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dos Santos CA, Eler JP, Oliveira ECDM, Espigolan R, Giacomini G, Ferraz JBS, Paim TDP. Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation. PLoS One 2024; 19:e0301937. [PMID: 38662691 PMCID: PMC11045132 DOI: 10.1371/journal.pone.0301937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Genomic regions related to tropical adaptability are of paramount importance for animal breeding nowadays, especially in the context of global climate change. Moreover, understanding the genomic architecture of these regions may be very relevant for aiding breeding programs in choosing the best selection scheme for tropical adaptation and/or implementing a crossbreeding scheme. The composite MONTANA TROPICAL® population was developed by crossing cattle of four different biological types to improve production in harsh environments. Pedigree and genotype data (51962 SNPs) from 3215 MONTANA TROPICAL® cattle were used to i) characterize the population structure; ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to each selected region. The population structure based on principal components had a weak relationship with the genetic contribution of the different biological types. Clustering analyses (ADMIXTURE) showed different clusters according to the number of generations within the composite population. Considering results of both selection signatures approaches, we identified only one consensus region on chromosome 20 (35399405-40329703 bp). Genes in this region are related to immune function, regulation of epithelial cell differentiation, and cell response to ionizing radiation. This region harbors the slick locus which is related to slick hair and epidermis anatomy, both of which are related to heat stress adaptation. Also, QTLs in this region were related to feed intake, milk yield, mastitis, reproduction, and slick hair coat. The signatures of selection detected here arose in a few generations after crossbreeding between contrasting breeds. Therefore, it shows how important this genomic region may be for these animals to thrive in tropical conditions. Further investigations on sequencing this region can identify candidate genes for animal breeding and/or gene editing to tackle the challenges of climate change.
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Affiliation(s)
- Camila Alves dos Santos
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
| | - Joanir Pereira Eler
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Rafael Espigolan
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Gabriela Giacomini
- Associação Internacional de criadores de Montana, Mogi Mirim, São Paulo, Brazil
| | - José Bento Sterman Ferraz
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Tiago do Prado Paim
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
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Amandykova M, Akhatayeva Z, Kozhakhmet A, Kapassuly T, Orazymbetova Z, Yergali K, Khamzin K, Iskakov K, Dossybayev K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat-Wool Sheep Breed. Genes (Basel) 2023; 14:1988. [PMID: 38002931 PMCID: PMC10671688 DOI: 10.3390/genes14111988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH1-2 Mb were much higher than ROH2-4 Mb and ROH8-16 Mb in the three sheep populations. Most of individuals had small number of ROH>16 Mb. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated FROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.
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Affiliation(s)
- Makpal Amandykova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zhanerke Akhatayeva
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Altynay Kozhakhmet
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Tilek Kapassuly
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zarina Orazymbetova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
| | - Kanagat Yergali
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kadyrzhan Khamzin
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Iskakov
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Dossybayev
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
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3
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Carmickle AT, Larson CC, Hernandez FS, Pereira JMV, Ferreira FC, Haimon MLJ, Jensen LM, Hansen PJ, Denicol AC. Physiological responses of Holstein calves and heifers carrying the SLICK1 allele to heat stress in California and Florida dairy farms. J Dairy Sci 2022; 105:9216-9225. [PMID: 36114060 DOI: 10.3168/jds.2022-22177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022]
Abstract
Inheritance of the SLICK1 allele of the prolactin receptor gene improves thermotolerance of lactating Holstein cows under humid heat stress conditions. The aim of this study was to investigate whether pre- and postweaning Holstein heifers carrying the SLICK1 allele would show physiological responses indicative of higher tolerance to heat stress in high- and low-humidity climates. A total of 101 heifer calves of two age groups heterozygous for the SLICK1 allele and 103 wild-type half-siblings were evaluated during July 2020 in 3 dairy farms in central California and 2 in south Florida. Dry bulb temperature and relative humidity data were recorded during evaluation and used to calculate the temperature-humidity index (THI). Physiological measurements were obtained between 1600 and 1900 h in California, and 1200 and 1400 h in Florida and included rectal temperature, respiration rate, skin temperature, and sweating rate. Data were analyzed via Generalized Linear Mixed Models including the main effects of genotype, state, group, sire, farm within state, and interactions, with THI included as a covariate. The correlations between THI and dependent variables were analyzed via linear regression. The average 24-h THI was higher in Florida compared with California (90 vs. 72, respectively); the main driver of the higher THI in Florida was the high relative humidity (average 85.6% in Florida vs. 36.7% in California). In Florida, the rectal temperature of slick calves was 0.4°C lower than non-slick calves (39.5 ± 0.1 vs 39.9 ± 0.1°C); no differences were detected between slick and non-slick calves in California. Regardless of genotype, heifer calves in Florida had higher respiration rate, higher rectal and skin temperatures, and lower sweating rate than in California. This study is the first to evaluate physiological responses of calves carrying the SLICK1 allele under heat stress conditions in different climates. Our findings demonstrate that the presence of this allele is associated with lower rectal temperatures in pre- and post-weaning Holstein females. According to the physiological parameters evaluated, calves raised in Florida appeared to be under more severe heat stress; in those conditions, the SLICK1 allele was advantageous to confer thermotolerance as evidenced by lower rectal temperature in slick animals.
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Affiliation(s)
| | - Colleen C Larson
- Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | | | - Jessica M V Pereira
- Veterinary Teaching and Research Center, School of Veterinary Medicine, University of California-Davis, Tulare 93274
| | - Fernanda C Ferreira
- Veterinary Teaching and Research Center, School of Veterinary Medicine, University of California-Davis, Tulare 93274
| | | | - Laura M Jensen
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - Anna C Denicol
- Department of Animal Science, University of California, Davis 95616.
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4
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Balbi M, Bonamy M, Fernandez ME, Cecco P, Vaca RJA, Rogberg Muñoz A, Peral Gacía P, Prando AJ, Giovambattista G. Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001-48,100,000 bp. Anim Biotechnol 2022:1-7. [PMID: 35130466 DOI: 10.1080/10495398.2022.2029464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (n = 108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446-48,030,219 bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.
