9 results on '"Agraw Amane"'
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2. Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing
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Agraw Amane, Gurja Belay, Abdulfatai Tijjani, Tadelle Dessie, Hassan H. Musa, and Olivier Hanotte
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genetic diversity ,population structure ,local sheep populations ,Sudan ,whole-genome sequence ,Biology (General) ,QH301-705.5 - Abstract
Local Sudanese sheep populations inhabiting diverse environmental conditions and holding opposing morphologies provide opportunities for molecular-genetic research. Characterizing their genome is crucial for sustainable breeding improvement and targeting favorable genes in breeding programs. However, the genome of these sheep populations, which comprises several subtypes, remains uncharacterized using whole-genome sequence data. This study aimed to elucidate genome-wide genetic diversity and population structure of 11 local Sudanese sheep populations, namely, Hammari, Kabbashi, Meidobe, Ashgar, Dubasi, Watish, Bega, Naili, Fulani, Zagawi, and Garag. Ninety whole blood samples were collected, and we extracted DNA using a Qiagen DNeasy® extraction kit. We used the Illumina HiSeq 2000 platform to sequence all the DNA samples. We included whole-genome sequence data of three Ethiopian sheep (Doyogena, Kefis, and Gafera) and one Libyan sheep (Libyan Barbary) in the study to infer the genetic relationships of local Sudanese sheep populations from a continental perspective. A total of 44.8 million bi-allelic autosomal SNPs were detected; 28.5% and 63.3% occur in introns and intergenic regions, respectively. The mean genetic diversity ranged from 0.276 for Garag to 0.324 for Kabbashi sheep populations. The lowest FST estimates were observed between Kabbashi and Ashgar and the highest between Bega and Fulani local Sudanese sheep populations. The principal component and population structure analyses of the 11 local Sudanese sheep populations indicated three separate genetic groups categorized following their tail morphotype, geographical distribution, and population subtype. The thin-tailed local Sudanese sheep populations exhibited independent clustering from the fat-tailed Ethiopian and Libyan sheep. We also observed distinct clustering between the fat-tailed Ethiopian and Libyan sheep. The present study’s findings demonstrated the population structure and principal components related to tail morphotype, geographical distribution, and population subtype of local Sudanese sheep populations. A clear signature of admixture was observed among the studied local Sudanese sheep populations.
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- 2022
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3. Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography
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Getinet Mekuriaw Tarekegn, Tesfaye Getachew, Adebabay Kebede, Yao Nasser, Agraw Amane, Tadelle Dessie, Zewdu Edea, Olivier Hanotte, Gurja Belay, Martina Kyalo, and Jean-Baka Domelevo Entfellner
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Tail ,0106 biological sciences ,0301 basic medicine ,Animal breeding ,Genotype ,Zoology ,Biology ,Population structure ,Disease cluster ,Polymorphism, Single Nucleotide ,010603 evolutionary biology ,01 natural sciences ,Biochemistry ,Genome ,Genetic diversity ,Indigenous ,Fat-tail ,03 medical and health sciences ,Population Groups ,Genetics ,Animals ,Humans ,Ovine 50 K SNP ,Molecular Biology ,Sheep ,Genetic Variation ,Phylogeography ,030104 developmental biology ,Genetic structure ,Ethiopia ,Genome-Wide Association Study ,Research Article - Abstract
Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. Methods A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. Results Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. Conclusion The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations
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- 2020
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4. Analysis of tail morphology and osteology in Ethiopian indigenous sheep
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Agraw Amane, Gurja Belay, Adebabay Kebede, Tadelle Dessie, Setegn Worku, Olivier Hanotte, and Emmanuelle Vila
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Archeology - Published
- 2023
