Large-scale genomic analysis reveals the genetic cost of chicken domestication

	Large-scale genomic analysis reveals the genetic cost of chicken domestication
	Wang, MS; Zhang, JJ; Guo, X; Li, M; Meyer, R; Ashari, H; Zheng, ZQ; Wang, S; Peng, MS; Jiang, Y; Thakur, M; Suwannapoom, C; Esmailizadeh, A; Hirimuthugoda, NY; Zein, MSA; Kusza, S; Kharrati-Koopaee, H; Zeng, L; Wang, YM; Yin, TT; Yang, MM; Li, ML; Lu, XM; Lasagna, E; Ceccobelli, S; Gunwardana, HGTN; Senasig, TM; Feng, SH; Zhang, H; Bhuiyan, AFH; Khan, MS; Silva, GLLP; Thuy, LT; Mwai, OA; Ibrahim, MNM; Zhang, GJ; Qu, KX; Hanotte, O; Shapiro, B; Bosse, M; Wu, DD; Han, JL; Zhang, YP
	2021
发表期刊	BMC BIOLOGY
卷号	19 期号:1
摘要	Background Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. Results We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average pi, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the cost of domestication hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. Conclusion This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.
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/152453/13157
专题	科研部门_适应性进化与进化医学（吕雪梅）昆明动物研究所
推荐引用方式 GB/T 7714	Wang, MS,Zhang, JJ,Guo, X,et al. Large-scale genomic analysis reveals the genetic cost of chicken domestication[J]. BMC BIOLOGY,2021,19(1).
APA	Wang, MS.,Zhang, JJ.,Guo, X.,Li, M.,Meyer, R.,...&Zhang, YP.(2021).Large-scale genomic analysis reveals the genetic cost of chicken domestication.BMC BIOLOGY,19(1).
MLA	Wang, MS,et al."Large-scale genomic analysis reveals the genetic cost of chicken domestication".BMC BIOLOGY 19.1(2021).

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