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Affiliation(s)
- Marianela Balbi
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martín Bonamy
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Elena Fernandez
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Paulo Cecco
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Roberto J A Vaca
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Facultad de Agronomía, INPA-Instituto de Producción Animal UBA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pilar Peral Gacía
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Alberto J Prando
- Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
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5
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Macedo VP, Ribeiro RDX, de Araújo SA, Souza MNS, de Andrade EA, Di Mambro Ribeiro CV, de Souza CO, Silva TM, Barbosa AM, Bezerra LR, da Silva Júnior JM, Oliveira RL. Physicochemical composition, fatty acid profile and sensory attributes of meat (longissimus lumborum muscle) from Nellore and Nellore-cross bulls. Trop Anim Health Prod 2022; 54:47. [PMID: 35018555 DOI: 10.1007/s11250-022-03059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
This study aimed to compare the physicochemical characteristics, fatty acid composition, and sensory attributes of the meat from three genetic groups: Nellore (Nell), ½ Nellore × ½ Angus (NeAn), and ¼ Nellore × ¼ Angus × ½ Senepol (NASe). Longissimus lumborum muscle from 30 slaughtered bulls with a body weight of 549 ± 32.5 kg was used. The water holding capacity was greater for the Nell and NeAn groups than for the NASe group. Meat samples from the NASe group exhibited a higher L* index than those from the NeAn group and lower a* and b* color indexes than those from the Nell group. The meat fatty acid profiles showed that the Nell group had higher concentrations of 12:0, 14:0, 18:1 t11, 14:1 c9, 16:1 c9, 18:1 c9, 18:1 c11, 18:2 c9, t11 (conjugated linoleic acid (CLA)), and 20:3 n-6 polyunsaturated fatty acid (PUFA) than the NeAn and NASe groups. The total saturated (ΣSFA), unsaturated (ΣUFA), and monounsaturated (ΣMUFA) fatty acid concentrations were higher and the ΣPUFA:ΣSFA ratio was lower in the Nell group than in the NeAn group. The Δ9-desaturase C16 activity was significantly higher in the Nell and NASe groups than in the NeAn group. The atherogenicity index (AI) tended to be lower in the crossbreeds than in the Nell breed. The NASe group presented meat with better tenderness, juiciness, and overall acceptance than the Nell and NeAn groups and was therefore the best genetic group for beef production of the tested groups.
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Affiliation(s)
- Vanessa Pereira Macedo
- Food Science Graduate Program, Pharmacy College, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170115, Brazil
| | - Rebeca Dantas Xavier Ribeiro
- Food Science Graduate Program, Pharmacy College, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170115, Brazil
| | - Sergiane Alves de Araújo
- Food Science Graduate Program, Pharmacy College, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170115, Brazil
| | - Mateus Neto Silva Souza
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Ederson Américo de Andrade
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Cláudio Vaz Di Mambro Ribeiro
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Carolina Oliveira de Souza
- Food Science Graduate Program, Pharmacy College, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170115, Brazil
| | - Thadeu Mariniello Silva
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Analívia Martins Barbosa
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Leilson Rocha Bezerra
- Department of Animal Science, Federal University of Campina Grande, Avenida Universitária, s/n - Jatobá, Patos, Paraíba, 58708110, Brazil
| | - Jarbas Miguel da Silva Júnior
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil
| | - Ronaldo Lopes Oliveira
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Av. Ademar de Barros, 500, Ondina, Salvador, Bahia, 40170110, Brazil.
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Kava R, Peripolli E, Berton MP, Lemos M, Lobo RB, Stafuzza NB, Pereira AS, Baldi F. Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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9
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Gorssen W, Meyermans R, Janssens S, Buys N. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species. Genet Sel Evol 2021; 53:2. [PMID: 33397285 PMCID: PMC7784028 DOI: 10.1186/s12711-020-00599-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/11/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. RESULTS The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). CONCLUSIONS We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.
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Affiliation(s)
- Wim Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Roel Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium.
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10
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Rodríguez-Valera Y, Rocha D, Naves M, Renand G, Pérez-Pineda E, Ramayo-Caldas Y, Ramos-Onsins SE. The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle. Animals (Basel) 2020; 10:ani10122233. [PMID: 33261195 PMCID: PMC7760288 DOI: 10.3390/ani10122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Charolais de Cuba cattle is a tropical adapted breed founded in Cuba around 120 years ago from Charolais French specimens. Nowadays, it is still a closed breed and remains as a small population. In this work, we analyzed the inbreeding and diversity patterns, as well as the population size, of this recent adapted breed via a run of homozygosity (ROH) analysis. We found that the genomic inbreeding levels are higher in the Charolais de Cuba breed compared to French and British Charolais populations. Nevertheless, we detected that the effective population size experienced a very similar decline during the last century in the three Charolais populations studied. Finally, a number of regions with exceptional patterns of long homozygosity were identified in this breed, and these could be related to processes of adaptation to tropical conditions. Abstract Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
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Affiliation(s)
- Yoel Rodríguez-Valera
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Dominique Rocha
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Michel Naves
- INRAE, URZ, 97170 Petit Bourg, Guadeloupe, France;
| | - Gilles Renand
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Eliecer Pérez-Pineda
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Yuliaxis Ramayo-Caldas
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre of Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
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11
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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12
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Hansen PJ. Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle. Theriogenology 2020; 154:190-202. [PMID: 32622199 DOI: 10.1016/j.theriogenology.2020.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022]
Abstract
In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.
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Affiliation(s)
- Peter J Hansen
- Department of Animal Sciences, D.H Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL, 32611-0910, USA.
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13
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Flori L, Moazami-Goudarzi K, Alary V, Araba A, Boujenane I, Boushaba N, Casabianca F, Casu S, Ciampolini R, Coeur D'Acier A, Coquelle C, Delgado JV, El-Beltagi A, Hadjipavlou G, Jousselin E, Landi V, Lauvie A, Lecomte P, Ligda C, Marinthe C, Martinez A, Mastrangelo S, Menni D, Moulin CH, Osman MA, Pineau O, Portolano B, Rodellar C, Saïdi-Mehtar N, Sechi T, Sempéré G, Thévenon S, Tsiokos D, Laloë D, Gautier M. A genomic map of climate adaptation in Mediterranean cattle breeds. Mol Ecol 2019; 28:1009-1029. [PMID: 30593690 DOI: 10.1111/mec.15004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022]
Abstract
Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.
