Biology of RICE Dec. 09.pmd - Department of Biotechnology

CONTENTS 

1. RICE AS A CROP PLANT ...................................................................................... 01 

2. TAXONOMY, GEOGRAPHIC ORIGIN AND GENOMIC EVOLUTION .......... 03 

2.1 Taxonomy ...................................................................................................... 03 

2.2 Geographic origin .......................................................................................... 03 

2.3 Rice gene pool and species complexes ............................................................ 04 

2.4 Sub-specific differentiation of the Asian cultivated rice .................................. 07 

2.5 Important cultivated species/wild relatives in India ........................................ 08 

2.6 Germplasm conservation ............................................................................... 09 

3. REPRODUCTIVE BIOLOGY................................................................................. 11 

3.1 Growth and development .............................................................................. 11 

3.2 Floral biology (adopted from Siddiq and Viraktamath, 2001) ........................ 16 

3.3 Pollination and fertilization............................................................................ 17 

3.4 Seed dispersal ................................................................................................. 18 

3.5 Seed Dormancy ............................................................................................. 18 

3.6 Mating systems .............................................................................................. 19 

3.7 Asexual reproduction ..................................................................................... 19 

3.8 Methods of reproductive isolation .................................................................. 19 

4. ECOLOGICAL INTERACTIONS .......................................................................... 20 

4.1 Potential for gene transfer .............................................................................. 20 

4.2 Gene flow to non Oryza species ..................................................................... 23

4.3 Gene flow to other organisms ........................................................................ 23 

4.4 Weediness of rice ............................................................................................ 23 

5. FREE LIVING POPULATIONS ............................................................................. 23 

6. HUMAN HEALTH CONSIDERATIONS .............................................................. 24 

7. RICE CULTIVATION IN INDIA ........................................................................... 24 

7.1 Climate and Soil Type .................................................................................... 24 

7.2 Rice ecosystems .............................................................................................. 25 

7.3 Zonal distribution .......................................................................................... 25 

7.4 Rice Growing Seasons .................................................................................... 26 

7.5 Cropping Patterns .......................................................................................... 26 

7.6 Breeding objectives and milestones ................................................................. 27 

7.7 Varietal testing of rice ..................................................................................... 28 

7.8 Key insect pests and diseases............................................................................ 29 

8. STATUS OF RICE CULTIVATION ....................................................................... 29 

9. BIOTECH INTERVENTIONS IN RICE ................................................................ 30 

10 ANNEXES ................................................................................................................ 32 

1. Botanical features ........................................................................................... 32 

2. Key Insect/Pests of Rice .................................................................................. 36 

3. Major Diseases of Rice.................................................................................... 40 

4. Naturally Occurring Predators ........................................................................ 42

1. 1. RICE RICE RICE AS AS A A CROP CROP PLANT 

PLANT 

Rice (Oryza sativa L.) is a plant belonging to the family of grasses, Gramineae. It is one of the three major 

food crops of the world and forms the staple diet of about half of the world’s population. The global 

production of rice has been estimated to be at the level of 650 million tones and the area under rice 

cultivation is estimated at 156 million hectares (FAOSTAT, 2008). Asia is the leader in rice production 

accounting for about 90% of the world’s production. Over 75% of the world supply is consumed by 

people in Asian countries and thus rice is of immense importance to food security of 

Asia. The demand for rice is expected to increase further keeping in view the expected increase 

in the population. 

India has a long history of rice cultivation. Globally, it stands first in rice area and second in rice 

production, after China. It contributes 21.5 percent of global rice production. Within the country, rice 

occupies one-quarter of the total cropped area, contributes about 40 to 43 percent of total food grain 

production and continues to play a vital role in the national food and livelihood security system. India 

is one of the leading exporter of rice, particularly basmati rice. 

O. Sativa has many ecotypes or cultivars adopted to various environmental conditions. It is grown in all 

continents except Antarctica. In fact, there is hardly any crop plant that grows under as diverse agro 

climatic condition as rice does (Box 1). 

BIOLOGY OF RICE 


Box 1: Diverse growing condition of rice 

Rice is now cultivated as far north as the banks of the Amur River (53º N) on the border between Russia and 

China, and as far south as central Argentina (40º S) (IRRI, 1985). It is grown in cool climates in the mountains 

of Nepal and India, and under irrigation in the hot deserts of Pakistan, Iran and Egypt. It is an upland crop in 

parts of Asia, Africa and Latin America. At the other environmental extreme are floating rices, which thrive in 

seasonally deeply flooded areas such as river deltas - the Mekong in Vietnam, the Chao Phraya in Thailand, 

the Irrawady in Myanmar, and the Ganges-Brahmaputra in Bangladesh and eastern India, for example. Rice 

can also be grown in areas with saline, alkali or acidsulphate soils. Clearly, it is well adapted to diverse growing 

conditions. 

Source: OECD, 1999 

The morphology, physiology, agronomy, genetics and biochemistry of O. sativa have been intensely 

studies over a long time. More than 40,000 varieties of rice had been reported worldwide. Crop 

improvement research in case of rice had been stated more than a century back. Extensive adoption of 

higher yielding varieties has enabled many countries in Asia to achieved sustained self sufficiency in 

food. In India rice is grown under four ecosystems: irrigated, rainfed lowland, rainfed upland and flood 

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prone. More than half of the rice area (55%) is rainfed and distribution wise 80% of the rainfed rice areas 

is in eastern India, making its cultivation vulnerable to vagaries of monsoon. 

Rice is a nutritious cereal crop, used mainly for human consumption. It is the main source of energy and 

is an important source of protein providing substantial amounts of the recommended nutrient intake of 

zinc and niacin (Table 1). However, rice is very low in calcium, iron, thiamine and riboflavin and nearly 

devoid of beta-carotene. 

Rice protein is biologically the richest by virtue of its high true digestibility (88%) among cereal proteins 

and also provides minerals and fiber. Calories from rice are particularly important for the poor accounting 

for 50-80% of the daily caloric intake. Rice can also be found in cereals, snack foods, brewed beverages, 

flour, oil, syrup and religious ceremonies to name a few other uses. Rice is also believed to have 

medicinal properties. Although, this is not scientifically proven, it has been used in many countries for 

medicinal purposes. 

Often times, rice is categorized by its size as being either short grain, medium grain or long grain. Short 

grain, which has the highest starch content, makes the stickiest rice, while long grain is lighter and 

tends to remain separate when cooked. The qualities of medium grain fall between the other two types. 

Another way that rice is classified is according to the degree of milling that it undergoes. This is what 

makes a brown rice different than a white rice. Thus, the primary differences in different varieties of 

rice are their cooking characteristics, shapes and even colors and in some cases, a subtle aroma difference. 

Husk, bran and broken rice are the by-products of the rice milling industries. These by-products can be 

used in better and profitable manner both for industrial and feed purposes. Rice husk constitutes the 

largest by-product of rice milling and one fifth of the paddy by weight consists of rice husk. Rice husk 

has a considerable fuel value for a variety of possible industrial uses. Hence, the major use of husk at the 

moment is as boiler fuel. Rice bran is the most valuable by-product of the rice milling industry. It is 

obtained from the outer layers of the brown rice during milling. Rice bran consists of pericarp, aleurone 

layer, germ and a part of endosperm. Rice bran can be utilized in various ways. It is a potential source 

of vegetable oil, feed, fertilizers etc. 


Table 1: Composition per 100 g of edible portion of milled rice 

Moisture 13.7 g Minerals 0.6 g 

Protein 6.8 g Carbohydrates 78.2 g 

Fat 0.5 g Calcium 10 mg 

Fibre 0.2 g Iron 0.7 mg 

Calories 345 kcal Thiamine 0.06 mg 

Phosphorus 160 mg Niacin 1.9 mg 

Riboflavin 0. 06 mg Folic acid 8 mg 

Essential amino acids 1.09 mg Magnesium 90 mg 

Copper 0.14 mg 

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2. 2. 2. TAX AX AXONOMY AX ONOMY ONOMY, ONOMY , GEOGRAPHIC GEOGRAPHIC ORIGIN ORIGIN AND AND GENOMIC GENOMIC EV EVOL EV EVOL 

OL OLUTION OL UTION 

2.1 2.1 Taxonomy axonomy 

Rice belongs to the genus Oryza and the tribe Oryzeae of the family Gramineae (Poaceae). The genus 

Oryza contains 25 recognized species, of which 23 are wild species and two, O. sativa and O. glaberrima 

are cultivated (Morishima 1984; Vaughan, 1994; Brar and Khush, 2003). O. sativa is the most widely 

grown of the two cultivated species. It is grown worldwide including in Asian, North and South American, 

European Union, Middle Eastern and African countries. O. glaberrima however is grown solely in 

West African countries. 

2.2 2.2 Geographic Geographic origin 

origin 


Kingdom Plantae 

Division Magnoliophyta 

Class Liliopsida 

Order Poales 

Family Gramineae o Poaceae 

Tribe Oryzeae 

Genus Oryza 

Species Sativa 

The centre of origin and centres of diversity of two cultivated species O. sativa and O. glaberrima have 

been identified using genetic diversity, historical and archaeological evidences and geographical 

distribution. It is generally agreed that river valleys of Yangtze, Mekon rivers could be the primary 

centre of origin of O. sativa while Delta of Niger River in Africa as the primary centre of origin of O. 

glaberrima (Porteres, 1956; OECD. 1999). The foothills of the Himalayas, Chhattisgarh, Jeypore Tract 

of Orissa, northeastern India, northern parts of Myanmar and Thailand, Yunnan Province of China 

etc., are some of the centres of diversity for Asian cultigens. The Inner delta of Niger River and some 

areas around Guinean coast of the Africa are considered to be centre of diversity of the African species 

of O. glaberrima (Chang, 1976; Oka, 1988). 

O. Sativa and O. glaberrima are believed to have evolved independently from two different progenitors, 

viz. O. Nivara and O. barthii and they are believed to be domesticated in South or South East Asia and 

tropical West Africa respectively. The progenitors of O sativa are considered to be the Asian AA genome 

diploid species and those of O. glaberrima to be African AA genome diploid species O. barthii 

and O longistaminata as indicated in various reviews by Chang, 1976, Siddiq, 2000 and NBPGR, 

2006 (Figure 1). 

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Domestication of Asian rice, O. sativa, is considered to have occurred in 7,000 BC (OECD, 1999). It 

spread and diversified to form two ecological groups, Indica and Japonica (Oka, 1988). There are other 

studies indicating that the two groups were derived independently from the domestication of two 

divergent wild rices in China and India, respectively (Second, 1982; 1986). 

2.3 2.3 Rice Rice gene gene pool pool and and species species complexes 

complexes 

There are 23 recognized species in the genus Oryza including the Asian and African cultivated rices. 

The species of the genus Oryza are broadly classified into four complexes (Vaughan 1994) viz. Sativa, 

Officinalis, Ridley and Meyeriana (Table 2). Of these, Sativa and Officinalis complexes are the best 

studied. The Sativa complex comprises the cultivated species O. sativa and O. glaberrima and their 

weedy /wild ancestors viz., perennial rhizomatous O.longistaminata, O.barthii (formerly O. breviligulata) 

and O. rufipogon , O. nivara and O. sativa f spontanea respectively. 


