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3. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats

Author

Shumuye Belay, Gurja Belay, Helen Nigussie, Abulgasim M. Ahbara, Abdulfatai Tijjani, Tadelle Dessie, Getinet M. Tarekegn, Han Jian-Lin, Siobhan Mor, Helina S. Woldekiros, Keith Dobney, Ophelie Lebrasseur, Olivier Hanotte, and Joram M. Mwacharo

Subjects
Medicine, Science
Abstract

Abstract Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.

Published
2024
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4. Whole-genome resource sequences of 57 indigenous Ethiopian goats

Author

Shumuye Belay, Gurja Belay, Helen Nigussie, Han Jian-Lin, Abdulfatai Tijjani, Abulgasim M. Ahbara, Getinet M. Tarekegn, Helina S. Woldekiros, Siobhan Mor, Keith Dobney, Ophelie Lebrasseur, Olivier Hanotte, and Joram M. Mwacharo

Subjects
Science
Abstract

Abstract Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species’ evolutionary trajectory.

Published
2024
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6. Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

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

Subjects
Biotechnology, Genetics, Human Genome, Animals, Animals, Domestic, Chickens, Domestication, Genome, Genomics, Humans, Bottleneck, Genetic load, Deleterious mutation, Domestic chicken, Developmental Biology
Abstract

BackgroundSpecies 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.ResultsWe 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.ConclusionThis 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.

Published
2021

8. Author Correction: 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Biochemistry and Cell Biology, Biological Sciences, Clinical Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

9. 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Genetics, Animal Distribution, Animals, Animals, Domestic, Asia, Chickens, Domestication, Gene Pool, Genome, Geography, Likelihood Functions, Phylogeny, Poultry, Selection, Genetic, Biochemistry and Cell Biology, Clinical Sciences, Developmental Biology
Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Published
2020

16. Rapid evolution of fine-scale recombination during domestication

Author

Liu, Zheng-Xi, primary, Li, Ming, additional, Si, Si, additional, Chen, Jian-Hai, additional, Hu, Li-Rong, additional, Peng, Min-Sheng, additional, Yin, Ting-Ting, additional, Esmailizadeh, Ali, additional, Zhang, Chang, additional, Qu, Lu-Jiang, additional, Lu, Xue-Mei, additional, Han, Jian-Lin, additional, Zhang, Ya-Ping, additional, and Wang, Ming-Shan, additional

Published
2024
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21. Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

Author

Li, Chao, primary, Chen, Bingchun, additional, Langda, Suo, additional, Pu, Peng, additional, Zhu, Xiaojia, additional, Zhou, Shiwei, additional, Kalds, Peter, additional, Zhang, Ke, additional, Bhati, Meenu, additional, Leonard, Alexander, additional, Huang, Shuhong, additional, Li, Ran, additional, Cuoji, Awang, additional, Wang, Xiran, additional, Zhu, Haolin, additional, Wu, Yujiang, additional, Cuomu, Renqin, additional, Gui, Ba, additional, Li, Ming, additional, Wang, Yutao, additional, Li, Yan, additional, Fang, Wenwen, additional, Jia, Ting, additional, Pu, Tianchun, additional, Pan, Xiangyu, additional, Cai, Yudong, additional, He, Chong, additional, Wang, Liming, additional, Jiang, Yu, additional, Han, Jian-Lin, additional, Chen, Yulin, additional, Zhou, Ping, additional, Pausch, Hubert, additional, and Wang, Xiaolong, additional

Published
2024
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25. ABE-induced PDGFD start codon silencing unveils new insights into the genetic architecture of sheep fat tails

Author

Kalds, Peter, primary, Huang, Shuhong, additional, Zhou, Shiwei, additional, Xi, Siyuan, additional, Fang, Yumeng, additional, Gao, Yawei, additional, Sun, Kexin, additional, Li, Chao, additional, Cai, Bei, additional, Liu, Yao, additional, Ding, Yige, additional, Kou, Qifang, additional, Sonstegard, Tad, additional, Petersen, Björn, additional, Kemp, Stephen, additional, Ma, Baohua, additional, Han, Jian-Lin, additional, Chen, Yulin, additional, and Wang, Xiaolong, additional

