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1. Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

Author

Xu, Songsong, Akhatayeva, Zhanerke, Liu, Jiaxin, Feng, Xueyan, Yu, Yi, Badaoui, Bouabid, Esmailizadeh, Ali, Kantanen, Juha, Amills, Marcel, Lenstra, Johannes A., Johansson, Anna M., Coltman, David W., Liu, George E., Curik, Ino, Orozco-terWengel, Pablo, Paiva, Samuel R., Zinovieva, Natalia A., Zhang, Linwei, Yang, Ji, Liu, Zhihong, Wang, Yachun, Yu, Ying, and Li, Menghua

Published
2024
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4. Evolution and legacy of East Asian aurochs

Author

Hou, Jiawen, Guan, Xiwen, Xia, Xiaoting, Lyu, Yang, Liu, Xin, Mazei, Yuri, Xie, Ping, Chang, Fengqin, Zhang, Xiaonan, Chen, Jialei, Li, Xinyi, Zhang, Fengwei, Jin, Liangliang, Luo, Xiaoyu, Sinding, Mikkel-Holger S., Sun, Xin, Achilli, Alessandro, Migliore, Nicola Rambaldi, Zhang, Dongju, Lenstra, Johannes A., Han, Jianlin, Fu, Qiaomei, Liu, Xinyi, Zhang, Xiaoming, Chen, Ningbo, Lei, Chuzhao, and Zhang, Hucai

Published
2024
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5. Recent selection and introgression facilitated high-altitude adaptation in cattle

Author

Lyu, Yang, Wang, Fuwen, Cheng, Haijian, Han, Jing, Dang, Ruihua, Xia, Xiaoting, Wang, Hui, Zhong, Jincheng, Lenstra, Johannes A., Zhang, Hucai, Han, Jianlin, MacHugh, David E., Medugorac, Ivica, Upadhyay, Maulik, Leonard, Alexander S., Ding, He, Yang, Xiaorui, Wang, Ming-Shan, Quji, Suolang, Zhuzha, Basang, Quzhen, Pubu, Wangmu, Silang, Cangjue, Nima, Wa, Da, Ma, Weidong, Liu, Jianyong, Zhang, Jicai, Huang, Bizhi, Qi, Xingshan, Li, Fuqiang, Huang, Yongzhen, Ma, Yun, Wang, Yu, Gao, Yuanpeng, Lu, Wenfa, Lei, Chuzhao, and Chen, Ningbo

Published
2024
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6. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Author

Chen, Ningbo, Xia, Xiaoting, Hanif, Quratulain, Zhang, Fengwei, Dang, Ruihua, Huang, Bizhi, Lyu, Yang, Luo, Xiaoyu, Zhang, Hucai, Yan, Huixuan, Wang, Shikang, Wang, Fuwen, Chen, Jialei, Guan, Xiwen, Liu, Yangkai, Li, Shuang, Jin, Liangliang, Wang, Pengfei, Sun, Luyang, Zhang, Jicai, Liu, Jianyong, Qu, Kaixing, Cao, Yanhong, Sun, Junli, Liao, Yuying, Xiao, Zhengzhong, Cai, Ming, Mu, Lan, Siddiki, Amam Zonaed, Asif, Muhammad, Mansoor, Shahid, Babar, Masroor Ellahi, Hussain, Tanveer, Silva, Gamamada Liyanage Lalanie Pradeepa, Gorkhali, Neena Amatya, Terefe, Endashaw, Belay, Gurja, Tijjani, Abdulfatai, Zegeye, Tsadkan, Gebre, Mebrate Genet, Ma, Yun, Wang, Yu, Huang, Yongzhen, Lan, Xianyong, Chen, Hong, Migliore, Nicola Rambaldi, Colombo, Giulia, Semino, Ornella, Achilli, Alessandro, Sinding, Mikkel-Holger S., Lenstra, Johannes A., Cheng, Haijian, Lu, Wenfa, Hanotte, Olivier, Han, Jianlin, Jiang, Yu, and Lei, Chuzhao

Published
2023
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8. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

Author

Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Pausch, Hubert, Leonard, Alexander S., Crysnanto, Danang, Wang, Shikang, Tong, Bin, Lenstra, Johannes A., Han, Jianlin, Li, Fuyong, Xu, Tieshan, Gu, Lihong, Jin, Liangliang, Dang, Ruihua, Huang, Yongzhen, Lan, Xianyong, Ren, Gang, Wang, Yu, Gao, Yuanpeng, Ma, Zhijie, Cheng, Haijian, Ma, Yun, Chen, Hong, Pang, Weijun, Lei, Chuzhao, and Chen, Ningbo

Published
2023
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10. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

Author

Chen, Ze-Hui, Xu, Ya-Xi, Xie, Xing-Long, Wang, Dong-Feng, Aguilar-Gómez, Diana, Liu, Guang-Jian, Li, Xin, Esmailizadeh, Ali, Rezaei, Vahideh, Kantanen, Juha, Ammosov, Innokentyi, Nosrati, Maryam, Periasamy, Kathiravan, Coltman, David W, Lenstra, Johannes A, Nielsen, Rasmus, and Li, Meng-Hua

Subjects
Human Genome, Genetics, Animals, Domestication, Gene Flow, Phylogeny, Selection, Genetic, Sheep, Sheep, Bighorn, Sheep, Domestic, Whole Genome Sequencing
Abstract

The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.

