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Zhang L, Duan Y, Zhao S, Xu N, Zhao Y. Caprine and Ovine Genomic Selection-Progress and Application. Animals (Basel) 2024; 14:2659. [PMID: 39335248 PMCID: PMC11428554 DOI: 10.3390/ani14182659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/28/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.
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Affiliation(s)
| | | | | | - Naiyi Xu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China; (L.Z.); (Y.D.); (S.Z.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China; (L.Z.); (Y.D.); (S.Z.)
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2
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Freitas LA, Savegnago RP, Alves AAC, Stafuzza NB, Pedrosa VB, Rocha RA, Rosa GJM, Paz CCP. Genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep using parametric models and artificial neural networks. Res Vet Sci 2024; 166:105099. [PMID: 38091815 DOI: 10.1016/j.rvsc.2023.105099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 01/01/2024]
Abstract
This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inês sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genotyped animals was 551 (PCV), 548 (FEC), and 565 (FAM), and 41,676 SNP. The average prediction accuracy (ACC) calculated by Pearson correlation between observed and predicted values and mean squared errors (MSE) were obtained using genomic best unbiased linear predictor (GBLUP), BayesA, BayesB, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayesian regularized artificial neural network (three and four hidden neurons, BRANN_3 and BRANN_4, respectively) in a 5-fold cross-validation technique. The average ACC varied from moderate to high according to the trait and models, ranging between 0.418 and 0.546 (PCV), between 0.646 and 0.793 (FEC), and between 0.414 and 0.519 (FAM). Parametric models presented nearly the same ACC and MSE for the studied traits and provided better accuracies than BRANN. The GBLUP, BayesA, BayesB and BLASSO models provided better accuracies than the BRANN_3 method, increasing by around 23% for PCV, and 18.5% for FEC. In conclusion, parametric models are suitable for genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep. Due to the small differences in accuracy found between them, the use of the GBLUP model is recommended due to its lower computational costs.
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Affiliation(s)
- L A Freitas
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo 14049-900, Brazil; University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - R P Savegnago
- Michigan State University, Department of Animal Science, MI 48864, USA.
| | - A A C Alves
- University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - N B Stafuzza
- Sustainable Livestock Research Center, Animal Science Institute, São José do Rio Preto, São Paulo 15130-000, Brazil
| | - V B Pedrosa
- State University of Ponta Grossa, Ponta Grossa, Paraná 84030-900, Brazil.
| | - R A Rocha
- State University of Ponta Grossa, Ponta Grossa, Paraná 84030-900, Brazil.
| | - G J M Rosa
- University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - C C P Paz
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo 14049-900, Brazil; Sustainable Livestock Research Center, Animal Science Institute, São José do Rio Preto, São Paulo 15130-000, Brazil.
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3
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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4
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Hayes BJ, Copley J, Dodd E, Ross EM, Speight S, Fordyce G. Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available. Genet Sel Evol 2023; 55:71. [PMID: 37845626 PMCID: PMC10578004 DOI: 10.1186/s12711-023-00847-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used in the reference population for these genomic evaluations, this could allow for very large reference populations. In tropical beef systems, such animals often have no pedigree information. Here we investigate potential models for such data, using marker heterozygosity (to model heterosis) and breed composition derived from genetic markers, as covariates in the model. Models treated breed effects as either fixed or random, and included genomic best linear unbiased prediction (GBLUP) and BayesR. A tropically-adapted beef cattle dataset of 29,391 purebred, crossbred and composite commercial animals was used to evaluate the models. RESULTS Treating breed effects as random, in an approach analogous to genetic groups allowed partitioning of the genetic variance into within-breed and across breed-components (even with a large number of breeds), and estimation of within-breed and across-breed genomic estimated breeding values (GEBV). We demonstrate that moderately-accurate (0.30-0.43) GEBV can be calculated using these models. Treating breed effects as random gave more accurate GEBV than treating breed as fixed. A simple GBLUP model where no breed effects were fitted gave the same accuracy (and correlations of GEBV very close to 1) as a model where GEBV for within-breed and the GEBV for (random) across-breed effects were included. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy, with 3% accuracy improvement averaged across traits, especially when the validation population was less related to the reference population. Estimates of heterosis from our models were in line with previous estimates from beef cattle. A method for estimating the number of effective breed comparisons for each breed combination accumulated across contemporary groups is presented. CONCLUSIONS When no pedigree is available, breed composition and heterosis for inclusion in multi-breed genomic evaluation can be estimated from genotypes. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy.