Figure 1: Schematic representation of the evolutionary pathways of Asian and African cultivated rices 

4


Table 2: Species complexes of the genus Oryza and their geographical distribution 

Species Complex Chromosome Genome Geographical 

Number Distribution 

I. Sativa complex 

1. O. sativa L. 24 AA Worldwide: originally 

South & Southeast Asia 

2. O. nivara Sharma et Shastry 24 AA South & Southeast Asia 

3. O. rufipogon Griff. 24 AA South & Southeast Asia, 

South China 

4. O. meridionalis Ng 24 AA Tropical Australia 

5. O. glumaepetula Steud. 24 AA Tropical America 

6. O. glaberrima Steud. 24 AA Tropical West Africa 

7. O. barthii A. Chev. et Roehr 24 AA West Africa 

8. O. longistaminata A. Chev. et Roehr. 24 AA Tropical Africa 

II. Officinalis Complex/ Latifolia complex 

9. O. punctata Kotschy ex Steud. 24 BB East Africa 

10. O. rhizomatis Vaughan 24 CC Sri Lanka 

11. O. minuta J.S.Pesl. ex C.B.Presl. 48 BBCC Philippines, New Guinea 

12. O. malamphuzaensis Krishn. et Chandr. 48 BBCC Kerala & Tamil Nadu 

13. O. officinalis Wall. ex Watt 24 CC South & Southeast Asia 

14. O. eichingeri A. Peter 24 CC East Africa & Sri Lanka 

15. O. latifolia Desv. 48 CCDD Central & South America 

16. O. alta Swallen 48 CCDD Central & South America 

17. O. grandiglumis (Doell) Prod. 48 CCDD South America 

18. O. australiensis Domin. 24 EE Northern Australia 

19. O. schweinfurthiana Prod. 48 BBCC Tropical Africa 

III. Meyeriana Complex 

20. O. granulata Nees et Arn. ex Watt 24 GG South & Southeast Asia 

21. O. meyeriana (Zoll. et Mor. ex Steud.) Baill. 24 GG Southeast Asia 

IV. Ridleyi Complex 

22. O. longiglumis Jansen 48 HHJJ Indonesia, New Guinea 

23. O. ridleyi Hook. f. 48 HHJJ Southeast Asia 

V. Unclassified (belonging to no complex) 

24. O. brachyantha A. Chev. et Roehr. 24 FF West & Central Africa 

25. O. schlechteri Pilger 48 HHKK Indonesia, New Guinea 

Source: Brar and Khush, 2003 

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The basic chromosome number of the genus Oryza is 12. O. sativa, O. glaberrima and 14 wild species 

are diploids with 24 chromosomes, and eight wild species are tetraploids with 48 chromosomes. Genome 

analysis done on the basis of chromosome pairing behavior and fertility in interspecific hybrids and 

degree of sexual compatability, has made possible to group them under nine distinct genomes, viz., A, 

B, C, D, E, F, G, H and J. On the basis of crossability and ease of gene transfer, the primary gene pool 

of rice is known to comprise the species of Sativa complex, while the species belonging to Officinalis 

complex constitute the secondary gene pool. Crosses between O. sativa and the species of Officinalis 

complex can be accomplished through embryo rescue technique. The species belonging to Meyeriana, 

Ridleyi complexes and O. schlechteri constitute the tertiary gene pool (Chang, 1964). A brief description 

of each of these complexes is given in Box 2. 


Box 2: Species complexes of Oryza 

Sativa complex: This complex consists of two cultivated species and six wild taxa. All of them have the AA 

genome and form the primary gene pool for rice improvement. Wild species closely related to O. sativa 

have been variously named. The weedy types of rice have been given various names, such as ‘fatua’ and 

‘spontanea’ in Asia and Oryza stapfii in Africa. These weedy forms usually have red endosperm – hence the 

common name ‘red rice’. These weedy species may be more closely related to Oryza rufipogon and Oryza 

nivara in Asia and to Oryza longistaminata or Oryza breviligulata in Africa. One of the species, Oryza 

meridionalis, is distributed across tropical Australia. This species is often sympatric with Oryza oustraliensis 

in Australia. 

Officinalis complex: The Officinalis complex consists of nine species and is also called the Oryza latifolia 

complex (Tateoka, 1962). This complex has related species groups in Asia, Africa and Latin America. The 

tetraploid species Oryza minata is sympatric with Oryza officinalis in the central islands of Bohol and 

Leyte in the Philippines. Oryza eichingeri, grows in forest shade in Uganda. It was found distributed in Sri 

Lanka (Vaughan, 1969). Two species of this complex, Oryza punctala and O. eichingeri, are distributed in 

Africa. Three American species of this complex, O. latifolia, Oryza alta and Oryza grandiglumis are tetraploid. 

Oryza latifolia is widely distributed in Central and South America, as well as in the Caribbean Islands. A 

diploid species O. australiensis, occurs in northern Australia in isolated populations. 

Meyeriana complex: This complex has two diploid species, Oryza granulate and Oryza meyeriana. Oryza 

granulate grows in South Asia, South-East Asia and south-west China. Oryza meyeriana is found in South- 

East Asia. Another species, Oryza indandamanica from the Andaman Islands (India), is a sub-species of O. 

granulate. The species of this complex have unbranched panicles with small spikelets. 

Ridleyi complex: This complex has two tetraploid species, Oryza ridleyi and Oryza longiglumis. Both 

species usually grow in shaded habitats, near rivers, streams or pools. Oryza longiglumis is found along the 

Komba River, Irian Jaya, Indonesa, and in Papua New Guinea. Oryza ridleyi grows across South-East Asia 

and as far as Papua New Guinea. 

Oryza brachyantha: This species is distributed in the African continent. It grows in the Sahel zone and in 

East Africa, often in the laterile soils. It is often sympatric with O. langistaminata. 

Oryza schlechtri: This is the least studied species of the genus. It was collected from north-east New 

Guinea. It is a tufted perennial, with 4-5 cm panicles and small, unawned spikelets. It is tetraploid, but its 

relationship to other species is unknown. 

Source: OECD, 1999 

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2.4 2.4 Sub Sub-specific Sub specific differentiation differentiation of of the the Asian Asian cultivated cultivated cultivated rice 

rice 

The subspecies or varietal groups of O. sativa viz., indica, japonica and javanica (Table 3), are the result 

of centuries of selection by man and nature for desired quality and adaptation to new niches. Most 

differentiation occurred in the region extending from the southern foothills of the Himalayas to Vietnam. 

These can be distinguished on few key characteristics such as glume size, number of secondary panicle 

branches (rachii), panicle thickness etc. 


Table 3: Characteristics of Oryza sativa ecotypes 

Characteristics Subspecies 

Indica Japonica javanica 

Tillering High Low Low 

Height Tall Medium Tall 

Lodging Easily Not easily Not easily 

Photoperiod Sensitive Non-sensitive Non-sensitive 

Cool temperature Sensitive Tolerant Tolerant 

Grain shattering Easily Not easily Not easily 

Grain type Long to medium Short and round Large and bold 

Grain texture Non-sticky Sticky Intermediate 

According to Sharma et al. (2000), the subspecies are believed to have evolved from 3 different populations 

of O. nivara existed then in different regions. The hill rices of south east India, the japonica like types 

of south-west China and the hill rices of Indo-China are said to have directly evolved from the annual 

wild species in the respective regions. The aus ecotype of West Bengal seems to have directly evolved 

from the upland rices of south east India, whereas aman type from introgression of rufipogon genes 

into aus type somewhere in the lower Gangetic Valley. The sali type of Assam had possibly evolved from 

introgression of O rufipogon genes into japonica like type somewhere in the Brahmaputra Valley. 

Migration of the hill rice of mainland Southeast Asia to Indonesia following introgression of genes 

from O rufipogon had possibly led to the evolution of javanica type. The primary ecotypes (aus and 

japonica) of O.sativa have retained photoperiod insensitivity of annual wild species (O. nivara), whereas 

the secondary ecotypes (aman, javanica and sali) have acquired photoperiod sensitivity and adaptation 

to lowland ecologies. 

The genetic affinity between the three subspecies as studied from chromosome pairing behaviour F1 

sterility and F2 segregation pattern reveal indica-japonica to show the least compatibility as compared 

to indica-javanica and javanica-japonica crosses. The genetic differences between indica and japonica 

have been explained through genic (Oka, 1953; 1974) and chromosomal (Sampath, 1962; Henderson 

et al., 1959) models. 

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2.5 2.5 Important Important cultivated cultivated cultivated species/wild species/wild relatives relatives in in South South South East East Asia Asia 

Asia 

India has abundant resources of wild rices particularly O. nivara, O.rufipogon, O.officinalis, and O. 

granulata. The wild species of rices can be found in many different natural habitats, from shade to full 

sunlight, and can be either annual or perennial in nature. The habitats of O. nivara are ditches, water 

holes, and edges of ponds, whereas O.rufipogon is usually found in deepwater swamps.Some wild 

species occur as weeds in and around rice fields and even hybridize naturally with the cultivated forms. 

This complex association between cultivated and wild forms has also enhanced the diversity of rice 

crop in traditional agricultural systems 

Northeastern hills , Koraput region of Orissa, Raipur region of Chattisgarh and peninsular region of 

India are considered important centres of diversity based on germplasm collections The distribution 

pattern of the four species in South East Asia is depicted in Figure 2. 


8

The diversity of rice crop has evolved over thousands of years, as the peasants and farmers selected different 

types to suit local cultivation practices and needs. This process of selection has led 

to a multiplicity of rice varieties adapted to a wide range of agro-ecological conditions.. India has 

also seen the release of more than 650 varities in last 50 years. The full spectrum of rice germplasm in 

India includes: 


Wild Oryza species and related genera 

Natural hybrids between the cultigen and wild relatives and primitive cultivars of the cultigen in 

areas of rice diversity. 

Germplasm generated in the breeding programs including pureline or inbred selections of farmers 

varieties, F1 hybrids and elite varieties of hybrid origin, breeding materials, mutants, polyploids, 

aneuploids, intergeneric and interspecific hybrids, composites, etc. 

Commercial types, obsolete varieties, minor varieties, and special purpose types in the centers of 

cultivation 

Diverse ecological situations in areas of rice cultivation have given rise to the following major 

ecospecific rice varieties with specificity for season, situation, and system: 

The aus group: Early maturing, photoinsensitive types - can be grown across the seasons except in 

the winter. 

The aman group: Late types mostly photoperiod sensitive and flower during specific time regardless 

of when they aresown or transplanted. 

The boro group: Perform best as a summer crop. When sown during winter they tolerate cold 

temperature in the early vegetative stage better than the other groups. 

The gora group: Short duration, can withstand a certain degree of moisture stress during its growing 

period. 

The basmati group: Specific to regions in the northern parts of Indian subcontinent, possessing 

extremely valuable quality traits like elongation, aroma, flavor, etc. 

2.6 2.6 GERMPLASM GERMPLASM GERMPLASM CONSERV CONSERV CONSERVATION 

CONSERV TION 

Rice germplasm comprising of over 150000 cultivars and large accessions of 22 wild species, is one of 

the richest among crop species. Most countries in Asia maintain collections of rice germplasm, and the 

largest are in China, India, Thailand and Japan. In Africa, there are significant collections in Nigeria 

and Madagascar, while in Latin America, the largest collections are in Brazil, Peru, Cuba and Ecuador. 