Published
2021

11. Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Author

Baazaoui, Imen, Bedhiaf-Romdhani, Sonia, Mastrangelo, Salvatore, Lenstra, Johannes A, Da Silva, Anne, Benjelloun, Badr, Ciani, Elena, Baazaoui, Imen, Bedhiaf-Romdhani, Sonia, Mastrangelo, Salvatore, Lenstra, Johannes A, Da Silva, Anne, Benjelloun, Badr, and Ciani, Elena

Abstract

INTRODUCTION: The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.METHODS: In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.RESULTS AND DISCUSSION: We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian F ST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism ( BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation ( SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

Published
2024

12. Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Author

One Health Toxicologie, IRAS – One Health Toxicology, Baazaoui, Imen, Bedhiaf-Romdhani, Sonia, Mastrangelo, Salvatore, Lenstra, Johannes A, Da Silva, Anne, Benjelloun, Badr, Ciani, Elena, One Health Toxicologie, IRAS – One Health Toxicology, Baazaoui, Imen, Bedhiaf-Romdhani, Sonia, Mastrangelo, Salvatore, Lenstra, Johannes A, Da Silva, Anne, Benjelloun, Badr, and Ciani, Elena

Published
2024

13. IBD sharing patterns as intra-breed admixture indicators in small ruminants

Author

One Health Toxicologie, IRAS – One Health Toxicology, Blondeau Da Silva, Stéphane, Mwacharo, Joram M, Li, Menghua, Ahbara, Abulgasim, Muchadeyi, Farai Catherine, Dzomba, Edgar Farai, Lenstra, Johannes A, Da Silva, Anne, One Health Toxicologie, IRAS – One Health Toxicology, Blondeau Da Silva, Stéphane, Mwacharo, Joram M, Li, Menghua, Ahbara, Abulgasim, Muchadeyi, Farai Catherine, Dzomba, Edgar Farai, Lenstra, Johannes A, and Da Silva, Anne

Published
2024

17. Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Author

Yurtman, Erinç, Özer, Onur, Yüncü, Eren, Dağtaş, Nihan Dilşad, Koptekin, Dilek, Çakan, Yasin Gökhan, Özkan, Mustafa, Akbaba, Ali, Kaptan, Damla, Atağ, Gözde, Vural, Kıvılcım Başak, Gündem, Can Yümni, Martin, Louise, Kılınç, Gülşah Merve, Ghalichi, Ayshin, Açan, Sinan Can, Yaka, Reyhan, Sağlıcan, Ekin, Lagerholm, Vendela Kempe, Krzewińska, Maja, Günther, Torsten, Morell Miranda, Pedro, Pişkin, Evangelia, Şevketoğlu, Müge, Bilgin, C. Can, Atakuman, Çiğdem, Erdal, Yılmaz Selim, Sürer, Elif, Altınışık, N. Ezgi, Lenstra, Johannes A., Yorulmaz, Sevgi, Abazari, Mohammad Foad, Hoseinzadeh, Javad, Baird, Douglas, Bıçakçı, Erhan, Çevik, Özlem, Gerritsen, Fokke, Özbal, Rana, Götherström, Anders, Somel, Mehmet, Togan, İnci, and Özer, Füsun

Published
2021
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19. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

Author

Asadollahpour Nanaei, Hojjat, Cai, Yudong, Alshawi, Akil, Wen, Jiayue, Hussain, Tanveer, Fu, Wei-Wei, Xu, Nai-Yi, Essa, Abdulameer, Lenstra, Johannes A, Wang, Xihong, Jiang, Yu, and One Health Toxicologie

Subjects
Nubian ibex, Ecology, Evolution, Goats, Genomics, Southwest Asia, Behavior and Systematics, Goat, Animals, Pakistan, KITLG, Animal Science and Zoology, Desert Climate, Adaptation, Alleles, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
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.

