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Stafuzza NB, Freitas ACD, Mioto MB, Silva RMDO, Fragomeni BDO, Pedrosa VB, Costa RLDD, Paz CCPD. Weighted single-step genome-wide association study and functional enrichment analyses for gastrointestinal nematode resistance traits in Santa Ines sheep. Vet Parasitol 2023; 323:110047. [PMID: 37857178 DOI: 10.1016/j.vetpar.2023.110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
This study aimed to identify genomic regions, pathways, and putative candidate genes associated with resistance to gastrointestinal nematode in Santa Ines sheep. The phenotypic information comprised 5529 records from 1703 naturally infected animals. After genomic data quality control, 37,511 SNPs from 589 animals were available. The weighted single-step approach for genome-wide association study was performed to estimate the SNP effects and variances accounted by 10-SNP sliding windows. Confirming the polygenic nature of the studied traits, 20, 22, 21, and 19 genomic windows that explained more than 0.5% of the additive genetic variance were identified for fecal egg counts (FEC), Famacha© (FAM), packed cell volume (PCV), and total plasma protein (TPP), respectively. A total of 81, 122, 106, and 101 protein-coding genes were found in windows associated with FEC, FAM, PCV, and TPP, respectively. Several protein-coding genes related to the immune system and inflammatory response functions were identified within those genomic regions, such as ADCY9, ADRB2, BRAF, CADM1, CCL20, CD70, CREBBP, FNBP1, HTR4, IL16, IL22, IL26, MAPK8, NDFIP1, NLRC3, PAK5, PLCB1, PLCB4, ROCK1, TEK, TNFRSF12A, and VAV1. Functional enrichment analysis by DAVID tool also revealed many significant (P < 0.05) pathways and Gene Ontology terms that could be related to resistance to gastrointestinal nematode in Santa Ines sheep, such as chemokine signaling pathway (oas04062), cAMP signaling pathway (oas04024), cGMP-PKG signaling pathway (Oas04022), platelet activation (Oas04611), Rap1 signaling pathway (oas04015), and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705). These results contribute to improving the knowledge of the genetic architecture of resistance to gastrointestinal nematode in Santa Ines sheep.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Sustainable Livestock Research Center, Animal Science Institute, 15130-000 São José do Rio Preto, SP, Brazil.
| | - Ana Claudia de Freitas
- São Paulo Agency of Agribusiness and Technology, Animal Science Institute, 13380-011 Nova Odessa, SP, Brazil; Agricultural Research Agency of the State of Minas Gerais, 38709-899 Patos de Minas, MG, Brazil
| | - Marina B Mioto
- Sustainable Livestock Research Center, Animal Science Institute, 15130-000 São José do Rio Preto, SP, Brazil
| | | | | | - Victor Breno Pedrosa
- Department of Animal Science, State University of Ponta Grossa, 84030-900 Ponta Grossa, PR, Brazil
| | - Ricardo Lopes Dias da Costa
- São Paulo Agency of Agribusiness and Technology, Animal Science Institute, 13380-011 Nova Odessa, SP, Brazil
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Castillo-Salas CA, Luna-Nevárez G, Reyna-Granados JR, Luna-Ramirez RI, Limesand SW, Luna-Nevárez P. Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment. J Therm Biol 2023; 112:103475. [PMID: 36796920 DOI: 10.1016/j.jtherbio.2023.103475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st.- March 31st.; n = 101) or warm (April 1st.- August 31st.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.
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Affiliation(s)
- Candelario A Castillo-Salas
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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McManus CM, Lucci CM, Maranhão AQ, Pimentel D, Pimentel F, Rezende Paiva S. Response to heat stress for small ruminants: Physiological and genetic aspects. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ahbara AM, Musa HH, Robert C, Abebe A, Al-Jumaili AS, Kebede A, Latairish S, Agoub MO, Clark E, Hanotte O, Mwacharo JM. Natural adaptation and human selection of northeast African sheep genomes. Genomics 2022; 114:110448. [PMID: 35964803 DOI: 10.1016/j.ygeno.2022.110448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/25/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.