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5. Are petrous bones just a repository of ancient biomolecules? Investigating biosystematic signals in sheep petrous bones using 3D geometric morphometrics
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Camille Bader, Christophe Mallet, Jwana Chahoud, Agraw Amane, Bea De Cupere, Remi Berthon, Franck Lavenne, Azadeh Mohaseb, Hossein Davoudi, Moussab Albesso, Homa Fathi, Manon Vuillien, Joséphine Lesur, Daniel Helmer, Lionel Gourichon, Olivier Hanotte, Marjan Mashkour, Emmanuelle Vila, and Thomas Cucchi
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Archeology - Published
- 2022
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6. EvoSheep : The Makeup of Sheep Breeds in the Ancient Near East
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Sofiane Bouzid, François Pompanon, Bea De Cupere, Camille Bader, Hossein Davoudi, Philippe Abrahami, Daniel Helmer, Catherine Breniquet, Azadeh Fatemeh Mohaseb, Thomas Cucchi, Rémi Berthon, Moussab Albesso, Oscar Estrada, Lionel Gourichon, Emmanuelle Vila, Marjan Mashkour, Daniel G. Bradley, Manon Vuillien, Jwana Chahoud, Ludovic Orlando, Jacqueline Studer, Wei Huangfu, Cécile Michel, Gilles Escarguel, Joséphine Lesur, Agraw Amane, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 (HALMA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Addis Ababa University (AAU), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Trinity College Dublin, Centre d'Histoire 'Espaces et Cultures' (CHEC), Université Clermont Auvergne (UCA), Lebanese University [Beirut] (LU), University of Tehran, Royal Belgian Institute of Natural Sciences (RBINS), Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution (P3E), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Maison de l'Orient et de la Méditerranée - Jean Pouilloux (MOM), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Natural History Museum [Geneva], ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), Histoire Archéologie Littérature des Mondes Anciens - UMR 8164 (HALMA), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Archaeozoological section, Bioarchaeological laboratory, Directorate Earth & History of Life, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Archaeozoology, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Ministère de la Culture (MC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Microbial, Cellular and Molecular Biology, ILRI Ethiopia (ILRI), ILRI, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland, Department of Archaeology, Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), ARCHEORIENT - Environnements et sociétés de l'Orient ancien [Archéorient], Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 [HALMA], Archéozoologie, archéobotanique : sociétés, pratiques et environnements [AASPE], Centre d'Histoire 'Espaces et Cultures' [CHEC], Anthropologie Moléculaire et Imagerie de Synthèse [AMIS], Archéologies et Sciences de l'Antiquité [ArScAn], Laboratoire d'Ecologie Alpine [LECA ], Culture et Environnements, Préhistoire, Antiquité, Moyen-Age [CEPAM], Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution [P3E]
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Near East ,010506 paleontology ,Archeology ,[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory ,Textile production ,01 natural sciences ,[SHS]Humanities and Social Sciences ,0601 history and archaeology ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Levant ,Archaeozoology ,0105 earth and related environmental sciences ,2. Zero hunger ,Morphometrics ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Geometric morphometrics ,Middle East ,Plateau ,geography.geographical_feature_category ,Africa ,Sheep ,060102 archaeology ,General Arts and Humanities ,Mesopotamia ,06 humanities and the arts ,Archaeology ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,Geography ,[SDE]Environmental Sciences ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
International audience; The EVOSHEEP project combines archaeozoology, geometric morphometrics and genetics to study archaeo- logical sheep assemblages dating from the sixth to the first millennia BC in eastern Africa, the Levant, the Ana- tolian South Caucasus, the Iranian Plateau and Mesopotamia. The project aims to understand changes in the physical appearance and phenotypic characteristics of sheep and how these related to the appearance of new breeds and the demand for secondary products to supply the textile industry.
