Fig 1.
Common wild rice lines at reproductive stage in the field.
(A) Huaye 1. (B) Huaye 2. Right panels are representing grains of respective lines. These lines were developed from non-shattering plant with high seed setting of common wild rice.
Table 1.
Summary of the genome wide resequencing data of wild rice lines mapped onto the reference genomes.
Table 2.
Summary of the whole genome sequence variations between wild rice lines and reference genomes.
Table 3.
The frequency of SNP bases substitution between wild rice lines and reference genomes.
Fig 2.
Annotation and distribution of SNPs and InDels between common wild rice lines and Nipponbare reference genome.
SNPs, insertions and deletions on the rice pseudomolecules were classified as genic and intergenic regions, and locations within the gene models were annotated. The number of SNPs, insertions and deletions in each class is shown. A and B indicate the distributions of SNPs and InDels in the comparisons of Huaye 1 and Nipponbare reference genome, and Huaye 2 and Nipponbare reference genome, respectively.
Fig 3.
Functional characterization of the resistance genes into gene ontology (GO) terms.
(A) and (B) indicate the annotation of resistance genes that were detected in the comparisons of Huaye 1 and reference genomes, and Huaye 2 and reference genomes of Nipponbare and 93–11, respectively.
Table 4.
Classification of NBS-LRR genes that showed sequence variations in two wild rice lines.
Fig 4.
Validation of NBS like genes in wild rice genome.
(A) and (B) indicate the PCR products of Huaye 1 and Huaye 2 mapped onto the reference genomes, respectively. M represents DNA Marker, and the vertical letters indicate the gene ID.
Fig 5.
Density map of NBS-LRR resistance genes that were detected between Huaye 1 and reference genome of 93–11.
Fig 6.
Phylogenetic relationships between NBS regions in two wild rice lines.
The names in each branch represent wild rice lines, chromosome number and gene ID. *indicates the novel NBS like genes that were explored from particular reference genome. The scale bar indicates the genetic distance.
Table 5.
Tajima's neutrality test on the NBS sequence data of two wild rice lines.
Fig 7.
Protein-protein interaction network of NBS-related genes associated with the resistant factors.
(A) and (B) indicate the protein-protein interaction network of NBS-related genes between wild rice lines and reference genome of 93–11, (C) indicates the protein-protein interaction network of NBS-related genes between wild rice lines and reference genome of Nipponbare.