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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #296675
Title: Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in catfish

Author
item SUN, LUYANG - Auburn University
item LIU, SHIKAI - Auburn University
item WANG, RUIJIA - Auburn University
item JIANG, YANLIANG - Auburn University
item ZHANG, YU - Auburn University
item ZHANG, JIAREN - Auburn University
item BOA, LISUI - Auburn University
item KALTENBOECK, LUDMILLA - Auburn University
item KUCUKTAS, HUSEYIN - Auburn University
item DUNHAM, REX - Auburn University
item Waldbieser, Geoffrey - Geoff
item LIU, ZHANJIANG - Auburn University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2014
Publication Date: 10/14/2014
Citation: Sun, L., Liu, S., Wang, R., Jiang, Y., Zhang, Y., Zhang, J., Boa, L., Kaltenboeck, L., Kucuktas, H., Dunham, R., Waldbieser, G.C., Liu, Z. 2014. Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in catfish. PLoS One. 9:e109666.

Interpretive Summary: In order to correlate DNA sequence variation with positive performance in catfish populations, it is necessary to first identify the sequence variants. Genomic DNA from channel catfish of four domestic and one wild population was sequenced and aligned to catfish reference contigs in order to identify single nucleotide polymorphisms (SNP) between individuals and groups. Criteria were developed to remove SNPs due to random sequencing artifact or sequence represented in repetitive areas of the genome, and the analysis resulted in 8.4 million putative SNP loci. A statistical analysis revealed that 407,861 loci had significant differences in allele frequencies between the domestic and wild populations, with evidence that domestication led to selection in 23 genomic regions that contained 11 genes. The more significant difference was in the gene encoding hypoxia-inducible factor 1 beta, which was implicated in response to low oxygen conditions. These markers will be useful in the selection of broodstock from these and other populations to improve performance for commercial production through selective breeding.

Technical Abstract: SNPs are one of the genomic variations accounting for biological diversity and function. They have become the molecular markers of choice because of their high abundance, even genomic distribution, and suitability for automation. However, genomic SNPs have not been systematically identified from catfish. In this study, we conducted Illumina sequencing analysis of pooled DNA samples from four domestic and one wild channel catfish populations to discover genomic SNPs and to determine the impact of domestication and selection. With a set of relatively reliable parameters, a total of 8.4 million SNPs were identified. On average, the 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 Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. A total of 407,861 SNPs had significant difference in allele frequencies between domestic and wild populations. With these SNPs, we identified 23 putative selective sweeps that included 11 genes. In spite of the lack of knowledge of their functions in catfish with the majority of these genes, hypoxia-inducible factor 1b was found within the selective sweep with the most significant probability, suggesting that selection for tolerance against low oxygen was predominantly important during the domestication processes for aquaculture. The large numbers of SNPs identified from this study should be useful for the development of high density SNP arrays for genetic and genomic analysis in catfish.