Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

Hojjat Asadollahpour Nanaei; Yudong Cai; Akil Alshawi; Jiayue Wen; Tanveer Hussain; Wei-Wei Fu; Nai-Yi Xu; Abdulameer Essa; Johannes A. Lenstra; Xihong Wang; Yu Jiang

doi:10.24272/j.issn.2095-8137.2022.242

Volume 44 Issue 1

Jan. 2023

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Hojjat Asadollahpour Nanaei, Yudong Cai, Akil Alshawi, Jiayue Wen, Tanveer Hussain, Wei-Wei Fu, Nai-Yi Xu, Abdulameer Essa, Johannes A. Lenstra, Xihong Wang, Yu Jiang. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate. Zoological Research, 2023, 44(1): 20-29. doi: 10.24272/j.issn.2095-8137.2022.242

Citation:

Hojjat Asadollahpour Nanaei, Yudong Cai, Akil Alshawi, Jiayue Wen, Tanveer Hussain, Wei-Wei Fu, Nai-Yi Xu, Abdulameer Essa, Johannes A. Lenstra, Xihong Wang, Yu Jiang. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate. Zoological Research, 2023, 44(1): 20-29. doi: 10.24272/j.issn.2095-8137.2022.242

Citation:

Hojjat Asadollahpour Nanaei, Yudong Cai, Akil Alshawi, Jiayue Wen, Tanveer Hussain, Wei-Wei Fu, Nai-Yi Xu, Abdulameer Essa, Johannes A. Lenstra, Xihong Wang, Yu Jiang. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate. Zoological Research, 2023, 44(1): 20-29. doi: 10.24272/j.issn.2095-8137.2022.242

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Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

doi: 10.24272/j.issn.2095-8137.2022.242

1.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
2.
Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Baghdad, Iraqi Ministry of Higher Education and Scientific Research, Bagdad 10090, Iraq
3.
Department of Molecular Biology, Virtual University of Pakistan, Lahore 54000, Pakistan
4.
Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad 10081, Iraq
5.
Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands

Raw sequencing data that support the findings of this study have been deposited in the NCBI database (BioProjectID PRJNA801057). Furthermore, whole-genome sequencing data have been submitted to the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa) and Science Data Bank (https://www.scidb.cn/en) under accession No. CRA007867 and 10. 57760/sciencedb.j00139.00032, respectively.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
Y.J. and X.W. led the project and designed and conceived the study. H.A.N., Y. C., and J.Y.W. performed the data analysis. A.A., T.H., and A.E. collected the local goat samples. A.A. provided critical information about Iraqi goats. H.A.N. prepared the first draft of the manuscript. Y.J., X.W., J.A.L., W.W.F., and N.Y.X. reviewed and edited the manuscript. All authors read and approved the final version of the manuscript.
#Authors contributed equally to this work

Funds: This work was supported by the National Natural Science Foundation of China (32050410304, 32002140, 31822052, 91431572381) and National Thousand Youth Talents Plan to Y.J.

More Information

Corresponding author: E-mail: rebecca_830410@163.com; yu.jiang@nwafu.edu.cn
Received Date: 2022-08-09
Accepted Date: 2022-10-11

Published Online: 2022-10-13

Publish Date: 2023-01-18

Abstract

Abstract

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex (C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.
- Goat,
- Adaptation,
- KITLG,
- Southwest Asia,
- Nubian ibex

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References(59)

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