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Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023; 54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Seo D, Lee DH, Jin S, Won JI, Lim D, Park M, Kim TH, Lee HK, Kim S, Choi I, Lee JH, Gondro C, Lee SH. Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. Sci Rep 2022; 12:6438. [PMID: 35440706 PMCID: PMC9018707 DOI: 10.1038/s41598-022-09425-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/01/2022] [Indexed: 11/09/2022] Open
Abstract
Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < –6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.
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Affiliation(s)
- Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Jung Il Won
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Mina Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, RDA, Seonghwan, South Korea
| | - Tae Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, South Korea
| | - Sidong Kim
- Poultry Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Inchul Choi
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Cedric Gondro
- Beacon Center for the Study of Evolution in Action and Department of Animal Science, Michigan State University, East Lansing, USA
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea.
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Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
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Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
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Fonseca PADS, Caldwell T, Mandell I, Wood K, Cánovas A. Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages. Meat Sci 2022; 186:108733. [PMID: 35007800 DOI: 10.1016/j.meatsci.2022.108733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tim Caldwell
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ira Mandell
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Katharine Wood
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
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Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
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8
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Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U, Lasagna E. The genetics of phenotypic plasticity in livestock in the era of climate change: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1809540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Giacomo Rovelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Eymen Demir
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Fabio Abeni
- Centro di ricerca Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Lodi, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | - Martino Cassandro
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| | - Umberto Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Viterbo, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
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Mastrangelo S, Ben Jemaa S, Sottile G, Casu S, Portolano B, Ciani E, Pilla F. Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations. J Anim Breed Genet 2019; 136:526-534. [PMID: 31206848 DOI: 10.1111/jbg.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022]
Abstract
Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and FST analyses. Moreover, one candidate marker identified by GWAS and FST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Gianluca Sottile
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, Sassari, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
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Zhang R, Miao J, Song Y, Zhang W, Xu L, Chen Y, Zhang L, Gao H, Zhu B, Li J, Gao X. Genome-wide association study identifies the PLAG1-OXR1 region on BTA14 for carcass meat yield in cattle. Physiol Genomics 2019; 51:137-144. [DOI: 10.1152/physiolgenomics.00112.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Carcass meat yield is an important carcass trait that contributes to the production efficiency and economic benefits in beef cattle. It is therefore critical to identify quantitative trait loci associated with carcass traits to enable selection. Our previous studies have identified several causal variants within the pleomorphic adenoma gene 1 ( PLAG1) and coiled-coil-helix-coiled-coil-helix domain-containing 7 ( CHCHD7) genes on BTA14 for carcass traits in Chinese Simmental. In the current study, we carried out a genome-wide association study for carcass meat yield in 472 Wagyu cattle with Bovine HD SNP array. Our results showed that 27 single nucleotide polymorphisms (SNPs) were identified for tenderloin weight (TDW), striploin weight (SPW), chuck roll weight (CRW), bicep weight (BPW), knuckle weight (KCW), and flank steak weight (FSW) in Wagyu cattle. Of these SNPs, 10 distinct SNPs were detected within the oxidation resistance 1 ( OXR1), fatty acid binding protein 5 ( FABP5), TNF receptor superfamily member 11b ( TNFRSF11B), and zinc finger CCCH-type containing 3 ( ZC3H3) genes on BTA14. Notably, three significant SNPs, BovineHD1400016738, BovineHD1400016743, and BovineHD1400016665 within OXR1, were shown strong linkage disequilibrium (r2 > 0.8) and significantly associated with CRW ( P = 1.37 × 10−8 ~ 1.94 × 10−8). Moreover, Ingenuity Pathway Analysis showed that OXR1, FABP5, and CAP1A genes were involved in a single network and FABP5 may regulate the expression of OXR1 gene via node gene, peroxisome proliferator-activated receptor gamma ( PPARG). Overall, this study suggests that OXR1 and FABP5 are candidate genes affecting carcass traits in Wagyu and the PLAG1-OXR1 region on BTA14 as a putative susceptibility locus for carcass meat yield for both Chinese Simmental and Wagyu.
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Affiliation(s)
- Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Song
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Manzari Z, Mehrabani-Yeganeh H, Nejati-Javaremi A, Moradi MH, Gholizadeh M. Detecting selection signatures in three Iranian sheep breeds. Anim Genet 2019; 50:298-302. [PMID: 30883840 DOI: 10.1111/age.12772] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
Abstract
The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype-phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP-EHH (cross-population extend haplotype homozygosity) and FST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori-Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.
