Abstract
Genomic selection and genome-wide association studies need thousands to millions of SNPs. However, many non-model species do not have reference chips for detecting variation. Our goal was to develop and validate an inexpensive but effective method for detecting SNP variation. Genotyping by sequencing (GBS) can be a highly efficient strategy for genome-wide SNP detection, as an alternative to microarray chips. Here, we developed a GBS protocol for ducks and tested it to genotype 49 Pekin ducks. A total of 169,209 SNPs were identified from all animals, with a mean of 55,920 SNPs per individual. The average SNP density reached 1156 SNPs/MB. In this study, the first application of GBS to ducks, we demonstrate the power and simplicity of this method. GBS can be used for genetic studies in to provide an effective method for genome-wide SNP discovery.
Highlights
The domestic duck is an economically important agriculture animal and is consumed worldwide, especially in Asia[1]
There is a limitation for population genetics studies and genomic selection due to the lack of a duck-specific DNA chip platform
Genotyping by sequencing (GBS) is one such highly efficient strategy for genome-wide SNP detection and this approach has been successfully applied to aquatic, plants, and animals like chicken, pig and cattle[5,6,7,8,9,10,11,12]
Summary
The domestic duck is an economically important agriculture animal and is consumed worldwide, especially in Asia[1]. Duck is a suitable material for population genetics and evolutionary studies[2,3]. There is a limitation for population genetics studies and genomic selection due to the lack of a duck-specific DNA chip platform. Genotyping by sequencing (GBS) is one such highly efficient strategy for genome-wide SNP detection and this approach has been successfully applied to aquatic, plants, and animals like chicken, pig and cattle[5,6,7,8,9,10,11,12]. We developed a GBS strategy (Fig. 1) and applied it for SNP detection in the domestic Pekin duck, and evaluated the results by PCR-RFLP. Our theoretic analysis and experimental data showed this is a low cost and effective method for discovering SNPs in animal genomes for which chip microarrays are not yet available
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