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.
Highlights
Strong selection can lead to significant allele frequency shifts with alleles directly affecting a trait reaching high frequencies
In addition to such hard selective sweeps where a single allele is selected for, recent work indicated that in some cases, more than one positive allele can be present within the selected loci, in this scenario drastic reduction in genetic variation in the genomic region does not occur
Reference mapping was conducted by aligning sequence reads from each strain with the preliminary catfish genome assembly
Summary
Strong selection can lead to significant allele frequency shifts with alleles directly affecting a trait reaching high frequencies. Selective sweeps have been detected in several agricultural animals such as chicken [2,3], pig [4], and cattle [5,6] In addition to such hard selective sweeps where a single allele is selected for, recent work indicated that in some cases, more than one positive allele can be present within the selected loci, in this scenario drastic reduction in genetic variation in the genomic region does not occur. This type of selective sweep has been defined as soft selective sweep [7,8,9]. The number of soft sweeps is likely underestimated [7]
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