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Affiliation(s)
- Ben J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia.
| | - James Copley
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia
| | - Elsie Dodd
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia
| | - Shannon Speight
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia
- BlackBox Co, Mareeba, QLD, 4880, Australia
| | - Geoffry Fordyce
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4067, Australia
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5
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Wu H, Ma W, Yan L, Liu F, Xu S, Ji P, Gao S, Zhang L, Liu G. Investigation of SNP markers for the melatonin production trait in the Hu sheep with bulked segregant analysis. BMC Genomics 2023; 24:502. [PMID: 37648999 PMCID: PMC10466869 DOI: 10.1186/s12864-023-09494-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/29/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND As an important reproductive hormone, melatonin plays an important role in regulating the reproductive activities of sheep and other mammals. Hu sheep is a breed favoring for meat, with prolific traits. In order to explore the relationship between melatonin and reproductive function of Hu sheep, 7,694,759 SNPs were screened out through the whole genome sequencing analysis from high and low melatonin production Hu sheep. RESULTS A total of 68,673 SNPs, involving in 1126 genes, were identified by ED association analysis. Correlation analysis of SNPs of AANAT/ASMT gene and MTNR1A/MTNR1B gene were carried out. The melatonin level of CG genotype 7,981,372 of AANAT, GA genotype 7,981,866 of ASMT and GG genotype 17,355,171 of MTNR1A were higher than the average melatonin level of 1.64 ng/mL. High melatonin Hu sheep appear to have better multiple reproductive performance. CONCLUSIONS By using different methods, three SNPs which are associated with high melatonin production trait have been identified in Hu sheep. These 3 SNPs are located in melatonin synthetase AANAT/ASMT and receptor MTNR1A, respectively. Considering the positive association between melatonin production and reproductive performance in ruminants, these three SNPs can be served as the potential molecular markers for breading Hu sheep with the desirable reproductive traits.
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Affiliation(s)
- Hao Wu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Wenkui Ma
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Laiqing Yan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Fenze Liu
- Inner Mongolia Golden Grassland Ecological Technology Group Co., LTD., Bayannaoer, 015000, China
| | - Shang Xu
- Inner Mongolia Golden Grassland Ecological Technology Group Co., LTD., Bayannaoer, 015000, China
| | - Pengyun Ji
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Shuai Gao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Lu Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Guoshi Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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Krivoruchko A, Likhovid A, Kanibolotskaya A, Saprikina T, Safaryan E, Yatsyk O. Genome-Wide Search for Associations with Meat Production Parameters in Karachaevsky Sheep Breed Using the Illumina BeadChip 600 K. Genes (Basel) 2023; 14:1288. [PMID: 37372468 DOI: 10.3390/genes14061288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
In a group of Karachaevsky rams, a genome-wide associations analysis of single nucleotide polymorphisms (SNPs) with live parameters of meat production was performed. We used for genotyping the Ovine Infinium HD BeadChip 600 K, which consists of points to detection of 606,000 polymorphisms. A total of 12 SNPs was found to be significantly associated with live meat quality parameters of the corpus and legs and ultrasonic traits. In this case, 11 candidate genes were described, the polymorphic variants of which can change in sheep body parameters. We found SNPs in the exons, introns, and other regions of some genes and transcripts: CLVS1, EVC2, KIF13B, ENSOART00000000511.1, KCNH5, NEDD4, LUZP2, MREG, KRT20, KRT23 and FZD6. The described genes involved in the metabolic pathways of cell differentiation, proliferation and apoptosis are connected with the regulation of the gastrointestinal, immune and nervous systems. In known productivity genes (MSTN, MEF2B, FABP4, etc.), loci were not found to be a significant presence of influence on the meat productivity of the Karachaevsky sheep phenotypes. Our study confirms the possible involvement of the identified candidate genes in the formation of the phenotypes of productivity traits in sheep and indicates the need for new research into candidate genes structure in point to detect their polymorphisms.