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Affiliation(s)
- Abulgasim M Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya; School of Life Sciences, University of Nottingham, University Park, Nottingham, UK; Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia; LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia; Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK.
| | - Hassan H Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan
| | - Christelle Robert
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Ahmed S Al-Jumaili
- Department of Medical Laboratory Techniques, Al-Maarif University College, Ramadi, Anbar, Iraq
| | - Adebabay Kebede
- LiveGene-CTLGH, International Livestock Research Institute (ILRI) Ethiopia, Addis Ababa, Ethiopia; Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Suliman Latairish
- Department of Animal Production, Faculty of Agriculture, Misurata University, Misurata, Libya
| | | | - Emily Clark
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK; LiveGene-CTLGH, International Livestock Research Institute (ILRI) Ethiopia, Addis Ababa, Ethiopia.
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia; Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK; Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK.
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Cesarani A, Gaspa G, Correddu F, Dimauro C, Macciotta NPP. Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity. J Anim Breed Genet 2022; 139:292-306. [PMID: 34984736 DOI: 10.1111/jbg.12666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 02/04/2023]
Abstract
Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.
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Affiliation(s)
- Alberto Cesarani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Giustino Gaspa
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Fabio Correddu
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Corrado Dimauro
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
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7
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Santos WB, Schettini GP, Maiorano AM, Bussiman FO, Balieiro JCC, Ferraz GC, Pereira GL, Baldassini WA, Neto ORM, Oliveira HN, Curi RA. Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping. BMC Genomics 2021; 22:737. [PMID: 34645387 PMCID: PMC8515666 DOI: 10.1186/s12864-021-08053-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 09/07/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifying genomic regions affected by different selection pressures, mainly highlighting the recent positive selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the Mangalarga Marchador genome. Besides, we seek to direct the discussion about genes and traits of importance in this breed, especially traits related to the type and quality of gait, temperament, conformation, and locomotor system. RESULTS Three different methods were used to search for signals of selection: Tajima's D (TD), the integrated haplotype score (iHS), and runs of homozygosity (ROH). The samples were composed of males (n = 62) and females (n = 130) that were initially chosen considering well-defined phenotypes for gait: picada (n = 86) and batida (n = 106). All horses were genotyped using a 670 k Axiom® Equine Genotyping Array (Axiom MNEC670). In total, 27, 104 (chosen), and 38 candidate genes were observed within the signatures of selection identified in TD, iHS, and ROH analyses, respectively. The genes are acting in essential biological processes. The enrichment analysis highlighted the following functions: anterior/posterior pattern for the set of genes (GLI3, HOXC9, HOXC6, HOXC5, HOXC4, HOXC13, HOXC11, and HOXC10); limb morphogenesis, skeletal system, proximal/distal pattern formation, JUN kinase activity (CCL19 and MAP3K6); and muscle stretch response (MAPK14). Other candidate genes were associated with energy metabolism, bronchodilator response, NADH regeneration, reproduction, keratinization, and the immunological system. CONCLUSIONS Our findings revealed evidence of signatures of selection in the MM breed that encompass genes acting on athletic performance, limb development, and energy to muscle activity, with the particular involvement of the HOX family genes. The genome of MM is marked by recent positive selection. However, Tajima's D and iHS results point also to the presence of balancing selection in specific regions of the genome.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil.
| | - Gustavo P Schettini
- Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil
| | - Fernando O Bussiman
- Department of Animal Science, University of São Paulo (USP) - FZEA, Pirassununga, Brazil
| | - Júlio C C Balieiro
- Department of Animal Science, University of São Paulo (USP) - FZEA, Pirassununga, Brazil
| | - Guilherme C Ferraz
- Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil
| | - Welder Angelo Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil
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Kominakis A, Tarsani E, Hager-Theodorides AL, Mastranestasis I, Gkelia D, Hadjigeorgiou I. Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PLoS One 2021; 16:e0257461. [PMID: 34529728 PMCID: PMC8445479 DOI: 10.1371/journal.pone.0257461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of 'mainland-island' populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.