Published
2023
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21. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Author

Li, Xin, Yang, Ji, Shen, Min, Xie, Xing-Long, Liu, Guang-Jian, Xu, Ya-Xi, Lv, Feng-Hua, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Zhou, Ping, Wan, Peng-Cheng, Zhang, Yun-Sheng, Gao, Lei, Yang, Jing-Quan, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Deng, Juan, Xu, Song-Song, Salehian-Dehkordi, Hosein, Hehua, Eer, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Štěpánek, Ondřej, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Lenstra, Johannes A., Kantanen, Juha, Coltman, David W., Kijas, James W., Bruford, Michael W., Periasamy, Kathiravan, Wang, Xin-Hua, and Li, Meng-Hua

Published
2020
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22. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Author

Li, Ran, Gong, Mian, Zhang, Xinmiao, Wang, Fei, Liu, Zhenyu, Zhang, Lei, Yang, Qimeng, Xu, Yuan, Xu, Mengsi, Zhang, Huanhuan, Zhang, Yunfeng, Dai, Xuelei, Gao, Yuanpeng, Zhang, Zhuangbiao, Fang, Wenwen, Yang, Yuta, Fu, Weiwei, Cao, Chunna, Yang, Peng, Ghanatsaman, Zeinab Amiri, Negari, Niloufar Jafarpour, Nanaei, Hojjat Asadollahpour, Yue, Xiangpeng, Song, Yuxuan, Lan, Xianyong, Deng, Weidong, Wang, Xihong, Pan, Chuanying, Xiang, Ruidong, Ibeagha-Awemu, Eveline M, Heslop-Harrison, Pat J S, Rosen, Benjamin D, Lenstra, Johannes A, Gan, Shangquan, Jiang, Yu, Li, Ran, Gong, Mian, Zhang, Xinmiao, Wang, Fei, Liu, Zhenyu, Zhang, Lei, Yang, Qimeng, Xu, Yuan, Xu, Mengsi, Zhang, Huanhuan, Zhang, Yunfeng, Dai, Xuelei, Gao, Yuanpeng, Zhang, Zhuangbiao, Fang, Wenwen, Yang, Yuta, Fu, Weiwei, Cao, Chunna, Yang, Peng, Ghanatsaman, Zeinab Amiri, Negari, Niloufar Jafarpour, Nanaei, Hojjat Asadollahpour, Yue, Xiangpeng, Song, Yuxuan, Lan, Xianyong, Deng, Weidong, Wang, Xihong, Pan, Chuanying, Xiang, Ruidong, Ibeagha-Awemu, Eveline M, Heslop-Harrison, Pat J S, Rosen, Benjamin D, Lenstra, Johannes A, Gan, Shangquan, and Jiang, Yu

Abstract

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Published
2023

23. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

Author

Cheng, Hong, Zhang, Zhuangbiao, Wen, Jiayue, Lenstra, Johannes A, Heller, Rasmus, Cai, Yudong, Guo, Yingwei, Li, Ming, Li, Ran, Li, Wenrong, He, Sangang, Wang, Jintao, Shao, Junjie, Song, Yuxuan, Zhang, Lei, Billah, Masum, Wang, Xihong, Liu, Mingjun, Jiang, Yu, Cheng, Hong, Zhang, Zhuangbiao, Wen, Jiayue, Lenstra, Johannes A, Heller, Rasmus, Cai, Yudong, Guo, Yingwei, Li, Ming, Li, Ran, Li, Wenrong, He, Sangang, Wang, Jintao, Shao, Junjie, Song, Yuxuan, Zhang, Lei, Billah, Masum, Wang, Xihong, Liu, Mingjun, and Jiang, Yu

Abstract

The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.

Published
2023

24. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Author

IRAS OH Toxicology, Li, Ran, Gong, Mian, Zhang, Xinmiao, Wang, Fei, Liu, Zhenyu, Zhang, Lei, Yang, Qimeng, Xu, Yuan, Xu, Mengsi, Zhang, Huanhuan, Zhang, Yunfeng, Dai, Xuelei, Gao, Yuanpeng, Zhang, Zhuangbiao, Fang, Wenwen, Yang, Yuta, Fu, Weiwei, Cao, Chunna, Yang, Peng, Ghanatsaman, Zeinab Amiri, Negari, Niloufar Jafarpour, Nanaei, Hojjat Asadollahpour, Yue, Xiangpeng, Song, Yuxuan, Lan, Xianyong, Deng, Weidong, Wang, Xihong, Pan, Chuanying, Xiang, Ruidong, Ibeagha-Awemu, Eveline M, Heslop-Harrison, Pat J S, Rosen, Benjamin D, Lenstra, Johannes A, Gan, Shangquan, Jiang, Yu, IRAS OH Toxicology, Li, Ran, Gong, Mian, Zhang, Xinmiao, Wang, Fei, Liu, Zhenyu, Zhang, Lei, Yang, Qimeng, Xu, Yuan, Xu, Mengsi, Zhang, Huanhuan, Zhang, Yunfeng, Dai, Xuelei, Gao, Yuanpeng, Zhang, Zhuangbiao, Fang, Wenwen, Yang, Yuta, Fu, Weiwei, Cao, Chunna, Yang, Peng, Ghanatsaman, Zeinab Amiri, Negari, Niloufar Jafarpour, Nanaei, Hojjat Asadollahpour, Yue, Xiangpeng, Song, Yuxuan, Lan, Xianyong, Deng, Weidong, Wang, Xihong, Pan, Chuanying, Xiang, Ruidong, Ibeagha-Awemu, Eveline M, Heslop-Harrison, Pat J S, Rosen, Benjamin D, Lenstra, Johannes A, Gan, Shangquan, and Jiang, Yu

