Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.
Bottom Line: 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.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.
Affiliation: 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.Show MeSH
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Mentions: The sex-specific maps were constructed using markers that were heterozygous in only female or male parent. The female genetic map consisted of 18,444 SNPs including 9,746 unique markers, with a total genetic length of 4,495.1 cM (Table 3; Fig. 1). The marker intervals estimated based on the unique marker positions ranged from 0.37 cM/marker pair in LG12 to 0.7 cM/marker pair in LG18 with the average marker interval of 0.46 cM/marker pair in female genetic map. The male genetic map comprised 15,148 SNPs with 7,250 unique markers and a total genetic length of 2,593.7 cM, which was much shorter than female genetic map. The marker intervals of male genetic map ranged from 0.25 cM/marker pair (LG18) to 0.55 cM/marker pair (LG1), with an average marker interval of 0.36 cM (Table 3, Fig. 2). It should be noted that these distances refer to intervals where recombination was detected and of course it should be recognized that in both sexes, the minimum distance observed was 0 cM for completely linked markers. The female- and male-specific maps are illustrated in Figs 1 and 2, respectively. The detailed map information was provided in Supplementary data S1.Table 3.
Affiliation: 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.