ArticlePloS one2014
Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus).
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 61 citations in OpenAlex.
- Draft genome sequences and comparative analyses of Spiroplasma citri strains from various hosts.Folia microbiologica · 2026Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping inInternational journal of molecular sciences · 2024Article
- Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss).Genetics, selection, evolution : GSE · 2024Article
- Fine-scale population structure of the northern hard clam (Evolutionary applications · 2023Article
- High Genetic Connectivity Inferred from Whole-Genome Resequencing Provides Insight into the Phylogeographic Pattern of Larimichthys polyactis.Marine biotechnology (New York, N.Y.) · 2022Article
- Exploring genetic variation and population structure in a threatened species, Noturus placidus, with whole-genome sequence data.G3 (Bethesda, Md.) · 2022Article
- Genomics applied to livestock and aquaculture breeding.Evolutionary applications · 2022Review
- Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture.Frontiers in genetics · 2022Review
- Domestication of farmed fishFrontiers in endocrinology · 2022Review
- Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.BMC genomics · 2020Article
- Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems.Genetics, selection, evolution : GSE · 2020Article
- Non-synonymous polymorphisms in candidate gene associated with growth traits in Channel catfish (Ictalurus punctatus, Rafinesque, 1818).Molecular biology reports · 2020Article
- Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Frontiers in genetics · 2020Article
- GWAS Analysis Indicated Importance of NF-κB Signaling Pathway in Host Resistance Against Motile Aeromonas Septicemia Disease in Catfish.Marine biotechnology (New York, N.Y.) · 2019Article
- Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms.Scientific reports · 2019Article
- Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish.Marine biotechnology (New York, N.Y.) · 2018Article
- GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish.Molecular genetics and genomics : MGG · 2018Article
- Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula.Scientific reports · 2018Article
- Whole Genome Sequencing of Greater Amberjack (International journal of genomics · 2018Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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