Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map

Parichart Ninwichian, Eric Peatman, Hong Liu, Huseyin Kucuktas, Benjaporn Somridhivej, Shikai Liu, Ping Li, Yanliang Jiang, Zhenxia Sha, Ludmilla Kaltenboeck, Jason W. Abernathy, Wenqi Wang, Fei Chen, Yoona Lee, Lilian Wong, Shaolin Wang, Jianguo Lu, Zhanjiang Liu

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ̃52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.

Original languageEnglish (US)
Pages (from-to)1233-1241
Number of pages9
JournalG3: Genes, Genomes, Genetics
Volume2
Issue number10
DOIs
StatePublished - Oct 2012

Keywords

  • Catfish
  • Genome
  • Linkage map
  • Map integration
  • Physical map

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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    Ninwichian, P., Peatman, E., Liu, H., Kucuktas, H., Somridhivej, B., Liu, S., Li, P., Jiang, Y., Sha, Z., Kaltenboeck, L., Abernathy, J. W., Wang, W., Chen, F., Lee, Y., Wong, L., Wang, S., Lu, J., & Liu, Z. (2012). Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map. G3: Genes, Genomes, Genetics, 2(10), 1233-1241. https://doi.org/10.1534/g3.112.003962