Published
2023
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29. Mapping molecular diversity of indigenous goat genetic resources of Asia

Author

Periasamy, Kathiravan, Vahidi, S.M.F., Silva, Pradeepa, Faruque, M.O., Naqvi, A.N., Basar, Muladno, Cao, JianHua, Zhao, ShuHong, Thuy, Le Thi, Pichler, Rudolf, Podesta, Mario Garcia, Shamsuddin, Mohammed, Boettcher, Paul, Garcia, Jose Fernando, Han, Jian-Lin, Marsan, Paolo Ajmone, Diallo, Adama, and Viljoen, Gerrit J.

Published
2017
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31. 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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32. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun

Abstract

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Published
2023

33. Thai Local Chicken Breeds, Chee Fah and Fah Luang, Originated from Chinese Black-Boned Chicken with Introgression of Red Junglefowl and Domestic Chicken Breeds

Author

Budi, Trifan, primary, Singchat, Worapong, additional, Tanglertpaibul, Nivit, additional, Wongloet, Wongsathit, additional, Chaiyes, Aingorn, additional, Ariyaraphong, Nattakan, additional, Thienpreecha, Worawit, additional, Wannakan, Wannapa, additional, Mungmee, Autchariyapron, additional, Thong, Thanyapat, additional, Wattanadilokchatkun, Pish, additional, Panthum, Thitipong, additional, Ahmad, Syed Farhan, additional, Lisachov, Artem, additional, Muangmai, Narongrit, additional, Chuenka, Rattanaphon, additional, Prapattong, Pollavat, additional, Nunome, Mitsuo, additional, Chamchumroon, Wiyada, additional, Han, Kyudong, additional, Pornpipatsiri, Santi, additional, Supnithi, Thepchai, additional, Peng, Min-Sheng, additional, Han, Jian-Lin, additional, Matsuda, Yoichi, additional, Duengkae, Prateep, additional, Noinafai, Phuechphol, additional, and Srikulnath, Kornsorn, additional

Published
2023
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34. Additional file 2 of Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation

Author

Wang, Chen, Wu, Dong-Dong, Yuan, Yao-Hua, Yao, Meng-Cheng, Han, Jian-Lin, Wu, Ya-Jiang, Shan, Fen, Li, Wan-Ping, Zhai, Jun-Qiong, Huang, Mian, Peng, Shi-Ming, Cai, Qin-Hui, Yu, Jian-Yi, Liu, Qun-Xiu, Liu, Zhao-Yang, Li, Lin-Xiang, Teng, Ming-Sheng, Huang, Wei, Zhou, Jun-Ying, Zhang, Chi, Chen, Wu, and Tu, Xiao-Long