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Affiliation(s)
- Z Manzari
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - H Mehrabani-Yeganeh
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - A Nejati-Javaremi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - M H Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran
| | - M Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, Sari, 4818168984, Iran
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12
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Xu L, Zhu B, Wang Z, Xu L, Liu Y, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle. Animals (Basel) 2019; 9:ani9030083. [PMID: 30845681 PMCID: PMC6466336 DOI: 10.3390/ani9030083] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Evaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle. Abstract Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.
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Affiliation(s)
- Lei Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zezhao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ling Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ying Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lupei Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xue Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huijiang Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Peripolli E, Stafuzza NB, Munari DP, Lima ALF, Irgang R, Machado MA, Panetto JCDC, Ventura RV, Baldi F, da Silva MVGB. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics 2018; 19:34. [PMID: 29316879 PMCID: PMC5759835 DOI: 10.1186/s12864-017-4365-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Results ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Conclusions Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. Electronic supplementary material The online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - André Luís Ferreira Lima
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Renato Irgang
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Marco Antonio Machado
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | | | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, 13635-900, Brazil.,Beef Improvement Opportunities, Elora, ON, N0B 1S0, Canada.,University of Guelph, Centre for Genetic Improvement of Livestock, ABScBG, Guelph, N1G 2W1, Canada
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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14
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de Simoni Gouveia JJ, Paiva SR, McManus CM, Caetano AR, Kijas JW, Facó O, Azevedo HC, de Araujo AM, de Souza CJH, Yamagishi MEB, Carneiro PLS, Braga Lôbo RN, de Oliveira SMP, da Silva MVG. Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Niu H, Zhu B, Guo P, Zhang W, Xue J, Chen Y, Zhang L, Gao H, Gao X, Xu L, Li J. Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Asif AR, Qadri S, Ijaz N, Javed R, Ansari AR, Awais M, Younus M, Riaz H, Du X. Genetic signature of strong recent positive selection at interleukin-32 gene in goat. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:912-919. [PMID: 27165029 PMCID: PMC5495668 DOI: 10.5713/ajas.15.0941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/06/2016] [Accepted: 03/25/2016] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. METHODS By using fixation index (FST ) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and FST . Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. RESULTS IL-32 is detected under positive selection using the FST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. CONCLUSION This study provides evidence for IL-32 gene as under significant positive selection in goat.
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Affiliation(s)
- Akhtar Rasool Asif
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Theriogenology Department, College of Veterinary and Animal Science, Jhang, Sub campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Sumayyah Qadri
- Theriogenology Department, College of Veterinary and Animal Science, Jhang, Sub campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Nabeel Ijaz
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruheena Javed
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Abdur Rahman Ansari
- Theriogenology Department, College of Veterinary and Animal Science, Jhang, Sub campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.,Department of Anatomy, Histology and Embryology, College of Animal and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammd Awais
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Younus
- Theriogenology Department, College of Veterinary and Animal Science, Jhang, Sub campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Hasan Riaz
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal 57000, Pakistan
| | - Xiaoyong Du
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan China
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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: 58] [Impact Index Per Article: 7.3] [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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18
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Biegelmeyer P, Gulias-Gomes CC, Caetano AR, Steibel JP, Cardoso FF. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genet 2016; 17:32. [PMID: 26832943 PMCID: PMC4736111 DOI: 10.1186/s12863-016-0339-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Background The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (RH,B) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Results Mean LD estimates, measured using the squared correlation of alleles at two loci (r2), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r2 was > 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r2 > 0.2) was found spanning to ~50 Kb. Conclusions Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.
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Affiliation(s)
- Patrícia Biegelmeyer
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil.
| | | | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. .,Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, Distrito Federal, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
| | | | - Fernando F Cardoso
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil. .,Embrapa Pecuária Sul, Bagé, Rio Grande do Sul, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
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19
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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: 60] [Impact Index Per Article: 6.7] [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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20
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Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus. G3-GENES GENOMES GENETICS 2015; 5:1391-401. [PMID: 25931611 PMCID: PMC4502373 DOI: 10.1534/g3.115.017772] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the evolution and molecular architecture of complex traits is important in domestic animals. Due to phenotypic selection, genomic regions develop unique patterns of genetic diversity called signatures of selection, which are challenging to detect, especially for complex polygenic traits. In this study, we applied the composite selection signals (CSS) method to investigate evidence of positive selection in a complex polygenic trait by examining stature in phenotypically diverse cattle comprising 47 European and 8 African Bos taurus breeds, utilizing a panel of 38,033 SNPs genotyped on 1106 animals. CSS were computed for phenotypic contrasts between multibreed cohorts of cattle by classifying the breeds according to their documented wither height to detect the candidate regions under selection. Using the CSS method, clusters of signatures of selection were detected at 26 regions (9 in European and 17 in African cohorts) on 13 bovine autosomes. Using comparative mapping information on human height, 30 candidate genes mapped at 12 selection regions (on 8 autosomes) could be linked to bovine stature diversity. Of these 12 candidate gene regions, three contained known genes (i.e., NCAPG-LCORL, FBP2-PTCH1, and PLAG1-CHCHD7) related to bovine stature, and nine were not previously described in cattle (five in European and four in African cohorts). Overall, this study demonstrates the utility of CSS coupled with strategies of combining multibreed datasets in the identification and discovery of genomic regions underlying complex traits. Characterization of multiple signatures of selection and their underlying candidate genes will elucidate the polygenic nature of stature across cattle breeds.