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Affiliation(s)
- Laurence Flori
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Véronique Alary
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, ICARDA, Rabat, Morocco
| | - Abdelillah Araba
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Ismaïl Boujenane
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Nadjet Boushaba
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | | | - Sara Casu
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | | | | | | | | | | | | | | | - Vincenzo Landi
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Anne Lauvie
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Philippe Lecomte
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, Montpellier, France
| | - Christina Ligda
- HAO-Demeter, Veterinary Research Institute, Thessaloniki, Greece
| | | | - Amparo Martinez
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Dalal Menni
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Charles-Henri Moulin
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | | | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Clementina Rodellar
- LAGENBIO, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Nadhira Saïdi-Mehtar
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | - Tiziana Sechi
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | - Guilhem Sempéré
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | - Sophie Thévenon
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | | | - Denis Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, University of Montpellier, Montferrier-sur-Lez, France.,Institut de Biologie Computationnelle (IBC), Montpellier, France
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14
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About the inconvenience of handling mixed-breed herds; aspects of social behavior as a potential source of stress and economic losses. Trop Anim Health Prod 2019; 52:743-751. [PMID: 31595384 DOI: 10.1007/s11250-019-02065-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
The objective of this study was to assess aspects of the social behavior of a mixed-breed herd of beef cows as a potential source for stress and economic losses. Angus (AN; N = 10), Brahman (BR; N = 10), and Senepol (SE; N = 10) cows were assigned to two groups (N = 15 each containing equal breed numbers) on separate pastures. Agonistic interactions (win/loss) during feeding were recorded daily for 45 days. Dominance values were estimated as the proportion of individuals dominated to total herdmates. From this, individuals were placed into social categories based upon linear ranking as follows: dominants (D), intermediate (I), and subordinates (S). Breed influenced (P < 0.01) social category, with SE cows being dominants (P < 0.05) over AN and BR cows. Interactions between AN and BR cows were less (P < 0.0005) than interactions between AN and SE (53 vs 140, respectively). Within breeds, BR (152) and SE (182) cows had more (P < 0.0005) agonistic interactions than AN (107) cows. Although apparently influenced by breed, agonistic interactions occurred more frequently (P < 0.005) between social categories than within social categories (814 vs 310, respectively). Dominant cows were involved in more agonistic interactions with cows from different social categories than were intermediate and subordinate cows (P < 0.0005). However, intermediate (100) and subordinate (157) cows generated more (P < 0.0005) agonistic interactions within their own social category than dominant cows (53). It was concluded that, in mixed-breed herds, breed influences both social organization and agonistic interactions which could be considered as potential sources of stress and economic losses.
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15
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Falomir-Lockhart AH, Ortega Masague MF, Rudd Garces G, Zappa ME, Peral García P, Morales HF, Holgado FD, Rogberg Muñoz A, Giovambattista G. Polledness in Argentinean Creole cattle, five centuries surviving. Anim Genet 2019; 50:381-385. [PMID: 31179563 DOI: 10.1111/age.12803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2019] [Indexed: 11/26/2022]
Abstract
Polledness has been shown to have autosomal Mendelian inheritance, with the polled locus being dominant to the horned locus. This trait was mapped to the BTA1 centromeric end in several breeds. One of the distinctive attributes of Creole cattle, such as the Argentinean Creole, is the presence of long, lyre-shaped horns. However, polled native animals were reported before the introduction of modern selected European breeds. Here, we studied the origin of the polled mutation, either independent or introgressed, in a Creole line from the Creole cattle founder group at the IIACS-INTA Leales Experimental Station (northwest Argentina). The study sample (65 animals: 26 horned and 39 polled) was genotyped using high-density SNP microarrays and three previously reported genetic markers (P202 ID , P80kb ID and PG ). A genome-wide association study, selection signatures, linkage disequilibrium analysis and copy number variations were used to detect the responsible region and the segregating haplotypes/alleles. The interval mapped in the Leales herd (1.23-2.13 Mb) overlapped with the region previously reported in several European cattle breeds, suggesting that the same locus could be segregating in this population. The previously reported variants PF and PG were not detected, thus dismissing the Holstein-Friesian and Nellore origins of the polled phenotype in this native breed. Conversely, the presence of the Celtic variant PC suggests an almost complete co-segregation. The cluster analysis rejected the hypothesis of recent introgression, which is compatible with the historical record of polled Creole cattle in northwest Argentina.
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Affiliation(s)
- A H Falomir-Lockhart
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
| | - M F Ortega Masague
- IIACS - Instituto de Investigación Animal del Chaco Semiárido, (CIAP-INTA), Chañar Pozo s/n, 4113, Leales, Tucumán, Argentina
| | - G Rudd Garces
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
| | - M E Zappa
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
| | - P Peral García
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
| | - H F Morales
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
| | - F D Holgado
- IIACS - Instituto de Investigación Animal del Chaco Semiárido, (CIAP-INTA), Chañar Pozo s/n, 4113, Leales, Tucumán, Argentina
| | - A Rogberg Muñoz
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina.,Departamento de Producción Animal, Facultad de Agronomía, Cátedra de Mejoramiento Genético Animal, Universidad de Buenos Aires, Av. San Martin 4453, C1417DSE, Buenos Aires, Argentina
| | - G Giovambattista
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Calle 60 y 118 s/n, CC 296, 1900, La Plata, Buenos Aires, Argentina
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16
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Siripan S, Wonnapinij P, Auetrakulvit P, Wangthongchaicharoen N, Surat W. Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:609-617. [PMID: 30957607 DOI: 10.1080/24701394.2019.1597072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.
