AUTHOR=Kumar Anuj , Gupta Chirag , Thomas Julie , Pereira Andy 

TITLE=Genetic Dissection of Grain Yield Component Traits Under High Nighttime Temperature Stress in a Rice Diversity Panel

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.712167

DOI=10.3389/fpls.2021.712167

ISSN=1664-462X

ABSTRACT=To dissect the genetic complexity of rice grain yield and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions of the USDA rice mini-core (URMC) were treated with high nighttime (HNT) stress at the reproductive stage of panicle initiation, and the quantifiable yield component response traits measured. The traits panicle length (PL) and number of spikelets per panicle (NSP) were evaluated in sub-sets of the panel comprising the rice sub-species O. sativa s.sp indica and s.sp. japonica. Under HNT stress the japonica s.sp. exhibited lower reduction in PL and NSP and showed higher level of genetic variation compared to the other sub-populations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for genome-wide association studies (GWAS) of the PL and NSP traits. The GWAS analysis in the combined, indica, and japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major grain yield component QTLs under heat stress. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules involved in primary and secondary metabolism pathways. The findings in this study could be useful to understand the pathways/mechanisms involved in rice grain yield and its components under HNT stress, for acceleration of rice-breeding programs and further functional analysis by molecular geneticists. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the japonica population, and 20 putative candidate genes were common in the combined, indica and japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules involved in primary and secondary metabolism. The findings in this study could be useful to understand the pathways/mechanisms involved in rice grain yield and its components under HNT stress, for rice breeders to accelerate breeding programs and molecular geneticists for further functional analysis.