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

文献类型： 外文期刊

第一作者： Wang, Ming-Shan

作者： Wang, Ming-Shan;Zhang, Jin-Jin;Wang, Sheng;Peng, Min-Sheng;Thakur, Mukesh;Esmailizadeh, Ali;Hirimuthugoda, Nalini Yasoda;Zeng, Lin;Yin, Ting-Ting;Yang, Min-Min;Li, Ming-Li;Lu, Xue-Mei;Feng, Shao-Hong;Zhang, Guojie;Wu, Dong-Dong;Zhang, Ya-Ping;Wang, Ming-Shan;Zhang, Jin-Jin;Wang, Sheng;Peng, Min-Sheng;Zeng, Lin;Yin, Ting-Ting;Yang, Min-Min;Li, Ming-Li;Lu, Xue-Mei;Wu, Dong-Dong;Zhang, Ya-Ping;Wang, Ming-Shan;Shapiro, Beth;Wang, Ming-Shan;Meyer, Rachel;Shapiro, Beth;Guo, Xing;Li, Ming;Jiang, Yu;Ashari, Hidayat;Zein, Moch Syamsul Arifin;Ashari, Hidayat;Han, Jian-Lin;Zheng, Zhu-Qing;Thakur, Mukesh;Suwannapoom, Chatmongkon;Suwannapoom, Chatmongkon;Esmailizadeh, Ali;Kharrati-Koopaee, Hamed;Hirimuthugoda, Nalini Yasoda;Gunwardana, Humpita Gamaralalage Thilini Nisanka;Senasig, Thilina Madusanka;Kusza, Szilvia;Kharrati-Koopaee, Hamed;Wang, Yun-Mei;Lu, Xue-Mei;Zhang, Guojie;Wu, Dong-Dong;Zhang, Ya-Ping;Lasagna, Emiliano;Ceccobelli, Simone;Feng, Shao-Hong;Zhang, Hao;Bhuiyan, Abul Kashem Fazlul Haque;Khan, Muhammad Sajjad;Silva, Gamamada Liyanage Lalanie Pradeepa;Le Thi Thuy;Mwai, Okeyo A.;Ibrahim, Mohamed Nawaz Mohamed;Han, Jian-Lin;Zhang, Guojie;Zhang, Guojie;Qu, Kai-Xing;Hanotte, Olivier;Hanotte, Olivier;Bosse, Mirte;Zhang, Ya-Ping

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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

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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.

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