Published
2023

25. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

Author

One Health Toxicologie, Cheng, Hong, Zhang, Zhuangbiao, Wen, Jiayue, Lenstra, Johannes A, Heller, Rasmus, Cai, Yudong, Guo, Yingwei, Li, Ming, Li, Ran, Li, Wenrong, He, Sangang, Wang, Jintao, Shao, Junjie, Song, Yuxuan, Zhang, Lei, Billah, Masum, Wang, Xihong, Liu, Mingjun, Jiang, Yu, One Health Toxicologie, Cheng, Hong, Zhang, Zhuangbiao, Wen, Jiayue, Lenstra, Johannes A, Heller, Rasmus, Cai, Yudong, Guo, Yingwei, Li, Ming, Li, Ran, Li, Wenrong, He, Sangang, Wang, Jintao, Shao, Junjie, Song, Yuxuan, Zhang, Lei, Billah, Masum, Wang, Xihong, Liu, Mingjun, and Jiang, Yu

Published
2023

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

Author

One Health Toxicologie, Asadollahpour Nanaei, Hojjat, Cai, Yudong, Alshawi, Akil, Wen, Jiayue, Hussain, Tanveer, Fu, Wei-Wei, Xu, Nai-Yi, Essa, Abdulameer, Lenstra, Johannes A, Wang, Xihong, Jiang, Yu, One Health Toxicologie, Asadollahpour Nanaei, Hojjat, Cai, Yudong, Alshawi, Akil, Wen, Jiayue, Hussain, Tanveer, Fu, Wei-Wei, Xu, Nai-Yi, Essa, Abdulameer, Lenstra, Johannes A, Wang, Xihong, and Jiang, Yu

Published
2023

27. Global dispersal and adaptive evolution of domestic cattle:a genomic perspective

Author

Xia, Xiaoting, Qu, Kaixing, Wang, Yan, Sinding, Mikkel Holger S., Wang, Fuwen, Hanif, Quratulain, Ahmed, Zulfiqar, Lenstra, Johannes A., Han, Jianlin, Lei, Chuzhao, Chen, Ningbo, Xia, Xiaoting, Qu, Kaixing, Wang, Yan, Sinding, Mikkel Holger S., Wang, Fuwen, Hanif, Quratulain, Ahmed, Zulfiqar, Lenstra, Johannes A., Han, Jianlin, Lei, Chuzhao, and Chen, Ningbo

Abstract

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations., Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.

Published
2023

28. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Author

Sub Data Intensive Systems, One Health Toxicologie, IRAS – One Health Toxicology, Chen, Ningbo, Xia, Xiaoting, Hanif, Quratulain, Zhang, Fengwei, Dang, Ruihua, Huang, Bizhi, Lyu, Yang, Luo, Xiaoyu, Zhang, Hucai, Yan, Huixuan, Wang, Shikang, Wang, Fuwen, Chen, Jialei, Guan, Xiwen, Liu, Yangkai, Li, Shuang, Jin, Liangliang, Wang, Pengfei, Sun, Luyang, Zhang, Jicai, Liu, Jianyong, Qu, Kaixing, Cao, Yanhong, Sun, Junli, Liao, Yuying, Xiao, Zhengzhong, Cai, Ming, Mu, Lan, Siddiki, Amam Zonaed, Asif, Muhammad, Mansoor, Shahid, Babar, Masroor Ellahi, Hussain, Tanveer, Silva, Gamamada Liyanage Lalanie Pradeepa, Gorkhali, Neena Amatya, Terefe, Endashaw, Belay, Gurja, Tijjani, Abdulfatai, Zegeye, Tsadkan, Gebre, Mebrate Genet, Ma, Yun, Wang, Yu, Huang, Yongzhen, Lan, Xianyong, Chen, Hong, Migliore, Nicola Rambaldi, Colombo, Giulia, Semino, Ornella, Achilli, Alessandro, Sinding, Mikkel-Holger S, Lenstra, Johannes A, Cheng, Haijian, Lu, Wenfa, Hanotte, Olivier, Han, Jianlin, Jiang, Yu, Lei, Chuzhao, Sub Data Intensive Systems, One Health Toxicologie, IRAS – One Health Toxicology, Chen, Ningbo, Xia, Xiaoting, Hanif, Quratulain, Zhang, Fengwei, Dang, Ruihua, Huang, Bizhi, Lyu, Yang, Luo, Xiaoyu, Zhang, Hucai, Yan, Huixuan, Wang, Shikang, Wang, Fuwen, Chen, Jialei, Guan, Xiwen, Liu, Yangkai, Li, Shuang, Jin, Liangliang, Wang, Pengfei, Sun, Luyang, Zhang, Jicai, Liu, Jianyong, Qu, Kaixing, Cao, Yanhong, Sun, Junli, Liao, Yuying, Xiao, Zhengzhong, Cai, Ming, Mu, Lan, Siddiki, Amam Zonaed, Asif, Muhammad, Mansoor, Shahid, Babar, Masroor Ellahi, Hussain, Tanveer, Silva, Gamamada Liyanage Lalanie Pradeepa, Gorkhali, Neena Amatya, Terefe, Endashaw, Belay, Gurja, Tijjani, Abdulfatai, Zegeye, Tsadkan, Gebre, Mebrate Genet, Ma, Yun, Wang, Yu, Huang, Yongzhen, Lan, Xianyong, Chen, Hong, Migliore, Nicola Rambaldi, Colombo, Giulia, Semino, Ornella, Achilli, Alessandro, Sinding, Mikkel-Holger S, Lenstra, Johannes A, Cheng, Haijian, Lu, Wenfa, Hanotte, Olivier, Han, Jianlin, Jiang, Yu, and Lei, Chuzhao