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Affiliation(s)
- Alexander Krivoruchko
- Federal Seфey Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Centre, 356241 Mikhailovsk, Russia
- Department of Genetic and Selection, FSAEIHE, North-Caucasus Federal University, 355017 Stavropol, Russia
| | - Andrey Likhovid
- Department of Genetic and Selection, FSAEIHE, North-Caucasus Federal University, 355017 Stavropol, Russia
| | - Anastasiya Kanibolotskaya
- Federal Seфey Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Centre, 356241 Mikhailovsk, Russia
| | - Tatiana Saprikina
- Federal Seфey Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Centre, 356241 Mikhailovsk, Russia
| | - Elena Safaryan
- Federal Seфey Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Centre, 356241 Mikhailovsk, Russia
| | - Olesya Yatsyk
- Federal Seфey Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Centre, 356241 Mikhailovsk, Russia
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7
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Vahedi SM, Salek Ardetani S, Brito LF, Karimi K, Pahlavan Afshari K, Banabazi MH. Expanding the application of haplotype-based genomic predictions to the wild: A case of antibody response against Teladorsagia circumcincta in Soay sheep. BMC Genomics 2023; 24:335. [PMID: 37330501 PMCID: PMC10276919 DOI: 10.1186/s12864-023-09407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/24/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Genomic prediction of breeding values (GP) has been adopted in evolutionary genomic studies to uncover microevolutionary processes of wild populations or improve captive breeding strategies. While recent evolutionary studies applied GP with individual single nucleotide polymorphism (SNP), haplotype-based GP could outperform individual SNP predictions through better capturing the linkage disequilibrium (LD) between the SNP and quantitative trait loci (QTL). This study aimed to evaluate the accuracy and bias of haplotype-based GP of immunoglobulin (Ig) A (IgA), IgE, and IgG against Teladorsagia circumcincta in lambs of an unmanaged sheep population (Soay breed) based on Genomic Best Linear Unbiased Prediction (GBLUP) and five Bayesian [BayesA, BayesB, BayesCπ, Bayesian Lasso (BayesL), and BayesR] methods. RESULTS The accuracy and bias of GPs using SNP, haplotypic pseudo-SNP from blocks with different LD thresholds (0.15, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, and 1.00), or the combinations of pseudo-SNPs and non-LD clustered SNPs were obtained. Across methods and marker sets, higher ranges of genomic estimated breeding values (GEBV) accuracies were observed for IgA (0.20 to 0.49), followed by IgE (0.08 to 0.20) and IgG (0.05 to 0.14). Considering the methods evaluated, up to 8% gains in GP accuracy of IgG were achieved using pseudo-SNPs compared to SNPs. Up to 3% gain in GP accuracy for IgA was also obtained using the combinations of the pseudo-SNPs with non-clustered SNPs in comparison to fitting individual SNP. No improvement in GP accuracy of IgE was observed using haplotypic pseudo-SNPs or their combination with non-clustered SNPs compared to individual SNP. Bayesian methods outperformed GBLUP for all traits. Most scenarios yielded lower accuracies for all traits with an increased LD threshold. GP models using haplotypic pseudo-SNPs predicted less-biased GEBVs mainly for IgG. For this trait, lower bias was observed with higher LD thresholds, whereas no distinct trend was observed for other traits with changes in LD. CONCLUSIONS Haplotype information improves GP performance of anti-helminthic antibody traits of IgA and IgG compared to fitting individual SNP. The observed gains in the predictive performances indicate that haplotype-based methods could benefit GP of some traits in wild animal populations.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Karim Karimi
- Molecular Diagnostics Program, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Kian Pahlavan Afshari
- Department of Animal Sciences, Islamic Azad University, Varamin, Varamin-Pishva Branch3381774895, Iran
| | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden.
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj, 3146618361, Iran.
