Haplotype-based multi-locus genome-wide association study reveals genomic regions associated with reproductive stage high temperature stress tolerance in rice.

Abstract

High temperature causes harmful effects on growth, quality and yield of rice (Oryza sativa L.). Higher spikelet fertility is the most desirable trait for mitigating the effects of climate change, and thus need to develop rice varieties with climate resilience under future climate scenario for sustainable rice productivity. In our study, spikelet fertility and panicle weight were investigated under controlled environmental conditions in a set of 241 rice genotypes, which were sequenced in 3000 rice genomes project. High temperature significantly reduced the spikelet fertility and panicle wight by over 50% in this study. Genome wide association mapping was performed on spikelet fertility and panicle weight with 1 million SNPs using an efficient mixed model. Three promising MTAs viz., qHTSF19_5.2, qHTSF19_5.4 and qHTPW19_9.2 and haplotype variants of four putative candidate genes namely, LOC_Os05g15160 (a triose phosphate/phosphate translocator 2), LOC_Os05g16420 (SHR5-receptor-like kinase), LOC_Os09g15670 (an ABA-induced protein phosphatase 2Cs) and LOC_Os09g15700 (a receptor like protein kinase) were identified. The variations of non-synonymous SNPs (nsSNPs) in the gene sequences were used to group the association panel and identify superior donors and haplotypes. IRIS 313-8704 and IRIS 313-11307 were identified as superior donors with higher spikelet fertility and panicle weight under HT stress. Moreover, both the identified donors were found to be in the same haplotype group, highlighting their significance in developing haplotype specific markers that could be beneficial for marker-assisted breeding and making reproductive stage high temperature stress tolerant rice globally.