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Affiliation(s)
- Sirianong Siripan
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand
| | - Passorn Wonnapinij
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
| | - Prasit Auetrakulvit
- c Department of Archaeology, Faculty of Archaeology , Silpakorn University , Bangkok , Thailand
| | | | - Wunrada Surat
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
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17
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Pitt D, Bruford MW, Barbato M, Orozco‐terWengel P, Martínez R, Sevane N. Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics. Evol Appl 2019; 12:105-122. [PMID: 30622639 PMCID: PMC6304683 DOI: 10.1111/eva.12641] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 02/06/2023] Open
Abstract
The introduction of Iberian cattle in the Americas after Columbus' arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and N e Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) and population differentiation (F ST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic N e contraction. NeS analysis provided insights into short-term complexity in population change and depicted a decrease/expansion episode at the end of the ABC-inferred expansion, as well as several additional fluctuations in N e with the attainment of the current small N e only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future-proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | - Michael W. Bruford
- School of BiosciencesCardiff UniversityCardiffUK
- Sustainable Places Research InstituteCardiff UniversityCardiffUK
| | - Mario Barbato
- Institute of ZootechnicsUniversità Cattolica del Sacro CuorePiacenzaItaly
| | | | - Rodrigo Martínez
- Centro de investigaciones TibaitatáCorporación Colombiana De Investigación Agropecuaria (Corpoica)BogotáColombia
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18
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Cardoso DF, de Albuquerque LG, Reimer C, Qanbari S, Erbe M, do Nascimento AV, Venturini GC, Scalez DCB, Baldi F, de Camargo GMF, Mercadante MEZ, do Santos Gonçalves Cyrillo JN, Simianer H, Tonhati H. Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle. Genet Sel Evol 2018; 50:22. [PMID: 29720080 PMCID: PMC5930444 DOI: 10.1186/s12711-018-0381-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (FST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. Electronic supplementary material The online version of this article (10.1186/s12711-018-0381-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diercles F Cardoso
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lucia Galvão de Albuquerque
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Malena Erbe
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Grub, Germany
| | - André V do Nascimento
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Guilherme C Venturini
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Daiane C Becker Scalez
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Fernando Baldi
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Gregório M Ferreira de Camargo
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Maria E Zerlotti Mercadante
- National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil.,APTA Beef Cattle Center, Institute of Animal Science, Sertãozinho, SP, Brazil
| | | | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Humberto Tonhati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
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19
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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20
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Porto-Neto LR, Bickhart DM, Landaeta-Hernandez AJ, Utsunomiya YT, Pagan M, Jimenez E, Hansen PJ, Dikmen S, Schroeder SG, Kim ES, Sun J, Crespo E, Amati N, Cole JB, Null DJ, Garcia JF, Reverter A, Barendse W, Sonstegard TS. Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor. Front Genet 2018. [PMID: 29527221 PMCID: PMC5829098 DOI: 10.3389/fgene.2018.00057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Evolutionary adaptations are occasionally convergent solutions to the same problem. A mutation contributing to a heat tolerance adaptation in Senepol cattle, a New World breed of mostly European descent, results in the distinct phenotype known as slick, where an animal has shorter hair and lower follicle density across its coat than wild type animals. The causal variant, located in the 11th exon of prolactin receptor, produces a frameshift that results in a truncated protein. However, this mutation does not explain all cases of slick coats found in criollo breeds. Here, we obtained genome sequences from slick cattle of a geographically distinct criollo breed, namely Limonero, whose ancestors were originally brought to the Americas by the Spanish. These data were used to identify new causal alleles in the 11th exon of the prolactin receptor, two of which also encode shortened proteins that remove a highly conserved tyrosine residue. These new mutations explained almost 90% of investigated cases of animals that had slick coats, but which also did not carry the Senepol slick allele. These results demonstrate convergent evolution at the molecular level in a trait important to the adaptation of an animal to its environment.
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Affiliation(s)
| | - Derek M Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture, Agricultural Research Service, Madison, WI, United States
| | - Antonio J Landaeta-Hernandez
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Yuri T Utsunomiya
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, São Paulo, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Melvin Pagan
- Department of Animal Science, University of Puerto Rico-Mayagüez, Mayagüez, Puerto Rico
| | - Esbal Jimenez
- Department of Animal Science, University of Puerto Rico-Mayagüez, Mayagüez, Puerto Rico
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Serdal Dikmen
- Department of Animal Science, Faculty of Veterinary Medicine, Uludağ University, Bursa, Turkey
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Eui-Soo Kim
- Recombinetics, Inc., Saint Paul, MN, United States
| | - Jiajie Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Edward Crespo
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Norman Amati
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Daniel J Null
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jose F Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, São Paulo, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, São Paulo, Brazil
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21
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Abstract
There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.
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Affiliation(s)
- W Barendse
- CSIRO Agriculture, St. Lucia 4067, Australia.,School of Veterinary Science, University of Queensland, Gatton 4343, Australia;
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22
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Davis SR, Spelman RJ, Littlejohn MD. BREEDING AND GENETICS SYMPOSIUM:Breeding heat tolerant dairy cattle: the case for introgression of the "slick" prolactin receptor variant into dairy breeds. J Anim Sci 2017; 95:1788-1800. [PMID: 28464106 DOI: 10.2527/jas.2016.0956] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increasing environmental temperatures are a threat to the sustainability of livestock production and, because of the high metabolic demands of lactation, to dairy production in particular. Summer heat waves in temperate climates reduce feed intake, milk production, and cow comfort. In extreme heat events, there is an increase in cow mortality. In tropical climates, dairy cattle are mostly (zebu) type or zebu crossbred with temperate dairy breeds. Crossbreeding is undertaken to combine the heat tolerance and tick resistance of zebu with the productivity of temperate dairy breeds. In the absence of improved heat tolerance, milk production and fertility of temperate cattle is severely impaired. We have recently identified a key role for the prolactin pathway in regulating heat tolerance. A de novo mutation in prolactin that impairs prolactin activity was discovered in hairy and heat intolerant, New Zealand dairy cattle. The phenotypes produced were remarkably similar to those seen in fescue toxicosis, a syndrome seen in grazing cattle in the U.S. where ingestion of ergovaline, a fungal toxin from infected pasture, inhibits prolactin secretion. Recognition of the role of prolactin in hairy cattle led us to identify a deletion in exon 10 of the long-form of the prolactin receptor in Senepol cattle that causes truncation of the protein and determines the slick coat and heat tolerance traits found in this , beef breed. The short form of the prolactin receptor is predicted to be unaffected by the deletion. Knowledge of this dominant mutation has provided the impetus to begin a crossbreeding program to investigate performance and heat tolerance of temperate dairy cattle carrying the slick, prolactin receptor variant. The perceived opportunity is to introgress this variant into temperate dairy cattle to enable performance and welfare improvement in hot climates. Heat tolerance of cattle with slick coats appears to be mostly associated with coat type although sweating ability may also be enhanced. Further investigation is required of performance traits in cows homozygous for the slick variant because the published data are almost exclusively from heterozygous animals. Combination of the slick mutation with other favorable genes for heat tolerance, especially those for coat color, will be particularly enabled by gene editing technologies, offering opportunities for further improvement in bovine thermotolerance.