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Affiliation(s)
- Antonios Kominakis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Eirini Tarsani
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | | | | | - Dimitra Gkelia
- Association of Pastoral Farmers of Epirus, Ioannina, Greece
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9
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Gurgul A, Jasielczuk I, Miksza-Cybulska A, Kawęcka A, Szmatoła T, Krupiński J. Evaluation of genetic differentiation and genome-wide selection signatures in Polish local sheep breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Serranito B, Taurisson-Mouret D, Harkat S, Laoun A, Ouchene-Khelifi NA, Pompanon F, Benjelloun B, Cecchi G, Thevenon S, Lenstra JA, Da Silva A. Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats. Front Genet 2021; 12:715732. [PMID: 34413881 PMCID: PMC8369930 DOI: 10.3389/fgene.2021.715732] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.
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Affiliation(s)
- Bruno Serranito
- Museum National d’Histoire Naturelle, CRESCO, Dinard, France
- University of Limoges, PEREINE, E2LIM, Limoges, France
| | | | - Sahraoui Harkat
- Science Veterinary Institute, University of Blida, Blida, Algeria
| | | | | | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- National Institute of Agronomic Research, Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Giuliano Cecchi
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Sophie Thevenon
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Anne Da Silva
- University of Limoges, PEREINE, E2LIM, Limoges, France
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Ghoreishifar SM, Rochus CM, Moghaddaszadeh-Ahrabi S, Davoudi P, Salek Ardestani S, Zinovieva NA, Deniskova TE, Johansson AM. Shared Ancestry and Signatures of Recent Selection in Gotland Sheep. Genes (Basel) 2021; 12:genes12030433. [PMID: 33802939 PMCID: PMC8002741 DOI: 10.3390/genes12030433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran;
| | - Christina Marie Rochus
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands;
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz 5157944533, Iran;
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Siavash Salek Ardestani
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Correspondence:
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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13
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Saravanan K, Panigrahi M, Kumar H, Bhushan B, Dutt T, Mishra B. Genome-wide analysis of genetic diversity and selection signatures in three Indian sheep breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Liu Y, Xu L, Yang L, Zhao G, Li J, Liu D, Li Y. Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle. Front Genet 2020; 11:533052. [PMID: 33391332 PMCID: PMC7775540 DOI: 10.3389/fgene.2020.533052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 11/27/2020] [Indexed: 01/20/2023] Open
Abstract
Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.
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Affiliation(s)
- Yuqiang Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liu Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guoyao Zhao
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
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15
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Vanvanhossou SFU, Scheper C, Dossa LH, Yin T, Brügemann K, König S. A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits. BMC Genomics 2020; 21:783. [PMID: 33176675 PMCID: PMC7656759 DOI: 10.1186/s12864-020-07170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.
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Affiliation(s)
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
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16
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Salles TT, Beijo LA, Nogueira DA, Almeida GC, Martins TB, Gomes VS. Modelling the growth curve of Santa Ines sheep using Bayesian approach. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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17
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Heat stress effects on sheep: Are hair sheep more heat resistant? Theriogenology 2020; 155:157-167. [PMID: 32679441 DOI: 10.1016/j.theriogenology.2020.05.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 12/19/2022]
Abstract
Climatic variables can trigger physiological, biochemical, haematological and hormonal alterations that influence the maintenance of homeothermy and can affect production and productivity in sheep. Different mechanisms are responsible for tolerance to heat stress (HS) including coat and skin colour, body size, fat distribution, physiological reactions and not just coat type (hair/wool). This review looks at physical, physiological, molecular and genetic aspects of heat tolerance in sheep and how they affect hair and wool sheep. We propose that it is the adaptation to hot environments and not the type of coat (wool/hair) itself that determines the capacity of the resistance of the animal to HS, due to modifications in essential pathways such as energy metabolism, physiological responses and body size. When studied in similar environments, commercial wool breeds tend to show higher heat stress, but hair breeds tend not to differ from wool breeds that are adapted to hot environments.