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21
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Kim ES, Sonstegard TS, Rothschild MF. Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions. BMC Genomics 2015; 16:302. [PMID: 25887761 PMCID: PMC4409734 DOI: 10.1186/s12864-015-1500-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/30/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genome signatures of artificial selection in U.S. Jersey cattle were identified by examining changes in haplotype homozygosity for a resource population of animals born between 1953 and 2007. Genetic merit of this population changed dramatically during this period for a number of traits, especially milk yield. The intense selection underlying these changes was achieved through extensive use of artificial insemination (AI), which also increased consanguinity of the population to a few superior Jersey bulls. As a result, allele frequencies are shifted for many contemporary animals, and in numerous cases to a homozygous state for specific genomic regions. The goal of this study was to identify those selection signatures that occurred after extensive use of AI since the 1960, using analyses of shared haplotype segments or Runs of Homozygosity. When combined with animal birth year information, signatures of selection associated with economically important traits were identified and compared to results from an extended haplotype homozygosity analysis. RESULTS Overall, our results reveal that more recent selection increased autozygosity across the entire genome, but some specific regions increased more than others. A genome-wide scan identified more than 15 regions with a substantial change in autozygosity. Haplotypes found to be associated with increased milk, fat and protein yield in U.S. Jersey cattle also consistently increased in frequency. CONCLUSIONS The analyses used in this study was able to detect directional selection over the last few decades when individual production records for Jersey animals were available.
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Affiliation(s)
- Eui-Soo Kim
- United States Department of Agriculture, Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, 20705, USA.
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
| | - Tad S Sonstegard
- United States Department of Agriculture, Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, 20705, USA.
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
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22
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Bomba L, Nicolazzi EL, Milanesi M, Negrini R, Mancini G, Biscarini F, Stella A, Valentini A, Ajmone-Marsan P. Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection. Genet Sel Evol 2015; 47:25. [PMID: 25888030 PMCID: PMC4383072 DOI: 10.1186/s12711-015-0113-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/19/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds. RESULTS A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production. CONCLUSIONS Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production.
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Affiliation(s)
- Lorenzo Bomba
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Ezequiel L Nicolazzi
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Marco Milanesi
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Riccardo Negrini
- Associazione Italiana Allevatori (AIA), Via Tomassetti 9, Rome, 00161, Italy.
| | - Giordano Mancini
- Center for Computational Chemistry and Cosmology, Scuola Normale Superiore, Via Consoli del Mare 2, Pisa, 56126, Italy.
| | - Filippo Biscarini
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. .,Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
| | - Alessio Valentini
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), via de Lellis, Viterbo, 01100, Italy.
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
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Beltrán NAR, Meira CT, de Oliveira HN, Pereira GL, Silva JAIIV, da Mota MDS, Curi RA. Prospection of genomic regions divergently selected in cutting line of Quarter Horses in relation to racing line. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Howard JT, Maltecca C, Haile-Mariam M, Hayes BJ, Pryce JE. Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations. BMC Genomics 2015; 16:187. [PMID: 25879195 PMCID: PMC4460752 DOI: 10.1186/s12864-015-1352-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/18/2015] [Indexed: 11/19/2022] Open
Abstract
Background Dairy cattle breeding objectives are in general similar across countries, but environment and management conditions may vary, giving rise to slightly different selection pressures applied to a given trait. This potentially leads to different selection pressures to loci across the genome that, if large enough, may give rise to differential regions with high levels of homozygosity. The objective of this study was to characterize differences and similarities in the location and frequency of homozygosity related measures of Jersey dairy cows and bulls from the United States (US), Australia (AU) and New Zealand (NZ). Results The populations consisted of a subset of genotyped Jersey cows born in US (n = 1047) and AU (n = 886) and Jersey bulls progeny tested from the US (n = 736), AU (n = 306) and NZ (n = 768). Differences and similarities across populations were characterized using a principal component analysis (PCA) and a run of homozygosity (ROH) statistic (ROH45), which counts the frequency of a single nucleotide polymorphism (SNP) being in a ROH of at least 45 SNP. Regions that exhibited high frequencies of ROH45 and those that had significantly different ROH45 frequencies between populations were investigated for their association with milk yield traits. Within sex, the PCA revealed slight differentiation between the populations, with the greatest occurring between the US and NZ bulls. Regions with high levels of ROH45 for all populations were detected on BTA3 and BTA7 while several other regions differed in ROH45 frequency across populations, the largest number occurring for the US and NZ bull contrast. In addition, multiple regions with different ROH45 frequencies across populations were found to be associated with milk yield traits. Conclusion Multiple regions exhibited differential ROH45 across AU, NZ and US cow and bull populations, an interpretation is that locations of the genome are undergoing differential directional selection. Two regions on BTA3 and BTA7 had high ROH45 frequencies across all populations and will be investigated further to determine the gene(s) undergoing directional selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1352-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeremy T Howard
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA.
