Kumar Anuj, Gupta Chirag, Thomas Julie, Pereira Andy
Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, Untied States.
Front Plant Sci. 2021 Sep 28;12:712167. doi: 10.3389/fpls.2021.712167. eCollection 2021.
To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies ssp. and ssp. . Under HNT stress, the ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, , and populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 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 GY component quantitative trait loci (QTLs) under heat stress. 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 population, with 20 putative candidate genes being common in the Combined, and populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.
为剖析水稻在生殖阶段响应热胁迫时籽粒产量（GY）和品质的遗传复杂性，对美国农业部（USDA）水稻微核心种质库（URMC）多样性面板中的190份不同水稻种质在幼穗分化生殖阶段进行夜间高温（HNT）胁迫处理。然后测量可量化的产量构成响应性状。在包含水稻亚种ssp.和ssp.的面板子集中评估了穗长（PL）和每穗小穗数（NSP）等性状。在HNT胁迫下，与其他亚群相比，ssp.在PL和NSP上的降低幅度较小，且遗传变异水平较高。全基因组测序鉴定出650万个单核苷酸多态性（SNP），用于PL和NSP性状的全基因组关联研究（GWAS）。在HNT胁迫下，组合群体、群体和群体中与PL相关的高度显著SNP分别为83个、60个和803个，而与NSP相关的高度显著SNP分别为30个、30个和11个。在这些与性状相关的SNP中’140个与先前报道的热胁迫下主要GY构成数量性状基因座（QTL）的基因组区域重合。利用水稻群体中的连锁不平衡程度，维恩图分析表明在群体中鉴定出的假定候选基因数量最多，有20个假定候选基因在组合群体、群体和群体中共有。对与PL和NSP相关的显著SNP连锁的基因进行网络分析，确定了参与初级和次级代谢的模块。本研究结果有助于理解HNT胁迫下水稻GY及其组成部分所涉及的途径/机制，以加速水稻育种计划，并为分子遗传学家进行进一步的功能分析提供帮助。
