Liu Dong, Ma Mengjuan, Yu Fengjiang, Li Qiulin, Li Ming, Li Rui, Fu Jing, Wang Yuetao, Wang Fuhua, Yin Haiqing, Zhang Zhanying, Li Zichao, Wang Ya
Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
School of Agriculture, Yunnan University, Kunming, Yunnan, 650091, China.
BMC Plant Biol. 2025 Sep 1;25(1):1172. doi: 10.1186/s12870-025-07269-0.
Submergence stress is a major obstacle limiting the application of direct seeding in rice cultivation. Therefore, understanding the genetic basis of submergence tolerance in rice is of great significance for identifying favorable genes and developing superior rice varieties. However, few studies have focused on submergence tolerance during seed germination; thus, the genetic basis of submergence tolerance at this stage deserves more attention.
In this study, a natural population of 432 rice varieties collected from 25 provinces in China and other countries was used for the first time to evaluate submergence tolerance during seed germination. Population structure analysis revealed that this population was divided into two groups and was rich in genetic diversity. Our findings confirm that japonica rice is more tolerant to submergence than indica rice during seed germination. A genome-wide association study (GWAS) was performed using the phenotypic data of 432 rice varieties and a 3,548,101 single-nucleotide polymorphism (SNP) dataset using a mixed linear model. Thirteen QTLs (P < 0.0001) were identified for the coleoptile length (CL) under submergence (10 cm depth of water), of which four QTLs (qCL3-1, qCL4-2, qCL5-1, and qCL5-2) colocalized with those from previous studies, while nine QTLs (qCL2-1, qCL2-2, qCL2-3, qCL2-4, qCL3-2, qCL4-1, qCL8-1, qCL8-2, and qCL9) were reported for the first time. Among these QTLs, qCL9, which harbored the most significant SNP, explained most of the phenotypic variation. Using quantitative real-time polymerase chain reaction (qRT-PCR) analysis and phenotypic identification of the knockout lines, three genes (LOC_Os09g11590, LOC_Os09g11660, and LOC_Os09g11760) were identified as candidates for qCL9. There were 28, 13, and 13 non-synonymous SNPs in LOC_Os09g11590, LOC_Os09g11660, and LOC_Os09g11760, respectively, from which 5, 3, and 5 haplotypes were detected in rice varieties.
This natural population, consisting of 432 rice varieties combined with high-density SNPs, provides a valuable resource for identifying rice QTLs/genes in the future. The detected QTLs/genes associated with submergence tolerance during seed germination in rice offer new insights for gene discovery and will facilitate the breeding of rice varieties with improved tolerance to submergence stress.
淹水胁迫是限制水稻直播栽培应用的主要障碍。因此，了解水稻耐淹性的遗传基础对于鉴定有利基因和培育优良水稻品种具有重要意义。然而，很少有研究关注种子萌发过程中的耐淹性；因此，这一阶段耐淹性的遗传基础值得更多关注。
在本研究中，首次使用从中国25个省份及其他国家收集的432个水稻品种的自然群体来评估种子萌发过程中的耐淹性。群体结构分析表明，该群体分为两组，具有丰富的遗传多样性。我们的研究结果证实，在种子萌发过程中，粳稻比籼稻更耐淹。使用432个水稻品种的表型数据和一个包含3,548,101个单核苷酸多态性（SNP）的数据集，采用混合线性模型进行全基因组关联研究（GWAS）。在淹水条件下（水深10厘米），鉴定出13个与胚芽鞘长度（CL）相关的QTL（P < 0.0001），其中4个QTL（qCL3-1、qCL4-2、qCL5-1和qCL5-2）与先前研究中的QTL共定位，而9个QTL（qCL2-1、qCL2-2、qCL2-3、qCL2-4、qCL3-2、qCL4-1、qCL8-1、qCL8-2和qCL9）为首次报道。在这些QTL中，具有最显著SNP的qCL9解释了大部分表型变异。通过定量实时聚合酶链反应（qRT-PCR）分析和敲除系的表型鉴定，鉴定出三个基因（LOC_Os09g11590、LOC_Os09g11660和LOC_Os09g11760）作为qCL9的候选基因。LOC_Os09g11590、LOC_Os09g11660和LOC_Os09g11760分别有28个、13个和13个非同义SNP，在水稻品种中检测到5种、3种和5种单倍型。
这个由432个水稻品种组成并结合高密度SNP的自然群体为未来鉴定水稻QTL/基因提供了宝贵资源。检测到的与水稻种子萌发过程中耐淹性相关的QTL/基因为基因发现提供了新的见解，并将促进耐淹水胁迫水稻品种的培育。