Published
2023

29. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

Author

One Health Toxicologie, Sub Data Intensive Systems, IRAS – One Health Toxicology, Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Pausch, Hubert, Leonard, Alexander S, Crysnanto, Danang, Wang, Shikang, Tong, Bin, Lenstra, Johannes A, Han, Jianlin, Li, Fuyong, Xu, Tieshan, Gu, Lihong, Jin, Liangliang, Dang, Ruihua, Huang, Yongzhen, Lan, Xianyong, Ren, Gang, Wang, Yu, Gao, Yuanpeng, Ma, Zhijie, Cheng, Haijian, Ma, Yun, Chen, Hong, Pang, Weijun, Lei, Chuzhao, Chen, Ningbo, One Health Toxicologie, Sub Data Intensive Systems, IRAS – One Health Toxicology, Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Pausch, Hubert, Leonard, Alexander S, Crysnanto, Danang, Wang, Shikang, Tong, Bin, Lenstra, Johannes A, Han, Jianlin, Li, Fuyong, Xu, Tieshan, Gu, Lihong, Jin, Liangliang, Dang, Ruihua, Huang, Yongzhen, Lan, Xianyong, Ren, Gang, Wang, Yu, Gao, Yuanpeng, Ma, Zhijie, Cheng, Haijian, Ma, Yun, Chen, Hong, Pang, Weijun, Lei, Chuzhao, and Chen, Ningbo

Published
2023

30. Evolutionary origin of genomic structural variations in domestic yaks

Author

One Health Toxicologie, IRAS – One Health Toxicology, Liu, Xinfeng, Liu, Wenyu, Lenstra, Johannes A, Zheng, Zeyu, Wu, Xiaoyun, Yang, Jiao, Li, Bowen, Yang, Yongzhi, Qiu, Qiang, Liu, Hongyu, Li, Kexin, Liang, Chunnian, Guo, Xian, Ma, Xiaoming, Abbott, Richard J, Kang, Minghui, Yan, Ping, Liu, Jianquan, One Health Toxicologie, IRAS – One Health Toxicology, Liu, Xinfeng, Liu, Wenyu, Lenstra, Johannes A, Zheng, Zeyu, Wu, Xiaoyun, Yang, Jiao, Li, Bowen, Yang, Yongzhi, Qiu, Qiang, Liu, Hongyu, Li, Kexin, Liang, Chunnian, Guo, Xian, Ma, Xiaoming, Abbott, Richard J, Kang, Minghui, Yan, Ping, and Liu, Jianquan

Published
2023

31. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Author

Afd Pharmaceutics, One Health Toxicologie, IRAS – One Health Toxicology, Xia, Xiaoting, Qu, Kaixing, Wang, Yan, Sinding, Mikkel-Holger S, Wang, Fuwen, Hanif, Quratulain, Ahmed, Zulfiqar, Lenstra, Johannes A, Han, Jianlin, Lei, Chuzhao, Chen, Ningbo, Afd Pharmaceutics, One Health Toxicologie, IRAS – One Health Toxicology, Xia, Xiaoting, Qu, Kaixing, Wang, Yan, Sinding, Mikkel-Holger S, Wang, Fuwen, Hanif, Quratulain, Ahmed, Zulfiqar, Lenstra, Johannes A, Han, Jianlin, Lei, Chuzhao, and Chen, Ningbo

Published
2023

32. Genetic homogenization of indigenous sheep breeds in Northwest Africa

Author

Belabdi, Ibrahim, Ouhrouch, Abdessamad, Lafri, Mohamed, Gaouar, Semir Bechir Suheil, Ciani, Elena, Benali, Ahmed Redha, Ould Ouelhadj, Hakim, Haddioui, Abdelmajid, Pompanon, François, Blanquet, Véronique, Taurisson-Mouret, Dominique, Harkat, Sahraoui, Lenstra, Johannes A., Benjelloun, Badr, and Da Silva, Anne

Published
2019
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33. High-Density Genomic Characterization of Native Croatian Sheep Breeds

Author

Drzaic, Ivana, Curik, Ino, Lukic, Boris, Shihabi, Mario, Li, Meng-Hua, Kantanen, Juha, Mastrangelo, Salvatore, Ciani, Elena, Lenstra, Johannes A, Cubric-Curik, Vlatka, Afd Pharmacology, One Health Toxicologie, Drzaic, Ivana, Curik, Ino, Lukic, Bori, Shihabi, Mario, Li, Meng-Hua, Kantanen, Juha, Mastrangelo, Salvatore, Ciani, Elena, Lenstra, Johannes A, Cubric-Curik, Vlatka, Afd Pharmacology, and One Health Toxicologie

Subjects
Croatian sheep breed, Croatian sheep breeds, Genetics, Molecular Medicine, inbreeding, Genetics(clinical), population structure, genomic characterization, Genetics (clinical), effective population size, populationstructure
Abstract

A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.