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8
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Johnson PL, McEwan JC, Hickey SM, Dodds KG, Hitchman S, Agnew MP, Bain WE, Newman SAN, Pickering NK, Craigie CR, Clarke SM. Potential of in-plant intramuscular fat predictions to enable sheep breeders to incorporate consumer preferences in breeding programmes. Meat Sci 2023; 199:109140. [PMID: 36822055 DOI: 10.1016/j.meatsci.2023.109140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
The inclusion of eating quality traits in sheep genetic improvement programmes is desirable. Intramuscular fat (IMF) plays a key role in ensuring consumer satisfaction when eating lamb, but genetic progress for IMF is constrained by a lack of routine data collection. This study investigated the potential for IMF predictor traits to substitute for measured IMF in genetic improvement programmes. Carcass and predicted IMF (near-infrared estimated IMF and marbling score) data were available on 10,113 New Zealand lambs, 1678 of which also had measured chemical IMF on a slice of M. longissimus lumborum on which the predictions of IMF had been made. Genetic antagonisms were observed between carcass lean traits and IMF. The genetic correlation between the predictors and measured IMF approached one, indicating that predictors of IMF can be used in genetic improvement programmes. Through using selection indexes, simultaneous increases in IMF and the existing terminal selection index are possible, provided all traits are measured. This study highlights the importance and potential of predicted IMF to achieve genetic improvement in traits of importance to consumers.
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Affiliation(s)
- P L Johnson
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand.
| | - J C McEwan
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand
| | - S M Hickey
- AgResearch Ruakura Research Centre, 10 Bisley Road, Hamilton 3214, New Zealand
| | - K G Dodds
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand
| | - S Hitchman
- AgResearch Grasslands, Palmerston North, 4410, New Zealand
| | - M P Agnew
- AgResearch Grasslands, Palmerston North, 4410, New Zealand
| | - W E Bain
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand
| | - S-A N Newman
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand
| | | | - C R Craigie
- AgResearch Lincoln, Springs Road, New Zealand
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Private Bag 50-034, Mosgiel 9053, New Zealand
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9
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Haslin E, Pettigrew EJ, Hickson RE, Kenyon PR, Gedye KR, Lopez-Villalobos N, Jayawardana JMDR, Morris ST, Blair HT. Genome-Wide Association Studies of Live Weight at First Breeding at Eight Months of Age and Pregnancy Status of Ewe Lambs. Genes (Basel) 2023; 14:genes14040805. [PMID: 37107563 PMCID: PMC10137859 DOI: 10.3390/genes14040805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
This study estimated genetic parameters and identified candidate genes associated with live weight, and the occurrence of pregnancy in 1327 Romney ewe lambs using genome-wide association studies. Phenotypic traits considered were the occurrence of pregnancy in ewe lambs and live weight at eight months of age. Genetic parameters were estimated, and genomic variation was assessed using 13,500 single-nucleotide polymorphic markers (SNPs). Ewe lamb live weight had medium genomic heritability and was positively genetically correlated with occurrence of pregnancy. This suggests that selection for heavier ewe lambs is possible and would likely improve the occurrence of pregnancy in ewe lambs. No SNPs were associated with the occurrence of pregnancy; however, three candidate genes were associated with ewe lamb live weight. Tenascin C (TNC), TNF superfamily member 8 (TNFSF8) and Collagen type XXVIII alpha 1 chain (COL28A1) are involved in extracellular matrix organization and regulation of cell fate in the immune system. TNC may be involved in ewe lamb growth, and therefore, could be of interest for selection of ewe lamb replacements. The association between ewe lamb live weight and TNFSF8 and COL28A1 is unclear. Further research is needed using a larger population to determine whether the genes identified can be used for genomic selection of replacement ewe lambs.
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Affiliation(s)
- Emmanuelle Haslin
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
- Correspondence:
| | | | | | - Paul R. Kenyon
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
| | - Kristene R. Gedye
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand;
| | - Nicolas Lopez-Villalobos
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
| | - J. M. D. R. Jayawardana
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Stephen T. Morris
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
| | - Hugh T. Blair
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (P.R.K.); (N.L.-V.); (J.M.D.R.J.); (S.T.M.); (H.T.B.)