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18
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Abied A, Bagadi A, Bordbar F, Pu Y, Augustino SM, Xue X, Xing F, Gebreselassie G, Han JL, Mwacharo JM, Ma Y, Zhao Q. Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments. Genes (Basel) 2020; 11:genes11050494. [PMID: 32365888 PMCID: PMC7290715 DOI: 10.3390/genes11050494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (FST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by FST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.
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Affiliation(s)
- Adam Abied
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Alnoor Bagadi
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Farhad Bordbar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Yabin Pu
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Serafino M.A. Augustino
- College of Animal Science and Technology, China Agricultural University (CAU), Beijing 100193, China;
| | - Xianglan Xue
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Feng Xing
- College of Animal Science, Talimu University (TU), Xinjiang, Alar 843300, China;
| | - Gebremedhin Gebreselassie
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Joram M. Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa 1108-2010, Ethiopia;
| | - Yuehui Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Qianjun Zhao
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Correspondence:
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Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types. Animals (Basel) 2020; 10:ani10050773. [PMID: 32365604 PMCID: PMC7278473 DOI: 10.3390/ani10050773] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023] Open
Abstract
Simple Summary According to the tail types, sheep can be briefly classified into three groups (fat-tailed, fat-rumped, and thin-tailed sheep). In this study, we used these three typical breeds from Chinese indigenous sheep breeds to perform a genome scan for selective sweeps using Ovine Infinium HD SNP BeadChip genotype data. Results showed that 25 genomic regions exhibited selection signals and harbored 73 positional candidate genes. These genes were documented not only to be associated with tail fat formation, but also be related to reproduction, body conformation, and appearance. Our findings contributed to understanding genetic basis of fat deposition in sheep tail and provide a reference for developing new sheep breeds with an ideal tail type. Abstract It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.
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Hernández-Montiel W, Martínez-Núñez MA, Ramón-Ugalde JP, Román-Ponce SI, Calderón-Chagoya R, Zamora-Bustillos R. Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep. Animals (Basel) 2020; 10:ani10030434. [PMID: 32143402 PMCID: PMC7143297 DOI: 10.3390/ani10030434] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/22/2022] Open
Abstract
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10-3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.
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Affiliation(s)
- Wilber Hernández-Montiel
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
- Departamento de Ciencias Agropecuarias, Universidad del Papaloapan, Loma Bonita Oaxaca 68400, Mexico
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico;
| | - Julio Porfirio Ramón-Ugalde
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
| | - Sergio Iván Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán Colón, Querétaro 76280, Mexico;
- Correspondence: (S.I.R.-P.); (R.Z.-B.); Tel.: +52-5538718700 (ext. 80208) (S.I.R.-P.); +52-999-341-0860 (ext. 7631) (R.Z.-B.)
| | - Rene Calderón-Chagoya
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán Colón, Querétaro 76280, Mexico;
| | - Roberto Zamora-Bustillos
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
- Correspondence: (S.I.R.-P.); (R.Z.-B.); Tel.: +52-5538718700 (ext. 80208) (S.I.R.-P.); +52-999-341-0860 (ext. 7631) (R.Z.-B.)
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21
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Naderi S, Moradi MH, Farhadian M, Yin T, Jaeger M, Scheper C, Korkuc P, Brockmann GA, König S, May K. Assessing selection signatures within and between selected lines of dual-purpose black and white and German Holstein cattle. Anim Genet 2020; 51:391-408. [PMID: 32100321 DOI: 10.1111/age.12925] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2020] [Indexed: 12/29/2022]
Abstract
The aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual-purpose black and white (DSN) population, as well as from generated sub-populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East-DSN and West-DSN sub-populations. In addition, two further sub-populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross-population extended haplotype homozygosity methodology (XP-EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright's fixation index (FST ). Chromosomal segments for the top 0.1 percentile of negative or positive XP-EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP-EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP-EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29-38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average FST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.
