Evaluation of genetic diversity and population structure for anaerobic germination under saline submergence condition using hypervariable SSR markers in a diverse set of global rice accessions

Saline submergence is an important stress for the vast coastal regions of many countries including India. A total of 21 polymorphic simple sequence repeat (SSR) markers distributed across 11 chromosomes of rice were used to study the genetic diversity in a diverse collection of 143 rice accessions from different parts of the world. The polymerase chain reaction profile obtained from 21 SSR markers generated a total of 139 allelic variations. Four genotypes Annakulam Pokkali (IC145150A), Annakulam Pokkali (IC145150B), Pokkali-Ezhikkara-IC324580, and Pokkali-IC324587 showed the higher number of alleles (16) for the miR169j SSR at Chr 9. The population structure analysis divided all the 143 genotypes into three sub-populations and phylogeny analysis revealed three  distinct genetic clusters suggesting how these genotypes were highly diversified and evolutionarily related to each other. We further treated the genotypes under low saline submergence (5 dSm⁻¹; 42.92 mM NaCl) and high saline submergence (10 dSm⁻¹; 85.83 mM NaCl) at germination stage for 5 days to evaluate the germination percentage. A total of 133 accessions were found to have moderate to high level of tolerance and 10 accessions were susceptible to anaerobic germination under saline-submergence. Our results indicated that Carolina Gold (EC792285) and Pokkali-BJJ/10-2 genotypes are highly tolerant and promising to the saline submergence condition for anaerobic germination. All of the tolerant Pokkali accessions were seen to cluster in the same clade in the phylogenetic tree whereas susceptible accessions grouped in the same cluster. Clear distinction in the pattern of clustering among tolerant and susceptible accessions were visible. Hence, some of the highly tolerant genotypes identified in our study can be used as donors for rice breeding programme. Improved rice ultivars can be developed further by introgression of promising candidate genes associated with saline submergence tolerance in anaerobic condition.