College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
Key laboratory for physiology biochemistry and application, Heze University, Heze, 274015, Shandong, China.
BMC Genomics. 2020 Oct 7;21(1):700. doi: 10.1186/s12864-020-07115-7.
A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits.
By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map' length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation.
We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.
高密度遗传连锁图谱对于 QTL 精细定位、比较基因组分析、候选基因鉴定和水产养殖品种的标记辅助选择至关重要。瓦氏黄颡鱼是亚洲非常受欢迎的商业鱼类。然而，一些特定的特征阻碍了基于表型的传统选择性育种的实现，例如缺乏大规模的基因组资源和与生长、性别决定和耐低氧相关性状紧密相关的标记。
利用 5059 个 ddRAD 标记，成功构建了瓦氏黄颡鱼的高分辨率遗传连锁图谱。该图谱长度为 4047.01cM，标记间隔为 0.11cm，平均标记密度为 1 个标记/cm。比较基因组作图表明，瓦氏黄颡鱼和黄颡鱼之间有 83.2%的标记具有一对一的对应关系。基于遗传图谱，在 4 条 LG 上检测到 4 个体重、1 个体比例、2 个性别决定和 1 个耐低氧相关性状的 8 个全基因组显著 QTL。通过 Kompetitive Allele Specific PCR 在其他个体中观察到这些全基因组显著 QTL 的一些 SNP 与这些表型性状显著相关。此外，体重相关的两个候选基因 Sipa1 和 HSD11B2 在生长迅速、生长中等和生长缓慢的瓦氏黄颡鱼之间存在差异表达。与耐低氧相关的 Sema7a 在缺氧暴露和复氧后被诱导表达。
我们利用 SNP 标记为黄颡鱼构建了一个高密度遗传连锁图谱，对 12 个生长、1 个性别决定和 1 个耐低氧相关性状进行了一组提示性和显著 QTL 以及候选基因的定位。我们的研究结果为水产养殖行业提供了一种更有效的生产全雄、快速生长和耐低氧瓦氏黄颡鱼的方法。