Abstract

Additional file 2: Figure S1. Distribution of 17-mer depth for estimating the genome size. The x-axis represents k-mer depths while y-axis represents the proportions. The blue line represents the proportion of 17-mer in each depth. The peak depth is at 25-fold and total number of 17-mer is 61,791,522,108. The South China tiger (P. t. amoyensis) genome size was estimated to be 2471.66 Mb from the formula: Genome size = K-mer_number/K_depth of peak. Figure S2. Hi-C chromosomal contact heat map. A 500 kb resolution was used to calculate the number of Hi-C read pairs in any two bins. Figure S3. The collinearity between the South China tiger and domestic cat (Felis catus) genomes. Each dot represents an aligned region while the minimum length is 10 kb. The red dot represents forward comparison and the blue dot reverse comparison. Figure S4. Q30 and GC content for each sample. The average Q30 and GC content are 93.24% and 42.04%, respectively. Their very low variation reflected our re-sequencing data to be high quality. Figure S5. The distribution of mapping rates and average mapping depths for each individual. The depths ranged from 12.91× to 18.96 × while the rates varied from 96.03% to 98.92%. Figure S6. The distribution of the SNP number and frequency. Number of genome-wide SNPs (top) and frequency of SNPs per 1 kb of each tiger sample (bottom). Figure S7. Nucleotide diversity π estimates of six tiger subspecies. Figure S8. Heterozygosity statistics of genome-wide SNPs. (a) Observed heterozygosity across all individual genomes of each tiger subspecies. (b) Genomic heterozygosity in each tiger subspecies at population level. Figure S9. Pairwise FST values between six tiger subspecies. The weighted FST values are shown above the diagonal while their standard deviations below the diagonal. Figure S10. Principal component analysis using genome-wide SNPs of six tiger subspecies. Figure S11. A maximum likelihood tree was built using TreeMix software with whole-genome sequencing data of six tiger subspecies and cat. Figure S12. Cluster analysis based on the matrix of genome-wide identity-by-state (IBS) pairwise distances between six tiger subspecies determined by a permutation score. Figure S13. Analysis of genome-wide average identity-by-state (IBS) pairwise identities between six tiger subspecies. Figure S14. Population genetic structure of the South China tigers estimated by the ADMIXTURE. Figure S15. Demographic histories of tiger subspecies. PSMC analysis shows the change in effective population size over time. The dash lines represent 100 bootstraps. The representative individuals sequenced at a high read coverage were selected for each graph, South China tiger (ptam_4, mean 25.38×), Amur tiger (ptal_1, mean 14.76×), Indochinese tiger (ptco_2, mean 13.98×), Malayan tiger (ptja_7, mean 13.13×), Bengal tiger (ptti_3, mean 13.79×), and Sumatran tiger (ptsu_1, mean 13.41×). Figure S16. The results of Dsuite. Heatmap showing statistical support for introgression between pairs of tiger subspecies. Cells in the heatmap indicate the pairwise Z score values between the branch b identified on the expanded tree on the Y axis (relative to its sister branch) and the taxa P3 identified on the X-axis. The grey color indicates the none. (a) Result of branch for South China tiger (lineage 1) with the other tiger subspecies populations. (b) Result of branch for South China tiger (lineage 2) with the other tiger subspecies populations. (c) Result of branch for South China tiger (ptam1 individual) with the other tiger subspecies populations. Figure S17. The graph of ABBA-BABA test. The values of D (pop1, pop2; pop3, pop4) >0 indicates that there are gene flows between pop1 and pop3. Here, only the introgression occurred in South China tiger will be shown. (a) D-statistic for South China tiger (lineage 1) with other tiger subspecies. (b) D-statistic for South China tiger (lineage 2) with other tiger subspecies. (c) D-statistic for South China tiger (ptam1 individual) with other tiger subspecies. Figure S18. Plot of inferred introgression between the South China tiger lineage 1 and other tiger subspecies populations detected by the TreeMix method. The scale bar shows 10 times the average standard error of the entries in the sample covariance matrix. Figure S19. Plot of inferred introgression between the South China tiger lineage 2 and other tiger subspecies populations detected by the TreeMix method. The scale bar shows 10 times the average standard error of the entries in the sample covariance matrix. Figure S20. Plot of inferred introgression between the South China tiger ptam_1 individual and other tiger subspecies populations detected by the TreeMix method. The scale bar shows 10 times the average standard error of the entries in the sample covariance matrix. Figure S21. Genomic inbreeding coefficients FH in each tiger subspecies. Figure S22. The plot of three inbreeding coefficients (FP, FH, and FROH) of the South China tiger. Figure S23. Comparison of homozygote and heterozygote percentage of per mutation category among six tiger subspecies. The significant value was calculated by t-test.

