Table6_A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia.XLSX

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

栀子是中国传统药用园艺植物，但其分子遗传学研究整体滞后。本研究构建了包含200个真实杂交个体的F1群体。采用测序分型（genotyping-by-sequencing, GBS）技术，构建了一张高密度性别平均遗传图谱，该图谱包含4249个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，总图距为1956.28 cM，平均遗传距离为0.46 cM。本研究开发了17个基于SNP的竞争性等位基因特异性PCR（Kompetitive Allele-Specific PCR, KASP）标记，其中15个SNP可成功完成分型；对96个F1个体进行分型后发现，13个SNP的分型结果与GBS获得的基因型一致。本研究对栀子与茜草科物种阿拉伯咖啡（Coffea arabica）、刚果咖啡（Coffea canephora）以及矮小蛇根草（Ophiorrhiza pumila）进行了基因组共线性分析，结果显示栀子连锁群LG11分别与NC_039919.1、HG974438.1及Bliw01000011.1具有相对较强的保守共线性关系。最后，本研究对2019、2020、2021三个表型鉴定时间点的数据进行数量性状位点（quantitative trait loci, QTL）分析，共获得18个与生长相关性状相关的QTL以及31个与叶片相关性状相关的QTL，其中qBSBN7-1、qCD8和qLNP2-1可被重复检测到。本研究还观测到5个具有潜在多效性的QTL区域，分别为qCD8与qSBD8、qBSBN7与qSI7、qCD4-1与qLLLS4、qLNP10与qSLWS10-2以及qSBD10与qLLLS10。本研究为栀子的分子遗传学研究提供了新的视角，可为后续栀子生长发育早期性状的基因克隆及标记辅助选择提供参考。