title: Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus).
abstract: Domestication and selection for important performance traits can impact the genome, which is most often reflected by reduced heterozygosity in and surrounding genes related to traits affected by selection. In this study, analysis of the genomic impact caused by domestication and artificial selection was conducted by investigating the signatures of selection using single nucleotide polymorphisms (SNPs) in channel catfish (Ictalurus punctatus). A total of 8.4 million candidate SNPs were identified by using next generation sequencing. On average, the channel catfish genome harbors one SNP per 116 bp. Approximately 6.6 million, 5.3 million, 4.9 million, 7.1 million and 6.7 million SNPs were detected in the Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. The allele frequencies of 407,861 SNPs differed significantly between the domestic and wild populations. With these SNPs, 23 genomic regions with putative selective sweeps were identified that included 11 genes. Although the function for the majority of the genes remain unknown in catfish, several genes with known function related to aquaculture performance traits were included in the regions with selective sweeps. These included hypoxia-inducible factor 1β. HIFιβ.. and the transporter gene ATP-binding cassette sub-family B member 5 (ABCB5). HIF1β. is important for response to hypoxia and tolerance to low oxygen levels is a critical aquaculture trait. The large numbers of SNPs identified from this study are valuable for the development of high-density SNP arrays for genetic and genomic studies of performance traits in catfish.
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Luyang
authors.initials: L
authors.lastname: Sun
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Ruijia
authors.initials: R
authors.lastname: Wang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Jiaren
authors.initials: J
authors.lastname: Zhang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Lisui
authors.initials: L
authors.lastname: Bao
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Ludmilla
authors.initials: L
authors.lastname: Kaltenboeck
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Rex
authors.initials: R
authors.lastname: Dunham
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, Mississippi, United States of America.
authors.forename: Geoff
authors.initials: G
authors.lastname: Waldbieser
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D000829:Animals, Domestic; D001483:Base Sequence; D002874:Chromosome Mapping; D005787:Gene Frequency; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D007059:Ictaluridae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D018626:Retroelements; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018626:Retroelements