Published
2023
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35. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, primary, Alfieri, James M., additional, Anthony, Nick, additional, Arensburger, Peter, additional, Athrey, Giridhar N., additional, Balacco, Jennifer, additional, Balic, Adam, additional, Bardou, Philippe, additional, Barela, Paul, additional, Bigot, Yves, additional, Blackmon, Heath, additional, Borodin, Pavel M., additional, Carroll, Rachel, additional, Casono, Meya C., additional, Charles, Mathieu, additional, Cheng, Hans, additional, Chiodi, Maddie, additional, Cigan, Lacey, additional, Coghill, Lyndon M., additional, Crooijmans, Richard, additional, Das, Neelabja, additional, Davey, Sean, additional, Davidian, Asya, additional, Degalez, Fabien, additional, Dekkers, Jack M., additional, Derks, Martijn, additional, Diack, Abigail B., additional, Djikeng, Appolinaire, additional, Drechsler, Yvonne, additional, Dyomin, Alexander, additional, Fedrigo, Olivier, additional, Fiddaman, Steven R., additional, Formenti, Giulio, additional, Frantz, Laurent A.F., additional, Fulton, Janet E., additional, Gaginskaya, Elena, additional, Galkina, Svetlana, additional, Gallardo, Rodrigo A., additional, Geibel, Johannes, additional, Gheyas, Almas, additional, Godinez, Cyrill John P., additional, Goodell, Ashton, additional, Graves, Jennifer A. M., additional, Griffin, Daren K., additional, Haase, Bettina, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Henderson, Lindsay J., additional, Hou, Zhuo-Cheng, additional, Howe, Kerstin, additional, Huynh, Lan, additional, Ilatsia, Evans, additional, Jarvis, Erich, additional, Johnson, Sarah M., additional, Kaufman, Jim, additional, Kelly, Terra, additional, Kemp, Steve, additional, Kern, Colin, additional, Keroack, Jacob H., additional, Klopp, Christophe, additional, Lagarrigue, Sandrine, additional, Lamont, Susan J., additional, Lange, Margaret, additional, Lanke, Anika, additional, Larkin, Denis M., additional, Larson, Greger, additional, Layos, John King N., additional, Lebrasseur, Ophélie, additional, Malinovskaya, Lyubov P., additional, Martin, Rebecca J., additional, Martin Cerezo, Maria Luisa, additional, Mason, Andrew S., additional, McCarthy, Fiona M., additional, McGrew, Michael J., additional, Mountcastle, Jacquelyn, additional, Muhonja, Christine Kamidi, additional, Muir, William, additional, Muret, Kévin, additional, Murphy, Terence, additional, Ng’ang’a, Ismael, additional, Nishibori, Masahide, additional, O’Connor, Rebecca E., additional, Ogugo, Moses, additional, Okimoto, Ron, additional, Ouko, Ochieng, additional, Patel, Hardip R., additional, Perini, Francesco, additional, Pigozzi, María Ines, additional, Potter, Krista C., additional, Price, Peter D., additional, Reimer, Christian, additional, Rice, Edward S., additional, Rocos, Nicolas, additional, Rogers, Thea F., additional, Saelao, Perot, additional, Schauer, Jens, additional, Schnabel, Robert, additional, Schneider, Valerie, additional, Simianer, Henner, additional, Smith, Adrian, additional, Stevens, Mark P., additional, Stiers, Kyle, additional, Tiambo, Christian Keambou, additional, Tixier-Boichard, Michele, additional, Torgasheva, Anna A., additional, Tracey, Alan, additional, Tregaskes, Clive A., additional, Vervelde, Lonneke, additional, Wang, Ying, additional, Warren, Wesley C., additional, Waters, Paul D., additional, Webb, David, additional, Weigend, Steffen, additional, Wolc, Anna, additional, Wright, Alison E., additional, Wright, Dominic, additional, Wu, Zhou, additional, Yamagata, Masahito, additional, Yang, Chentao, additional, Yin, Zhong-Tao, additional, Young, Michelle C., additional, Zhang, Guojie, additional, Zhao, Bingru, additional, and Zhou, Huaijun, additional

Published
2023
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37. Markhor-derived Introgression of a Genomic Region EncompassingPAPSS2Confers High-altitude Adaptability in Tibetan Goats