Published
2022

34. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Author

Li, Ran, primary, Gong, Mian, additional, Zhang, Xinmiao, additional, Wang, Fei, additional, Liu, Zhenyu, additional, Zhang, Lei, additional, Yang, Qimeng, additional, Xu, Yuan, additional, Xu, Mengsi, additional, Zhang, Huanhuan, additional, Zhang, Yunfeng, additional, Dai, Xuelei, additional, Gao, Yuanpeng, additional, Zhang, Zhuangbiao, additional, Fang, Wenwen, additional, Yang, Yuta, additional, Fu, Weiwei, additional, Cao, Chunna, additional, Yang, Peng, additional, Ghanatsaman, Zeinab Amiri, additional, Negari, Niloufar Jafarpour, additional, Nanaei, Hojjat Asadollahpour, additional, Yue, Xiangpeng, additional, Song, Yuxuan, additional, Lan, Xianyong, additional, Deng, Weidong, additional, Wang, Xihong, additional, Pan, Chuanying, additional, Xiang, Ruidong, additional, Ibeagha-Awemu, Eveline M., additional, Heslop-Harrison, Pat (J.S.), additional, Rosen, Benjamin D., additional, Lenstra, Johannes A., additional, Gan, Shangquan, additional, and Jiang, Yu, additional

Published
2023
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35. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

Author

Cheng, Hong, primary, Zhang, Zhuangbiao, additional, Wen, Jiayue, additional, Lenstra, Johannes A., additional, Heller, Rasmus, additional, Cai, Yudong, additional, Guo, Yingwei, additional, Li, Ming, additional, Li, Ran, additional, Li, Wenrong, additional, He, Sangang, additional, Wang, Jintao, additional, Shao, Junjie, additional, Song, Yuxuan, additional, Zhang, Lei, additional, Billah, Masum, additional, Wang, Xihong, additional, Liu, Mingjun, additional, and Jiang, Yu, additional

Published
2023
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36. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

Author

Colli, Licia, Milanesi, Marco, Talenti, Andrea, Bertolini, Francesca, Chen, Minhui, Crisà, Alessandra, Daly, Kevin Gerard, Del Corvo, Marcello, Guldbrandtsen, Bernt, Lenstra, Johannes A., Rosen, Benjamin D., Vajana, Elia, Catillo, Gennaro, Joost, Stéphane, Nicolazzi, Ezequiel Luis, Rochat, Estelle, Rothschild, Max F., Servin, Bertrand, Sonstegard, Tad S., Steri, Roberto, Van Tassell, Curtis P., Ajmone-Marsan, Paolo, Crepaldi, Paola, Stella, Alessandra, and the AdaptMap Consortium

Published
2018
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38. High-Density Genomic Characterization of Native Croatian Sheep Breeds

Author

Afd Pharmacology, One Health Toxicologie, Drzaic, Ivana, Curik, Ino, Lukic, Boris, Shihabi, Mario, Li, Meng-Hua, Kantanen, Juha, Mastrangelo, Salvatore, Ciani, Elena, Lenstra, Johannes A, Cubric-Curik, Vlatka, Afd Pharmacology, One Health Toxicologie, Drzaic, Ivana, Curik, Ino, Lukic, Boris, Shihabi, Mario, Li, Meng-Hua, Kantanen, Juha, Mastrangelo, Salvatore, Ciani, Elena, Lenstra, Johannes A, and Cubric-Curik, Vlatka