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- 2021
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7. Adaptation and Yield Performance of Different Cowpea (Vigna unguiculata L.) Varieties in Western Gojjam, Ethiopia
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Wondmeneh Mekonnen, Biyadglegne Hunegnaw, Misganaw Walie, Agraw Amane, and Likawent Yeheyis
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Wet season ,Vigna ,Horticulture ,Point of delivery ,Yield (wine) ,Field experiment ,Randomized block design ,Dry matter ,General Medicine ,Biology ,biology.organism_classification ,Legume - Abstract
Field experiment was conducted during 2013/14 rainy season in two selected districts of north western Ethiopia with the objective of evaluate the adaptability and yield performance of cowpea ( Vigna unguiculata ) varieties under sole cropping. Treatments consisted of seven cowpea (TVU, Bekur, 9333, 9334, 12688, Kenkety and Black eye bean) varieties in randomized complete block design with three replication per district. Variety showed highly significance difference in their Dry Matter Yield (DMY) and the value ranged 2.07 to 4.19 t/ha. Cowpea variety 9334 showed highly significance (4.19) difference in its DMY as compared to12688 (3.09), black eye bean (2.85), TVU (2.79) and bekur (2.07t/ha). Seed yield also showed highly significance difference by variety and district. Cowpea variety 9333 gave significantly higher (1235.4kg/ha) seed yield compared to TVU (733.3), 9334 (722.9), black eye bean (511.8) and bekur 487.5 kg/ha. There was also significant variation between the number of seeds per pod obtained from kenkety and 12688 with that of most cowpea varieties. Black eye bean significantly differed from all cowpea varieties evaluated in its thousand seed weight. Based on yield data kenkety 9333 and 9334 recommended as alternative legume forage crops from cowpea varieties evaluated under sole cropping for Jabitehnan and South Achefer areas.
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- 2016
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8. EVOSHEEP project: Documenting morphological diversity of early sheep 'breeds' in Southwest Asian societies (6th - 1rst millennia BC) using 3D geometric morphometric of appendicular bones
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Manon Vuillien, Emmanuelle Vila, Jwana Chahoud, Moussab Albesso, Agraw Amane, Rémi Berthon, Sofiane Bouzid, Bea de Cupere, Hossein Davoudi, Homa Fathi, Daniel Helmer, Joséphine Lesur, Azadeh Mohaseb, Lionel Gourichon, Marjan Mashkour, Thomas CUCCHI, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Lebanese University [Beirut] (LU), Université d'Addis Abéba, Musée national d'Éthiopie, International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut Royal des Sciences Naturelles de Belgique (IRSNB), Archaeozoological section, Bioarchaeological laboratory, University of Tehran, Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
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[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory ,[SHS]Humanities and Social Sciences - Abstract
International audience; The EVOSHEEP project focuses on the complex history of early sheep (Ovis aries) husbandry in Southwest Asia between the Late Neolithic and Late Bronze Age using a multi proxy approach (morphometrics, genetics, iconography) to identify the biological and anthropological components behind the emergence and development of early sheep breeds. One of the challenges in this approach is to be able to disentangle the impact of anthropogenic selective pressure from ecological conditions on the skeletal morphology of sheep on a large scale. As a first step towards this understanding, we first explored the extent of morphology diversity and change in domestic sheep populations across southwestern Asia over the last 8,000 years. Using the recent development in virtual morphometrics on distal humerus, calcaneum and astragalus bones, this paper will present our latest thoughts from the comparative study of ancient sheep from forty archaeological sites across Syria, Lebanon, Iraq, Azerbaijan, Georgia and Iran between the 6th and the 1st millennium BC with current traditional breeds of sheep from Middle East and Eastern Africa whose husbandry practices are well documented.
9. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci
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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, 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 M., Hallsson, Jón H., Kantanen, Juha, Coltman, David W., Bruford, Michael W., Lenstra, Johannes A., Li, Meng-Hua, Nowick, Katja, National Natural Science Foundation of China, National Key Research and Development Program (China), Chinese Academy of Sciences, FENG-HUA LV, China Agricultural University, China, YIN-HONG CAO, Chinese Academy of Sciences (CAS), China, GUANG-JIAN LIU, Novogene Bioinformatics Institute, China, LING-YUN LUO, China Agricultural University, China, RAN LU, China Agricultural University, China, MING-JUN LIU, Xinjiang Academy of Animal Science, China, WEN-RONG LI, Xinjiang Academy of Animal Science, China, PING ZHOU, Xinjiang Academy of Agricultural and Reclamation Sciences, China, XIN-HUA WANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, MIN SHEN, Xinjiang Academy of Agricultural and Reclamation Sciences, China, LEI GAO, Xinjiang Academy of Agricultural and Reclamation Sciences, China, JING-QUAN YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, HUA YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YONG-LIN YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, CHANG-BIN LIU, Xinjiang Academy of Agricultural and Reclamation Sciences, China, PENG-CHENG WAN, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YUN-SHENG ZHANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, WEN-HUI PI, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YAN-LING REN, Shandong Binzhou Academy of Animal Science and Veterinary Medicine, China, ZHI-QIANG SHEN, Shandong Binzhou Academy of Animal Science and Veterinary Medicine, China, FENG WANG, Nanjing Agricultural University, China, YU-TAO WANG, Kashi University, China, JIN-QUAN LI, Inner Mongolia Agricultural University, China, HOSEIN SALEHIAN-DEHKORDI, Chinese Academy of Sciences (CAS), China, EER HEHUA, Ningxia Academy of Agriculture and Forestry Sciences, China, YONG-GANG LIU, Yunnan Agricultural University, China, JIAN-FEI CHEN, China Agricultural University, China, JIAN-KUI WANG, China Agricultural University, China, XUE-MEI DENG, China Agricultural University, China, ALI ESMAILIZADEH, Shahid Bahonar University of Kerman, Iran, MOSTAFA DEHGHANI-QANATQESTANI, Shahid Bahonar University of Kerman, Iran, HADI CHARATI, Shahid Bahonar University of Kerman, Iran, MARYAM NOSRATI, Payame Noor University, Iran, ONDREJ STEPANEK, State Veterinary Institute Jihlava, Czech Republic, HOSSAM E. RUSHDI, Cairo University, Egypt, INGRID OLSAKER, Norwegian University of Life Sciences, Norway, INO CURIK, University of Zagreb, Croatia, NEENA A. GORKHALI, Nepal Agriculture Research Council (NARC), Nepal, SAMUEL REZENDE PAIVA, Cenargen, ALEXANDRE RODRIGUES CAETANO, Cenargen, ELENA CIANI, Universita degli Studi di Bari Aldo 24 Moro, Italy, MARCEL AMILLS, Campus de la Universitat Autonoma de Barcelona, Spain, CHRISTINA WEIMANN, Justus-Liebig-University Giessen, Germany, GEORG ERHARDT, Justus-Liebig-University Giessen, Germany, AGRAW AMANE, Addis Ababa University, Ethiopia, JORAM M. MWACHARO, International Centre for Agricultural Research in the Dry Areas (ICARDA), Ethiopia, JIAN-LIN HAN, Chinese Academy of Agricultural Sciences (CAAS), China, OLIVIER HANOTTE, International Livestock Research Institute, Ethiopia, KATHIRAVAN PERIASAMY, International Atomic Energy Agency (IAEA), Austria, ANNA M. JOHANSSON, Swedish University of Agricultural Sciences, Sweden, JON H. HALLSSON, Agricultural University of Iceland, Iceland, JUHA KANTANEN, Natural Resources Institute Finland (Luke), Finland, DAVID W. COLTMAN, University of Alberta, Edmonton, Canada, MICHAEL W. BRUFORD, Cardiff University, United Kingdom, JOHANNES A. LENSTRA, Utrecht University, The Netherlands, and MENG-HUA LI, China Agricultural University, China.
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Asia ,Genome ,Sheep ,Whole-genome sequences ,Genetic Variation ,Genetic selection ,Sequence Analysis, DNA ,Iran ,Polymorphism, Single Nucleotide ,Genetic diversity ,whole-genome sequences ,genetic diversity ,adaptive introgression ,genetic selection ,agronomic traits ,migration ,Europe ,Adaptive introgression ,Genetics ,Animals ,Agronomic traits ,Molecular Biology ,Sheep, Domestic ,Ecology, Evolution, Behavior and Systematics ,Migration - 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., This study was financially supported by grants from the National Natural Science Foundation of China (Nos. 32061133010, 31825024, 31661143014, and 31972527), the National Key Research and Development Program-Key Projects of International Innovation Cooperation between Governments (2017YFE0117900), the External Cooperation Program of Chinese Academy of Sciences (152111KYSB20150010), and the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (No. 2019QZKK0501), and the Special Funds of the State Key Laboratory of Sheep Genetic Improvement and Healthy Production (Nos. 2018CA001, and 2019CA009, 2020CA001).
- Published
- 2022
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