Author

Li, Chao, primary, Wu, Yujiang, additional, Chen, Bingchun, additional, Cai, Yudong, additional, Guo, Jiazhong, additional, Leonard, Alexander S, additional, Kalds, Peter, additional, Zhou, Shiwei, additional, Zhang, Jingchen, additional, Zhou, Ping, additional, Gan, Shangqu, additional, Jia, Ting, additional, Pu, Tianchun, additional, Suo, Langda, additional, Li, Yan, additional, Zhang, Ke, additional, Li, Lan, additional, Purevdorj, Myagmarsuren, additional, Wang, Xihong, additional, Li, Ming, additional, Wang, Yu, additional, Liu, Yao, additional, Huang, Shuhong, additional, Sonstegard, Tad, additional, Wang, Ming-Shan, additional, Kemp, Stephen, additional, Pausch, Hubert, additional, Chen, Yulin, additional, Han, Jian-Lin, additional, Jiang, Yu, additional, and Wang, Xiaolong, additional

Published
2022
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38. Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation

Author

Li, Xin, primary, He, San-Gang, additional, Li, Wen-Rong, additional, Luo, Ling-Yun, additional, Yan, Ze, additional, Mo, Dong-Xin, additional, Wan, Xing, additional, Lv, Feng-Hua, additional, Yang, Ji, additional, Xu, Ya-Xi, additional, Deng, Juan, additional, Zhu, Qiang-Hui, additional, Xie, Xing-Long, additional, Xu, Song-Song, additional, Liu, Chen-Xi, additional, Peng, Xin-Rong, additional, Han, Bin, additional, Li, Zhong-Hui, additional, Chen, Lei, additional, Han, Jian-Lin, additional, Ding, Xue-Zhi, additional, Dingkao, Renqing, additional, Chu, Yue-Feng, additional, Wu, Jin-Yan, additional, Wang, Li-Min, additional, Zhou, Ping, additional, Liu, Ming-Jun, additional, and Li, Meng-Hua, additional

Published
2022
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41. 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

42. 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. 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

44. Population genomic analysis provides strong evidence of the past success and future strategies of South China tiger breeding

Author

Wang, Chen, primary, Wu, Dong-Dong, additional, Yuan, Yao-Hua, additional, Yao, Meng-Cheng, additional, Han, Jian-Lin, additional, Wu, Ya-Jiang, additional, Shan, Fen, additional, Li, Wan-Ping, additional, Zhai, Jun-Qiong, additional, Huang, Mian, additional, Peng, Shi-Ming, additional, Cai, Qin-Hui, additional, Yu, Jian-Yi, additional, Liu, Qun-Xiu, additional, Liu, Zhao-Yang, additional, Li, Lin-Xiang, additional, Teng, Ming-Sheng, additional, Huang, Wei, additional, Zhou, Jun-Ying, additional, Zhang, Chi, additional, Chen, Wu, additional, and Tu, Xiao-Long, additional

Published
2021
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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, primary, Cao, Yin-Hong, additional, Liu, Guang-Jian, additional, Luo, Ling-Yun, additional, Lu, Ran, additional, Liu, Ming-Jun, additional, Li, Wen-Rong, additional, Zhou, Ping, additional, Wang, Xin-Hua, additional, Shen, Min, additional, Gao, Lei, additional, Yang, Jing-Quan, additional, Yang, Hua, additional, Yang, Yong-Lin, additional, Liu, Chang-Bin, additional, Wan, Peng-Cheng, additional, Zhang, Yun-Sheng, additional, Pi, Wen-Hui, additional, Ren, Yan-Ling, additional, Shen, Zhi-Qiang, additional, Wang, Feng, additional, Wang, Yu-Tao, additional, Li, Jin-Quan, additional, Salehian-Dehkordi, Hosein, additional, Hehua, Eer, additional, Liu, Yong-Gang, additional, Chen, Jian-Fei, additional, Wang, Jian-Kui, additional, Deng, Xue-Mei, additional, Esmailizadeh, Ali, additional, Dehghani-Qanatqestani, Mostafa, additional, Charati, Hadi, additional, Nosrati, Maryam, additional, Štěpánek, Ondřej, additional, Rushdi, Hossam E, additional, Olsaker, Ingrid, additional, Curik, Ino, additional, Gorkhali, Neena A, additional, Paiva, Samuel R, additional, Caetano, Alexandre R, additional, Ciani, Elena, additional, Amills, Marcel, additional, Weimann, Christina, additional, Erhardt, Georg, additional, Amane, Agraw, additional, Mwacharo, Joram M, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Periasamy, Kathiravan, additional, Johansson, Anna M, additional, Hallsson, Jón H, additional, Kantanen, Juha, additional, Coltman, David W, additional, Bruford, Michael W, additional, Lenstra, Johannes A, additional, and Li, Meng-Hua, additional