Published
2022

39. Supplementary Material for Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci

Author

Li, Meng-Hua [menghua.li@cau.edu.cn], Lv, Feng-Hua, Cao, Yin-Hong, Liu, Guang-Jian, Luo, Ling-Yun, Lu, Ran, Liu, Ming-Jun, Li, Wen-Rong, Zhou, Ping, Wang, Xin-Hua, Shen, Min, Gao, Lei, Yang, Jing-Quan, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Wan, Peng-Cheng, Zhang, Yun-Sheng, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Wang, Yu-Tao, Li, Jin-Quan, Salehian-Dehkordi, Hosein, Hehua, Eer, Liu, Yong-Gang, Chen, Jian-Fei, Wang, Jian-Kui, Deng, Xue-Mei, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Charati, Hadi, Nosrati, Maryam, Štěpánek, Ondřej, Rushdi, Hossam E., Olsaker, Ingrid, Curik, Ino, Gorkhali, Neena A., Paiva, S. R., Caetano, Alexander R., Ciani, Elena, Amills, Marcel, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Periasamy, Kathiravan, Johansson, Anna M., Hallsson, Jón H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., Li, Meng-Hua, Li, Meng-Hua [menghua.li@cau.edu.cn], Lv, Feng-Hua, Cao, Yin-Hong, Liu, Guang-Jian, Luo, Ling-Yun, Lu, Ran, Liu, Ming-Jun, Li, Wen-Rong, Zhou, Ping, Wang, Xin-Hua, Shen, Min, Gao, Lei, Yang, Jing-Quan, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Wan, Peng-Cheng, Zhang, Yun-Sheng, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Wang, Yu-Tao, Li, Jin-Quan, Salehian-Dehkordi, Hosein, Hehua, Eer, Liu, Yong-Gang, Chen, Jian-Fei, Wang, Jian-Kui, Deng, Xue-Mei, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Charati, Hadi, Nosrati, Maryam, Štěpánek, Ondřej, Rushdi, Hossam E., Olsaker, Ingrid, Curik, Ino, Gorkhali, Neena A., Paiva, S. R., Caetano, Alexander R., Ciani, Elena, Amills, Marcel, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Periasamy, Kathiravan, Johansson, Anna M., Hallsson, Jón H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., and Li, Meng-Hua

Published
2022

40. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci

Author

National Natural Science Foundation of China, National Key Research and Development Program (China), Chinese Academy of Sciences, Lv, Feng-Hua, Cao, Yin-Hong, Liu, Guang-Jian, Luo, Ling-Yun, Lu, Ran, Liu, Ming-Jun, Li, Wen-Rong, Zhou, Ping, Wang, Xin-Hua, Shen, Min, Gao, Lei, Yang, Jing-Quan, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Wan, Peng-Cheng, Zhang, Yun-Sheng, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Wang, Yu-Tao, Li, Jin-Quan, Salehian-Dehkordi, Hosein, Hehua, Eer, Liu, Yong-Gang, Chen, Jian-Fei, Wang, Jian-Kui, Deng, Xue-Mei, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Charati, Hadi, Nosrati, Maryam, Štěpánek, Ondřej, Rushdi, Hossam E., Olsaker, Ingrid, Curik, Ino, Gorkhali, Neena A., Paiva, S. R., Caetano, Alexander R., Ciani, Elena, Amills, Marcel, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Periasamy, Kathiravan, Johansson, Anna M., Hallsson, Jón H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., Li, Meng-Hua, National Natural Science Foundation of China, National Key Research and Development Program (China), Chinese Academy of Sciences, Lv, Feng-Hua, Cao, Yin-Hong, Liu, Guang-Jian, Luo, Ling-Yun, Lu, Ran, Liu, Ming-Jun, Li, Wen-Rong, Zhou, Ping, Wang, Xin-Hua, Shen, Min, Gao, Lei, Yang, Jing-Quan, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Wan, Peng-Cheng, Zhang, Yun-Sheng, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Wang, Yu-Tao, Li, Jin-Quan, Salehian-Dehkordi, Hosein, Hehua, Eer, Liu, Yong-Gang, Chen, Jian-Fei, Wang, Jian-Kui, Deng, Xue-Mei, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Charati, Hadi, Nosrati, Maryam, Štěpánek, Ondřej, Rushdi, Hossam E., Olsaker, Ingrid, Curik, Ino, Gorkhali, Neena A., Paiva, S. R., Caetano, Alexander R., Ciani, Elena, Amills, Marcel, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Periasamy, Kathiravan, Johansson, Anna M., Hallsson, Jón H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., and Li, Meng-Hua

Abstract

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Published
2022

43. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

Author

Cheng, Hong, primary, Zhang, Zhuangbiao, additional, Wen, Jiayue, additional, Lenstra, Johannes A., additional, Heller, Rasmus, additional, Cai, Yudong, additional, Guo, Yingwei, additional, Li, Ming, additional, Li, Ran, additional, Li, Wenrong, additional, He, Sangang, additional, Wang, Jintao, additional, Shao, Junjie, additional, Song, Yuxuan, additional, Zhang, Lei, additional, Billah, Masum, additional, Wang, Xihong, additional, Liu, Mingjun, additional, and Jiang, Yu, additional

Published
2022
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45. Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Author

Lv, Feng-Hua, Cao, Yin-Hong, Liu, Guang-Jian, Luo, Ling-Yun, Lu, Ran, Liu, Ming-Jun, Li, Wen-Rong, Zhou, Ping, Wang, Xin-Hua, Shen, Min, Gao, Lei, Yang, Jing-Quan, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Wan, Peng-Cheng, Zhang, Yun-Sheng, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Li, Jin-Quan, Salehian-Dehkordi, Hosein, Hehua, Eer, Liu, Yong-Gang, Chen, Jian-Fei, Wang, Jian-Kui, Deng, Xue-Mei, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Charati, Hadi, Nosrati, Maryam, Stepanek, Ondrej, Rushdi, Hossam E., Olsaker, Ingrid, Curik, Ino, Gorkhali, Neena A., Paiva, Samuel R., Caetano, Alexandre R., Ciani, Elena, Amills, Marcel, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Periasamy, Kathiravan, Johansson, Anna Maria, Hallsson, Jon H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., and Li, Meng-Hua

