title: Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.
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.
authors.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.
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.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.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.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.
authors.forename: Zhenkui
authors.initials: Z
authors.lastname: Qin
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS 38776, USA.
authors.forename: Geoff
authors.initials: G
authors.lastname: Waldbieser
authors.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.
authors.forename: Ruijia
authors.initials: R
authors.lastname: Wang
authors.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.
authors.forename: Luyang
authors.initials: L
authors.lastname: Sun
authors.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.
authors.forename: Lisui
authors.initials: L
authors.lastname: Bao
authors.affiliation: Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
authors.forename: Roy G
authors.initials: RG
authors.lastname: Danzmann
authors.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.
authors.forename: Rex
authors.initials: R
authors.lastname: Dunham
authors.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 liuzhan@auburn.edu.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D005260:Female; D016678:Genome; D007059:Ictaluridae / Q000235:genetics*; D008297:Male; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: SNP; catfish; genome; linkage map; physical map