Exploring genetic diversity, population structure and stability for yield related traits in rice germplasm of northeastern India

The northeastern region of India, being a biodiversity hotspot and the probable origin of rice, harbors enormous diversity for the crop. However, many of the landraces have become extinct due to increasing human interference, favoring improved cultivars over local landraces, urbanization, and climate change. Systematic evaluation of landraces for their genetic potential and population structure is scanty. Yield potential and stability were investigated based on agro-morphological evaluation during Kharif (monsoon or rainy season) 2020-2022. In additive main effects and multiplicative interaction (AMMI) analysis, genotype by environment (G x E) interactions derived interactions principal component axes 1 (IPCA1) and 2 (IPCA2) explained 59.8% and 40.2% of total multiplicative variations for yield per plant, respectively. The first five principal components cumulatively explained 78.02% of the variance. Genotyping of 88 rice genotypes along with five checks was performed with 50 Simple Sequence Repeat (SSR) markers. A total of 111 alleles were identified using 42 polymorphic SSRs, with an average of 2.64 alleles per locus. The Shannon information content ranged from 0.035 (RM454) to 1.284 (RM1). High values of expected heterozygosity (0.43) and polymorphism information content (0.65) were observed with markers RM1, RM152, and RM334 with a high PIC value (> 0.5). Genetic distance and model-based clustering have differentiated the 93 genotypes into three major groups. The analysis of molecular variance (AMOVA) explained 6.7% variation among the population and 93.3% variation within the population. Based on FST calculations, landraces from Manipur and Meghalaya were similar at the molecular level, whereas landraces from Assam, Arunachal Pradesh, Sikkim, and Nagaland were significantly different. Based on AMMI stability value, the sum of absolute values of the IPC scores, the absolute value of the relative contribution of IPCs to interactions, weighted average of absolute scores, and multi-trait genotype ideotype distance index values calculated over three-year performances, landraces namely, Manipur Special, GR-12, Bhumap, PR-26850, Yemshea Ngha, Welhinyi, Kezurd, Chini Dhan, Dalbao, and Ruboke-30, were selected and would be utilized in a sustainable manner to increase the yield potential vis a vis farmers' income.