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10
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Kravitz A, Tyler R, Manohar BM, Ronald BSM, Collins MT, Sriranganathan N. Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis. Vet Res Commun 2023; 47:131-139. [PMID: 35618986 PMCID: PMC9873697 DOI: 10.1007/s11259-022-09937-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
Abstract
Archived formalin fixed paraffin-embedded (FFPE) tissues are powerful tools in medicine, capable of harboring diagnostic and genetic answers to challenging clinical questions. Successful utilization of DNA derived from FFPE samples is dependent upon repairing DNA damage generated from the fixation process. Methods to repair FFPE DNA have been successful in human medicine for a variety of research and clinical applications, yet remain underutilized in veterinary medicine. Despite the available technology, our study is the first to evaluate the repair of FFPE derived DNA from veterinary species for single-nucleotide polymorphism (SNP) analysis using the Illumina OvineSNP50 BeadChip and Illumina FFPE QC and DNA Restore kit. To accomplish this, 48 ovine FFPE samples were run using the Illumina OvineSNP50 BeadChip with and without restoration. Compared to pre-restore data, we found increased sample call rates, SNP call frequency, and assay metrics for all samples post-restoration. Further, we utilized four sheep with available parallel fresh DNA and FFPE DNA to compare assay metrics and genotype calls between the two starting sample types. Although fresh samples generated increased call rates, we found 99% concordance in allele calls between restored FFPE and fresh DNA for all four samples. Our results indicate successful restoration and genotyping of ovine FFPE samples using this technology, with potential for utilization in other veterinary species.
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Affiliation(s)
- Amanda Kravitz
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Ron Tyler
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - B. Murali Manohar
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - B. Samuel Masilamoni Ronald
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - Michael T. Collins
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI USA
| | - Nammalwar Sriranganathan
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
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11
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Karimi K, Do DN, Wang J, Easley J, Borzouie S, Sargolzaei M, Plastow G, Wang Z, Miar Y. A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison). Commun Biol 2022; 5:1381. [PMID: 36526733 PMCID: PMC9757699 DOI: 10.1038/s42003-022-04341-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.
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Affiliation(s)
- Karim Karimi
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Duy Ngoc Do
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Jingy Wang
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - John Easley
- Joint Mink Research Committee, Fur Commission USA, Preston, ID USA ,Mink Veterinary Consulting and Research Service, Plymouth, WI USA
| | - Shima Borzouie
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Mehdi Sargolzaei
- grid.34429.380000 0004 1936 8198Department of Pathobiology, University of Guelph, Guelph, ON Canada ,Select Sires Inc., Plain City, OH USA
| | - Graham Plastow
- grid.17089.370000 0001 2190 316XLivestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Zhiquan Wang
- grid.17089.370000 0001 2190 316XLivestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Younes Miar
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
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12
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Ashraf B, Hunter DC, Bérénos C, Ellis PA, Johnston SE, Pilkington JG, Pemberton JM, Slate J. Genomic prediction in the wild: A case study in Soay sheep. Mol Ecol 2022; 31:6541-6555. [PMID: 34719074 DOI: 10.1111/mec.16262] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
Genomic prediction, the technique whereby an individual's genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30 year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.
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Affiliation(s)
- Bilal Ashraf
- School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Anthropology, Durham University, Durham, UK
| | - Darren C Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK.,School of Biology, University of St Andrews, St Andrews, UK
| | - Camillo Bérénos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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13
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A Genome-Wide Search for Candidate Genes of Meat Production in Jalgin Merino Considering Known Productivity Genes. Genes (Basel) 2022; 13:genes13081337. [PMID: 35893074 PMCID: PMC9331477 DOI: 10.3390/genes13081337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
In a group of Jalgin merino rams with no significant influence on the dispersion of the phenotypes of known productivity genes (MSTN, MEF2B, FABP4, etc.), a genome-wide search for associations of individual polymorphisms with intravital indicators of meat productivity was performed. Using the Ovine Infinium HD BeadChip 600K, 606,000 genome loci were evaluated. Twenty-three substitutions were found to be significantly associated with external measurements of the body and ultrasonic parameters. This made it possible to describe 14 candidate genes, the structural features of which can cause changes in animal phenotypes. No closely spaced genes were found for two substitutions. The identified polymorphisms were found in the exons, introns, and adjacent regions of the following genes and transcripts: CDCA2, ENSOARG00000014477, C4BPA, RIPOR2, ENSOARG00000007198, ENSOARG00000026965 (LincRNA), ENSOARG00000026436 (LincRNA), ENSOARG00000026782 (LincRNA), TENM3, RTL8A, MOSPD1, RTL8С, RIMS2, and P4HA3. The detected genes affect the metabolic pathways of cell differentiation and proliferation and are associated with the regulation of the immune system. This confirms their possible participation in the formation of the phenotypes of productivity parameters in animals and indicates the need for further study of the structure of candidate genes in order to identify their internal polymorphisms.