Subjects
Evolutionary Biology
Abstract

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (similar to 16.10x) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, similar to 121.2 million single nucleotide polymorphisms, similar to 61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3 '-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Published
2022

46. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author

Consortium, Vargoats, primary, Nijman, Isaäc, additional, Rosen, Benjamin, additional, Bardou, Philippe, additional, Faraut, Thomas, additional, Cumer, Tristan, additional, Daly, Kevin, additional, Zheng, Zhuqing, additional, Cai, Yudong, additional, Asadollahpour, Hojjat, additional, Cinar-Kul, Bengi, additional, Zhang, Wei-Yi, additional, e, guangxin, additional, Ayin, A, additional, Baird, Hayley, additional, Bakhtin, Meirat, additional, Balteanu, Valentin, additional, Barfield, Diana, additional, Berger, Beate, additional, Blichfeldt, Thor, additional, Boink, Geert, additional, Bugiwati, Sri Rachma, additional, Cai, Zexi, additional, Carolan, Sean, additional, Clark, Emily, additional, Curik, Vladka Cubrić, additional, Dagong, Muhammad, additional, Dorji, Tashi, additional, Drew, Louise, additional, Guo, Jiazhong, additional, Hallsson, Jón, additional, Horvat, Simon, additional, Kantanen, Juha, additional, Kawaguchi, Fuki, additional, Kazymbet, Polat, additional, khayatzadeh, Negar, additional, Kim, Namshin, additional, Shah, Manoj Kumar, additional, Liao, Yuying, additional, Martinez, Amparo, additional, Masangkay, Joseph, additional, Masaoka, Maho, additional, Mazza, Raffaele, additional, McEwan, John, additional, Milanesi, Marco, additional, Faruque, Md Omar, additional, Nomura, Yuto, additional, Ouchene-Khelifi, Nadjet-Amina, additional, Pereira, Filipe, additional, Sahana, Goutam, additional, Salavati, Mazdak, additional, Sasazaki, Shinji, additional, SILVA, Anne DA, additional, Simčič, Mojca, additional, Soelkner, Johann, additional, Sutherland, Alison, additional, Tigchelaar, Johannes, additional, Zhang, Hongping, additional, Consortium, Econogene, additional, Marsan, Paolo Ajmone, additional, Bradley, Daniel, additional, Colli, Licia, additional, Drögemüller, Cord, additional, Jiang, Yu, additional, Lei, chuzhao, additional, Mannen, H, additional, Pompanon, Francois, additional, TOSSER-KLOPP, GWENOLA, additional, and Lenstra, Johannes A., additional

Published
2022
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47. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate.

Author

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

Subjects
GENOMICS, GOATS, COPPER Age, NATURAL selection, DOMESTIC animals, GENE flow
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 wholegenome 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 theKITLG 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. [ABSTRACT FROM AUTHOR]

Published
2023
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48. Geographic distribution of haplotype diversity at the bovine casein locus

Author

Moazami-Goudarzi Katy, Lenstra Johannes A, Ajmone-Marsan Paolo, Williams John L, Zaragoza Pilar, Özbeyaz Ceyhan, Ibeagha-Awemu Eveline M, Jann Oliver C, and Erhardt Georg

Subjects
casein, haplotype, Bos taurus, Bos indicus, phylogeny, Animal culture, SF1-1100, Genetics, QH426-470
Abstract

Abstract The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed.

Published
2004
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50. The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Author

Li, Ran, primary, Gong, Mian, additional, Zhang, Xinmiao, additional, Wang, Fei, additional, Liu, Zhenyu, additional, Zhang, Lei, additional, Xu, Mengsi, additional, Zhang, Yunfeng, additional, Dai, Xuelei, additional, Zhang, Zhuangbiao, additional, Fang, Wenwen, additional, Yang, Yuta, additional, Zhang, Huanhuan, additional, Fu, Weiwei, additional, Cao, Chunna, additional, Yang, Peng, additional, Ghanatsaman, Zeinab Amiri, additional, Negari, Niloufar Jafarpour, additional, Nanaei, Hojjat Asadollahpour, additional, Yue, Xiangpeng, additional, Song, Yuxuan, additional, Lan, Xianyong, additional, Deng, Weidong, additional, Wang, Xihong, additional, Xiang, Ruidong, additional, Ibeagha-Awemu, Eveline M., additional, Heslop-Harrison, Pat (J.S.), additional, Lenstra, Johannes A., additional, Gan, Shangquan, additional, and Jiang, Yu, additional

Published
2021
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