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23
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Evidence of positive selection towards Zebuine haplotypes in the BoLA region of Brangus cattle. Animal 2017; 12:215-223. [PMID: 28707606 DOI: 10.1017/s1751731117001380] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Brangus breed was developed to combine the superior characteristics of both of its founder breeds, Angus and Brahman. It combines the high adaptability to tropical and subtropical environments, disease resistance, and overall hardiness of Zebu cattle with the reproductive potential and carcass quality of Angus. It is known that the major histocompatibility complex (MHC, also known as bovine leucocyte antigen: BoLA), located on chromosome 23, encodes several genes involved in the adaptive immune response and may be responsible for adaptation to harsh environments. The objective of this work was to evaluate whether the local breed ancestry percentages in the BoLA locus of a Brangus population diverged from the estimated genome-wide proportions and to identify signatures of positive selection in this genomic region. For this, 167 animals (100 Brangus, 45 Angus and 22 Brahman) were genotyped using a high-density single nucleotide polymorphism array. The local ancestry analysis showed that more than half of the haplotypes (55.0%) shared a Brahman origin. This value was significantly different from the global genome-wide proportion estimated by cluster analysis (34.7% Brahman), and the proportion expected by pedigree (37.5% Brahman). The analysis of selection signatures by genetic differentiation (F st ) and extended haplotype homozygosity-based methods (iHS and Rsb) revealed 10 and seven candidate regions, respectively. The analysis of the genes located within these candidate regions showed mainly genes involved in immune response-related pathway, while other genes and pathways were also observed (cell surface signalling pathways, membrane proteins and ion-binding proteins). Our results suggest that the BoLA region of Brangus cattle may have been enriched with Brahman haplotypes as a consequence of selection processes to promote adaptation to subtropical environments.
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24
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Bahbahani H, Tijjani A, Mukasa C, Wragg D, Almathen F, Nash O, Akpa GN, Mbole-Kariuki M, Malla S, Woolhouse M, Sonstegard T, Van Tassell C, Blythe M, Huson H, Hanotte O. Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu. Front Genet 2017. [PMID: 28642786 PMCID: PMC5462927 DOI: 10.3389/fgene.2017.00068] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait UniversityKuwait, Kuwait
| | - Abdulfatai Tijjani
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | | | - David Wragg
- Centre for Tropical Livestock Genetics and Health, Roslin InstituteEdinburgh, United Kingdom
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal UniversityAl-Hasa, Saudi Arabia
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | - Gerald N Akpa
- Department of Animal Science, Ahmadu Bello UniversityZaria, Nigeria
| | - Mary Mbole-Kariuki
- School of Life Sciences, University of NottinghamNottingham, United Kingdom
| | - Sunir Malla
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Mark Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of EdinburghEdinburgh, United Kingdom
| | | | - Curtis Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Martin Blythe
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Heather Huson
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Olivier Hanotte
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,International Livestock Research Institute (ILRI)Addis Ababa, Ethiopia
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25
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Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. A Meta-Assembly of Selection Signatures in Cattle. PLoS One 2016; 11:e0153013. [PMID: 27045296 PMCID: PMC4821596 DOI: 10.1371/journal.pone.0153013] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/31/2022] Open
Abstract
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
- * E-mail:
| | - Mehar S. Khatkar
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Peter C. Thomson
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Herman W. Raadsma
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
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26
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Sempéré G, Moazami-Goudarzi K, Eggen A, Laloë D, Gautier M, Flori L. WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle. BMC Genomics 2015; 16:940. [PMID: 26573482 PMCID: PMC4647285 DOI: 10.1186/s12864-015-2181-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/31/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. However, efficient storage, management, cross-analyzing and exploration of such dense genotyping datasets remain challenging. This is particularly true for the bovine species where many SNP datasets have been generated in various cattle populations with different genotyping tools. DESCRIPTION We developed WIDDE, a Web-Interfaced Next Generation Database that stands as a generic tool applicable to a wide range of species and marker types ( http://widde.toulouse.inra.fr). As a first illustration, we hereby describe its first version dedicated to cattle biodiversity, which includes a large and evolving cattle genotyping dataset for over 750,000 SNPs available on 129 (89 public) different cattle populations representative of the world-wide bovine genetic diversity and on 7 outgroup bovid species. This version proposes an optional marker and individual filtering step, an export of genotyping data in different popular formats, and an exploration of genetic diversity through a principal component analysis. Users can also explore their own genotyping data together with data from WIDDE, assign their samples to WIDDE populations based on distance assignment method and supervised clustering, and estimate their ancestry composition relative to the populations represented in the database. CONCLUSION The cattle version of WIDDE represents to our knowledge the first database dedicated to cattle biodiversity and SNP genotyping data that will be very useful for researchers interested in this field. As a generic tool applicable to a wide range of marker types, WIDDE is overall intended to the genetic diversity exploration of any species and will be extended to other species shortly. The structure makes it easy to include additional output formats and new tools dedicated to genetic diversity exploration.
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Affiliation(s)
| | | | | | - Denis Laloë
- INRA, UMR 1313 GABI, F78350, Jouy-en-Josas, France.
| | - Mathieu Gautier
- INRA, UMR CBGP (INRA/CIRAD/IRD/Supagro), F34988, Montferrier-sur-Lez, France.
| | - Laurence Flori
- CIRAD, UMR INTERTRYP, F34398, Montpellier, France. .,INRA, UMR 1313 GABI, F78350, Jouy-en-Josas, France.
