Song Xiaoming, Ge Tingting, Li Ying, Hou Xilin
State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
BMC Genomics. 2015 Apr 20;16(1):328. doi: 10.1186/s12864-015-1534-0.
Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC.
A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future.
This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.
不结球白菜属于十字花科，是亚洲一种重要的叶菜类蔬菜。尽管已经通过传统的选择和育种方法进行了遗传分析，但不结球白菜的驯化历史及其形态多样性的遗传基础仍不清楚。因此，在不结球白菜的分子辅助选择中需要代表全基因组的可靠分子标记。
在不结球白菜中总共检测到20,836个简单序列重复（SSR），包含从单核苷酸到九核苷酸的重复类型。平均密度为62.93个SSR/Mb。在基因区域，在4,569个基因中鉴定出5,435个SSR。总共设计了5,008对引物，并随机选择了74对进行验证。其中，60对（81.08%）在18个十字花科植物中具有多态性。多态性条带的数量从2到5不等，每个引物的平均值为2.70。多态性信息含量、观察杂合度、哈迪-温伯格平衡和香农信息指数的平均值分别为0.2970、0.4136、0.5706和0.5885。根据非加权组平均法对18个基因型进行聚类分析，分为4个簇。此外，通过与大白菜基因组比较，在不结球白菜中总共鉴定出1,228,979个单核苷酸多态性（SNP），全基因组的平均SNP密度为4.33/Kb。在10个材料中，SNP的数量从341,939到591,586不等，平均杂合SNP比例约为42.53%。所有分析表明这些标记质量高且可靠。因此，它们可用于构建连锁图谱以及未来不结球白菜的遗传多样性研究。
这是首次对不结球白菜及17个物种中的SSR进行系统全面的分析和鉴定。成功为不结球白菜开发了大量的SNP和SSR标记。这些新型标记对于构建遗传连锁图谱、比较基因组分析、数量性状位点（QTL）定位、全基因组关联研究以及不结球白菜育种系统研究中的标记辅助选择具有重要价值。
