Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Yun Li, Shikai Liu, Zhenkui Qin, Geoff Waldbieser, Ruijia Wang, Luyang Sun, Lisui Bao, Roy G. Danzmann, Rex Dunham, Zhanjiang Liu

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)39-52
Number of pages14
JournalDNA Research
Issue number1
StatePublished - Feb 1 2015
Externally publishedYes


  • Catfish
  • Genome
  • Linkage map
  • Physical map
  • SNP

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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