文献类型： 外文期刊

作者： Wang, Ming-Shan ¹ ; Zhang, Jin-Jin ¹ ; Guo, Xing ⁵ ; Li, Ming ⁶ ; Meyer, Rachel ⁴ ; Ashari, Hidayat ⁷ ; Zheng, Zhu-Qin ¹ ;

作者机构： 1.Chinese Acad Sci, Kunming Inst Zool, Yunnan Lab Mol Biol Domest Anim, State Key Lab Genet Resources & Evolut, Kunming 650223, Yunnan, Peoples R China

2.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650204, Yunnan, Peoples R China

3.Univ Calif Santa Cruz, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA

4.Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA

5.Anhui Agr Univ, Coll Anim Sci & Technol, Hefei 230036, Peoples R China

6.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Shaanxi, Peoples R China

7.Indonesian Inst Sci LIPI, Res Ctr Biol, Museum Zool Bogoriense, Bogor 16911, Indonesia

8.Chinese Acad Agr Sci CAAS, Inst Anim Sci, CAAS ILRI Joint Lab Livestock & Forage Genet Reso, Beijing 100193, Peoples R China

9.Huazhong Agr Univ, Cooperat Innovat Ctr Sustainable Pig Prod, Minist Educ, Key Lab Agr Anim Genet Breeding & Reprod, Wuhan 430070, Peoples R China

10.Zool Survey India, Kolkata 700053, W Bengal, India

11.Univ Phayao, Sch Agr & Nat Resources, Phayao 56000, Thailand

12.Univ Phayao, Unit Excellence Biodivers & Nat Resources Managem, Phayao 56000, Thailand

13.Shahid Bahonar Univ Kerman, Dept Anim Sci, POB 76169133, Kerman, Iran

14.Univ Ruhuna, Fac Agr, Matara, Sri Lanka

15.Univ Debrecen, Inst Anim Husb Biotechnol & Nat Conservat, H-4032 Debrecen, Hungary

16.Shiraz Univ, Sch Agr, Inst Biotechnol, POB 1585, Shiraz, Iran

17.Skolkovo Inst Sci & Technol, Ctr Neurobiol & Brain Restorat, Moscow 143026, Russia

18.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650204, Yunnan, Peoples R China

19.Univ Perugia, Dipartimento Sci Agr Alimentarie Ambientali, I-06123 Perugia, Italy

20.BGI Shenzhen, Shenzhen 518083, Peoples R China

21.China Agr Univ, Coll Anim Sci & Technol, Natl Engn Lab Anim Breeding, Minist Agr China,Lab Anim Genet Breeding & Reprod, Beijing 100193, Peoples R China

22.Bangladesh Agr Univ, Mymensingh 2202, Bangladesh

23.Cholistan Univ Vet & Anim Sci, Bahawalpur, Pakistan

24.Univ Peradeniya, Dept Anim Sci, Peradeniya 20400, Sri Lanka

25.Natl Inst Anim Husb, Hanoi, Vietnam

26.Int Livestock Res Inst ILRI, Livestock Genet Program, Nairobi 00100, Kenya

27.BGI Shenzhen, China Natl Genebank, Shenzhen 518083, Peoples R China

28.Univ Copenhagen, Ctr Social Evolut, Dept Biol, DK-1870 Copenhagen, Denmark

29.Yunnan Acad Grassland & Anim Sci, Kunming 650212, Yunnan, Peoples R China

30.Univ Nottingham, Sch Life Sci, Cells Organisms & Mol Genet, Nottingham NG7 2RD, England

31.Int Livestock Res Inst ILRI, Livestock Genet Program, POB 5689, Addis Ababa, Ethiopia

32.Wageningen Univ & Res Anim Breeding & Genom, NL-6708 PB Wageningen, Netherlands

33.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresource, Kunming 650091, Yunnan, Peoples R China

关键词： Domestication; Bottleneck; Genetic load; Deleterious mutation; Domestic chicken

期刊名称：BMC BIOLOGY （ 影响因子：7.431； 五年影响因子：8.182 ）

ISSN：

年卷期： 2021 年 19 卷 1 期

页码：

收录情况： SCI

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.