Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens
[Display omitted] •The genomes of modern purebred broilers carried fewer deleterious mutations compared to local chickens and wild ancestors.•163 protein-coding genes were selected positively in purebred broilers during long term selection.•The MYH1 gene family harbored the top significant selective...
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Veröffentlicht in: | Journal of advanced research 2024-01, Vol.55, p.1-16 |
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•The genomes of modern purebred broilers carried fewer deleterious mutations compared to local chickens and wild ancestors.•163 protein-coding genes were selected positively in purebred broilers during long term selection.•The MYH1 gene family harbored the top significant selective sweep windows and displays muscle-specific expression in purebred broilers.•SOX6 gene provided key regulatory function to breast muscle traits and adaptation to artificial selection.•A haplotype within SOX6 appeared differential pattern in gene expression, breast muscle traits, and haplotype frequency.
Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems.
Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood.
We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping and the Mendelian randomization was applied.
We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes.
Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory targe |
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ISSN: | 2090-1232 2090-1224 2090-1224 |
DOI: | 10.1016/j.jare.2023.02.016 |