Artificial selection footprints in indigenous and commercial chicken genomes

	Artificial selection footprints in indigenous and commercial chicken genomes
	Wu, SW; Dou, TF; Wang, K; Yuan, SS; Yan, SX; Xu, ZQ; Liu, Y; Jian, ZH; Zhao, JY; Zhao, RH; Wu, H; Gu, DH; Liu, LX; Li, QH; Wu, DD; Ge, CR; Su, ZC; Jia, JJ
	2024
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	25 期号:1
摘要	Background Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. Results We found 30 million non-redundant single nucleotide variants and small indels (<50bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (similar to 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds. Conclusion We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14515
专题	科研部门_进化与发育转录组学（吴东东）
推荐引用方式 GB/T 7714	Wu, SW,Dou, TF,Wang, K,et al. Artificial selection footprints in indigenous and commercial chicken genomes[J]. BMC GENOMICS,2024,25(1).
APA	Wu, SW.,Dou, TF.,Wang, K.,Yuan, SS.,Yan, SX.,...&Jia, JJ.(2024).Artificial selection footprints in indigenous and commercial chicken genomes.BMC GENOMICS,25(1).
MLA	Wu, SW,et al."Artificial selection footprints in indigenous and commercial chicken genomes".BMC GENOMICS 25.1(2024).

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