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14
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Association Analysis between Genetic Variants of elovl5a and elovl5b and Poly-Unsaturated Fatty Acids in Common Carp (Cyprinus carpio). BIOLOGY 2022; 11:biology11030466. [PMID: 35336839 PMCID: PMC8945013 DOI: 10.3390/biology11030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 01/14/2023]
Abstract
Simple Summary PUFAs have an essential impact on human health, but their availability constitutes a critical bottleneck in food production. Although fish is the traditional source of PUFAs, it is limited by the stagnation of fisheries. Many studies aim to increase the PUFA products of fish. Genetic markers are efficient in aquaculture breeding. Fatty acid desaturase 2 (fads2) and elongase 5 (elovl5) are the rate-limiting enzymes in the synthesis of PUFAs. The allo-tetraploid common carp is able to biosynthesize endogenous PUFAs. However, selective breeding common carp with high PUFA contents was hindered due to a lack of effective molecular markers. For future breeding common carp capable of producing endogenous PUFAs more effectively, we previously identified the polymorphisms in the coding regions of two duplicated fads2, fads2a and fads2b. However, the polymorphisms in the duplicated elovl5, elovl5a and elovl5b, were not detected. This study screened the genetic variants in the coding regions of elovl5a and elovl5b. Moreover, the joint effects of multiple coding SNPs in fads2b and elovl5b, two major genes regulating the PUFA biosynthesis, were evidenced with the increased explained percentages of the PUFA contents. These polymorphisms in these two genes were used to evaluate the breeding values of PUFAs. These SNPs would be potential markers for future selection to improve the PUFA contents in common carp. Abstract The allo-tetraploid common carp, one widely cultured food fish, is able to produce poly-unsaturated fatty acids (PUFAs). The genetic markers on the PUFA contents for breeding was limited. The polymorphisms in elovl5a and elovl5b, the rate-limiting enzymes in the PUFA biosynthesis, have not been investigated yet. Herein, we identified one coding SNP (cSNP) in elovl5a associated with the content of one PUFA and two cSNPs in elovl5b with the contents of eight PUFAs. The heterozygous genotypes in these three loci were associated with higher contents than the homozygotes. Together with previously identified two associated cSNPs in fads2b, we found the joint effect of these four cSNPs in fads2b and elovl5b on the PUFA contents with the increased explained percentages of PUFA contents. The genotype combinations of more heterozygotes were associated with higher PUFA contents than the other combinations. Using ten genomic selection programs with all cSNPs in fads2b and elovl5b, we obtained the high and positive correlations between the phenotypes and the estimated breeding values of eight PUFAs. These results suggested that elovl5b might be the major gene corresponding to common carp PUFA contents compared with elovl5a. The cSNP combinations in fads2b and elovl5b and the optimal genomic selection program will be used in the future selection breeding to improve the PUFA contents of common carp.
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15
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Massender E, Brito LF, Maignel L, Oliveira HR, Jafarikia M, Baes CF, Sullivan B, Schenkel FS. Single-step genomic evaluation of milk production traits in Canadian Alpine and Saanen dairy goats. J Dairy Sci 2022; 105:2393-2407. [PMID: 34998569 DOI: 10.3168/jds.2021-20558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022]
Abstract
Genomic evaluations are routine in most plant and livestock breeding programs but are used infrequently in dairy goat breeding schemes. In this context, the purpose of this study was to investigate the use of the single-step genomic BLUP method for predicting genomic breeding values for milk production traits (milk, protein, and fat yields; protein and fat percentages) in Canadian Alpine and Saanen dairy goats. There were 6,409 and 12,236 Alpine records and 3,434 and 5,008 Saanen records for each trait in first and later lactations, respectively, and a total of 1,707 genotyped animals (833 Alpine and 874 Saanen). Two validation approaches were used, forward validation (i.e., animals born after 2013 with an average estimated breeding value accuracy from the full data set ≥0.50) and forward cross-validation (i.e., subsets of all animals included in the forward validation were used in successive replications). The forward cross-validation approach resulted in similar validation accuracies (0.55 to 0.66 versus 0.54 to 0.61) and biases (-0.01 to -0.07 versus -0.03 to 0.11) to the forward validation when averaged across traits. Additionally, both single and multiple-breed analyses were compared, and similar average accuracies and biases were observed across traits. However, there was a small gain in accuracy from the use of multiple-breed models for the Saanen breed. A small gain in validation accuracy for genomically enhanced estimated breeding values (GEBV) relative to pedigree-based estimated breeding values (EBV) was observed across traits for the Alpine breed, but not for the Saanen breed, possibly due to limitations in the validation design, heritability of the traits evaluated, and size of the training populations. Trait-specific gains in theoretical accuracy of GEBV relative to EBV for the validation animals ranged from 17 to 31% in Alpine and 35 to 55% in Saanen, using the cross-validation approach. The GEBV predicted from the full data set were 12 to 16% more accurate than EBV for genotyped animals, but no gains were observed for nongenotyped animals. The largest gains were found for does without lactation records (35-41%) and bucks without daughter records (46-54%), and consequently, the implementation of genomic selection in the Canadian dairy goat population would be expected to increase selection accuracy for young breeding candidates. Overall, this study represents the first step toward implementation of genomic selection in Canadian dairy goat populations.
