Multivariate analysis and genome wide association mapping for chlorophyll fluorescence and grain number per panicle under high temperature stress in rice

High temperature stress adversely impact rice production, posing a serious threat to global food security in the global climate change scenario. HT stress impairs growth and photosynthesis by causing damage to the Photosystem II (PSII) complex. Additionally, HT stress affects spikelet fertility, grain filling and grains per panicle during reproductive development, and significantly reduce grain yield. In this context, identification of efficient genotypes with high maximum quantum efficiency of PSII and high grain number per panicle is critical. We have studied chlorophyll fluorescence (F_v/F_m) and grain number per panicle in a set of 127 Indian rice accessions under natural and controlled environmental conditions. Plants grown in pots were subjected to high temperature (38 °C) stress from booting till physiological maturity to assess their tolerance to high temperatures. A genome-wide association mapping was carried out on both traits using one million SNPs. Three significant QTLs (one each on chromosome 2, chromosome 3, and chromosome 11, respectively) along with three promising putative candidate genes and their haplotype variants were identified. Furthermore, our study identified accessions with high F_v/F_m and grain number per panicle under high temperature stress, and thus can be used as donors in breeding for heat tolerance. The significant QTLs identified in this study may be further investigated for fine-mapping and map-based cloning in the future.