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Open Access Research article

Development of the catfish 250K SNP array for genome-wide association studies

Shikai Liu, Luyang Sun, Yun Li, Fanyue Sun, Yanliang Jiang, Yu Zhang, Jiaren Zhang, Jianbin Feng, Ludmilla Kaltenboeck, Huseyin Kucuktas and Zhanjiang Liu*

Author Affiliations

The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA

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BMC Research Notes 2014, 7:135  doi:10.1186/1756-0500-7-135

Published: 10 March 2014

Abstract

Background

Quantitative traits, such as disease resistance, are most often controlled by a set of genes involving a complex array of regulation. The dissection of genetic basis of quantitative traits requires large numbers of genetic markers with good genome coverage. The application of next-generation sequencing technologies has allowed discovery of over eight million SNPs in catfish, but the challenge remains as to how to efficiently and economically use such SNP resources for genetic analysis.

Results

In this work, we developed a catfish 250K SNP array using Affymetrix Axiom genotyping technology. The SNPs were obtained from multiple sources including gene-associated SNPs, anonymous genomic SNPs, and inter-specific SNPs. A set of 640K high-quality SNPs obtained following specific requirements of array design were submitted. A panel of 250,113 SNPs was finalized for inclusion on the array. The performance evaluated by genotyping individuals from wild populations and backcross families suggested the good utility of the catfish 250K SNP array.

Conclusions

This is the first high-density SNP array for catfish. The array should be a valuable resource for genome-wide association studies (GWAS), fine QTL mapping, high-density linkage map construction, haplotype analysis, and whole genome-based selection.

Keywords:
Catfish; Fish; Genome; SNP array; GWAS; Genotyping