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Affiliation(s)
- Erin Massender
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1.
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Laurence Maignel
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, Canada, K1A 0C6
| | - Hinayah R Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1; Canadian Centre for Swine Improvement Inc., Ottawa, ON, Canada, K1A 0C6
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Brian Sullivan
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, Canada, K1A 0C6
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1
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16
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Araujo AC, Carneiro PLS, Oliveira HR, Schenkel FS, Veroneze R, Lourenco DAL, Brito LF. A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study. Front Genet 2021; 12:729867. [PMID: 34721524 PMCID: PMC8551834 DOI: 10.3389/fgene.2021.729867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), leading to lower predictive ability of genomic breeding values (GEBVs) in high genetically diverse populations. Haplotype-based predictions could outperform individual SNP predictions by better capturing the LD between SNP and QTL. Therefore, we aimed to evaluate the accuracy and bias of individual-SNP- and haplotype-based genomic predictions under the single-step-genomic best linear unbiased prediction (ssGBLUP) approach in genetically diverse populations. We simulated purebred and composite sheep populations using literature parameters for moderate and low heritability traits. The haplotypes were created based on LD thresholds of 0.1, 0.3, and 0.6. Pseudo-SNPs from unique haplotype alleles were used to create the genomic relationship matrix ( G ) in the ssGBLUP analyses. Alternative scenarios were compared in which the pseudo-SNPs were combined with non-LD clustered SNPs, only pseudo-SNPs, or haplotypes fitted in a second G (two relationship matrices). The GEBV accuracies for the moderate heritability-trait scenarios fitting individual SNPs ranged from 0.41 to 0.55 and with haplotypes from 0.17 to 0.54 in the most (Ne ≅ 450) and less (Ne < 200) genetically diverse populations, respectively, and the bias fitting individual SNPs or haplotypes ranged between -0.14 and -0.08 and from -0.62 to -0.08, respectively. For the low heritability-trait scenarios, the GEBV accuracies fitting individual SNPs ranged from 0.24 to 0.32, and for fitting haplotypes, it ranged from 0.11 to 0.32 in the more (Ne ≅ 250) and less (Ne ≅ 100) genetically diverse populations, respectively, and the bias ranged between -0.36 and -0.32 and from -0.78 to -0.33 fitting individual SNPs or haplotypes, respectively. The lowest accuracies and largest biases were observed fitting only pseudo-SNPs from blocks constructed with an LD threshold of 0.3 (p < 0.05), whereas the best results were obtained using only SNPs or the combination of independent SNPs and pseudo-SNPs in one or two G matrices, in both heritability levels and all populations regardless of the level of genetic diversity. In summary, haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.