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Affiliation(s)
- S Naderi
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - M H Moradi
- Department of Animal Sciences, Arak University, Shahid Beheshti Street, Arak, Iran
| | - M Farhadian
- Department of Animal Science, University of Tabriz, 29 Bahman Boulevard, Tabriz, Iran
| | - T Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - M Jaeger
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - C Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - P Korkuc
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Invalidenstr. 42, Berlin, D-10115, Germany
| | - G A Brockmann
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Invalidenstr. 42, Berlin, D-10115, Germany
| | - S König
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - K May
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
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Álvarez I, Fernández I, Traoré A, Pérez-Pardal L, Menéndez-Arias NA, Goyache F. Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Rep 2020; 10:2824. [PMID: 32071365 PMCID: PMC7028950 DOI: 10.1038/s41598-020-59839-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
The Djallonké (West African Dwarf) sheep is a small-sized haired sheep resulting from a costly evolutionary process of natural adaptation to the harsh environment of West Africa including trypanosome challenge. However, genomic studies carried out in this sheep are scant. In this research, genomic data of 184 Djallonké sheep (and 12 Burkina-Sahel sheep as an outgroup) generated using medium-density SNP Chips were analyzed. Three different statistics (iHS, XP-EHH and nSL) were applied to identify candidate selection sweep regions spanning genes putatively associated with adaptation of sheep to the West African environment. A total of 207 candidate selection sweep regions were defined. Gene-annotation enrichment and functional annotation analyses allowed to identify three statistically significant functional clusters involving 12 candidate genes. Genes included in Functional Clusters associated to selection signatures were mainly related to metabolic response to stress, including regulation of oxidative and metabolic stress and thermotolerance. The bovine chromosomal areas carrying QTLs for cattle trypanotolerance were compared with the regions on which the orthologous functional candidate cattle genes were located. The importance of cattle BTA4 for trypanotolerant response might have been conserved between species. The current research provides new insights on the genomic basis for adaptation and highlights the importance of obtaining information from non-cosmopolite livestock populations managed in harsh environments.
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Affiliation(s)
- Isabel Álvarez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Iván Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou, 04 BP 8645, Burkina Faso
| | | | | | - Félix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain.
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Haines ML, Luikart G, Amish SJ, Smith S, Latch EK. Evidence for adaptive introgression of exons across a hybrid swarm in deer. BMC Evol Biol 2019; 19:199. [PMID: 31684869 PMCID: PMC6827202 DOI: 10.1186/s12862-019-1497-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
Background Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. Results We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. Conclusions Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret L Haines
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Gordon Luikart
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA.,Montana Conservation Genomics Laboratory, Flathead Lake Biological Station, Division of Biological Sciences, The University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, USA
| | - Stephen J Amish
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Seth Smith
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.
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Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F. Identifying loci under positive selection in complex population histories. Genome Res 2019; 29:1506-1520. [PMID: 31362936 PMCID: PMC6724678 DOI: 10.1101/gr.246777.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022]
Abstract
Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.
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Affiliation(s)
- Alba Refoyo-Martínez
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
| | - Rute R da Fonseca
- Centre for Macroecology, Evolution and Climate, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copehnagen 2100, Denmark
| | - Katrín Halldórsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
| | - Einar Árnason
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
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Signer-Hasler H, Burren A, Ammann P, Drögemüller C, Flury C. Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds. Anim Genet 2019; 50:512-525. [PMID: 31365135 DOI: 10.1111/age.12828] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 01/01/2023]
Abstract
A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between FPED and FROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean FROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.
