Genetic potential unravelling for anaerobic germination tolerances in North-eastern Indian rice (Oryza sativa L.) germplasm

Anaerobic germination is one of the constraints faced by direct-seeded rice (DSR) plants, causing poor and irregular germination. In this study, 281 rice germplasm lines were screened for anaerobic germination. Based on the phenotypic variation of root length, coleoptile length and percentage of germination, 24 genotypes were identified as anaerobic germination tolerant. The correlation analysis showed a significant association among phenotypic traits in aerobic and anaerobic germination. Out of 281, 24 rice germplasm lines were found to be tolerant to anaerobic germination based on a positive response index of >0.1. The genetic diversity among the 48 selected germplasm using 48 SSR markers of 12 rice chromosomes revealed a prevalence of enough diversity for marker-trait association analysis. The PIC value ranged from 0 to 0.375, with the maximum (0.375) in RM16238, RM7311, RM20228, RM22321, RM25866 and RM26603 markers. The dendrogram based on UPGMA-based clustered analysis and population structure clustered the 48 individuals into two major groups. Marker-traits association analyses identified five SSR markers (RM20948, RM26033, RM16730, RM23732 and RM25866) that were strongly associated with root length and coleoptile length with a phenotypic variance of 1.1 to 9.9%. These findings provide valuable insights into the genetic architecture and population structure underlying anaerobic germination tolerance in rice, facilitating future breeding efforts to develop improved DSR varieties.