Abstract
Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.
Highlights
The weight and size of breast muscle are crucial to production efficiency and economic benefit by affecting carcass appearance, especially for chicken
12 g)developm the genome before exploring the genetic markers associated with muscle was found in the selected population, which was consistent with a previous report distinct pattern based on global genomic variants identified a clear divergence b that a mild correlation was found between chicken intramuscular fat (IMF) and Breast muscle weight (BrW) [11]
The results of this study indicated that IGF2BP1 or its upstream regulatory element was directionally selected during the IMF enhancement, with confirmation by transcriptional activity differences between the two chicken lines
Summary
The weight and size of breast muscle are crucial to production efficiency and economic benefit by affecting carcass appearance, especially for chicken. Liu et al reported chromosome 4 and 27 had BrW associated SNPs and genes (LCORL and MAPT), and both of these two genes were expressed at significantly higher levels in chickens with larger breast muscle [16] These results suggest that candidate variants or genes differ among various subspecies, with no clear identification of the major functional genes related to BrW. In chicken advanced intercross line, an interval of chromosome 27 was recognized as a candidate genomic region (containing IGF2BP1, GIP, and other genes) that affected growth traits [13] Taken together these results suggest a possible role for IGF2BP1 in chicken breast muscle development. In this manner genetic changes and pivotal markers associated with enhanced BrW, due to directional breeding, were identified
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