Zhang Shiyong, Zhang Xinhui, Chen Xiaohui, Xu Tengfei, Wang Minghua, Qin Qin, Zhong Liqiang, Jiang Hucheng, Zhu Xiaohua, Liu Hongyan, Shao Junjie, Zhu Zhifei, Shi Qiong, Bian Wenji, You Xinxin
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.
National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.
Front Genet. 2019 Mar 26;10:251. doi: 10.3389/fgene.2019.00251. eCollection 2019.
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including , and , were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as , and . In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
高密度遗传连锁图谱对于水产养殖物种重要经济性状的精细定位和全基因组组装尤为重要。斑点叉尾鮰原产于北美，是世界上最重要的商业淡水鱼之一。在美国以外，中国在过去三十年经历快速发展后，已成为斑点叉尾鮰的主要生产国和消费国。在本研究中，基于限制性位点相关DNA测序（RAD-seq），利用一个由156个后代及其两个亲本个体组成的F家系中的单核苷酸多态性（SNP）构建了斑点叉尾鮰的高密度遗传连锁图谱。总共4768个SNP被分配到29个连锁群（LG）中，连锁图谱长度达到2480.25厘摩（cM），位点间平均距离为0.55 cM。基于此遗传连锁图谱，223个基因组支架被锚定到斑点叉尾鮰的29个LG上，组装总长为704.66 Mb。数量性状位点（QTL）定位和全基因组关联分析分别在LG17和LG28上鉴定出10个与性别相关的QTL和6个与生长相关性状的QTL。在LG17的QTL区间内鉴定出与性别二态性相关的候选基因，包括、和。LG17基因中一个具有简单序列重复（SSR）的性别连锁标记在斑点叉尾鮰性别实际鉴定中得到验证。因此，LG17被认为是与性别相关的LG。还鉴定出了潜在的与生长相关的基因，包括、和等重要调节因子。总之，我们构建了斑点叉尾鮰的高密度遗传连锁图谱并开发了性别连锁标记，这些都是该重要经济硬骨鱼未来标记辅助选择（MAS）的重要遗传资源。