Published
2021
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46. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep

Author

Lv, Feng-Hua, Peng, Wei-Feng, Yang, Ji, Zhao, Yong-Xin, Li, Wen-Rong, Liu, Ming-Jun, Ma, Yue-Hui, Zhao, Qian-Jun, Yang, Guang-Li, Wang, Feng, Li, Jin-Quan, Liu, Yong-Gang, Shen, Zhi-Qiang, Zhao, Sheng-Guo, Hehua, EEr, Gorkhali, Neena A., Farhad Vahidi, S. M., Muladno, Muhammad, Naqvi, Arifa N., Tabell, Jonna, Iso-Touru, Terhi, Bruford, Michael W., Kantanen, Juha, Han, Jian-Lin, and Li, Meng-Hua

Published
2015
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47. Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus).

Author

Ma, Zhi-Jie, Li, Guang-Zhen, Chen, Sheng-Mei, Han, Jian-Lin, and Hanif, Quratulain

Subjects
YAK, GENETIC variation, GERMPLASM conservation, HAPLOTYPES
Abstract

Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai-Tibetan Plateau. So far, most studies on the molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on the small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) and four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. The present study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species. [ABSTRACT FROM AUTHOR]

Published
2022
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49. Paternal Origins and Migratory Episodes of Domestic Sheep

Author

Deng, Juan, Xie, Xing-Long, Wang, Dong-Feng, Zhao, Chao, Lv, Feng-Hua, Li, Xin, Yang, Ji, Yu, Jia-Lin, Shen, Min, Gao, Lei, Yang, Jing-Quan, Liu, Ming-Jun, Li, Wen-Rong, Wang, Yu-Tao, Wang, Feng, Li, Jin-Quan, Hehua, EEr, Liu, Yong-Gang, Shen, Zhi-Qiang, Ren, Yan-Ling, Liu, Guang-Jian, Chen, Ze-Hui, Gorkhali, Neena A., Rushdi, Hossam E., Salehian-Dehkordi, Hosein, Esmailizadeh, Ali, Nosrati, Maryam, Paiva, Samuel R., Caetano, Alexandre R., Štěpánek, Ondřej, Olsaker, Ingrid, Weimann, Christina, Erhardt, Georg, Curik, Ino, Kantanen, Juha, Mwacharo, Joram M., Hanotte, Olivier, Bruford, Michael W., Ciani, Elena, Periasamy, Kathiravan, Amills, Marcel, Lenstra, Johannes A., Han, Jian-Lin, Zhang, Hong-Ping, Li, Li, and Li, Meng-Hua

Published
2020
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50. Additional file 1 of Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

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

Abstract

Additional file 1: Figure S1. Nucleotide diversity for G. g. spadiceus and chicken populations (grouped by samling locations and breeds). Figure S2. Demographic histories for G. g. spadiceus and diverse chicken groups by PSMC. A total of 18 chicken populations were included in this analysis. Figure S3. Four tested demographic models for dadi analysis. Nanc, ancestral population size before the split; T, timepoints; m, migrations; Napop, ancestral population size after split. Ncpop, current population size. Arrows depict migration directions. Figure S4. Comparing observed data and model allele frequency spectrum for the best model (Model 3). Figure S5. Provean-scores for nonsynonymous mutations (for all mutations, left; and for mutations with Provean-scores ≤ –2.5, right) in microchromosomes, macrochromosomes, and intermediate chromosomes. Figure S6. Pipeline for constructing the mouse model with a mutation at the mouse TSHR locus (p. Gly559Arg; c.1675G>A). Figure S7. Photograph showing TSHR-559Arg knock-in homozygous (HO) and wild-type mice at 10 months old. Figure S8. Gly558Arg knock-in mice consumed less food than wild-type. *, P

Published
2021
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