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

Luyang Sun, Shikai Liu, Ruijia Wang, Yanliang Jiang, Yu Zhang, Jiaren Zhang, Lisui Bao, Ludmilla Kaltenboeck, Rex Dunham, Geoff Waldbieser, Zhanjiang Liu

Research output: Contribution to journalArticle

28 Scopus citations

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 HIF1β 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.

Original languageEnglish (US)
Article numbere109666
JournalPloS one
Volume9
Issue number10
DOIs
StatePublished - Oct 14 2014

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Sun, L., Liu, S., Wang, R., Jiang, Y., Zhang, Y., Zhang, J., Bao, L., Kaltenboeck, L., Dunham, R., Waldbieser, G., & Liu, Z. (2014). Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus). PloS one, 9(10), [e109666]. https://doi.org/10.1371/journal.pone.0109666