Department of Genetics, Stellenbosch University, Matieland, South Africa.
Mkwawa University College of Education, University of Dar es Salaam, Iringa, Tanzania.
Anim Genet. 2024 Oct;55(5):744-760. doi: 10.1111/age.13462. Epub 2024 Jun 30.
Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.
鲍曼拟石鳖是南非商业水产养殖中最重要的贝类之一。在这项研究中，我们利用 2b-RADseq 对三个家系进行 SNP 基因型分析，构建了一个高分辨率的整合连锁图谱，并鉴定了 QTL。最终的整合连锁图谱是通过合并各个家系图谱得到的，结果共得到 3290 个信息 SNP 标记，映射到 18 个连锁群，与鲍曼拟石鳖的已知单倍体染色体数一致。总图谱覆盖 1798.25cM，平均标记间隔 0.55cM，代表了 98.76%的基因组覆盖度。通过对三个家系进行 QTL 分析，共鉴定到 5 个与生长相关性状（壳宽、壳长和体重）相关的 QTL。对于壳宽和体重，每个性状各鉴定到 1 个 QTL，而壳长则鉴定到 3 个 QTL。鉴定到的 QTL 分别解释了观察到的表型方差的 7.20%至 11.40%。三个性状之间均存在显著相关性（r=0.862-0.970；p<0.01），并共享重叠的 QTL。生长性状的 QTL 被映射回鲍曼拟石鳖的草图基因组，BLAST 搜索揭示了候选基因的身份，如 egf-1、megf10、megf6、tnx、sevp1、kcp、notch1 和 scube2，它们可能在鲍曼拟石鳖的生长中具有功能作用。构建的高密度连锁图谱和映射的 QTL 为生长相关性状的遗传结构提供了有价值的见解，将成为标记辅助选择的重要遗传资源。然而，在未来仍需要通过连锁不平衡精细作图来验证因果变异。
