Construction of a high-density,high-resolution genetic map and its integration with BAC-based physical map in channel catfish |
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Authors: | Yun Li Shikai Liu Zhenkui Qin Geoff Waldbieser Ruijia Wang Luyang Sun Lisui Bao Roy G. Danzmann Rex Dunham Zhanjiang Liu |
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Affiliation: | 1The 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;2USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS 38776, USA;3Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada |
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Abstract: | 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. |
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Keywords: | SNP catfish linkage map physical map genome |
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