Abstract
Copy number variations (CNVs) are important source of genetic variation, which can affect diverse economic traits through a variety of mechanisms. In addition, genome scan can identify many quantitative trait loci (QTLs) for the economic traits, while genome-wide association studies (GWAS) can localize genetic variants associated with the phenotypic variations. Here, we developed a method called GWAScore which collected GWAS summary data to identify potential candidates, and integrated CNVs into QTLs and high confidence GWAScore regions to detect crucial CNV markers for sheep growth traits. We got 197 candidate genes which were overlapping with the candidate CNVs. Some crucial genes (MYLK3, TTC29, HERC6, ABCG2, RUNX1, etc.) showed significantly elevated GWAScore peaks than other candidate genes. In this study, we developed the GWAScore method to excavate the potential value of candidate genes as markers for the sheep molecular breeding.
Highlights
Chaka sheep named Qinghai plateau half-fine wool sheep has been a geographical symbol of agricultural products by Ministry of Agriculture
Our method identifies Copy number variations (CNVs) using resequencing data which integrates with the existing genome-wide association studies (GWAS) and quantitative trait loci (QTL) data
We have developed a new method called GWAScore to look for important regions across the genome by summarizing the GWAS data, integrating QTLs and high confidence GWAScore regions with CNVs to identify positional candidates for sheep breeding to accelerate genetic improvement
Summary
Chaka sheep named Qinghai plateau half-fine wool sheep has been a geographical symbol of agricultural products by Ministry of Agriculture. Chaka sheep is famous for its excellent mutton quality, known as the tributary sheep in the ancient times. Its wool is exceptional for making woolen sweaters. Chaka sheep is reared as a multipurpose breed.
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