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA.
| | - Mekonnen Haile-Mariam
- Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. .,Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia.
| | - Ben J Hayes
- Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. .,La Trobe University, Bundoora, Victoria, 3086, Australia. .,Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia.
| | - Jennie E Pryce
- Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. .,La Trobe University, Bundoora, Victoria, 3086, Australia. .,Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia.
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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: 22] [Impact Index Per Article: 2.4] [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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26
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López ME, Neira R, Yáñez JM. Applications in the search for genomic selection signatures in fish. Front Genet 2015; 5:458. [PMID: 25642239 PMCID: PMC4294200 DOI: 10.3389/fgene.2014.00458] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022] Open
Abstract
Selection signatures are genomic regions harboring DNA sequences functionally involved in the genetic variation of traits subject to selection. Selection signatures have been intensively studied in recent years because of their relevance to evolutionary biology and their potential association with genes that control phenotypes of interest in wild and domestic populations. Selection signature research in fish has been confined to a smaller scale, due in part to the relatively recent domestication of fish species and limited genomic resources such as molecular markers, genetic mapping, DNA sequences, and reference genomes. However, recent genomic technology advances are paving the way for more studies that may contribute to the knowledge of genomic regions underlying phenotypes of biological and productive interest in fish.
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Affiliation(s)
- María E López
- Faculty of Agricultural Sciences, University of Chile Santiago, Chile ; Aquainnovo, Puerto Montt Chile
| | - Roberto Neira
- Faculty of Agricultural Sciences, University of Chile Santiago, Chile
| | - José M Yáñez
- Aquainnovo, Puerto Montt Chile ; Faculty of Veterinary and Animal Sciences, University of Chile Santiago, Chile
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27
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Ryu J, Lee C. Identification of contemporary selection signatures using composite log likelihood and their associations with marbling score in Korean cattle. Anim Genet 2014; 45:765-70. [DOI: 10.1111/age.12209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Jihye Ryu
- School of Systems Biomedical Science; Soongsil University; Seoul 156-743 Korea
| | - Chaeyoung Lee
- School of Systems Biomedical Science; Soongsil University; Seoul 156-743 Korea
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28
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Grasso AN, Goldberg V, Navajas EA, Iriarte W, Gimeno D, Aguilar I, Medrano JF, Rincón G, Ciappesoni G. Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep. Genet Mol Biol 2014; 37:389-95. [PMID: 25071404 PMCID: PMC4094612 DOI: 10.1590/s1415-47572014000300011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/16/2014] [Indexed: 02/08/2023] Open
Abstract
The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (FST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (FST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (FST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.
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Affiliation(s)
- Andrés N Grasso
- Meat and Wool National Program , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
| | - Virginia Goldberg
- Meat and Wool National Program , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
| | - Elly A Navajas
- Biotechnology Unit , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
| | - Wanda Iriarte
- Biotechnology Unit , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
| | - Diego Gimeno
- Department of Animal Genetic Improvement , Secretariado Uruguayo de la Lana , Montevideo , Uruguay
| | - Ignacio Aguilar
- Meat and Wool National Program , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
| | - Juan F Medrano
- Department of Animal Science , University of California Davis , USA
| | - Gonzalo Rincón
- Department of Animal Science , University of California Davis , USA
| | - Gabriel Ciappesoni
- Meat and Wool National Program , Instituto Nacional de Investigación Agropecuaria , Las Brujas, Canelones , Uruguay
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de Simoni Gouveia JJ, da Silva MVGB, Paiva SR, de Oliveira SMP. Identification of selection signatures in livestock species. Genet Mol Biol 2014; 37:330-42. [PMID: 25071397 PMCID: PMC4094609 DOI: 10.1590/s1415-47572014000300004] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/27/2014] [Indexed: 11/22/2022] Open
Abstract
The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.