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Affiliation(s)
- H Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
| | - A Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
| | - P Ammann
- ProSpecieRara, Unter Brüglingen 6, 4052, Basel, Switzerland
| | - C Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
| | - C Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
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Adaptation Mechanisms of Small Ruminants to Environmental Heat Stress. Animals (Basel) 2019; 9:ani9030075. [PMID: 30823364 PMCID: PMC6466405 DOI: 10.3390/ani9030075] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Heat stress is an intriguing factor that negatively influences livestock production and reproduction performance. Sheep and goat are among the livestock that can adapt to environmental heat stress via a combination of physiological, morphological, behavioral, and genetic bases. Sheep and goat are able to minimize adverse effect of high thermal stress by invoking behavioral responses such as feeding, water intake, shade seeking, and increased frequency of drinking. Their morphological mechanisms are comprised of body shape and size, light hair color, lightly pigmented skin, and less subcutaneous fat, and the physiological means are that of increased respiration rate (RR), increased sweating rate (SW), reduced metabolic rate, and change in endocrine function. Adaptation in terms of genetics is the heritable trait of animal characteristics which favor the survival of populations. For instance, genes like heat shock proteins 70 (HSP70) and ENOX2 are commonly expressed proteins which protect animals against heat stress. Abstract Small ruminants are the critical source of livelihood for rural people to the development of sustainable and environmentally sound production systems. They provided a source of meat, milk, skin, and fiber. The several contributions of small ruminants to the economy of millions of rural people are however being challenged by extreme heat stress difficulties. Heat stress is one of the most detrimental factors contributing to reduced growth, production, reproduction performance, milk quantity and quality, as well as natural immunity, making animals more vulnerable to diseases and even death. However, small ruminants have successfully adapted to this extreme environment and possess some unique adaptive traits due to behavioral, morphological, physiological, and largely genetic bases. This review paper, therefore, aims to provide an integrative explanation of small ruminant adaptation to heat stress and address some responsible candidate genes in adapting to thermal-stressed environments.
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27
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Ahbara A, Bahbahani H, Almathen F, Al Abri M, Agoub MO, Abeba A, Kebede A, Musa HH, Mastrangelo S, Pilla F, Ciani E, Hanotte O, Mwacharo JM. Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Front Genet 2019; 9:699. [PMID: 30687385 PMCID: PMC6334744 DOI: 10.3389/fgene.2018.00699] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 12/13/2018] [Indexed: 12/03/2022] Open
Abstract
Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.
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Affiliation(s)
- Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ayelle Abeba
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hassan Hussein Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, Università Palermo, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “Aldo Moro ”, Bari, Italy
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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El-Ashram S, Li C, Abouhajer F, Mehmood R, Al Nasr I, Zhang Y, Lu T, Yili D, Suo X, Haoji Z, Li Z, Huang S. An ex vivo abomasal ovine model to study the immediate immune response in the context of Haemonchus contortus larval-stage. Vet Parasitol 2018; 254:105-113. [PMID: 29656994 DOI: 10.1016/j.vetpar.2018.02.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/22/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Abstract
We have set up an ex vivo ovine abomasal model, which can mimic the multicellular process to explore the early steps in haemonchine nematode infection using RNA-seq technology. Ovine abomasal explants were collected for histological and transcriptional analysis and supernatants collected to quantitate lactate dehydrogenase (LDH) enzymes. Atotal of 233 were substantially induced genes between L4-inoculated and uninoculated-control tissues, respectively. However, a total of 14 were considerably down-regulated genes between the 51 aforementioned tissues. Fifteen pathways were annotated by Kyoto Encyclopedia of Genes, and Genomes pathway analysis accounted for the significant percentage in immediate response to larval-stage of H. contortus. Key genes upregulated in response to the addition of L4-inoculum of H. contortus were IL-6, IL-8, C1q, Atypical chemokine receptor-3, chemokine ligand-2, manganese superoxide dismutase, integrin alpha-7, -8, -9, integrin subunit beta-1, integrin subunit beta 6, intercellular adhesion molecule-1 and actin alpha-1. This study shows for the first time that galectin-1 is up-regulated in an ex vivo abomasal segment model exposed to L4-inoculum of H. contortus following 6 h of incubation. The abomasal segment model has been shown to be a suitable tool to study the haemonchine larval-stage effects on the ovine abomasal tissues prior to in vivo assessment.
