College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
Sci Rep. 2017 Apr 19;7:46509. doi: 10.1038/srep46509.
High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258.38 cM with an average distance of 0.57 cM among 5676 effective loci, thereby representing the first high-density genetic map reported for M. amblycephala. A total of eight positive quantitative trait loci (QTLs) were detected in QTL analysis. Of that, five QTL explained ≥35% of phenotypic variation for growth traits and three QTL explained ≥16% phenotypic variation for gonad related traits. A total of 176 mapped markers had significant hits in the zebrafish genome and almost all of the 24 putative-chromosomes of M. amblycephala were in relatively conserved synteny with chromosomes of zebrafish. Almost all M. amblycephala and zebrafish chromosomes had a 1:1 correspondence except for putative-chromosome 4, which mapped to two chromosomes of zebrafish caused by the difference in chromosome numbers between two species.
高密度基于 SNP 的遗传图谱对于精细定位控制鱼类特定性状的基因座至关重要。利用限制性酶切相关 DNA 标签测序 (RAD-Seq) 技术，我们在大口黑鲈基因组中鉴定出 42784 个均匀分布的 SNP。基于 2 个亲本和 187 个种内杂交后代，共鉴定出 14648 个高置信 SNP ，并分配到母本和父本图谱的 24 个共识连锁群 (LG)。整合图谱的总长度为 3258.38cM，在 5676 个有效位点之间的平均距离为 0.57cM，代表了大口黑鲈第一张高密度遗传图谱。在 QTL 分析中总共检测到 8 个阳性数量性状位点 (QTL)。其中，5 个 QTL 解释了生长性状的 35%以上的表型变异，3 个 QTL 解释了性腺相关性状的 16%以上的表型变异。总共 176 个映射标记在斑马鱼基因组中具有显著的命中，并且大口黑鲈的 24 个假定染色体中的大多数与斑马鱼的染色体具有相对保守的同线性。除了假定的第 4 号染色体，大口黑鲈和斑马鱼的染色体几乎都有 1:1 的对应关系，这是由于两个物种之间的染色体数量不同，导致第 4 号染色体映射到斑马鱼的两条染色体上。