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Affiliation(s)
- João José de Simoni Gouveia
- Colegiado Acadêmico de Zootecnia , Universidade Federal do Vale do São Francisco , Petrolina, PE , Brazil . ; Programa de Doutorado Integrado em Zootecnia , Universidade Federal do Ceará , Fortaleza, CE , Brazil
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30
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Cardoso DF, de Souza FRP, de Camargo GMF, Fonseca PDDS, Fonseca LFS, Braz CU, Boligon AA, Mercadante MEZ, de Albuquerque LG, Tonhati H. Polymorphism analysis in genes of the somatotropic axis in Nellore cattle selected for growth. Gene 2014; 545:215-9. [DOI: 10.1016/j.gene.2014.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/05/2014] [Accepted: 05/13/2014] [Indexed: 11/26/2022]
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31
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Pertoldi C, Purfield DC, Berg P, Jensen TH, Bach OS, Vingborg R, Kristensen TN. Genetic characterization of a herd of the endangered Danish Jutland cattle. J Anim Sci 2014; 92:2372-6. [PMID: 24671594 DOI: 10.2527/jas.2013-7206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this paper we present results from a genetic characterization of a herd of the Danish Jutland cattle breed named the Kortegaard herd (n = 135; 57 males and 78 females). The herd is genotyped on the Bovine HD BeadChip microarray with 697,548 evenly spaced SNP across the bovine genome. The aim of the study was to characterize the genetic profile of the Kortegaard herd, which has been closed for several generations, by quantifying the degree of genetic homogeneity within the herd and to compare its genetic profile to that of other cattle breeds. A total of 868 animals from the Angus, Belgian Blue, Charolais, Friesian, Hereford, Holstein, Holstein-Friesian crosses, Limousin, and Simmental breeds was used for genetic profile comparisons. The level of genetic variation within the breeds were quantified by the expected heterozygosity (H(E)), observed heterozygosity (H(O)), average minor allele frequency (MAF), the degree of polymorphism, and runs of homozygosity (ROH), which are contiguous lengths of homozygous genotypes of varying length. Interestingly, the Kortegaard herd had the lowest within-breed genetic variation (lowest H(E), H(O), and MAF), showed moderate levels of short ROH (<5 Mb), and had the highest mean long ROH (>5 Mb) compared to all the other breeds. This is possibly due to recent consanguineous matings, a strong founder effect, and a lack of gene flow from other herds and breeds. We further examined whether the observed genetic patterns in the Kortegaard herd can be used to design breeding strategies for the preservation of the genetic pool by focusing on a subset of SNP outside homozygote regions. By calculating the pairwise identical-by-state between all possible matings, we designed a breeding plan that maximized heterozygosity in the short term. The benefits and limitations of such a breeding strategy are discussed.
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Affiliation(s)
- C Pertoldi
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark Aalborg Zoo, Aalborg, Denmark
| | - D C Purfield
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - P Berg
- NordGen - Nordic Genetic Resource Center, Ås, Norway
| | - T H Jensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark Aalborg Zoo, Aalborg, Denmark
| | - O S Bach
- Randers Regnskov, Randers, Denmark
| | | | - T N Kristensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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Kim ES, Cole JB, Huson H, Wiggans GR, Van Tassell CP, Crooker BA, Liu G, Da Y, Sonstegard TS. Effect of artificial selection on runs of homozygosity in u.s. Holstein cattle. PLoS One 2013; 8:e80813. [PMID: 24348915 PMCID: PMC3858116 DOI: 10.1371/journal.pone.0080813] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 10/16/2013] [Indexed: 02/04/2023] Open
Abstract
The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins.
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Affiliation(s)
- Eui-Soo Kim
- Bovine Functional Genomics Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - John B. Cole
- Animal Improvement Programs Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - Heather Huson
- Bovine Functional Genomics Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - George R. Wiggans
- Animal Improvement Programs Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - Curtis P. Van Tassell
- Bovine Functional Genomics Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
- Animal Improvement Programs Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - Brian A. Crooker
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - George Liu
- Bovine Functional Genomics Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Tad S. Sonstegard
- Bovine Functional Genomics Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
- * E-mail:
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Sanz A, Serrano C, Uffo O, Acosta A, Ordovás L, Osta R, Zaragoza P, Rodellar C. 5′Cis regulatory polymorphisms in candidate genes in Bos taurus and Bos indicus. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.06.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pintus E, Sorbolini S, Albera A, Gaspa G, Dimauro C, Steri R, Marras G, Macciotta NPP. Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown cattle breeds. Anim Genet 2013; 45:1-11. [PMID: 23889699 DOI: 10.1111/age.12076] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2013] [Indexed: 11/27/2022]
Abstract
Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.