All these collections conserve landrace varieties as well as breeding materials. Four centres of the 

Consultative Group on International Agricultural Research (CGIAR) i.e. the International Rice Research 

Institute (IRRI) in the Philippines, the West Africa Rice Development Association (WARDA) in Côte 

9

d'Ivoire, the International Institute for Tropical Agriculture (IITA) in Nigeria (on behalf of WARDA), 

and the International Centre for Tropical Agriculture (CIAT) in Colombia, also maintain rice collections. 

IRRI holds nearly 100 000 accessions. It is also the most genetically diverse and complete rice collection 

in the world (Table 4). 

The International Rice Genebank (IRG) at IRRI was established in 1977, although shortly after its 

foundation in 1960 IRRI had already begun to assemble a germplasm collection to support its nascent 

breeding activities (Jackson, 1997). This rich biodiversity has been collected and maintained by various 

national agricultural research systems. The systematic collection campaign has been mainly coordinated 

by IRRI since 1972. The International Network for Genetic Evaluation of RICE (INGER) is the 

principal germplasm exchange and evaluation network worldwide. 

As one of the primary centers of origin of O.sativa, India contains rich and diverse genetic wealth of 

rice. According to an estimate, about 50,000 land races of rice are expected to exist in India. A total of 

66,745 accessions have so far been collected from various parts of the country. If it is presumed that 

almost 50% of the total germplasm are duplicates, about 17,000 land races of rice still remain to be 

collected. 

The IGKV's collection of rice germplasm, the largest such in India and the second largest in the world, 

includes the indica rice variety that originated from Chhattisgarh. Some 19,000 of the 22,972 varieties 


Table 4: Origin of the accessions in the International Rice Genebank Collection at IRRI 

Country Accessions 

India 16 013 

Lao PDR 15 280 

Indonesia 8 993 

China 8 507 

Thailand 5 985 

Bangladesh 5 923 

Philippines 5 515 

Cambodia 4 908 

Malaysia 4 028 

Myanmar 3 335 

Viet Nam 3 039 

Nepal 2 545 

Sri Lanka 2 123 

7 countries with > 1 000 and < 2 000 accessions 10 241 

105 countries < 1 000 accessions 11 821 

Total 108 256 

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in this collection are local to Chhattisgarh. These include those with varying harvesting periods (from 60 

days to 150 days); the largest (dokra-dokri), the longest and the shortest rice varieties; some varieties that 

can grow under 10 feet (three metres) of water (Naatrgoidi); those with high protein content and medicinal 

properties; and the scented rice varieties.The Assam Hills are another invaluable source of rice germplasm 

known as as Assam Rice collection. 

India is also known for its quality rices, like basmati and other fine grain aromatic types grown 

in northwest region of the country. The basmati rice is known globally for its special characteristics 

(Box 3). 

Source: http://www.rice-trade.com 


Box 3: Main characteristics of Indian Basmati Rice 

Origin: Authentic Basmati rice is sourced from northern India at the foothills of the Himalayas. Whilst 

Basmati rice can be sourced from India and Pakistan, Indian Basmati is traditionally considered premium. 

Colour: The colour of a basmati is translucent, creamy white. Brown Basmati Rice is also available but the 

most commonly used is white Basmati. 

Grain: Long Grain. The grain is long (6.61 - 7.5 mm) or very long (more than 7.50 mm and 2 mm 

breadth). 

Shape: Shape or length-to-width ratio is another criteria to identify basmati rice. This needs to be over 3.0 

in order to qualify as basmati. 

Texture: Dry, firm, separate grains. Upon cooking, the texture is firm and tender without splitting, and it 

is non-sticky. (This quality is derived from the amylose content in the rice. If this value is 20-22%, the 

cooked rice does not stick. The glutinous, sticky variety preferred by the chopsticks users has 0-19% 

amylose). 

Elongation: The rice elongates almost twice upon cooking but does not fatten much. When cooked the 

grains elongate (70-120 % over the pre-cooked grain) more than other varieties. 

Flavour: Distinctive fragrance. The most important characteristic of them all is the aroma. Incidentally, 

the aroma in Basmati arises from a cocktail of 100 compounds — hydrocarbons, alcohols, aldehydes and 

esters. A particular molecule of note is 2-acetyl-1-pyrroline. 

Uses: Flavour and texture complements curries because it is a drier rice and the grains stay separate. Also 

suits biryani and pilaf (where saffron is added to provide extra colour and flavour). Great for Indian & 

Middle Eastern dishes. 

Main benefits: Aromatic fragrance and dry texture. 

3. 3. REPRODUCTIVE REPRODUCTIVE BIOL BIOL BIOLOG BIOL BIOLOG 

OG OGY OG 

3.1 3.1 Growth Growth Growth and and development 

development 

In India, most of rice cultivation is done through transplanting. The young seedlings grown in nursery 

beds are transplanted by hands to rice fields. However, about 28% of rice area is under cultivation 

through direct seed, particularly in Eastern India (Pandey and Velasco 1999). The growth of the rice plant 

is divided into three phases viz. vegetative, reproductive and ripening phase (IRRI, 2002). The stages of 

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development in each phase are further divided according to 0-9 numerical scale to identify the growth 

stages of a rice plant. Each number in the scale corresponds to a specific growth stage. Therefore, three 

growth phases consist of a series of 10 distinct stages, as indicated in Table 5. These growth stages are 

based on data and characteristics of IR64, a modern, a high yielding, semi dwarf variety but apply generally 

to other rice varieties. 


Table 5: Growth phases and stages of rice 

Growth phase Stage 

I. Vegetative (germination to panicle initiation) Stage 0 from germination to emergence 

Stage 1 - seedling 

Stage 2 - tillering 

Stage 3 - Stem elongation 

II. Reproductive (panicle initiation to flowering); and Stage 4 - panicle initiation to booting 

Stage 5 - heading or panicle exsertion 

Stage 6 - flowering 

III. Ripening (flowering to mature grain) Stage 7 - milk grain stage 

Stage 8 - dough grain stage 

Stage 9 -- mature grain stage 

It has been indicated that in the tropical countries like India, the reproductive phase is about 35 days and 

the ripening phase is about 30 days (Figure 3). The differences in growth duration are determined by 

changes in the length of the vegetative phase. For example, IR64 which matures in 110 days has a 45-day 

vegetative phase, whereas IR8 which matures in 130 days has a 65-day vegetative phase. 

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i. i. i. Vegetative egetative phase 

phase 


Figure 3: Each of the growth phases are explained as under: 

Stage 0 - Germination to emergence: Seeds are usually pregerminated by soaking for 24 hours and 

incubating for another 24 hours. After pregermination the radicle and plumule protrude through 

the hull.By the second or third day after seeding in the seedbed or direct seeding, the first leaf 

breaks through the coleoptile. The end of stage 0 shows the emerged primary leaf still curled and an 

elongated radicle. 

Stage 1 – Seedling: The seedling stage starts right after emergence and lasts until just before the first 

tiller appears. During this stage, seminal roots and up to five leaves develop Leaves continue to 

develop at the rate of 1 every 3-4 days during the early stage. Secondary adventitious roots that 

form the permanent fibrous root system rapidly replace the temporary radicle and seminal roots. 

This is an 18-day-old seedling ready for transplanting. The seedling has 5 leaves and a rapidly 

developing root system. 

Stage 2 – Tillering: This stage extends from the appearance of the first tiller until the maximum 

tiller number is reached. Tillers emerge from the auxiliary buds of the nodes and displace the leaf as 

they grow and develop. This seedling shows the position of the two primary tillers with respect to 

13


the main culm and its leaves. After emerging, the primary tillers give rise to secondary tillers. This 

occurs about 30 days after transplanting. The plant is now increasing in length and tillering very 

actively. Besides numerous primary and secondary tillers, new tertiary tillers arise from the secondary 

tillers as the plant grows longer and larger. By this stage, the tillers have multiplied to the point that 

it is difficult to pick out the main stem. Tillers continuously develop as the plant enters the next 

stage which is stem elongation. 

Stage 3 - Stem elongation: This stage may begin before panicle initiation or it may occur during 

the latter part of the tillering stage. Thus, there may be an overlap of stages 2 and 3.The tillers 

continue to increase in number and height, with no appreciable senescence of leaves noticeable. 

Ground cover and canopy formation by the growing plants have advanced. Growth duration is 

significantly related to stem elongation. Stem elongation is more in varieties with longer growth 

duration. In this respect, rice varieties can be categorized into two groups: the short-duration varieties 

which mature in 105-120 days and the long-duration varieties which mature in 150 days. In earlymaturing 

semidwarfs like IR64, the fourth internode of the stem, below the point where the panicle 

emerges, elongates only from 2 to 4 cm before panicle initiation becomes visible. Maximum tillering, 

stem elongation, and panicle initiation occur almost simultaneously in short-duration varieties 

(105-120 days). In long-duration varieties (150 days), there is a so-called lag vegetative period 

during which maximum tillering 

14

ii. ii. ii. Reproductive eproductive phase 

phase 


Stage 4 - Panicle initiation to booting: The initiation of the panicle primordium at the tip of the 

growing shoot marks the start of the reproductive phase. The panicle primordium becomes visible 

to the naked eye about 10 days after initiation. At this stage, 3 leaves will still emerge before the 

panicle finally emerges. In short-duration varieties, the panicle becomes visible as a white feathery 

cone 1.0-1.5 mm long. It occurs first in the main culm and then in tillers where it emerges in 

uneven pattern. It can be seen by dissecting the stem. As the panicle continues to develop, the 

spikelets become distinguishable. The young panicle increases in size and its upward extension 

inside the flag leaf sheath causes the leaf sheath t bulge. This bulging of the flag leaf sheath is called 

booting. Booting is most likely to occur first in the main culm. At booting, senescence (aging and 

dying) of leaves and nonbearing tillers are noticeable at the base of the plant. 

Stage 5 – Heading: Heading is marked by the emergence of the panicle tip from the flag leaf 

sheath. The panicle continues to emerge until it partially or completely protrudes from the sheath. 

Stage 6 – Flowering: It begins when anthers protrude from the spikelet and then fertilization takes 

place. At flowering, the florets open, the anthers protrude from the flower glumes because of stamen 

elongation, and the pollen is shed. The florets then close.The pollen falls on the pistil, thereby 

fertilizing the egg. The pistil is the feathery structure through which the pollen tube of the germinating 

pollen (round, dark structures in this illustration) will extend into the ovary.The flowering process 

continues until most of the spikelets in the panicle are in bloom. From left to right, this frame 

shows anthesis or flowering at the top of the panicle, 1st day after heading; anthesis at the middle of 

the panicle, 2nd day after heading; anthesis at the lower third of the panicle, 3rd day after 

heading.Flowering occurs a day after heading. Generally, the florets open in the morning. It takes 

about 7 days for all spikelets in a panicle to open. At flowering, 3-5 leaves are still active.The tillers 

of this rice plant have been separated at the start of flowering and grouped into bearing and 

nonbearing tillers. 

15

iii. iii. Ripening Ripening phase 

phase 


Stage 7. Milk grain stage: In this stage, the grain beginsn to fill with a milky material.The grain 

starts to fill with a white, milky liquid, which can be squeezed out by pressing the grain between the 

fingers.The panicle looks green and starts to bend. Senescence at the base of the tillers is progressing. 

