Key Message

By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

Abstract

Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.

中文翻译：

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耐热水稻品种开发的生殖组织特异性meta-QTLs和候选基因。

关键信息

通过整合遗传学和基因组学数据，鉴定了生殖组织特异性和热应激响应的 35 个元 QTL 和 45 个候选基因，可通过标记辅助育种来快速开发耐热水稻品种。

抽象的

水稻掌握着未来粮食安全的关键。在水稻种植区，温度已经达到最适宜生长的水平，因此，全球气候变化导致的任何进一步升高都可能显着降低水稻产量。一些作图研究已经确定了过多的生殖组织特异性和热应激相关的不一致数量性状基因座 (QTL)，可用于提高耐热性。在这项研究中，我们对先前报道的 QTL 进行了荟萃分析，并在不同的遗传背景和环境中确定了 35 个最一致的元 QTL (MQTL)。近 66% MQTL 的遗传和物理间隔分别小于 5 cM 和 2 Mb，表明耐热性的热点基因组区域。MQTL 基础基因与基于微阵列和 RNA-seq 的转录组数据集的比较分析揭示了 45 个热响应基因的核心集，其中 24 个是生殖组织特异性基因，以前没有进行过详细研究。值得注意的是，所有这些基因都对应于各种胁迫相关功能，从非生物胁迫感应到调节植物胁迫反应，包括热休克基因。OsBiP2、OsMed37_1）、转录因子（OsNAS3、OsTEF1、OsWRKY10、OsWRKY21）、跨膜转运蛋白（OsAAP7A、OsAMT2;1）、糖代谢（OsSUS4、α-Gal III）和非生物胁迫（OsRCI2-7、SRWD1）基因。来自拟南芥热休克基因的功能数据证据也表明OsBIP2可能与花粉管在热应激条件下的耐热性有关。此外，已鉴定基因的启动子富含热、脱水、花粉和糖响应性顺式作用调节元件，表明水稻中可能存在一种共同的调节机制来减轻生殖期热应激。这些发现有力地支持了我们的结果，并为耐热水稻品种的快速开发提供了新的候选基因。