Li Yun, Liu Shikai, Qin Zhenkui, Waldbieser Geoff, Wang Ruijia, Sun Luyang, Bao Lisui, Danzmann Roy G, Dunham Rex, Liu Zhanjiang
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.
USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS 38776, USA.
DNA Res. 2015 Feb;22(1):39-52. doi: 10.1093/dnares/dsu038. Epub 2014 Nov 26.
Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.
构建遗传连锁图谱对于遗传和基因组研究至关重要。测序和基因分型技术的最新进展使得生成高密度和高分辨率的遗传连锁图谱成为可能，特别是对于缺乏丰富基因组资源的生物。在本研究中，我们利用鲶鱼250K单核苷酸多态性（SNP）阵列对三个大型资源家族进行基因分型，构建了鲶鱼的高密度和高分辨率遗传图谱。共有54,342个SNP被定位到连锁图谱上，据我们所知，这在水产养殖物种中具有最高的标记密度。对于性别平均遗传图谱，估计的遗传大小为3,505.4 cM，分辨率为0.22 cM。雌性特异性连锁图谱总长4,495.1 cM，雄性特异性连锁图谱总长2,593.7 cM，雌性和雄性的重组率之比为1.7 : 1。与先前建立的物理图谱整合后，超过87%的物理图谱重叠群被锚定到连锁群上，这些连锁群覆盖的物理长度为867 Mb，约占鲶鱼基因组的90%。该整合图谱为验证和改进鲶鱼全基因组组装提供了有价值的工具，并有助于精细定位数量性状位点以及对经济重要性状相关基因进行定位克隆。