The flag leaves and the two lower leaves are green. 

Stage 8 - Dough grain stage: During this stage, the milky portion of the grain first turns into soft 

dough and later into hard dough. The grains in the panicle begin to change from green to yellow. 

Senescence of tillers and leaves is noticeable. The field starts to look yellowish. As the panicle turns 

yellow, the last two remaining leaves of each tiller begin to dry at the tips. 

Stage 9 - Mature grain stage: The individual grain is mature, fully developed, hard, and has turned 

yellow. This slide shows rice plants at the mature grain stage. Ninety to one hundred percent of the filled 

grains have turned yellow and hard. The upper leaves are now drying rapidly although the leaves of some 

varieties remain green. A considerable amount of dead leaves accumulate at the base of the plant. 

3.2 3.2 Floral Floral biology biology biology (adopted (adopted from from Siddiq Siddiq and and Viraktamath, Viraktamath, 2001) 

2001) 

Precise knowledge of floral biology, which includes structural and functional aspects of rice flower is 

essential for breeders to plan and execute breeding strategies. Inflorescence of rice is a terminal panicle 

with single flowered spikelets. The panicle has a main axis, on which primary branches are borne. 

Secondary branches are borne towards the basal region of the primary branches. Tertiary branches, if 

any, are seen at the base of the secondary branches. Much of the variability for spikelet number is due 

to variation in the number of secondary branches. The spikelet consists of two short sterile lemma, a 

normal fertile lemma and palea. The fertile lemma is either awnless or short or long awned (Figure 4). 

The fertile lemma and palea enclose the sexual organs viz., six stamens arranged in whorls and a pistil 

at the centre. The stamen consists of bilobed anthers borne on slender filaments, while the pistil consists 

of ovary, style and feathery bifid stigma. 

Figure 4: Parts of spikelet (From Chang and Bardenas 1965) 

16

As indicated in the previous section, reproductive phase starts with panicle initiation, which occurs about 35 

days before panicle emergence. Complete emergence of panicle from flag leaf sheath takes place within a 

day. Days to complete heading varies with the variety, the range being between 5-15 days. Anthesis (spikelet 

opening and dehiscence of anther) occurring immediately after the panicle emergence, follows a specific 

pattern, in which spikelets on the primary branch followed by spikelets on the secondary/tertiary branches at 

the corresponding position of the panicle open (Figure 5). The lower most secondary/tertiary branches open 

last. Thus completion of anthesis on a panicle takes about 7 days. 

The process of anthesis is greatly influenced by weather conditions. The spikelets generally open on a 

sunny day between 10 AM and 2 PM, the maximum blooming being between 10 and 11 AM. About 

six days before heading, pollen grains mature and the flag leaf swells indicating the approach of booting 

stage. At the time of anthesis, lemma and palea get separated, filaments of stamens elongate and protrude 

out and anthers dehisce releasing the pollen. Most of the pollen is shed on the protruded stigma of the 

same spikelet or neighbouring spikelets of the same plant, thus causing self-pollination. After 20-30 

minutes of anthesis, anthers wither out and the spikelet closes leaving the stamens sticking out from the 

seams of lemma and palea. The pollen remain viable for not more than 3-5 minutes, while stigma is 

receptive for 2-3 days from the day of opening. Under tropical conditions, all the spikelets on a panicle 

complete flowering within 7-10 days and following fertilization, ovary starts developing into a caryopsis. 

3.3 3.3 Pollination ollination and and fertilization 

fertilization 

O. sativa is basically a self-pollinated crop, with limited degree of outcrossing(< 5%). The factors limiting 

the receptivity of rice flowers to outcrossing include a short style and stigma (1.5 to 4 mm in combined 


17

length), short anthers, limited pollen viability and brief period between opening of florets and release of 

pollen (between 30 seconds and 9 minutes) (Morishima 1984; Oka 1988). 

Immediately after the spikelet opens at flowering, pollen is shed on the protruded stigma of the same 

spikelet or neighboring spikelets of the same plant, thus causing self-pollination. The maturation of 

pollen in an anther is synchronized with the maturation of the ovule within the same spikelet. 

All wild and cultivated rice can also be wind-pollinated, with a few varieties having scented flowers that 

attract bees (Oka 1988). It has been reported that greater out crossing is observed when honeybees are 

present (Gealy et. al. 2003). Rice pollen is short-lived with most pollen grains loosing viability after 

approximately five minutes under typical environmental conditions (Koga et al. 1969). The morphology 

of pollen grain also changes dramatically after shedding from the anther. Initially grains are spherical 

but within minutes they begin to collapse and this collapse of the pollen grains coincide with a measured 

loss of viability. It has been reported by Koga et al. 1969 that 90% of the pollen grains were found to be 

viable for upto four minutes in one of the study, and the viability decreased to approximately 33% 

between five and eight minutes after shedding. The wind assisted pollen dispersal distances have been 

estimated at upto 110 metres (Song et. al. 2004). 

Although, the germinability of pollen lasts only for few minutes after being shed from anther under 

favorable temperatures and moisture conditions, ovules keep their viability to receive pollens for several 

days after maturation. Fertilization is completed within six hours and occurs in the spikelet. Only one 

pollen tube reaches an ovule to initiate double fertilization. During fertilization rice is most sensitive to 

cold temperatures (McDonald 1979). 

3.4 3.4 Seed Seed dispersal 

dispersal 

The probability of seed dispersal from rice plants varies widely within the O. sativa species (OGTR 

2005). Most cultivars have limited dispersal ability, whereas in wild rices and some cultivars mature rice 

seeds can be shed from the plant through seed shatter. Shattered seed can either be buried in the soil for 

subsequent germination or be eaten/dispersed by animals. Another cultivar specific trait is the presence 

or absence of awns at the tip of the lemma. When present, awns can be vary in their rate of development, 

length, diameter and bristle length. The presence or absence of awns influences the potential for seed 

dispersal through attachment to passing animals (Oka 1988). 

3.5 3.5 Seed Seed dormancy dormancy 

dormancy 

Seed dormancy is generally weaker in cultivated rice than in wild or weedy rice (Oka 1988; 

Vaughan1994)..The longevity of rice seeds has not been well studied however,wild rice seeds are 

believed to be long lived (Vaughan 1994) and may be dormant for several years ( Moldenhauer and 

Gibbons 2003). 

It has been reported that of the three O. sativa ecotypes, Indica cultivars display the greatest degree of 

dormancy, followed by Javanica and then Japonica cultivars (Ellis et al. 1983). Although, dormancy is 


18

a heritable trait but the environmental conditions during seed maturation also appear to influence the 

degree of dormancy present in the seeds. For example, Indica cultivars have stronger dormancy after 

maturation in rainy weather, but drying the seeds at high temperature (40oC to 50oC for upto two 

weeks) after harvest removes dormancy from all rice seeds (Takahashi 1984b). 

3.6 3.6 Mating Mating Mating systems 

systems 

O. sativa is largely an autogamous plant (self fertilizing) propagating through seeds produced by selfpollination 

(OECD, 1999). Cross pollination between wild species and O. sativa cultivars has been 

reported to occur in natural habitats (Oka and Chang 1961). The degree of outcrossing has 

been reported to be generally higher in Indica cultivars and wild species than in Japonica cultivars 

(Oka 1988). 

3.7 3.7 Asexual Asexual reproduction 

reproduction 

Although O. sativa is cultivated annually, the rice plants can grow vegetatively and continuously under 

favorable water and temperature conditions, even after they have borne seeds (OECD, 1999). This 

perennial character in O. sativa is considered to have been inherited from the ancestral species O. 

rufipogon (Morishima et al., 1963). 

Under natural conditions, tiller buds on the basal nodes of rice plants start to re-grow after rice grains 

have been harvested. These new tillers called ratoons grow best under long day conditions and are used 

in some countries to obtain second harvest (OECD,1999). 

Cell/tissue culture techniques can be used to propagate calli and reproduce tissues or plants asexually 

under the appropriate cultural conditions (OECD 1999). Haploid plants can be easily obtained through 

anther culture and they become diploid spontaneously or when artificially treated with chemicals (Niizeki 

and Oono, 1968). 

3.8 3.8 Methods Methods of of reproductive reproductive isolation 

isolation 

The commonly used method of reproductive isolation in case of rice is spatial isolation. In case of 

varieties, an isolation distance of about 3 metres have been recommended for seed production by most 

of the national agencies. However, for conducting the trials of genetically modified rice, various agencies/ 

experts have recommended different isolation distance requirement for reproductive isolation. It has 

been recommended that buffering isolation zones wider than 110 metres or consisting tall crops such 

as sugarcane are required to prevent gene flow (den Nijs et al., 2004). Proposed isolation distance is 

1320 feet by US Department of Agriculture. In Australia, the trials have been conducted with an 

isolation distance of ___ metres. 

As per the Indian Minimum Seed Certification Standards, an isolation distance of 200 meters is required 

for production of foundation seed of hybrid rice (Tunwar and Singh, 1998). The isolation distance of 

300 meters has been adopted for conducting various field trials of genetically modified rice. 


19

4. 4. ECOL ECOLOGICAL ECOL OGICAL INTERA INTERA INTERACTIONS 

INTERA INTERA CTIONS 

4.1 4.1 Potential otential for for gene gene transfer 

transfer 

Gene transfer can occur within a species or between different species of the same, or other genera, 

referred to as intraspecific and interspecific gene transfer respectively. Successful gene transfer requires 

that the plant population must overlap spatially, temporally and be sufficiently close biologically that 

the resulting hybrids are able to reproduce normally (den Nijs et al. 2004). The potential of gene 

transfer from O. sativa is discussed below: 

4.1.1 4.1.1 lntraspecific lntraspecific gene gene transfer 

transfer 

Although O. sativa is essentially a self pollinating plant, natural out crossing can occur at a rate of upto 

5% (Oka, 1988). However, natural out crossing occurs only when plants with synchronous or overlapping 

flowering times grow in close proximity (Gealy et al. 2003). Even if flowering periods overlap, the time 

of day that the flowers open is important as rice flowers often remain open for period of less than three 

hours (Moldenhauer & Gibbons 2003). Summary of some of the studies performed to study the 

extent of outcrossing in O. sativa is given in Box 4. Outcrossing can be avoided by allocating 

cultivars with sufficiently different maturity time to adjacent fields, or by separating cultivars with same 

maturity time. 


Box 4: Extent of outcrossing in O. sativa 

In the study by Reano & Pham (1998) to study cross-pollination between cultivars, ten varieties were 

grown in four different plot designs. The varieties chosen were paired in order to match, as closely as 

possible, plant height and flowering time. The pollen acceptor plants had various stigma lengths (ranging 

from 1.00 to 1.88 mm) and varying degrees of stigma exsertion (32 to 70%). In the first two plot designs, 

the pollen donor plants (carrying a gene for purple leaf colouration) and pollen acceptor plants were 

alternated within the rows, so that each acceptor was surrounded by donors. In one of these plots, the 

panicles of donor and acceptor plants were clipped together in pairs to ensure close contact between the 

flowers. In the third plot design, alternating rows of the donors and acceptors were planted. In the final 

plot, paired varieties were planted in adjacent blocs sepated by 1.5 m. The highest rate of gene flow 

(hybrid progeny identified by leaf pigmentation) found was 09%. This occurred between clipped panicles 

with the pollen acceptors that had the greatest degree of stigma exsertion and the longest stigmas. No 

hybrids were found amongst the 600-900 seeds tested from the plots that were separated by 1.5 m, 

indicated that if gene flow was occurring it was occurring at a rate of less than 0.8%, the lowest rate 

detected. 

