TY - JOUR
T1 - Large-scale genomic analysis reveals the genetic cost of chicken domestication
AU - Wang, Ming Shan
AU - Zhang, Jin Jin
AU - Guo, Xing
AU - Li, Ming
AU - Meyer, Rachel
AU - Ashari, Hidayat
AU - Zheng, Zhu Qing
AU - Wang, Sheng
AU - Peng, Min Sheng
AU - Jiang, Yu
AU - Thakur, Mukesh
AU - Suwannapoom, Chatmongkon
AU - Esmailizadeh, Ali
AU - Hirimuthugoda, Nalini Yasoda
AU - Zein, Moch Syamsul Arifin
AU - Kusza, Szilvia
AU - Kharrati-Koopaee, Hamed
AU - Zeng, Lin
AU - Wang, Yun Mei
AU - Yin, Ting Ting
AU - Yang, Min Min
AU - Li, Ming Li
AU - Lu, Xue Mei
AU - Lasagna, Emiliano
AU - Ceccobelli, Simone
AU - Gunwardana, Humpita Gamaralalage Thilini Nisanka
AU - Senasig, Thilina Madusanka
AU - Feng, Shao Hong
AU - Zhang, Hao
AU - Bhuiyan, Abul Kashem Fazlul Haque
AU - Khan, Muhammad Sajjad
AU - Silva, Gamamada Liyanage Lalanie Pradeepa
AU - Thuy, Le Thi
AU - Mwai, Okeyo A.
AU - Ibrahim, Mohamed Nawaz Mohamed
AU - Zhang, Guojie
AU - Qu, Kai Xing
AU - Hanotte, Olivier
AU - Shapiro, Beth
AU - Bosse, Mirte
AU - Wu, Dong Dong
AU - Han, Jian Lin
AU - Zhang, Ya Ping
PY - 2021/6/16
Y1 - 2021/6/16
N2 - 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 π, 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.
AB - 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 π, 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.
KW - Bottleneck
KW - Deleterious mutation
KW - Domestic chicken
KW - Domestication
KW - Genetic load
UR - https://doi.org/10.6084/m9.figshare.c.5468901
U2 - 10.1186/s12915-021-01052-x
DO - 10.1186/s12915-021-01052-x
M3 - Article
C2 - 34130700
AN - SCOPUS:85108111361
SN - 1741-7007
VL - 19
JO - BMC Biology
JF - BMC Biology
IS - 1
M1 - 118
ER -