Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.
University of Chinese Academy of Sciences, Beijing, China.
BMC Genomics. 2020 Apr 19;21(1):313. doi: 10.1186/s12864-020-6730-x.
Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture.
In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.
A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.
草鱼（Ctenopharyngodon idellus）是亚洲水产养殖的重要物种。2015 年已经发表了草鱼的基因组草图。然而，仍然需要合适的遗传连锁图谱将支架排列在染色体框架上。QTL 分析是检测数量性状关键位置的有力工具，特别是在水产养殖中。目前尚未发表草鱼生长相关的 QTL 。即使生长性状是草鱼养殖的重点之一。
在这项研究中，使用一对远缘亲本草鱼及其 100 只 6 月龄全同胞后代，通过 2b-RAD 技术构建了一个包含 6429 个单核苷酸多态性（SNP）的高密度遗传图谱。共识图谱的总长度为 5553.43cM，平均标记间隔为 1.92cM。该图谱与草鱼基因组草图和斑马鱼基因组具有良好的共线性，将基因组草图组装到染色体水平的 89.91%。此外，根据后代生长相关性状，在 5 个连锁群的 16 个位置鉴定出 30 个数量性状位点（QTL），包括 7 个体重、9 个体长、5 个体高和 9 个全长。这些 QTL 的表型方差解释率从 13.4%到 21.6%不等。最后，在这些区域中发现了 17 个基因，它们要么是根据父母重测序数据预测的功能突变，要么是功能未知的基因。
构建了草鱼高密度遗传连锁图谱，并将基因组草图组装到染色体水平。检测到 30 个与生长相关的 QTL。通过父母重测序数据的交叉分析，获得了 17 个候选基因，可进一步研究。