Messeguer et al. (2001) reported rates of less than 1% at 1 m and less than 0.05% at 5 m in concentric 

circle plots. In these experiments, wind direction was important in pollen transfer at 1 m but at 5 m the 

more random spread of hybrids around the circular plot indicated that wind direction was no longer 

important. Gene flow (measured as numbers of herbicide tolerant seedlings) was greater between plants 

of the same cultivar than between the cultivar and red rice plants, which were taller and flowered slightly 

earlier, but with a 10 day overlap. 

20

As regards crossability among various groups of O. sativa, it has been reported that F plants from crosses 

1 

within the indica or japonica group generally show high fertility in pollen and seed set. Those from crosses 

between the two groups have lower pollen fertility and lower seed set, with some exceptions (Oka, 1988). 

Sharma (2000) reviewed many studies on the intra specific differentiation of O. sativa ( Iso 1928, 

Mizushima 1939, Matsuo 1952, Waagenr et al 1952 , Oka 1958, Jennings 1966, Morinaga 1968, 

Glaszmann 1965, Sano et a 1985, Glaszmannan and Arrandeau 1968) and concluded that the cultivated 

rice of Asia has differentiated into many ecogenetic groups and when cultivars of two ecogenetic groups 

are crossed, their F1 hybrid often shows different degrees of sterility. 

Interspecific Interspecific gene gene transfer transfer to to other other Oryza Oryza species species 

species 

As mentioned in table 2, species in the Oryza genus can be grouped according to the compatibility of 

their genomes. O. sativa has an AA-type genome, which means that its chromosomes can pair correctly 

at meiosis with other AA-type species. Despite this, hybrids between AA rice species can be difficult to 

obtain and have been reported to show low fertility. However, this does not prevent gene flow between 

these species, as backcrossing to one of the parents can stabilize the hybrids (Vaughan & Morishima 

2003). In fact successful hybrid formation has been used to transfer beneficial traits from related species 

to O. sativa. Examples include transfer of resistance to grassy stunt virus from O. nivara (Khush 1977), 

cytoplasmic male sterility from weedy/rice rice (O. sativa f. spontanea (Lin & Yuan 1980)) and resistance 

to bacterial blight from O. longistaminata (Khush et al. 1990). Occurrence of gene flow has also been 

reported in studies conducted in India e.g. IGKV, Raipur undertook studies to assess the pollen flow 

between the cultivated rice i.e O.sativa and wild rice O. nivara and O. forma spontanea for two consecutive 

years (2001 and 2002) (Sidram, 2001 and Tamatwar, 2003). The two wild species included O.nivara 

and O.forma spontanea and O.sativa. The study clearly indicated that significant amount of gene flow 

occurred from O. sativa to O. nivara, O. sativa to O. spontanea, and vice versa. 

Hybridization between O. sativa and non AA type genome Oryza sp. is also possible with human assistance 

(Vaughan & Morishima, 2003) and has been used to introduce insect and disease resistance into new 

cultivars. However, these type of inter-specific hybridization do not occur naturally and rely on extensive 

embryo rescue and backcrossing efforts to obtain fertile hybrids. 


In a study by Zhang et al. (2004), three rice varieties (red seed, purple leaf and herbicide tolerant) were 

paired and grown in random plots in 50:50 mixes. No hybrid plants were recovered when seeds were 

collected from the taller red rice plants, indicating a lack of gene flow in that direction. However, hybrids 

were found in seeds collected from plants grown with the red rice with rates of 0.76% and 0.33% for 

purple rice and the herbicide tolerant rice respectively. The hybrids formed between the herbicide tolerant 

and red rice plants were very late in maturing and had to be removed from the field to a glasshouse at the 

end of the season to reach reproductive maturity. These would not have been able to set seed in the field, 

and in the glasshouse showed reduced fertility. · 

The relatively high seed-sets (9-73%) can be obtained through the artificial hybridization of O. sativa with AA 

21

genome wild species (Sitch et al., 1989). Further, species with the BB, BBCC, CC or CCDD genome are 

more crossable with O. sativa (0-30% seedset) than the more distantly related EE and FF genome species 

with O. sativa (0.2-3.8% seedset), but their hybrids are highly male and female sterile (Sitch, 1990) 

As regards the crossability of O. sativa with wild species occurring in India, O. nivara is easily crossable 

with different O. sativa varieties and occurs widely as weed in and around rice fields. Infact their F1 and 

segregating populations create significant problems with regard to seed impurity besides yield losses. In 

fact efforts have been made to eradicate this problem by releasing specific marker varieties for eradication. 

On such example is the Shyamala variety released by IGKV, Raipur which has purple leaves. O. rufipogon, 

the wild progenitor of O. sativa, can also be crossed with O. sativa and sometimes produces hybrid 

swarms in the field. Their hybrids show no sterility (Oka, 1988). The other two species O.officinalis, and 

O. granulate present in India do not cross with O. sativa in nature or by human intervention. 

In fact, relationship among different Asian AA species has been reviewed and reported by Sharma 2000. 

It has been indicated that in the coastal regions of south and southeast Asia, O. sativa is sympatric with O. 

rufipogon. The genetic barrier between these two species is not complete and, therefore, they easily 

hybridise in nature and form F hybrids. These F hybrids are partially sterile and hence get backcrossed 

1 1 

with either of the parents. As a result, various intergrades of these hybrids are found in nature. The single 

plant progenies of these plants segregate indicating their hybrid nature. In cultivated fields, one often 

comes across plants similar to O. sativa but with a few introgressed rufipogon characters such as presence 

of awn, black husk, red kernel, shattering of spikelet on maturity, etc. These plants are “wild” only in the 

sense that they shatter their spikelets on maturity and hence are not harvestable by the farmers. Instead, 

they become self-sown in the same field and germinate next year. The field thus comes up with more and 

more plants of these weedy spontanea rices in subsequent years. These plants compete with the cultivated 

rice (O. sativa) but, as they cannot be harvested, cause loss to the farmers. Since these weedy types 

resemble the cultivated rice closely in their vegetative stage, a farmer tries to weed any rice plant that 

appears off type at the vegetative stage. However, by such attempts, weedy types resembling cultivated 

varieties more and more closely have appeared (Oka, and Chang 1959). 

In plateau regions of south and southeast Asia where O. sativa and O. nivara are sympatric. The genetic 

barrier between these two species is incomplete leading to a situation similar to that between O. sativa 

and O. rufipogon in the coastal region. 

The natural hybrids (between O. sativa and O. nivara or between O. sativa and O. rufipogon) that get 

repeatedly backcrossed with the wild parent (nivara or rufipogon) acquire the characters of the wild 

parent and adapt more and more to the habitat of the wild parent. One, therefore, comes across forms 

that are similar to O. nivara or O. rufipogon but with a few sativa characters due to introgression of genes 

from the cultivated rice. 

O. nivara is a photoperiod insensitive species whereas O. rufipogon is a sensitive one and hence they flower 

in different seasons in south and southeast Asia. The natural hybrids between O. nivara and O. rufipogon 

are, therefore, rare. 


22

4.2 4.2 Gene Gene Gene flow flow to to non non Oryza Oryza species 

species 

As is evident from above, gene flow through conventional sexual hybridization is limited to O. sativa 

varieties and to the AA type genome species within this genus. Gene flow between more distantly 

related species, particularly those outside of the Oryza genus, is restricted to artificial breeding methods 

such as embryo rescue and somatic hybridisation (the regeneration of plants following the fusion of 

two protoplasts) (Liu et al. 1999; Multani et al. 2003). 

4.3 4.3 Gene Gene flow flow to to other other organisms 

organisms 

The only means by which genes could be transferred from plants to non-plant organisms is by horizontal 

gene transfer (HGT). Such transfers have not been demonstrated under natural conditions (Nielsen et 

al. 1997; Nielsen et al. 1998; Syvanen 1999) and deliberate attempts to induce them have so far failed 

(Schlüter et al. 1995; Coghlan 2000). Thus, gene transfer from rice to organisms other than plants is 

extremely unlikely. 

4.4 4.4 4.4 Weediness eediness of of rice rice 

rice 

Rice plants (O. sativa or other species) that are grown unintentionally in and around rice growing areas are 

regarded as weeds (Vaughan & Morishima 2003). Rice has a tendency to become weedy in areas where 

wild and cultivated rice plants grows sympatrically. In these areas, wild and cultivated rice plants can 

hybridize, producing plants that compete with the cultivars and produce inferior seed, thus decreasing the 

yield from the rice crop (Oka, 1988). However, weedy rice can also develop in areas without native wild 

rice populations (Bres-Patry et al. 2001; Vaughan & Morishima 2003). 

In the case of O. Sativa, the weeds are known as red rice due to the coloured pericarp associated with these 

plants. Red rice is viewed as a major economic problem when it occurs in rice fields as it causes losses in 

yield through competition with the cultivars as wells as decreasing the value of the harvested grain through 

its colour. Other Oryza species growing in and around rice fields are known as weedy rice and can also 

produce red seeds. 

Characteristics of weedy rice contributing to its potential weediness include similar growth attributes 

with cultivars due to common progenitors, high seed shedding rate, dormancy and persistence , adoption 

to different habitats and relatively higher outcrossing ability. In view of the above, populations of 

weedy/red rice tend to be genetically diverse and highly heterogeneous and often have intermediate 

characteristics between wild and cultivated characteristics. 

5. 5. 5. FREE FREE LIVING LIVING POPULA POPULATIONS 

POPULA TIONS 

The term “free living” is assigned to plant pollutants that are able to survive, without direct human 

assistance, over long term in competition with the native flora. This is a general ecological category that 

includes plants that colonize open, disturbed prime habitat that is either under human control (weedy 


23

populations) or natural disturbed areas such as river banks and sand bars(wild populations). There are no 

such free living populations of rice in India. 

6. 6. HUMAN HUMAN HEAL HEALTH HEAL TH CONSIDERA 

CONSIDERATIONS 

CONSIDERA TIONS 

There is no evidence of any toxicity or pathogenicity associated with use of rice grains as a food crop for 

humans. However the antinutrients including phytic acid, trypsin inhibitor, hemagglutinins (lectins) 

present in the bran fraction can present low levels of toxicity. Also the rice straw used as stock feed for 

animals in many parts of the world (Jackson 1978; Drake et al. 2002; FAO 2004), has the potential to 

cause toxicity if fed in large quantities due to the high levels (1 to 2%) of oxalates present in the straw 

(Jackson 1978) that can result in calcium deficiencies if supplements are not provided (FAO 2004). In 

general rice is considered to be of low allergenicity (Hill et al. 1997). 