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Affiliation(s)
- Saeed El-Ashram
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China; State Key Laboratory for Agrobiotechnology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Faculty of Science, Kafr ElSheikh University, Kafr ElSheikh, Egypt.
| | - Cuiping Li
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Fathi Abouhajer
- Faculty of Education, Asmarya University for Islamic Sciences, Zliten, Libya
| | - Rashid Mehmood
- Department of Computer Science and Information Technology, University of Kotli, AJ&K Pakistan
| | - Ibrahim Al Nasr
- College of Science and Arts in Unaizah, Qassim University, Unaizah, Saudi Arabia; College of Applied Health Sciences in Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Yinghui Zhang
- School of Food Science and Engineering, Foshan University (Northern Campus), Shishan, Naihai district of Foshan City, Guangdong Province 528231, China
| | - Tang Lu
- School of Food Science and Engineering, Foshan University (Northern Campus), Shishan, Naihai district of Foshan City, Guangdong Province 528231, China
| | - Ding Yili
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Xun Suo
- State Key Laboratory for Agrobiotechnology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhang Haoji
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Zhili Li
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China.
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Abouhajer F, El-Ashram S, Karama M, Huang S, Liu JF. An ex vivo ruminal ovine model to study the immediate immune response in the context of bacterial lipopolysaccharide. Funct Integr Genomics 2018; 18:277-285. [PMID: 29429072 DOI: 10.1007/s10142-018-0589-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
We have set up an ex vivo ovine ruminal model, which can mimic the multicellular process to explore the early steps in Salmonella typhimurium lipopolysaccharide (LPS) stimulation using RNA-seq technology. Ovine ruminal explants were collected for histological and transcriptional analysis and supernatants collected to quantitate lactate dehydrogenase (LDH) enzymes. A total of 8 and 523 genes were significantly over-expressed between LPS-treated and control tissues at 6 and 12 h, respectively. However, six and seven hundred and thirteen genes were substantially repressed between the aforementioned tissues, correspondingly. Key genes up-regulated in response to the addition of LPS were tumor necrosis factor (TNF), interlukin (IL)-1 beta(b), IL-6, IL-8, IL-17B, IL-19, MMP-1, MMP-3, and integrin alpha 2 (ITGA8, 9). This study shows for the first time that galectin-1 is up-regulated in an ex vivo ruminal segment model exposed to bacterial lipopolysaccharide following 6 h of incubation. The ruminal segment model has been shown to be a suitable tool to study the bacterial lipopolysaccharide effects on the ovine ruminal tissues prior to in vivo assessment.
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Affiliation(s)
- Fathi Abouhajer
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Faculty of Education, Asmarya University for Islamic Sciences, Zliten, Libya
| | - Saeed El-Ashram
- College of life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, Guangdong, 528231, China.
- Faculty of Science, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt.
| | - Musafiri Karama
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Shujian Huang
- College of life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, Guangdong, 528231, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world? Animal 2018; 12:1333-1340. [PMID: 29343308 DOI: 10.1017/s1751731117003688] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations. Molecular information has resulted in gains in accuracy of between 0.05 and 0.27 and proved useful in parentage verification and the identification of QTLs for economically important traits. Except for a few established breeds with some degree of infrastructure, the basic building blocks to support conventional breeding programmes in small holder systems are lacking in most developing countries. In these systems, molecular data could offer quick wins in undertaking parentage verification and genetic evaluations using G matrix, and determination of breed composition. The development of next-generation molecular tools has prompted investigations on genome-wide signatures of selection for mainly adaptive and reproduction traits in SR in developing countries. Here, the relevance of the developments and application of GS and other molecular tools in developed countries to developing countries context is examined. Worth noting is that in the latter, the application of GS in SR will not be a 'one-size fits all' scenario. For breeds with some degree of conventional genetic improvement, classical GS may be feasible. In small holder systems, where production is key, community-based breeding programmes can provide the framework to implement GS. However, in fragile growth systems, for example those found in marginal environments, innovative GS to maximize adaptive diversity will be required. A cost-benefit analysis should accompany any strategy of implementing GS in these systems.
