Xie Mimi, Ming Yao, Shao Feng, Jian Jianbo, Zhang Yaoguang, Peng Zuogang
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, People's Republic of China.
BGI Genomics, BGI-Shenzhen, Shenzhen 518083, People's Republic of China.
R Soc Open Sci. 2018 May 30;5(5):172054. doi: 10.1098/rsos.172054. eCollection 2018 May.
Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish (). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.
单核苷酸多态性（SNP）标记和高密度遗传图谱是标记辅助选择、数量性状基因座（QTL）定位及基因组结构分析的重要资源。尽管已获得某些鲶鱼物种的连锁图谱，但在经济价值重要的南方鲶鱼（）中仍缺乏高密度图谱。最近开发的限制性位点相关DNA（RAD）标记已被证明是SNP检测和遗传图谱构建的一种有前景的工具。本研究的目的是利用下一代RAD测序产生的SNP构建南方鲶鱼的高密度连锁图谱，以供未来的遗传和基因组研究使用。通过两个野生杂合个体的种内杂交获得了一个由100个个体组成的F1群体。通过将亲本的双末端RAD reads比对到来自双亲的参考重叠群上，总共发现了亲本之间77634个推定的高质量双等位基因SNP，其中54.7%为转换，45.3%为颠换（转换/颠换比为1.2）。最后，使用从头聚类方法（Stacks）将26714个高质量RAD标记分为29个连锁群。在这些标记中，4514个与雌性遗传图谱连锁，23718个与雄性图谱连锁，6715个有效位点与跨度为5918.31厘摩（cM）的整合图谱连锁，平均标记间隔为0.89 cM。高分辨率遗传图谱对于鲶鱼的标记辅助育种和各种基因组研究都是一种有用的工具，如序列组装、基因定位、QTL检测和基因组结构比较。因此，这样的高密度连锁图谱将成为鲶鱼物种比较基因组学和精细QTL定位的宝贵资源。