7. 7. RICE RICE CUL CULTIV CUL TIV TIVATION TIV TION IN IN INDIA 

INDIA 

7.1 7.1 Climate Climate and and Soil Soil T TType 

T Type 

ype 

Rice is grown under varied ecosystems on a variety of soils under varying climatic conditions. The 

climatic factors affecting the cultivation of rice are: 


Rainfall: Rainfall is the most important weather element for successful cultivation of rice. The 

distribution of rainfall in different regions of the country is greatly influenced by the physical 

features of the terrain, the situation of the mountains and plateau. 

Temperature: Temperature is another climatic factor which has a favorable and in some cases 

unfavorable influence on the development, growth and yield of rice. Rice being a tropical and subtropical 

plant, requires a fairly high temperature, ranging from 20° to 40°C. The optimum temperature 

of 30°C during day time and 20°C during night time seems to be more favorable for the development 

and growth of rice crop. 

Day length or Sunshine: Sunlight is very essential for the development and growth of the plants. In 

fact, sunlight is the source of energy for plant life. The yield of rice is influenced by the solar radiation 

particularly during the last 35 to 45 days of its ripening period. The effect of solar radiation is more 

profound where water, temperature and nitrogenous nutrients are not limiting factors. Bright sunshine 

with low temperature during ripening period of the crop helps in the development of carbohydrates 

in the grains. 

Rice can be grown in all types of soils. However soils capable of holding water for a longer period such as 

heavy neutral soils (clay, clay loam and loamy) are most suited for its cultivation. The most important 

group of soils for successful rice cultivation include alluvial soils, red soils, laterite soils and black soils. It 

is grown normally in soils with soil reaction ranging from 5 to 8 pH. Because of its better adaptation it 

24

is also grown under extreme soil conditions such as acid peaty soils of Kerala (pH 3) and highly alkaline 

soils (pH 10) of Punjab, Haryana and Uttar Pradesh. 

7.2 7.2 Rice Rice ecosystems 

ecosystems 

ecosystems 

Rice farming is practiced in several agro ecological zones in India. No other country in the world has such 

diversity in rice ecosystems than India. Because cultivation is so widespread, development of four distinct 

types of ecosystems has occurred in India, such as irrigated rice, rainfed upland rice, rainfed lowland and 

flood prone as explained below: 

i. Irrigated rice ecosystem: Rice is grown under irrigated conditions in the states of Punjab, Haryana, 

Uttar Pradesh, Jammu & Kashmir, Andhra Pradesh, Tamil Nadu, Sikkim, Karnataka, Himachal 

Pradesh and Gujarat. Irrigated rice is grown in bunded (embanked), paddy fields. The area under 

irrigated rice accounts for approx 50% of the total area under rice crop in the country 

ii. Rainfed upland rice ecosystem: Upland rice areas lies in eastern zone comprising of Assam, Bihar, 

Eastern M.P., Orissa, Eastern U.P., West Bengal and North-Eastern Hill region. Upland rice fields 

are generally dry, unbunded, and directly seeded. Land utilized in upland rice production can be low 

lying, drought-prone, rolling, or steep sloping. 

iii. Rainfed lowland rice ecosystem: Rainfed lowland farmers are typically challenged by poor soil 

quality, drought/flood conditions, and erratic yields. Production is variable because of the lack of 

technology used in rice production. The low land rice area accounts approx. 32% of the total area 

under rice crop in the country. 

iv. Flood prone rice ecosystem: Flood-prone ecosystems are characterized by periods of extreme flooding 

and drought. Yields are low and variable. Flooding occurs during the wet season from June to 

November, and rice varieties are chosen for their level of tolerance to submersion. 

7.3 7.3 Zonal Zonal distribution 

distribution 

On the basis of above classification of ecosystems, the rice growing areas in the country have been broadly 

grouped into the following five regions: 

i) North-eastern region comprising of Assam, eastern Uttar Pradesh receives very heavy rainfall and 

hence rice is grown under rain fed conditions. 

ii) Eastern region has the highest intensity of rice cultivation in the country including the states of 

Bihar, Chhattisgarh, Madhya Pradesh, Orissa, eastern Uttar Pradesh and West Bengal. In this region 

rice is grown in the basins of Ganga and Mahanadi rivers. This region receives heavy rainfall and rice 

is grown mainly under rain fed conditions. 

iii) Northern region includes Haryana, Himachal Pradesh, Jammu & Kashmir, Punjab, western Uttar 

Pradesh and Uttranchal. Rice is grown mainly as an irrigated crop from May/July to September/ 

December in these states. 


25

iv) Western region comprising of Gujarat, Maharashtra and Rajasthan have a largely grown, rain 

fed area. 

v) Southern region includes Andhra Pradesh, Karnataka, Kerala, Tamil Nadu and Pondicherry where 

rice is mainly grown as irrigated crop in the deltas of the rivers Godavari, Krishna, Cauvery and the 

non-deltaic rain fed area of Tamil Nadu and Andhra Pradesh. Rice is grown under irrigated condition 

in deltaic tracts. 

7.4 7.4 Rice Rice Growing Growing Seasons 

Seasons 

Rice is grown under widely varying conditions of altitude and climate in the country and therefore, the 

rice growing seasons vary in different parts of the country, depending upon temperature, rainfall, soil 

types, water availability and other climatic conditions. In eastern and southern regions of the country, the 

mean temperature is found favourable for rice cultivation throughout the year. Hence, two or three crops 

of rice are grown in a year in eastern and southern states. In northern and western parts of the country, 

where rainfall is high and winter temperature is fairly low, only one crop of rice is grown during the 

month from May to November. 

There are three seasons for growing rice in India. These three seasons are named according to the season of 

harvest of the crop. 

Autumn Rice/Pre-Kharif Rice 

Summer Rice/Rabi Rice 

Winter Rice/Kharif Rice 

7.5 7.5 Cropping Cropping patterns 

patterns 

Rice cropping pattern in India vary widely from region to region and to a lesser extent from one year to 

another year depending on a wide range of soil and climatic conditions. Some of the rice based cropping 

patterns being followed in the country are as follows: 


Rice-Rice-Rice: This is most suitable for areas having high rainfall and assured irrigation facilities 

in summer months, particularly, in soils which have high water holding capacity and low rate of 

infiltration. In some canal irrigated areas of Tamil Nadu, a cropping pattern of 300% intensity is 

followed. In such areas three crops of rice are grown in a year. 

Rice-Rice-Cereals (other than rice): This cropping pattern is being followed in the areas where the 

water is not adequate for taking rice crop in summer. The alternate cereal crops to rice being grown 

are Ragi, Maize and Jowar. 

Rice-Rice-Pulses: In the areas where, there is a water scarcity to take up cereal crops other than rice in 

summer, the short duration pulse crops are being raised. 

26


Rice-Groundnut: This cropping pattern is being followed by the farmers of Andhra Pradesh, Tamil 

Nadu and Kerala. After harvesting of rice crop, groundnut is grown in summer. 

Rice-Wheat: This crop rotation has become dominant cropping pattern in the Northern parts of the 

country. 

Rice-Wheat-Pulses: In this sequence of cropping pattern, after harvesting of wheat green gram and 

cowpea as fodder are grown in the alluvial soil belt of Northern states. Besides, cowpea is grown in 

red and yellow soils of Orissa and black gram is grown in the black soils. 

Rice-Toria-Wheat: Rice-wheat cropping pattern is the most common and largest one. The Ricewheat 

cropping pattern is being practiced in the Indo-Gangetic plains of India since long time. 

Rice-Fish farming system: The field with sufficient water retaining capacity for a long period and 

free from heavy flooding are suitable for rice-fish farming system. This system is being followed by 

the small and marginal poor farmers in rain fed lowland rice areas. 

7.6 7.6 Breeding Breeding objectives objectives and and milestones 

milestones 

Rice breeding programme in India was started way back in 1911 in Bengal followed by Madras province 

(Tamil Nadu). Subsequently, rice research projects were initiated after the establishment of Indian 

Council of Agricultural Research in 1929 in various provinces. By 1950, 82 research stations in 14 

provinces were established fully devoted to rice research. These research stations released 445 improved 

varieties mainly by pure line method of selection. These varieties were bred for various ecotypes and 

other traits such as earliness, deep water and flood resistant, lodging resistant, drought resistant, nonshredding 

of grains, dormancy of seed, control of wild rice, disease resistant and response to heavy 

manuring. Thus, during the pure line period of selection from 1911-1949, the advantage of natural 

selection have been fully exploited and there have been varieties available for every rice ecology. The 

Central Rice Research Institute (CRRI) established in 1946. An inter-racial hybridization programme 

between japonicas and indicas was initiated during 1950-54. This programme continued in India upto 

1964 without much success. The International Rice Research Institute was established in the Philippines 

in 1960. This institute helped in evolving dwarf high yielding varieties based on the use of a gene from 

semi-dwarf varieties from Taiwan. Major breeding efforts in rice were thus initiated in the early 1960s 

and resulted in improved productivity, higher quality and increased tolerance to various biotic and 

abiotic stresses. Maximum impetus was achieved with the advent of the spontaneous mutant Dee-Geo- 

Woo-Gen which possessed a dwarfing gene. Dwarf, photo-insensitive and upright-effective plant types 

which were highly responsive to added dosages of inputs then gave new direction to the rice improvement 

programmes Following this plant type concept, Indian rice breeders developed many semi-dwarf 

rice varieties that increased the productivity of rice in the country and India became self-reliant in 

its rice production. 

The breeding priority has changed over the decades from purification of landraces placing emphasis on 

early maturity , consumer quality and blast resistance to recombining of desired traits through hybridization 

27

and recombinant DNA technology giving emphasis to high yield and value addition. Other important 

breeding objectives include disease/ pest resistance, field resistance against rice blast, tolerance to unfavourable 

conditions 

nutritive quality 

such as drought,submergence,salinity etc and cooking and 

Cytoplasmic genetic male sterility (CMS) system is being widely utilized for development of rice hybrids. 

The first commercially usable CMS line was developed in China, 1973 from a spontaneous male sterile 

plant isolated in a population of the wild rice O. sativa f. spontanea (Yuan, 1977) This source ‘Wild 

Abortive’ or ‘WA’ type is considered a landmark in the history of rice breeding. The first rice hybrid for 

commercial cultivation was launched by China in 1976. Efforts to develop and use of hybrid rice 

technology in India was initiated during 1970 but the research works were systematized and intensified 

since 1989 with a mission mode project and this helped India earn the distinction of being the second 

country after China to make hybrid technology a field reality. The first four rice hybrids were released 

in the country viz. APHR-1, APHR-2, MGR-1 and KRH-1 during 1994. Subsequently, several more 

hybrids have been released. 

7.7 7.7 7.7 Varietal arietal arietal testing testing testing of of of rice rice 

rice 

Indian Council of Agricultural Research (ICAR) started All-India Coordinated Rice Improvement 

Project (AICRIP) in 1965 at Hyderabad. The coordinated variety improvement and testing programme 

covers 46 funded cooperating centres in addition to 72 voluntary centres in different rice growing 

ecologies in the country and involves more than 300 scientists (Source: Progress Report, 2008, Vol. 1, 

Varietal Improvement, AICRIP, ICAR, DRR, Hyderabad, India). 

Under AICRIP, the following trials are carried out at 118 locations spread across 26 Indian States and 2 

Union Territories. 