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27
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The genomics of ecological vicariance in threespine stickleback fish. Nat Commun 2015; 6:8767. [PMID: 26556609 PMCID: PMC4659939 DOI: 10.1038/ncomms9767] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/29/2015] [Indexed: 12/19/2022] Open
Abstract
Populations occurring in similar habitats and displaying similar phenotypes are increasingly used to explore parallel evolution at the molecular level. This generally ignores the possibility that parallel evolution can be mimicked by the fragmentation of an ancestral population followed by genetic exchange with ecologically different populations. Here we demonstrate such an ecological vicariance scenario in multiple stream populations of threespine stickleback fish divergent from a single adjacent lake population. On the basis of demographic and population genomic analyses, we infer the initial spread of a stream-adapted ancestor followed by the emergence of a lake-adapted population, that selective sweeps have occurred mainly in the lake population, that adaptive lake–stream divergence is maintained in the face of gene flow from the lake into the streams, and that this divergence involves major inversion polymorphisms also important to marine-freshwater stickleback divergence. Overall, our study highlights the need for a robust understanding of the demographic and selective history in evolutionary investigations. Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.
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Álvarez I, Pérez-Pardal L, Traoré A, Fernández I, Goyache F. Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle. J Anim Breed Genet 2015; 133:105-14. [DOI: 10.1111/jbg.12181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/24/2015] [Indexed: 01/22/2023]
Affiliation(s)
- I. Álvarez
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
| | - L. Pérez-Pardal
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | | | - I. Fernández
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
| | - F. Goyache
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
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29
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Bahbahani H, Clifford H, Wragg D, Mbole-Kariuki MN, Van Tassell C, Sonstegard T, Woolhouse M, Hanotte O. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis. Sci Rep 2015; 5:11729. [PMID: 26130263 PMCID: PMC4486961 DOI: 10.1038/srep11729] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 06/03/2015] [Indexed: 12/02/2022] Open
Abstract
The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics.
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Affiliation(s)
- Hussain Bahbahani
- 1] School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK [2] Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
| | - Harry Clifford
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX, Oxford, UK
| | - David Wragg
- Institut National de la Recherche Agronomique (INRA), UMR 1338 Génétique, Physiologie et Systèmes d'Elevage (GenPhySE), 31326 Castanet Tolosan, France
| | - Mary N Mbole-Kariuki
- African Union - InterAfrican Bureau of Animal Resources (AU-IBAR), P. O. Box 30786, 00100 Nairobi, Kenya
| | - Curtis Van Tassell
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA
| | - Tad Sonstegard
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA
| | - Mark Woolhouse
- Centre for Immunity, Infection &Evolution, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
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Orozco-terWengel P, Barbato M, Nicolazzi E, Biscarini F, Milanesi M, Davies W, Williams D, Stella A, Ajmone-Marsan P, Bruford MW. Revisiting demographic processes in cattle with genome-wide population genetic analysis. Front Genet 2015; 6:191. [PMID: 26082794 PMCID: PMC4451420 DOI: 10.3389/fgene.2015.00191] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/12/2015] [Indexed: 11/23/2022] Open
Abstract
The domestication of the aurochs took place approximately 10,000 years ago giving rise to the two main types of domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near the Fertile Crescent, and indicine (Bos indicus) domesticated in the Indus Valley. However, although cattle have historically played a prominent role in human society the exact origin of many extant breeds is not well known. Here we used a combination of medium and high-density Illumina Bovine SNP arrays (i.e., ~54,000 and ~770,000 SNPs, respectively), genotyped for over 1300 animals representing 56 cattle breeds, to describe the relationships among major European cattle breeds and detect patterns of admixture among them. Our results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin. We use these data to identify signatures of selection reflecting both domestication (hypothesized to produce a common signature across breeds) and local adaptation (predicted to exhibit a signature of selection unique to a single breed or group of related breeds with a common history) to uncover additional demographic complexity of modern European cattle.
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Affiliation(s)
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | | | - Marco Milanesi
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
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31
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Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front Genet 2015; 6:167. [PMID: 26029239 PMCID: PMC4429627 DOI: 10.3389/fgene.2015.00167] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022] Open
Abstract
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.
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Affiliation(s)
| | - Juan J Arranz
- Departamento de Producción Animal, Universidad de León León, Spain
| | - Pamela Wiener
- Division of Genetics and Genomics, Roslin Institute and R(D)SVS, University of Edinburgh Midlothian, UK
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32
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Tixier-Boichard M, Verrier E, Rognon X, Zerjal T. Farm animal genetic and genomic resources from an agroecological perspective. Front Genet 2015; 6:153. [PMID: 25983741 PMCID: PMC4415434 DOI: 10.3389/fgene.2015.00153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/05/2015] [Indexed: 01/16/2023] Open
Affiliation(s)
| | - Etienne Verrier
- GABI, INRA, AgroParisTech, Université Paris-Saclay Paris, France
| | - Xavier Rognon
- GABI, INRA, AgroParisTech, Université Paris-Saclay Paris, France
| | - Tatiana Zerjal
- GABI, INRA, AgroParisTech, Université Paris-Saclay Paris, France
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33
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Utsunomiya YT, Pérez O'Brien AM, Sonstegard TS, Sölkner J, Garcia JF. Genomic data as the "hitchhiker's guide" to cattle adaptation: tracking the milestones of past selection in the bovine genome. Front Genet 2015; 6:36. [PMID: 25713583 PMCID: PMC4322753 DOI: 10.3389/fgene.2015.00036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle "hitchhiked" on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field.
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Affiliation(s)
- Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture Beltsville, MA, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista (UNESP) Araçatuba, São Paulo, Brazil
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34
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Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle. Nat Commun 2014; 5:5861. [PMID: 25519203 PMCID: PMC4284646 DOI: 10.1038/ncomms6861] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/13/2014] [Indexed: 12/30/2022] Open
Abstract
Lactation, hair development and homeothermy are characteristic evolutionary features that define mammals from other vertebrate species. Here we describe the discovery of two autosomal dominant mutations with antagonistic, pleiotropic effects on all three of these biological processes, mediated through the prolactin signalling pathway. Most conspicuously, mutations in prolactin (PRL) and its receptor (PRLR) have an impact on thermoregulation and hair morphology phenotypes, giving prominence to this pathway outside of its classical roles in lactation. The hormone prolactin is a known modulator of mammalian lactation and hair growth. Here, the authors describe two dominant mutations in bovine prolactin and its receptor, demonstrating antagonistic effects on these traits and highlighting a role for this pathway in sweat gland function and thermoregulation.
