Table_2_QTL Mapping for Leaf Area of Tea Plants (Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing.XLS

High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on “Jinxuan,” “Yuncha 1” and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.

高质量遗传图谱在数量性状位点（Quantitative Trait Locus, QTL）定位与分子标记辅助育种中发挥着重要作用。茶叶不仅是茶树重要的营养器官，亦是兼具重要经济价值的收获器官。然而，调控叶片面积的关键基因及遗传机制尚未阐明。本研究对"金萱"、"云茶1号"及其96株F1杂交后代开展全基因组重测序，从1.84 TB的原始测序数据中共鉴定得到大量遗传变异位点，包括28144625个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）与2780380个插入缺失标记（Insertions-Deletions, indels）。结合已报道遗传图谱的标记，本研究构建了一套包含15个连锁群、涵盖8956个高质量单核苷酸多态性标记的高密度遗传图谱，该图谱总长度为1490.81 cM，与参考基因组展现出良好的共线性。本研究共鉴定得到25个与叶片面积相关的代表性标记（潜在QTL），且这些标记附近的大、小叶片样本中存在差异表达基因。全基因组关联分析（Genome-Wide Association Study, GWAS）进一步验证了QTL定位结果的可靠性。靶向这些潜在QTL区域新开发的31对插入缺失标记展现出较高的多态性，可有效区分大、小叶片茶树样本。本研究可为茶树遗传育种、数量性状定位及产量提升提供必要的技术支撑与全新研究视角。