Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus)

PLoS One. 2014 Oct 14;9(10):e109666. doi: 10.1371/journal.pone.0109666. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Animals, Domestic
  • Base Sequence
  • Chromosome Mapping
  • Gene Frequency
  • Genome
  • Heterozygote
  • High-Throughput Nucleotide Sequencing
  • Ictaluridae / genetics*
  • Polymorphism, Single Nucleotide*
  • Retroelements
  • Selection, Genetic
  • Sequence Analysis, DNA

Substances

  • Retroelements

Grant support

This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2010-65205-20356 and 2012-67015-19410 from the USDA National Institute of Food and Agriculture (NIFA). L. Sun was supported by a scholarship from the China Scholarship Council (CSC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.