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35
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Xu L, Bickhart DM, Cole JB, Schroeder SG, Song J, Tassell CPV, Sonstegard TS, Liu GE. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Mol Biol Evol 2014; 32:711-25. [PMID: 25431480 DOI: 10.1093/molbev/msu333] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.
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Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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36
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Abstract
Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i) domestication and subsequent wild introgression; (ii) natural adaptation to a diverse agricultural habitat; and (iii) breed development.
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37
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Dikmen S, Khan FA, Huson HJ, Sonstegard TS, Moss JI, Dahl GE, Hansen PJ. The SLICK hair locus derived from Senepol cattle confers thermotolerance to intensively managed lactating Holstein cows. J Dairy Sci 2014; 97:5508-20. [PMID: 24996281 DOI: 10.3168/jds.2014-8087] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/20/2014] [Indexed: 11/19/2022]
Abstract
The SLICK haplotype (http://omia.angis.org.au/OMIA001372/9913/) in cattle confers animals with a short and sleek hair coat. Originally identified in Senepol cattle, the gene has been introduced into Holsteins. The objectives of the current study were to determine (1) whether lactating Holsteins with the slick hair phenotype have superior ability for thermoregulation compared with wild-type cows or relatives not inheriting the SLICK haplotype, and (2) whether seasonal depression in milk yield would be reduced in SLICK cows. In experiment 1, diurnal variation in vaginal temperature in the summer was monitored for cows housed in a freestall barn with fans and sprinklers. Vaginal temperatures were lower in slick-haired cows than in relatives and wild-type cows. In experiment 2, acute responses to heat stress were monitored after cows were moved to a dry lot in which the only heat abatement was shade cloth. The increases in rectal temperature and respiration rate caused by heat stress during the day were lower for slick cows than for relatives or wild-type cows. Moreover, sweating rate was higher for slick cows than for cows of the other 2 types. In experiment 3, effects of season of calving (summer vs. winter) on milk yield and composition were determined. Compared with milk yield of cows calving in winter, milk yield during the first 90 d in milk was lower for cows calving in the summer. However, this reduction was less pronounced for slick cows than for wild-type cows. In conclusion, Holsteins with slick hair have superior thermoregulatory ability compared with non-slick animals and experience a less drastic depression in milk yield during the summer.
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Affiliation(s)
- S Dikmen
- University of Uludag, Faculty of Veterinary Medicine, Department of Animal Science, Bursa 16059, Turkey
| | - F A Khan
- University of Florida, Department of Animal Sciences, Gainesville 32611-0910
| | - H J Huson
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - T S Sonstegard
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - J I Moss
- University of Florida, Department of Animal Sciences, Gainesville 32611-0910
| | - G E Dahl
- University of Florida, Department of Animal Sciences, Gainesville 32611-0910
| | - P J Hansen
- University of Florida, Department of Animal Sciences, Gainesville 32611-0910.
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38
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Flori L, Thevenon S, Dayo GK, Senou M, Sylla S, Berthier D, Moazami-Goudarzi K, Gautier M. Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population. Mol Ecol 2014; 23:3241-57. [PMID: 24888437 DOI: 10.1111/mec.12816] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 12/01/2022]
Abstract
Understanding the adaptive response to environmental fluctuations represents a central issue in evolutionary biology. Population admixture between divergent ancestries has often been considered as an efficient short-term adaptation strategy. Cattle populations from the West African Bos taurus × Bos indicus hybrid zone represent a valuable resource to characterize the effect of such adaptive admixture at the genome level. We here provide a detailed assessment of the global and local genome ancestries of the Borgou breed, one of the most representative cattle of this hybrid zone. We analysed a large data set consisting of 38,100 SNPs genotyped on 203 Borgou and 591 individuals representative of all the different cattle ancestries. At the global genomic level, we show that Borgou is a stabilized admixed breed whose origin (c. 130 years ago) traces back to the great African rinderpest pandemic, several centuries after the last admixture events, the West African zebus originate from (c. 500 years ago). To identify footprints of adaptive admixture, we combined the identification of signatures of selection and the functional annotation of the underlying genes using systems biology tools. The detection of the SILV coat coloration gene likely under artificial selection may be viewed as a validation of our approach. Overall, our results suggest that the long-term presence of pathogens and the intermediate environmental conditions are the main acting selective pressures. Our analytical framework can be extended to other model or nonmodel species to understand the process that shapes the patterns of genetic variability in hybrid zones.
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Affiliation(s)
- Laurence Flori
- CIRAD, UMR INTERTRYP, Montpellier, F34398, France; INRA, UMR 1313 GABI, Jouy-en-Josas, F78350, France
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39
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Huson HJ, Kim ES, Godfrey RW, Olson TA, McClure MC, Chase CC, Rizzi R, O'Brien AMP, Van Tassell CP, Garcia JF, Sonstegard TS. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle. Front Genet 2014; 5:101. [PMID: 24808908 PMCID: PMC4010767 DOI: 10.3389/fgene.2014.00101] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/08/2014] [Indexed: 11/13/2022] Open
Abstract
The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (BTA) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principal component analysis (PCA) and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.
