Dissecting genetic variation for agro-morphological traits of elevated temperature under CO2-temperature gradient chamber and validation of markers linked to heat tolerance of rice (Oryza sativa L.)‏ cultivars of north-eastern Himalayan Region

Global warming is causing increased temperatures that are affecting crop yield and sustainability. To harness the diversity present in rice germplasm, 1100 rice genotypes from the north-eastern Himalayan region (NEHR) were evaluated for high yield stability and marker-trait associations using SSR markers under ambient and elevated temperature conditions in the CO 2 -temperature gradient chamber (CTGC). Compared to ambient temperature, most agro-morphological traits showed a decreasing trend under elevated temperature, while PCV, GCV, heritability, and GAM tended to increase with elevated temperature. Pollen fertility percentage ranged from 5.4 to 99.4% at ambient temperature and from 3.4 to 98.6% at elevated temperature. The yield per plant (YPP) was significantly positively associated with traits like plant height (PH), panicle length (PL), number of tillers per plant (NT), number of effective tillers per plant (NET), number of filled grains per panicle (NFGPP), spikelet fertility percentage (SFP), and panicle weight (PW), under ambient and elevated temperature conditions. The polymorphism information content (PIC) values of markers associated with heat tolerance ranged from 0.02 to 0.77, with an average of 0.26. A total of 91 alleles were detected, ranging from 2 (RM570, RM225) to 11 (RM364), with an average of 3.14 alleles per marker. The AMOVA results showed that a significant percentage of variation was attributed to the genotypes within the population (67.50%). Based on the F ST value (6.42%), genotypes from Meghalaya and Tripura were significantly differed from those outside the NEHR. Model-based clustering revealed that 86 genotypes had more than 80% genetic purity to their respective ancestry. In comparison, seven genotypes (Sojkyrleh, RCPL 1–123, RCPL 1–136, RCPL 1–74, RCPL 1–188, Sialkathi and Bapnah) had less than 80% genetic purity and were considered admixtures. Two markers, RM234 and RM7364, were found to be significantly associated with yield per plant under elevated temperature conditions using both the general linear model (GLM) and mixed linear model (MLM) approach. Genotypes such as TRC-2016–291, TRC-2007–1, TRC-2016–426, Daya, Badjhania, TRC-2016–624, TRC-2016–33, Nania, TRC-2016–51, Aati Ghal and TRC-2016–153, which exhibited superior performance for yield and component traits were selected as high yielding for the elevated temperature conditions of NEHR.