Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses

Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait.

热带地区气候变化背景下，水稻受精过程对高温的敏感性是一项核心关切问题。本研究针对由167份籼型地方品种与改良品种组成的关联群体开展表型鉴定：于开花期38℃胁迫条件下测定其小穗不育率（spikelet sterility, SPKST），并考察了若干可能影响穗部微气候、进而干扰受精过程的次级性状。该群体通过测序分型技术（genotyping by sequencing, GBS）完成基因分型，平均标记密度达到每29 kb一个标记。本研究分别采用单标记回归、单倍型回归以及全标记同时拟合三种分析方法开展全基因组关联分析（Genome-wide association analyses, GWAS），最终检测到14个可在至少两种GWAS方法中均表现出显著关联的小穗不育率相关位点。同时，次级性状也被检测到大量关联位点。通过将本研究鉴定的小穗不育率关联位点与已发表文献中双亲和杂交后代群体定位的数量性状位点（Quantitative Trait Locus, QTL）进行共定位分析，我们将其中8个QTL的位点区间进行了精准缩减，其中包括研究最为深入的qHTSF4.1。与小穗不育率关联位点对应的基因家族功能跨度广泛，涵盖非生物逆境感应与植物响应调控（如细胞壁相关激酶、热激蛋白）、细胞分裂以及配子体发育等多个生物学过程。基于水稻3000基因组计划中与小穗不育率关联位点邻近区域的多样性分析显示，有利等位基因在亚洲栽培稻（Oryza sativa）的各遗传类群中均呈现广泛分布，但尚未发现可在所有关联位点上聚合有利等位基因的材料。有效的耐热供体材料包括耐热品种N22以及部分印度和中国台湾地区的水稻品种。本研究结果可为开花期耐热水稻品种选育以及调控该性状的关键位点功能验证提供重要理论依据与研究基础。