Chen Wu, Hou Lu, Zhang Zhiyong, Pang Xiaoming, Li Yingyue
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China.
Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry UniversityBeijing, China.
Front Plant Sci. 2017 Apr 18;8:575. doi: 10.3389/fpls.2017.00575. eCollection 2017.
Chinese jujube ( Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.
枣（Mill）是原产于中国的一种具有重要经济价值的水果品种，具有很高的营养和药用价值。通过简化基因组测序对150份枣种质资源的核心收集品进行单核苷酸多态性（SNP）检测和基因分型，并进一步对其遗传多样性、群体结构和连锁不平衡（LD）进行表征。共鉴定出4680个高质量SNP，其中检测到38组三等位基因SNP。基于双等位基因SNP和三等位基因SNP的平均多态性信息含量（PIC）值分别为0.27和0.38。基于SNP的STRUCTURE和主坐标分析表明，150份种质可分为两组。然而，邻接法树状图表明这些种质应分为三个主要类群。我们的数据证实，SSR和SNP对遗传多样性的分辨能力相似。相比之下，在群体结构方面，SSR的分辨能力高于SNP。首次对枣的LD模式进行了研究。我们观察到所有假染色体和单个假染色体的LD在短距离（约10 kb）内相对快速衰减。我们的研究结果为枣未来的全基因组关联分析和标记辅助选择育种提供了重要信息。