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Affiliation(s)
- Elia Pintus
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy
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Ramey HR, Decker JE, McKay SD, Rolf MM, Schnabel RD, Taylor JF. Detection of selective sweeps in cattle using genome-wide SNP data. BMC Genomics 2013; 14:382. [PMID: 23758707 PMCID: PMC3681554 DOI: 10.1186/1471-2164-14-382] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 05/24/2013] [Indexed: 12/25/2022] Open
Abstract
Background The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps. Results Two datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour. Conclusions The bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.
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Affiliation(s)
- Holly R Ramey
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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Utsunomiya YT, Pérez O’Brien AM, Sonstegard TS, Van Tassell CP, do Carmo AS, Mészáros G, Sölkner J, Garcia JF. Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS One 2013; 8:e64280. [PMID: 23696874 PMCID: PMC3655949 DOI: 10.1371/journal.pone.0064280] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 04/13/2013] [Indexed: 12/21/2022] Open
Abstract
As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10−7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10−12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.
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Affiliation(s)
- Yuri Tani Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Ana Maria Pérez O’Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tad Stewart Sonstegard
- Bovine Functional Genomics Laboratory, ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Curtis Paul Van Tassell
- Bovine Functional Genomics Laboratory, ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Adriana Santana do Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
- * E-mail: (JS); (JFG)
| | - José Fernando Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
- * E-mail: (JS); (JFG)
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A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content. BMC Genomics 2012; 13:704. [PMID: 23241142 PMCID: PMC3557156 DOI: 10.1186/1471-2164-13-704] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/10/2012] [Indexed: 01/04/2023] Open
Abstract
Background Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. Results A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. Conclusions We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.
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Decker JE, Vasco DA, McKay SD, McClure MC, Rolf MM, Kim J, Northcutt SL, Bauck S, Woodward BW, Schnabel RD, Taylor JF. A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits. BMC Genomics 2012; 13:606. [PMID: 23140540 PMCID: PMC3532096 DOI: 10.1186/1471-2164-13-606] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection. RESULTS We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCπ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis. CONCLUSIONS We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.
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Affiliation(s)
- Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
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Glick G, Shirak A, Uliel S, Zeron Y, Ezra E, Seroussi E, Ron M, Weller JI. Signatures of contemporary selection in the Israeli Holstein dairy cattle. Anim Genet 2012; 43 Suppl 1:45-55. [DOI: 10.1111/j.1365-2052.2012.02348.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- G. Glick
- The Robert H. Smith Faculty of Agriculture; The Hebrew University of Jerusalem; Rehovot; 76100; Israel
| | - A. Shirak
- Institute of Animal Sciences; ARO; The Volcani Center; Bet Dagan; 50250; Israel
| | - S. Uliel
- Israel Cattle Breeders Association; Caesaria Industrial Park; Caesaria; 38900; Israel
| | - Y. Zeron
- Sion; AI Institute; Shikmim; 79800; Israel
| | - E. Ezra
- Israel Cattle Breeders Association; Caesaria Industrial Park; Caesaria; 38900; Israel
| | - E. Seroussi
- Institute of Animal Sciences; ARO; The Volcani Center; Bet Dagan; 50250; Israel
| | - M. Ron
- Institute of Animal Sciences; ARO; The Volcani Center; Bet Dagan; 50250; Israel
| | - J. I. Weller
- Institute of Animal Sciences; ARO; The Volcani Center; Bet Dagan; 50250; Israel
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Abstract
Maximum likelihood methods for the estimation of linkage disequilibrium between biallelic DNA-markers in half-sib families (half-sib method) are developed for single and multifamily situations. Monte Carlo computer simulations were carried out for a variety of scenarios regarding sire genotypes, linkage disequilibrium, recombination fraction, family size, and number of families. A double heterozygote sire was simulated with recombination fraction of 0.00, linkage disequilibrium among dams of δ=0.10, and alleles at both markers segregating at intermediate frequencies for a family size of 500. The average estimates of δ were 0.17, 0.25, and 0.10 for Excoffier and Slatkin (1995), maternal informative haplotypes, and the half-sib method, respectively. A multifamily EM algorithm was tested at intermediate frequencies by computer simulation. The range of the absolute difference between estimated and simulated δ was between 0.000 and 0.008. A cattle half-sib family was genotyped with the Illumina 50K BeadChip. There were 314,730 SNP pairs for which the sire was a homo-heterozygote with average estimates of r2 of 0.115, 0.067, and 0.111 for half-sib, Excoffier and Slatkin (1995), and maternal informative haplotypes methods, respectively. There were 208,872 SNP pairs for which the sire was double heterozygote with average estimates of r2 across the genome of 0.100, 0.267, and 0.925 for half-sib, Excoffier and Slatkin (1995), and maternal informative haplotypes methods, respectively. Genome analyses for all possible sire genotypes with 829,042 tests showed that ignoring half-sib family structure leads to upward biased estimates of linkage disequilibrium. Published inferences on population structure and evolution of cattle should be revisited after accommodating existing half-sib family structure in the estimation of linkage disequilibrium.