1. Upland trials 

2. Lowland trials 

3. Irrigated trials 

4. Hybrid rice trials 

5. Basmati trials 

6. Slender grain trials 

7. Aromatic short grain trials 

8. Saline-alkaline tolerant trials 

9. Hill rice trials 

10. Aerobic trials 

11. Boro season trials 

12. Near isogenic trials (to test rice lines derived through marker-assisted breeding) 

13. International observational nurseries 

14. Rabi trials 


28

The AICRIP programme helps to exchange and evaluate breeding material quickly across the country. 

The aim of AICRIP programme is to improve yielding ability, increase efficiency in the use of external 

inputs and incorporate resistance to biotic and abiotic stresses. The multi-locational testing of breeding 

stock developed at different research centres is organized by AICRIP. The evaluation of genotype x 

environment interactions in different ecosystems has been the rationale for the multidisciplinary approach 

to rice improvement research. Depending on genotype sensitivity to photoperiod, three to four years are 

needed to identify a promising superior genotype based on data from the multilocational tests. 

In the first year, the newly evolved genotypes are tested in replicated local yield trials. The selected 

breeding lines from these experiments are included in the zonal coordinated trials called initial 

variety trial (or initial evaluation trial). Simultaneously, these breeding lines are also put to screening 

nursery tests for identifying their reaction to pests and diseases. The breeding lines that yield 

consistently well for two years are grouped to form advanced variety trials (or uniform variety trials) 

and tested for two more seasons. Agronomic data on these elite breeding lines are also generated 

during this period. After a careful scrutiny by different research centres, selected breeding lines are 

evaluated in on-farm trials for obtaining reaction of farmers and extension workers on the yield 

performance and acceptability. Considering yield records, agronomic data and the reaction to pests 

and diseases, candidate breeding lines are identified for release as varieties at the annual workshop by 

the coordinating unit. These are then named and released as new high yielding varieties to cultivators 

by the state or central variety release committee. 

7.8 7.8 Key Key Key insect insect pests pests and and diseases 

diseases 

Insect pests and diseases take a heavy toll of rice crop and thus are one of the important constraints in 

achieving higher rice yields. Blast disease continues to be the major constraint particularly in rainfed 

uplands, ranfed lowlands and hill ecosystem. Neckblast damage on basmati varieties is getting increasingly 

severe. Sheath blight causes considerable damage at endemic sites. False smit and sheath rot diseases have 

emerged as new threats to rice production. Bacterial leaf blight occurs frequently in some location. Rice 

tungro virus becomes a problem at a few places along the east cost in some years (ICAR, 2006). The 

major Insect pests and diseases are explained in the Annexure 2 and 3 respectively. 

8. 8. ST STATUS ST TUS OF OF RICE RICE CUL CULTIV CUL TIV TIVATION TIV TION 

The area under rice cultivation in India has risen from 8. 6 million hectares to 9.2 million hectares 

and the estimated increase in rice production for the year 2007-08 is 96.43 million tonnes compared 

to 88.25 million tones of the previous year. The demand for rice in India is projected to be 128 

million tonnes for 2012 and will require a production level of 3,000 kg per hectare against the 

present average yield of 1,930 kg per hectare. The impressive growth is mainly owing to wide 

adoption of high yielding, semi-dwarf varieties, increased use of chemical fertilizers and improved 

package of cultural practices. 


29

Rice is grown from Kashmir to Kanyakumari and Amritsar to Nagaland almost in every district with 

variations in area of cultivation. The entire country has been divided into five rice growing zones. These 

zones are mentioned below along with the states falling in each zone. 

S. No. Name of the Zone Name of the States 

1. Southern zone Andhra Pradesh, Karnataka, Kerala, Tamil Nadu, Pondicherry, 

Andaman & Nicobar Islands 

2. Northern zone Haryana, Himachal Pradesh, Jammu & Kashmir, Punjab, Uttarakhand 

3. Western zone Goa, Gujarat, Maharashtra, Rajasthan 

4. Eastern zone Bihar, Jharkhand, Madhya Pradesh, Chhattisgarh, Orissa, 

Uttar Pradesh, West Bengal 

5. North-Eastern zone Assam, Arunachal Pradesh, Manipur, Meghalaya, Mizoram, 

Nagaland, Sikkim, Tripura 

9. 9. BIO BIOTECH BIO TECH INTERVENTIONS INTERVENTIONS IN IN RICE 

RICE 

Rice is the first food crop for which complete genome sequence is available. This offers an unprecedented 

opportunity to identify and functionally characterize the genes and biochemical pathways that are responsible 

for agronomic performance, adaptation to diverse environments, resistance to biotic stress and consumer 

quality. The progress achieved in biotechnology applications for rice improvement is in two major areas 

viz. the use of molecular markers for identifying and introgressing favourable genes and gene combinations 

with the rice species, the use of transgenic technologies to incorporate genes/traits of interest. 

Although no transgenic rice has yet been commercialized in Asian countries, GM rice containing herbicide 

tolerant trait have been granted regulatory approval in the United States and also approved for food and 

feed use in other countries like Canada, Mexico, Australia, Colombia etc. Extensive research and 

development efforts are underway to develop transgenic rice broadly into herbicide tolerance, bioticstress 

resistance, abiotic-stress resistance and nutritional traits. Herbicide tolerance has been the major 

focus for the private sector led by the United States. Biotic-stress tolerance, on the other hand been the 


30

primary focus for private sector as well as public sector research institutions including those in Asia. 

Specific traits being worked in this category include resistance to bacterial blight using Xa21 gene, rice 

blast, various viral diseases, the brown planthopper, and yellow stem borer, the latter-using Bt technologybeing 

the closest to commercialization. For abiotic-stress tolerance, transgenic rice plants have been 

developed with tolerance to various conditions viz. drought and salinity. Regarding the nutritional traits, 

one of the most promising application of transgenic technology has been the development of vitamin Aenriched 

varieties, popularly known as Golden Rice due to the slightly yellow colour conferred to the 

endosperm (Portrykus, 2000). 

Various research institutions working in the area of GM rice in India include Directorate of Rice Research, 

Hyderabad; Central Rice Research Institute, Cuttack; Indian Agricultural Research Institute, New Delhi; 

University of Delhi South Campus, New Delhi; M.S. Swaminathan Research Foundation, Chennai; 

Tamil Nadu Agricultural University, Coimbatore etc. 


31

BO BOTANICAL BO ANICAL FEA FEATURES FEA TURES 


ANNEXURE-1 

Rice is a monocarpic plant that flowers once, set seeds and then die. Cultivated rice plant is an annual 

grass growing to 1–1.8 m with round, hallow and jointed culms, flat leaves and a terminal inflorescences, 

called panicle. Each culm or tiller is a shoot, which includes root, stem and leaves. 

Root oot 

The root system is fairly well developed in all species of rice. The root system consists of two major 

types: crown roots (the adventitious roots, including mat roots) that develop from nodes below the soil 

surface and the nodal roots that develop from nodes above the soil surface; bedsides the primary (seminal) 

roots. Primary root is direct prolongation of radicle that usually dies within a month. Dimorphism is a 

regular feature of rice roots, as originally they are thick and white with numerous root hairs on their 

entire surface. They become thinner, branched and brownish having hairs left only towards the root 

apex afterwards. Root hairs are tubular extensions of outermost layer of root and theses are generally 

short lived. The main rooting system of the plant develops at later stages of plant growth, when roots 

develop horizontally from the nodes of the stem below ground level (crown roots). 

In the “floating rice”, whorls of adventitious roots are formed from the first three very short nodes, 

giving rise to whorls of permanent adventitious roots. Tillers are produced at the nodes and adventitious 

roots are produced from lower nodes of these culms, so that the plant quickly develops a mass of 

adventitious roots. 

Stem 

Stem 

The stem has 2 parts, underground and aerial. The aerial part, has well defined solid nodes and hollow 

internodes. Another name for the aerial part of the stem of the rice plant is the culm which consists of 

several nodes spaced apart by internodes. The culm is more or less erect, cylindrical, and hollow except 

at the nodes, and varies in thickness from about 6-8 mm. At the base of the culm is a bladeless bract 

called the prophyllum. The first leaves are generated at the first node. Their sheaths envelop the main 

culm and this is called the primary tiller. Primary tillers emerge alternatively from the main stem, 

projecting in upward direction. The lower point of origin on the main stem, the older is the tiller. 

Secondary tillers arise from the first node of the primary tiller and generally have a fewer number of 

leaves. At the leaf junction at the furthermost node, ligules and a pair of auricles occur. The panicle also 

forms at the uppermost node and gives rise to the spikelets or fruits of the rice plant. 

32

The nodes are clearly defined by the presence of a distinct thickening, the Pulvinus, immediately above 

the node. The pulvinus may be coloured, varying in intensity from a “touch” of purple to a deep 

uniform purple. A bud may form in the axil of each leaf of the main stem, but normally only the 

lowermost bud from the crowded nodes at ground level develop into branches, thus a typical tillered 

plant develops. 

Leaf eaf 

Leaves on the main stem are produced one at a time and are arranged alternatively. The number of 

leaves borne on an axis is equal to the number of nodes. The first leaf of the plant is the sheathing leaf 

or coleoptile. The second leaf emerging through the lateral sheath of the coleoptile is reduced in size 

and has no blade. The remaining leaves are normal, except the uppermost or “flag” which is slightly 

modified. The angle of flag leaf is oriented more vertically than of preceding leaves. The uppermost leaf 

or flag of the axis possesses a blade always shorter and broader than the lower leaves. As the panicle 

emerges from the sheath, its blade is nearly parallel to the panicle axis. After the panicle has emerged 

the blade falls. 

The leaves are born at an angle of every node and they possess two parts viz., leaf blade or expanded 

parts and the leaf sheath which wraps the culms. The bud of potential tiller is enclosed in the sheath. 

The normal vegetative leaf has sheath, auricles and blade. The leaf sheath is an elongated, cylindrical 

structure that encloses and so protects the younger shoots inside of it. The leaf blade is flat, elongated, 

and ribbon like, the “leafy” part of the leaf, it is usually longer than the sheath, its major function is to 

perform photosynthesis. 


Source: http://www.ikisan.com 

33

Rice leaf can be distinguished from other rice like grasses by the presence of ligule and auricle. The 

white band at the junction of the blade and the sheath is called collar. The ligule is the papery scale 

located inside the blade and it looks like continuation of the sheath. The auricle is a pair of hairy, sickleshaped 

appendages located in the junction of the collar and the sheath. 

Flowers 

Flowers 

Inflorescence of rice is a terminal panicle (compound raceme) with single flowered spikelets, born on a 

long peduncle, which is the last internode of the culm. Panicle formation occurs at the tip of the 

growing point of the shoot. The spikelet consists of two short sterile lemma, a normal fertile lemma 

and palea (Fig. ). The floral organs are present protected within the Lemma and Palea, the hardened, 

modified stem. When the spikelet is closed, the lemma partly encloses the palea. The flower consists of 

two small, oval, thick, and fleshing bodies, the lodicules situated at the base of the axis. When floral 

parts mature, the lodicules swell and open the spikelet to expose the mature floral parts. 

The fertile lemma and palea enclose the sexual organs viz., six stamens arranged in whorls and a pistil 

at the centre. The stamen consists of bilobed anthers borne on slender filaments, while the pistil consists 

of ovary, style and feathery bifid stigma. The anther present in the stamen includes 4 elongated sacs 

where pollen grains are stored. The stigma is some what longer than broad, smooth and bears two styles 

and sometimes a short, rudimentary third. 