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Mwacharo JM, Kim ES, Elbeltagy AR, Aboul-Naga AM, Rischkowsky BA, Rothschild MF. Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts. Sci Rep 2017; 7:17647. [PMID: 29247174 PMCID: PMC5732286 DOI: 10.1038/s41598-017-17775-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023] Open
Abstract
African indigenous sheep are classified as fat-tail, thin-tail and fat-rump hair sheep. The fat-tail are well adapted to dryland environments, but little is known on their genome profiles. We analyzed patterns of genomic variation by genotyping, with the Ovine SNP50K microarray, 394 individuals from five populations of fat-tail sheep from a desert environment in Egypt. Comparative inferences with other East African and western Asia fat-tail and European sheep, reveal at least two phylogeographically distinct genepools of fat-tail sheep in Africa that differ from the European genepool, suggesting separate evolutionary and breeding history. We identified 24 candidate selection sweep regions, spanning 172 potentially novel and known genes, which are enriched with genes underpinning dryland adaptation physiology. In particular, we found selection sweeps spanning genes and/or pathways associated with metabolism; response to stress, ultraviolet radiation, oxidative stress and DNA damage repair; activation of immune response; regulation of reproduction, organ function and development, body size and morphology, skin and hair pigmentation, and keratinization. Our findings provide insights on the complexity of genome architecture regarding dryland stress adaptation in the fat-tail sheep and showcase the indigenous stocks as appropriate genotypes for adaptation planning to sustain livestock production and human livelihoods, under future climates.
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Affiliation(s)
- Joram M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia.
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
| | - Ahmed R Elbeltagy
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Nadi Elsaid Street, Dokki, Cairo, Egypt
| | - Adel M Aboul-Naga
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Nadi Elsaid Street, Dokki, Cairo, Egypt
| | - Barbara A Rischkowsky
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
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Campos BM, do Carmo AS, da Silva TBR, Verardo LL, de Simoni Gouveia JJ, Mendes Malhado CH, Barbosa da Silva MVG, Souza Carneiro PL. Identification of artificial selection signatures in Caracu breed lines selected for milk production and meat production. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Early and late gene expression profiles of the ovine mucosa in response to Haemonchus contortus infection employing Illumina RNA-seq technology. Parasitol Int 2017; 66:681-692. [PMID: 28552633 DOI: 10.1016/j.parint.2017.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/03/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023]
Abstract
We conducted herein transcriptome sequencing of the ovine abomasal tissues using the Illumina HiSeq 4000 platform to segregate early and late H. contortus-infected sheep (7 and 50days post-infected groups, respectively) from the control naive ones. A total of 548, 357 and 7 were substantially induced genes in 7days post-infection versus uninfected-control group, 50days post-infection versus 7days post-infection (7dpi), and 50days post-infection (50dpi) versus uninfected-control group, respectively. However, a total of 301, 355 and 11 were significantly repressed genes between 7dpi versus uninfected-control group, 50dpi versus 7dpi, and 50dpi versus uninfected-control group, correspondingly. This indicates that H. contortus infection induced a more potent activation of abomasal gene expression in the early stage of infection as compared to the late stage. Seven pathways were annotated by Kyoto Encyclopedia of Genes, and Genomes pathway analysis accounted for the significant percentage in early H. contortus infection. This study shows for the first time that both galectin-11 and matricellular protein osteopontin are up-regulated in abomasal tissue after chronic H. contortus infection, while galectin-4 is specifically down-regulated in the early infection. Additionally, our results showed that the induction or repression of these molecules is likely to determine the infection progression.
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