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Affiliation(s)
- Heather J Huson
- Department of Animal Science, Cornell University Ithaca, NY, USA ; Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
| | - Eui-Soo Kim
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Department of Animal Science, Iowa State University Ames, IA, USA
| | - Robert W Godfrey
- Agricultural Experiment Station, University of the Virgin Islands St. Croix, Virgin Islands
| | - Timothy A Olson
- Department of Animal Science, University of Florida Gainsville, FL, USA
| | - Matthew C McClure
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Irish Cattle Breeding Federation Cork, Ireland
| | - Chad C Chase
- Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Services Clay Center, NE, USA
| | - Rita Rizzi
- Department of Veterinary Medicine, Milan University Milan, Italy
| | - Ana M P O'Brien
- Division of Livestock Sciences, BOKU University of Natural Resources and Life Sciences Vienna, Austria
| | - Curt P Van Tassell
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
| | - José F Garcia
- Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Brazil
| | - Tad S Sonstegard
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
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40
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Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep. BMC Genet 2014; 15:34. [PMID: 24636660 PMCID: PMC4101850 DOI: 10.1186/1471-2156-15-34] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/10/2014] [Indexed: 12/22/2022] Open
Abstract
Background Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse constituent tests. The extreme CSS scores capture highly differentiated loci and underlying common variants hauling excess haplotype homozygosity in the samples of a target population. Results The data on high-density genotypes were analyzed for evidence of an association with either polledness or double muscling in various cohorts of cattle and sheep. In cattle, extreme CSS scores were found in the candidate regions on autosome BTA-1 and BTA-2, flanking the POLL locus and MSTN gene, for polledness and double muscling, respectively. In sheep, the regions with extreme scores were localized on autosome OAR-2 harbouring the MSTN gene for double muscling and on OAR-10 harbouring the RXFP2 gene for polledness. In comparison to the constituent tests, there was a partial agreement between the signals at the four candidate loci; however, they consistently identified additional genomic regions harbouring no known genes. Persuasively, our list of all the additional significant CSS regions contains genes that have been successfully implicated to secondary phenotypic diversity among several subpopulations in our data. For example, the method identified a strong selection signature for stature in cattle capturing selective sweeps harbouring UQCC-GDF5 and PLAG1-CHCHD7 gene regions on BTA-13 and BTA-14, respectively. Both gene pairs have been previously associated with height in humans, while PLAG1-CHCHD7 has also been reported for stature in cattle. In the additional analysis, CSS identified significant regions harbouring multiple genes for various traits under selection in European cattle including polledness, adaptation, metabolism, growth rate, stature, immunity, reproduction traits and some other candidate genes for dairy and beef production. Conclusions CSS successfully localized the candidate regions in validation datasets as well as identified previously known and novel regions for various traits experiencing selection pressure. Together, the results demonstrate the utility of CSS by its improved power, reduced false positives and high-resolution of selection signals as compared to individual constituent tests.
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Affiliation(s)
- Imtiaz Ahmed Sajid Randhawa
- ReproGen - Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, 425 Werombi Road, Camden NSW 2570, Australia.
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41
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Hudson NJ, Porto-Neto LR, Kijas J, McWilliam S, Taft RJ, Reverter A. Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest. BMC Bioinformatics 2014; 15:66. [PMID: 24606587 PMCID: PMC4015654 DOI: 10.1186/1471-2105-15-66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/26/2014] [Indexed: 11/20/2022] Open
Abstract
Background Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains patterns in allele order and proportion. These patterns can be quantified by compression efficiency (CE). In principle, the composition of an entire genome can be represented by a CE number quantifying allele representation and order. Results We applied a compression algorithm (DEFLATE) to genome-wide high-density SNP data from 4,155 human, 1,800 cattle, 1,222 sheep, 81 dogs and 49 mice samples. All human ethnic groups can be clustered by CE and the clusters recover phylogeography based on traditional fixation index (FST) analyses. CE analysis of other mammals results in segregation by breed or species, and is sensitive to admixture and past effective population size. This clustering is a consequence of individual patterns such as runs of homozygosity. Intriguingly, a related approach can also be used to identify genomic loci that show population-specific CE segregation. A high resolution CE ‘sliding window’ scan across the human genome, organised at the population level, revealed genes known to be under evolutionary pressure. These include SLC24A5 (European and Gujarati Indian skin pigmentation), HERC2 (European eye color), LCT (European and Maasai milk digestion) and EDAR (Asian hair thickness). We also identified a set of previously unidentified loci with high population-specific CE scores including the chromatin remodeler SCMH1 in Africans and EDA2R in Asians. Closer inspection reveals that these prioritised genomic regions do not correspond to simple runs of homozygosity but rather compositionally complex regions that are shared by many individuals of a given population. Unlike FST, CE analyses do not require ab initio population comparisons and are amenable to the hemizygous X chromosome. Conclusions We conclude with a discussion of the implications of CE for a complex systems science view of genome evolution. CE allows one to clearly visualise the evolution of individual genomes and populations through a formal, mathematically-rigorous information space. Overall, CE makes a set of biological predictions, some of which are unique and await functional validation.
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Affiliation(s)
| | | | | | | | - Ryan J Taft
- Computational and Systems Biology, CSIRO Animal, Food and Health Sciences, St, Lucia, Brisbane, QLD 4067, Australia.
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Porto-Neto LR, Lee SH, Sonstegard TS, Van Tassell CP, Lee HK, Gibson JP, Gondro C. Genome-wide detection of signatures of selection in Korean Hanwoo cattle. Anim Genet 2014; 45:180-90. [PMID: 24494817 DOI: 10.1111/age.12119] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2013] [Indexed: 02/02/2023]
Abstract
The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.
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Affiliation(s)
- L R Porto-Neto
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia; School of Veterinary Science, The University of Queensland, Gatton, QLD, 4345, Australia
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Comparison of tick resistance of crossbred Senepol × Limousin to purebred Limousin cattle. Trop Anim Health Prod 2013; 46:447-53. [PMID: 24366717 DOI: 10.1007/s11250-013-0512-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
Abstract
The comparison of resistance to natural tick infestation by Rhipicephalus microplus (Canestrini, 1887) of crossbred Senepol × Limousin and purebred Limousin cattle was investigated. The Senepol breed, originated from St Croix Island in the Caribbean is considered as a Bos taurus breed adapted to tropical conditions. Despite its B. taurus genetic background, it is believed to have a good tick resistance, but this resistance has never been assessed previously. Tick counts under natural infestation were carried out to investigate the difference of susceptibility between crossbred Senepol × Limousin and purebred Limousin cattle. Mixed-effect models were used to assess the effect of the breed on the number of ticks. Results show that Senepol × Limousin are five times less infested by ticks than purebred Limousin. These results underline the opportunity to use Senepol cattle for crossing with susceptible B. taurus breeds in tick infested areas, to combine tick resistance with beef production abilities.
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