Fig : Parts of spikelet (From Chang and Bardenas 1965) 

34

The panicle has a main axis, known as ‘primary rachis’ which bears a number of secondary rachii. The 

secondary rachii further branch out into tertiary ones and produce in turn still smaller branches, known 

as ‘rachilla’. Each rachilla bears a spikelet at its tip. Much of the variability for spikelet number is due to 

variation in the number of secondary branches. 

Grain Grain 

Grain 

Rice grain, a caryopsis, is a dry one seeded fruit having its pericarp fused with seed coat. The outer 

protective covering of grain is called the Hull which consists of a lemma, a palea, an awn (tail), a rachilla 

(grain stem) and two sterile lemmas. The hull is hard cover of seed, which accounts for 20% of total seed 

weight. Other parts of the grain are the pericarp, seed coat and nucellus; and embryo and endosperm. 

The endosperm is made of starch, protein and fat. The endosperm consists of aleurone layer that 

encloses the embryo and the starchy or inner endosperm. It is the storehouse of food for embryo. The 

food needed for germination is stored here. 

Grain length varies with cultivar between 5 and 7 mm, and grains can be round, bold or slender. 


35

KEY KEY KEY INSECT INSECT PEST PEST PEST OF OF RICE 



ANNEXURE - 2 

Insect infestation is one of the most limiting factors in rice, as it is prompt to damage by various insects. 

More than 70 species are as pests of rice and about 20 have major significance. Together, they infest all 

parts of the plant at all growth stages. The yield losses vary from 20 to 50 per cent due to the damage 

caused by various insect Pests. 

1. 1. Rice Rice Stem Stem Borer Borer (Scirpophaga (Scirpophaga incertulas) 

incertulas) 

Rice stem borer is also commonly known as the yellow borer of rice. It is a regular pest in all parts of 

India and occurs both in kharif and rabi seasons. The pest affects the crop in the nursery, soon after 

transplanting and also in the pre-earhead stage. The caterpillars bore into stem and feed internally 

causing death of central shoot “dead hearts” in vegetative stage and “white earhead” at milky stage 

respectively. This results in chaffy grains. The larvae feed on green tissue of leaf sheath. 

Caterpillars bore into stem White ears in paddy due to YSB 

2. 2. Green Green L LLeaf 

L eaf F FFolder 

F older (Cnapholocrocis (Cnapholocrocis medinalis) 

medinalis) 

In India the rice leaf folder is another serious pest. Infestation usually occurs during late growth 

stages of the crop. Nymphs and Adults suck the sap from leaves. Infested leaves are characterized by 

small scratches like mark due to chlorophyll removal. They transmit “yellow dwarf” and “tungro 

virus” disease in rice. 

36

3. 3. Gundhi Gundhi Bug Bug (L (Leptocorisa (L eptocorisa oratorius) 

oratorius) 

Gundhi bugs also called stink bugs, are distributed in all rice growing areas in India. Nymphs and 

adults suck sap from the grain at the milk stage by which grains becomes chaffy, empty and some grains 

develop but break during milking. Damage by nymphs is more compared to adults. 

4. 4. Brown Brown Plant Plant Plant Hopper Hopper (Nilaparvata (Nilaparvata lugens) 

lugens) 


Leaf folder damage in paddy 

The brown plant hoppers are most serious pests of paddy. Nymphs and adults congregate at the base of 

plants, above water level, sucking the plant sap. The leaves turn yellow then brown and finally the 

plants dry and die. Sudden slumping of crop is the first sign of damage and affected patches give a 

scorched appearance called ‘Hopper-burn’. 

37

5. 5. Rice Rice Gall Gall Midge Midge (Orseolia (Orseolia oryzae) oryzae) 

oryzae) 

It is a serious pest of the rice growing countries, including India. The maggots crawl down the plant 

between leaf sheaths to reach the apical meristem on which they feed. The maggot feeding causes 

formation of a tubular sheath gall called silver shoot. The differentiation of tiler is affected and tiler is 

rendered sterile. 

6. 6. Rice Rice Hispa Hispa Hispa (Dicladispa (Dicladispa (Dicladispa armigera) 

armigera) 

It is common in wet-land environments and sporadic out breaks have been reported from almost all 

states of India including Andaaman & Nicobar Islands. Damage is caused by both the grubs and adult. 

Grubs feed by tunneling lower and upper epidermis resulting in regular translucent white patches. 

Adults scrape chlorophyll between the veins and so white parallel streaks are visible. Feeding on veins 

results in the formation of blotches on the leaves. 

7. 7. Climbing Climbing Climbing Cutworm Cutworm (Mythimma (Mythimma separate) 

separate) 

The climbing cut worm is also known as Rice Ear-eating caterpillar is a serious pest in Andhra Pradesh, 

Orissa and Uttar Pradesh. The early instar caterpillars feed on green leaves lemma and palea of the 

developing grains as well as anthers of flowers. Mature larvae, become gregarious and feed voraciously 

on young leaves at night. The final instar larvae cut off rice panicles from the peduncle. 


38

8. 8. Rice Rice Case Case W WWorm 

W Worm 

orm (Nymphula (Nymphula depunctalis depunctalis depunctalis guen) 

guen) 

The rice case worm is an important pest of irrigated and rain fed wet land. The pest attacks the crop in 

the early transplanted stage. The larvae cut the leaf tips and roll by spinning both margins to make 

tubular case. They live inside the tube, feed on leaves, float over the water to move from plant to plant 

and defoliate rice plant before maximum tillering. During heavy damage, leaves are skeletonised and 

appear whitish in color. 

9. 9. Rice Rice R RRoot 

R oot Aphid 

Aphid 

The nymphs and adults suck the sap from the tender roots. In heavy infestation seedlings growth is 

stunted, become pale yellow in color and do not flower. 


39

MAJOR MAJOR DISEASES DISEASES DISEASES OF OF RICE 



ANNEXURE-3 

Disease are considered major constraints in rice production. Rice diseases are mainly caused by fungi, 

bacteria or viruses. An over view of important fungal and bacterial diseases affecting the rice crop in 

India are as follows: 

Fungal ungal ungal diseases diseases of of Rice 

Rice 

1. Rice blast: Blast is caused by the fungus Pyricularia oryzae. Blast can infest any organ of the plant. 

Young seedlings, leaves, panicles and other aerial parts of the adult plant are affected and so often called 

as leaf blast, rotten neck, or panicle blast. The fungus produces spots or lesions on leaves, nodes, panicles, 

and collar of the flag leaves. Leaf spots are of spindle-shaped with brown or reddish-brown margins, 

ashy centers, and pointed ends. Infection of panicle base causes rotten neck or neck rot and causes the 

panicle to fall off. 

2. Sheath blight: The symptoms of sheath blight, another major fungal caused by Rhizoctonia solani. 

Symptoms become apparent at filtering or flowering stage. Spots or lesions first develop near the water 

level (in flooded fields) or soil (in upland fields) and spots initially appear on the leaf sheath. Spots may 

be oral or ellipsoidal and measure 1-3 cm long. Lesions on the leaf blade are usually irregular and 

banded with green, brown, and orange coloration. 

3. Brown spot: The disease symptoms of brown spot causes by Bipolaris oryzae are seen on leaves and 

glumes of maturing plants. Symptoms also appear on young seedlings and the panicle branches in older 

plants. Brown leaf spot is a seed-borne disease. The fungus causes brown, circular to oval spots on the 

coleoptile leaves of the seedlings. Leaf spots may be evident shortly after seedling emergence and continue 

to develop until maturity. 

4. False smut: False smut is caused by Ustilaginoidea virens is characterized by large orange to brown-green 

fruiting structures on one or more grains of the mature panicle. 

5. Black sheath rot: Gaeumannomyces graminis attacks the crown, lower leaf sheaths, and roots of the rice 

plant causing a dark brown to black discoloration of the leaf sheaths from the crown to considerably 

above the water line. As the discolored, infected sheaths decay, tiny, black the fungal reproductive 

structures (perithecia) form within the tissue. The disease is usually observed late in the main crop 

season and may cause reduced tillering, poor grain fill, and lodging. 

Bacterial diseases of Rice 

6. Bacterial leaf blight: The most serious bacterial disease is Bacterial leaf blight caused by Xanthomonas 

campestris pv oryzae. The first symptom of the disease is a water soaked lesion on the edges of the leaf 

40

lades near the leaf tip. The lesions expand and turn yellowish and eventually grayish-white. 

Leaves wilt and roll up and become grayish green to yellow. Entire plant wilt completely. Seedling 

wilt or kresek. 

7. Bacterial leaf streak: Xanthomonas oryzae pv. Oryzicola is responsible for bacterial leaf streak in which 

small, dark-green and water-soaked streaks appear initially on interveins from tillering to booting stage. 

Streaks dark-green at first and later enlarge to become yellowish gray and translucent. Numerous small 

yellow beads of bacterial exudates on surface of lesions on humid conditions. 

8. Bakanae disease: Gibberella fujikuroi causes Bakanae disease in which infected plants several inches 

taller than normal plants in seedbed and field. Thin plants with yellowish green leaves and pale green 

flag leaves. Dying seedlings at early tillering. Reduced tillering and drying leaves at late infection. 


41

NA NATURALL NA TURALL TURALLY TURALL Y OCCURRING OCCURRING PRED PREDATORS 

PRED ORS 

1. 1. Spiders 

Spiders 

2. 2. 2. Beetles Beetles 

Beetles 

3. 3. Bugs Bugs 

Bugs 


ANNEXURE-4 

The predominant predators that offer control of pests in rice crop are spiders, beetles, plant bug, 

damselfly etc as indicated below. 

Spiders play an important role in regulating insect pests in the agricultural ecosystem. Spiders as the 

wolf spiders, Lynx spider, Orb spider are known to consume a large number of prey and play an 

important role in reducing the densities of plant hoppers and leafhoppers in rice fields. 

Both the adults and nymphs prefer to prey upon various aphid, leafhopper and planthopper. In the 

absence of prey however they feed on the rice plant parts itself. Some e.g. are Ground beetle (Ophionea 

nigrofasciata), Rove beetle (Paederus fuscipes). Lady beetles are important insect predators in rice as 

Micraspis crocea (Mulsant) 

Microvelia douglasi atrolineata a short but broad small water bug can survive for long periods even 

without food provided the field is saturated or flooded as in rice fields. Both the adults and nymphs live 

on the water surface and attack insects that fall onto the surface. They are more successful as predators 

when they attack the host in groups. 

42

4. 4. Damselfy 

Damselfy 

5. 5. Crickets Crickets 

Crickets 

The narrow winged damselflies are weak fliers compared with their dragonfly cousins. The yellowgreen 

and black adults have a long slender abdomen. They feed on flying moths, butterflies, and hoppers. 

The following are common in rice Agriocnemis femina femina (Brauer), Agriocnemis pygmaea (Rambur). 

Two species of Crickets are common predators of rice insect pests i.e. Anaxipha longipennis (Serville) 

and Metioche vittaticollis (Sword-tailed Cricket). 


43

Biology of RICE Dec. 09.pmd - Department of Biotechnology

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