Biochemical and molecular marker-based screening of rice collections of the National Genebank of India reveals their japonica and wide compatibility status

Indica and japonica subspecies of rice represent different gene pools and agro-morphological characteristics. Inter sub-specific hybridization between them can result in heterosis and superior segregants for enhanced utilization. National Genebank of India comprises more than 0.12 million rice accessions, however, there is incomplete information with respect to the classification of rice germplasm for their indica and japonica status. In this study, 9172 indigenous rice accessions collected from Himalayan states of India were subjected to chemical based indica and japonica identification. Furthermore, the identified japonica lines were profiled with the S 5 InDel molecular marker for detecting the presence of a wide compatibility (WC) S 5 neutral ( S 5 n ) allele which enables normal fertility in the inter sub-specific F 1 hybrids. Out of the 9,172 accessions screened, 1,906 genotypes (20.78%) were identified as japonica, 6,375 (69.51%) as indica and 891 (9.71%) as mixed types. Collections from the state of Arunachal Pradesh contributed the highest number of japonica accessions, followed by Uttarakhand. Grain morphological studies revealed that 63.49% of the japonica types were medium bold, followed by medium slender and short bold grains. Accessions possessing the S 5 n allele predominantly emanated from Arunachal Pradesh (84%). The S 5 InDel markers identified the S 5 n allele in 613 japonica accessions, indicating their potential in hybrid breeding. These japonica accessions were further characterized for 53 agro-morphological traits and, genetic structure and inter trait relationship were estimated. The identification of japonica rice accessions containing S 5 n allele will infuse diverse ancestry in indica-japonica crosses for developing high yielding and stress-resilient varieties for sustainable rice production.