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Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 2012; 13:10. [PMID: 22364287 PMCID: PMC3351017 DOI: 10.1186/1471-2156-13-10] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Accepted: 02/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. RESULTS Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. CONCLUSIONS In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.
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Affiliation(s)
- Mohammad Hossein Moradi
- Department of Animal Science-Excellent centre for improving sheep carcass quality and quantity, University of Tehran, PO Box 3158711167-4111, Karaj, Iran.
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Schwarzenbacher H, Dolezal M, Flisikowski K, Seefried F, Wurmser C, Schlötterer C, Fries R. Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. BMC Genomics 2012; 13:48. [PMID: 22289501 PMCID: PMC3305582 DOI: 10.1186/1471-2164-13-48] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 01/30/2012] [Indexed: 12/29/2022] Open
Abstract
Background Hitchhiking mapping and association studies are two popular approaches to map genotypes to phenotypes. In this study we combine both approaches to complement their specific strengths and weaknesses, resulting in a method with higher statistical power and fewer false positive signals. We applied our approach to dairy cattle as they underwent extremely successful selection for milk production traits and since an excellent phenotypic record is available. We performed whole genome association tests with a new mixed model approach to account for stratification, which we validated via Monte Carlo simulations. Selection signatures were inferred with the integrated haplotype score and a locus specific permutation based integrated haplotype score that works with a folded frequency spectrum and provides a formal test of signifance to identify selection signatures. Results About 1,600 out of 34,851 SNPs showed signatures of selection and the locus specific permutation based integrated haplotype score showed overall good accordance with the whole genome association study. Each approach provides distinct information about the genomic regions that influence complex traits. Combining whole genome association with hitchhiking mapping yielded two significant loci for the trait protein yield. These regions agree well with previous results from other selection signature scans and whole genome association studies in cattle. Conclusion We show that the combination of whole genome association and selection signature mapping based on the same SNPs increases the power to detect loci influencing complex traits. The locus specific permutation based integrated haplotype score provides a formal test of significance in selection signature mapping. Importantly it does not rely on knowledge of ancestral and derived allele states.
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Affiliation(s)
- Hermann Schwarzenbacher
- Lehrstuhl für Tierzucht, Technische Universität München, Hochfeldweg 1, 85376 Freising-Weihenstephan, Germany
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Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, Taberlet P, Nicolazzi EL, Sölkner J, Simianer H, Ciani E, Garcia JF, Bruford MW, Ajmone-Marsan P, Weigend S. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 2012; 43:483-502. [DOI: 10.1111/j.1365-2052.2011.02309.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Affiliation(s)
- J. A. Lenstra
- Faculty of Veterinary Medicine; Utrecht University; Utrecht; The Netherlands
| | - L. F. Groeneveld
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
| | - H. Eding
- Animal Evaluations Unit; CRV; Arnhem; The Netherlands
| | - J. Kantanen
- Biotechnology and Food Research; MTT Agrifood Research Finland; FI-31600; Jokioinen; Finland
| | - J. L. Williams
- Parco Tecnologico Padano; via Einstein; 2600; Lodi; Italy
| | - P. Taberlet
- Laboratoire d'Ecologie Alpine; Université Joseph Fourier; BP 53; Grenoble; France
| | - E. L. Nicolazzi
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - J. Sölkner
- Department of Sustainable Agricultural Systems; Animal Breeding Group; BOKU - University of Natural Resources and Life Sciences; Vienna; Austria
| | - H. Simianer
- Department of Animal Sciences; Animal Breeding and Genetics Group; Georg-August-University Göttingen; 37075; Göttingen; Germany
| | - E. Ciani
- Department of General and Environmental Physiology; University of Bari “Aldo Moro”; Bari; Italy
| | - J. F. Garcia
- Universidade Estadual Paulista; Araçatuba; Brazil
| | - M. W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff; UK
| | - P. Ajmone-Marsan
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
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Wiener P, Wilkinson S. Deciphering the genetic basis of animal domestication. Proc Biol Sci 2011; 278:3161-70. [PMID: 21885467 DOI: 10.1098/rspb.2011.1376] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Genomic technologies for livestock and companion animal species have revolutionized the study of animal domestication, allowing an increasingly detailed description of the genetic changes accompanying domestication and breed development. This review describes important recent results derived from the application of population and quantitative genetic approaches to the study of genetic changes in the major domesticated species. These include findings of regions of the genome that show between-breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the genetics of behavioural traits and the implications for domestication. Despite the operation of severe bottlenecks, high levels of inbreeding and intensive selection during the history of domestication, most domestic animal species are genetically diverse. Possible explanations for this phenomenon are discussed. The major insights from the surveyed studies are highlighted and directions for future study are suggested.
