Xue Li, Wang Sen, Zhang Qiuyu, Han Bing, Cui Di, Han Longzhi, Deng Jianxin, Ma Xiaoding
College of Agriculture, Yangtze University, Hubei, China.
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Front Plant Sci. 2025 May 13;16:1546580. doi: 10.3389/fpls.2025.1546580. eCollection 2025.
Mesocotyl length is a key trait affecting seedling emergence and establishment in dry direct-seeded rice, with longer mesocotyls promoting rapid and uniform emergence, thereby forming larger effective populations. Therefore, mining genes associated with mesocotyl length will facilitate the development of rice varieties suitable for dry direct seeding. In this study, 300 rice germplasm resources with a wide range of sources were selected as experimental materials. Phenotypic traits such as mesocotyl length and seedling emergence rate were systematically determined in each variety by setting different mulch depth treatments. Genome-wide association analysis (GWAS) was used to locate QTL controlling mesocotyl length and predict candidate genes. The results showed that mesocotyl length increased significantly with greater soil cover depth, while excessively deep sowing treatments inhibited seedling emergence. The GWAS analysis identified four QTLs associated with mesocotyl length and two QTLs associated with seedling emergence, with phenotypic contributions of 6.96-8.48%. Among them, the mesocotyl length-related QTL located at 28.03-28.43 Mb on chromosome 3 was detected at both sowing depths. Gene annotation analysis identified nine candidate genes related to plant hormones and transcription factors for . Further investigation revealed three genes (, , and ) exhibiting distinct haplotypes with significant differences in mesocotyl length, suggesting they may be causal genes for . The results provide new clues to elucidate the molecular mechanism of rice mesocotyl development and lay an important foundation for subsequent gene function verification and molecular breeding. In the future, the functions of these candidate genes will be verified by transgenic and other methods, and molecular markers will be developed for genetic improvement of drought-tolerant rice varieties.
中胚轴长度是影响旱直播水稻种子萌发和幼苗建成的关键性状，较长的中胚轴有利于快速、均匀地出苗，从而形成更大的有效群体。因此，挖掘与中胚轴长度相关的基因将有助于适合旱直播的水稻品种的培育。本研究选取了300份来源广泛的水稻种质资源作为实验材料。通过设置不同的覆土深度处理，系统测定了每个品种的中胚轴长度和出苗率等表型性状。利用全基因组关联分析（GWAS）定位控制中胚轴长度的QTL并预测候选基因。结果表明，随着土壤覆盖深度的增加，中胚轴长度显著增加，而过深的播种处理会抑制种子萌发。GWAS分析鉴定出4个与中胚轴长度相关的QTL和2个与出苗率相关的QTL，表型贡献率为6.96-8.48%。其中，位于第3染色体28.03-28.43 Mb处的中胚轴长度相关QTL在两个播种深度均被检测到。基因注释分析鉴定出9个与植物激素和转录因子相关的候选基因。进一步研究发现3个基因（、和）表现出不同的单倍型，中胚轴长度存在显著差异，表明它们可能是中胚轴长度的因果基因。该结果为阐明水稻中胚轴发育的分子机制提供了新线索，为后续基因功能验证和分子育种奠定了重要基础。未来，将通过转基因等方法验证这些候选基因的功能，并开发分子标记用于耐旱水稻品种的遗传改良。
