Chen Lei, Chen Weiwei, Li Jin, Wei Yu, Qing Dongjin, Huang Juan, Yang Xinghai, Tang Maoyan, Zhang Zhanying, Yu Jianping, Deng Guofu, Dai Gaoxing, Chen Chao, Liang Tianfeng, Pan Yinghua
Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
Rice (N Y). 2025 Mar 11;18(1):13. doi: 10.1186/s12284-025-00770-y.
High temperature significantly impacts grain appearance quality, yet few studies have focused on identifying new quantitative trait loci (QTLs)/genes related to these traits under heat stress during the flowering stage in rice. In this study, a natural population of 525 rice accessions was used to identify QTLs and candidate genes associated with grain appearance quality using a Genome-Wide Association Study under heat stress. We identified 25 QTLs associated with grain length (GL), grain width (GW), and grain chalkiness (GC) under heat stress across 10 chromosomes in the three rice populations (full, indica, and japonica). Notably, three sets of overlapping QTLs were identified (set 1: qHTT-L3 and qHTT-XL3; set 2: qHTT-C5 and qHTT-XC5; set 3: qHTT-L11.1 and qHTT-GL11), located on chromosomes 3, 5, and 11, respectively. Haplotype analysis indicated that Hap1 is the superior haplotype, and pyramiding more than two superior alleles improved rice grain appearance quality (longer GL, wider GW, and lower GC) in high-temperature environments. Based on RNA-seq, qRT-PCR and functional annotations analysis, LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 were highly expressed, identifying them as the high-priority candidate genes for QTLs linked to grain appearance quality (GL, GW, and GC) under heat stress. Expression analysis revealed that LOC_Os05g06920, which encodes a relA-SpoT-like protein RSH4, and LOC_Os11g28104, which encodes a protein kinase with a DUF26 domain, were highly expressed in seeds, leaves, and shoots. And LOC_Os05g06970, encoding a peroxidase precursor, exhibited high expression levels in roots. Compared to the wild-type (WT) plants, the mutants of LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 exhibited increased GL and grain length-to-width ratio, but reduced GW under both natural and heat stress conditions, while the LOC_Os05g06970 and LOC_Os11g28104 mutants significantly increased the chalky grain rate and grain chalkiness degree under natural conditions. Furthermore, the LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 mutants showed a lower decline in grain appearance quality traits than the WT after high-temperature treatment. These findings suggest that LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 play crucial roles in regulating both grain development and heat tolerance under heat stress at anthesis, thus affecting grain appearance quality in rice. Our results provide a promising genetic resource for improving rice grain appearance quality under heat stress.
高温显著影响稻米外观品质，但在水稻开花期热胁迫下，很少有研究聚焦于鉴定与这些性状相关的新数量性状位点（QTL）/基因。在本研究中，利用一个包含525份水稻种质的自然群体，通过全基因组关联研究在热胁迫下鉴定与稻米外观品质相关的QTL和候选基因。我们在三个水稻群体（籼稻、粳稻和常规稻）的10条染色体上鉴定出25个与热胁迫下粒长（GL）、粒宽（GW）和粒垩白（GC）相关的QTL。值得注意的是，分别在第3、5和11号染色体上鉴定出三组重叠QTL（第1组：qHTT-L3和qHTT-XL3；第2组：qHTT-C5和qHTT-XC5；第3组：qHTT-L11.1和qHTT-GL11）。单倍型分析表明，单倍型1是优良单倍型，聚合两个以上优良等位基因可在高温环境下改善水稻籽粒外观品质（更长的粒长、更宽的粒宽和更低的垩白度）。基于RNA测序、qRT-PCR和功能注释分析，LOC_Os05g06920、LOC_Os05g06970和LOC_Os11g28104高表达，确定它们为热胁迫下与籽粒外观品质（粒长、粒宽和垩白度）相关QTL的高优先级候选基因。表达分析显示，编码relA-SpoT样蛋白RSH4的LOC_Os05g06920和编码具有DUF26结构域的蛋白激酶的LOC_Os11g28104在种子、叶片和茎中高表达。而编码过氧化物酶前体的LOC_Os05g06970在根中表达水平较高。与野生型（WT）植株相比，LOC_Os05g06920、LOC_Os05g06970和LOC_Os11g28104的突变体在自然和热胁迫条件下均表现出粒长和长宽比增加，但粒宽减小，而LOC_Os05g06970和LOC_Os11g28104的突变体在自然条件下显著增加了垩白粒率和垩白度。此外，高温处理后，LOC_Os05g06920、LOC_Os05g06970和LOC_Os11g28104的突变体籽粒外观品质性状的下降幅度低于野生型。这些结果表明，LOC_Os05g06920、LOC_Os05g06970和LOC_Os11g28104在花期热胁迫下对籽粒发育和耐热性的调节中起关键作用，从而影响水稻籽粒外观品质。我们的研究结果为提高热胁迫下水稻籽粒外观品质提供了有前景的遗传资源。