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Affiliation(s)
- Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, Moore S, Thaller G, Simianer H. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 2011; 12:318. [PMID: 21679429 PMCID: PMC3146955 DOI: 10.1186/1471-2164-12-318] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 06/16/2011] [Indexed: 11/12/2022] Open
Abstract
Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation.
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Affiliation(s)
- Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, 37075 Göttingen, Germany.
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Sodeland M, Kent M, Hayes BJ, Grove H, Lien S. Recent and historical recombination in the admixed Norwegian Red cattle breed. BMC Genomics 2011; 12:33. [PMID: 21232164 PMCID: PMC3030550 DOI: 10.1186/1471-2164-12-33] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 01/14/2011] [Indexed: 11/30/2022] Open
Abstract
Background Comparison of recent patterns of recombination derived from linkage maps to historical patterns of recombination from linkage disequilibrium (LD) could help identify genomic regions affected by strong artificial selection, appearing as reduced recent recombination. Norwegian Red cattle (NRF) make an interesting case study for investigating these patterns as it is an admixed breed with an extensively recorded pedigree. NRF have been under strong artificial selection for traits such as milk and meat production, fertility and health. While measures of LD is also crucial for determining the number of markers required for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies. Results A dataset containing more than 17,000 genome-wide distributed SNPs and 2600 animals was used to assess recombination rates and LD in NRF. Although low LD measured by r2 was observed in NRF relative to some of the breeds from which this breed originates, reports from breeds other than those assessed in this study have described more rapid decline in r2 at short distances than what was found in NRF. Rate of decline in r2 for NRF suggested that to obtain an expected r2 between markers and a causal polymorphism of at least 0.5 for genome-wide association studies, approximately one SNP every 15 kb or a total of 200,000 SNPs would be required. For well known quantitative trait loci (QTLs) for milk production traits on Bos Taurus chromosomes 1, 6 and 20, map length based on historic recombination was greater than map length based on recent recombination in NRF. Further, positions for 130 previously unpositioned contigs from assembly of the bovine genome sequence (Btau_4.0) found using comparative sequence analysis were validated by linkage analysis, and 28% of these positions corresponded to extreme values of population recombination rate. Conclusion While LD is reduced in NRF compared to some of the breeds from which this admixed breed originated, it is elevated over short distances compared to some other cattle breeds. Genomic regions in NRF where map length based on historic recombination was greater than map length based on recent recombination coincided with some well known QTL regions for milk production traits. Linkage analysis in combination with comparative sequence analysis and detection of regions with extreme values of population recombination rate proved to be valuable for detecting problematic regions in the Btau_4.0 genome assembly.
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Affiliation(s)
- Marte Sodeland
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, N-1432 Aas, Norway.
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Erbe M, Ytournel F, Pimentel E, Sharifi A, Simianer H. Power and robustness of three whole genome association mapping approaches in selected populations. J Anim Breed Genet 2010; 128:3-14. [DOI: 10.1111/j.1439-0388.2010.00885.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals. The validity of this approach was confirmed by obtaining extremely large CLLs at the sites of causative variation for polled (BTA1) and black-coat-color (BTA18) phenotypes. Across the 30 bovine chromosomes, 699 putative selection signatures were detected. The largest CLL was on BTA6 and corresponded to KIT, which is responsible for the piebald phenotype present in four of the five dairy breeds. Potassium channel-related genes were at the site of the largest CLL on three chromosomes (BTA14, -16, and -25) whereas integrins (BTA18 and -19) and serine/arginine rich splicing factors (BTA20 and -23) each had the largest CLL on two chromosomes. On the basis of the results of this study, the application of population genomics to farm animals seems quite promising. Comparisons between breed groups have the potential to identify genomic regions influencing complex traits with no need for complex equipment and the collection of extensive phenotypic records and can contribute to the identification of candidate genes and to the understanding of the biological mechanisms controlling complex traits.
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Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H. A genome-wide scan for signatures of recent selection in Holstein cattle. Anim Genet 2010; 41:377-89. [PMID: 20096028 DOI: 10.1111/j.1365-2052.2009.02016.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.
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Affiliation(s)
- S Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, 37075 Göttingen, Germany.
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Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H. The pattern of linkage disequilibrium in German Holstein cattle. Anim Genet 2010; 41:346-56. [PMID: 20055813 DOI: 10.1111/j.1365-2052.2009.02011.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r(2) statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r(2) = 0.30 +/- 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r(2) > or = 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < or =100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r(2). It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to approximately 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.
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Affiliation(s)
- S Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, 37075 Göttingen, Germany.
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