Whole-Genome Resequencing Reveals Adaptive Variants in Heat-Tolerant Rice Cultivars
DOI:
https://doi.org/10.5281/zenodo.22687627Keywords:
Oryza sativa, whole-genome resequencing, heat tolerance, spikelet fertility, selective sweep, genome-wide association studyAbstract
Heat stress during flowering is one of the most damaging climate-related threats to rice yield, since even a few
hours above the critical temperature threshold at anthesis can sharply reduce spikelet fertility, yet the genetic
basis of natural variation in heat tolerance at this stage remains only partially resolved. We performed
whole-genome resequencing at a mean depth of 14.8x on 120 Oryza sativa accessions -- 64 heat-tolerant
landraces sourced from historically hot rice-growing regions of South and Southeast Asia and 56 heat-sensitive
check varieties -- and combined genome-wide association analysis of spikelet fertility under controlled heat stress
(38C, 4 hours daily during a 7-day anthesis window) with a genome-wide selective-sweep scan (FST and
XP-CLR) contrasting the two phenotypic groups. Under heat stress, spikelet fertility ranged from 9.4% to 88.6%
across accessions and was strongly bimodal between the two source groups (tolerant group mean 71.2%,
sensitive group mean 24.6%; t-test P<0.001). Genome-wide association identified 14 SNPs reaching
genome-wide significance (P<8.2x10-8 after Bonferroni correction), clustering into six independent loci on
chromosomes 1, 3, 6, 9 and 10, with the strongest association (P=3.1x10-14) located approximately 8 kb
upstream of OsTT1, a proteasome alpha2 subunit gene previously implicated in thermotolerance through
enhanced clearance of heat-denatured proteins. The selective-sweep scan independently flagged four of these six
GWAS-identified regions among its top 20 genome-wide FST outlier windows, providing convergent evidence that
these loci have been under recent positive selection in heat-tolerant germplasm rather than representing chance
GWAS associations. Haplotype analysis at the OsTT1 locus identified a tolerant-associated haplotype carrying
three linked promoter-region variants, present in 89% of tolerant accessions but only 12% of sensitive accessions,
consistent with this haplotype being a primary driver of the locus's association signal. These results narrow the
genetic basis of heat tolerance at anthesis in rice to a tractable set of candidate loci suitable for marker-assisted
selection in breeding programmes targeting warming production environments.
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