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Affiliation(s)
- Andre C Araujo
- Postgraduate Program in Animal Sciences, State University of Southwestern Bahia, Itapetinga, Brazil.,Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Paulo L S Carneiro
- Department of Biology, State University of Southwestern Bahia, Jequié, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Renata Veroneze
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, Brazil
| | - Daniela A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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17
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18
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Oliveira HRD, McEwan JC, Jakobsen JH, Blichfeldt T, Meuwissen THE, Pickering NK, Clarke SM, Brito LF. Across-country genomic predictions in Norwegian and New Zealand Composite sheep populations with similar development history. J Anim Breed Genet 2021; 139:1-12. [PMID: 34418183 DOI: 10.1111/jbg.12642] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/29/2021] [Accepted: 08/06/2021] [Indexed: 01/11/2023]
Abstract
The goal of this study was to assess the feasibility of across-country genomic predictions in Norwegian White Sheep (NWS) and New Zealand Composite (NZC) sheep populations with similar development history. Different training populations were evaluated (i.e., including only NWS or NZC, or combining both populations). Predictions were performed using the actual phenotypes (normalized) and the single-step GBLUP via Bayesian inference. Genotyped NWS animals born in 2016 (N = 267) were used to assess the accuracy and bias of genomic estimated breeding values (GEBVs) predicted for birth weight (BW), weaning weight (WW), carcass weight (CW), EUROP carcass classification (EUC), and EUROP fat grading (EUF). The accuracy and bias of GEBVs differed across traits and training population used. For instance, the GEBV accuracies ranged from 0.13 (BW) to 0.44 (EUC) for GEBVs predicted including only NWS, from 0.06 (BW) to 0.15 (CW) when including only NZC, and from 0.10 (BW) to 0.41 (EUC) when including both NWS and NZC animals in the training population. The regression coefficients used to assess the spread of GEBVs (bias) ranged from 0.26 (BW) to 0.64 (EUF) for only NWS, 0.10 (EUC) to 0.52 (CW) for only NZC, and from 0.42 (WW) to 2.23 (EUC) for both NWS and NZC in the training population. Our findings suggest that across-country genomic predictions based on ssGBLUP might be possible for NWS and NZC, especially for novel traits.
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Affiliation(s)
- Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, ON, Canada
| | - John C McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Jette H Jakobsen
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Thor Blichfeldt
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Shannon M Clarke
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, ON, Canada
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19
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Bitaraf Sani M, Zare Harofte J, Banabazi MH, Esmaeilkhanian S, Shafei Naderi A, Salim N, Teimoori A, Bitaraf A, Zadehrahmani M, Burger PA, Landi V, Silawi M, Taghipour Sheshdeh A, Faghihi MA. Genomic prediction for growth using a low-density SNP panel in dromedary camels. Sci Rep 2021; 11:7675. [PMID: 33828208 PMCID: PMC8027435 DOI: 10.1038/s41598-021-87296-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/26/2021] [Indexed: 11/29/2022] Open
Abstract
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran.
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Saeid Esmaeilkhanian
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education and Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Nader Salim
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Abbas Teimoori
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Ahmad Bitaraf
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | | | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, 1160, Vienna, Austria
| | - Vincenzo Landi
- Departement of Veterinary Medicine, Università Di Bari "Aldo Moro", Bari, Italy
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran
| | | | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran.,Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, 33136, USA
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20
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Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep. Animals (Basel) 2021; 11:ani11010086. [PMID: 33466430 PMCID: PMC7824810 DOI: 10.3390/ani11010086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Parentage misassignments directly affect genetic gain in traditional breeding programs. The use of genetic markers facilitates parentage verification. In sheep, microsatellite markers and single nucleotide polymorphism (SNP) markers have been proposed by the International Society of Animal Sciences (ISAG) for parentage testing. Since the implementation of genomic selection, the microsatellite information used for parental testing in previous generations is gradually being replaced by SNPs. However, parentage verifications should all be performed using the same technology. A strategy for transitioning from microsatellites to SNP markers, while avoiding extra genotyping costs, is the imputation of microsatellite alleles from SNP haplotypes. This study aims to identify the optimum approach, using a minimum number of SNPs to accurately impute microsatellite markers and developing a low-density SNP chip for parentage verification in the Assaf sheep breed. The imputation approach described here reached high accuracies using a low number of SNP markers, which supports the development of a low-density SNP chip that could avoid the problems of genotyping with both technologies, being a cost-effective method for parentage testing. This study will help sheep breeders to perform parentage verification when different genotyping platforms have been used across generations. Abstract Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.
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Teissier M, Larroque H, Brito LF, Rupp R, Schenkel FS, Robert-Granié C. Genomic predictions based on haplotypes fitted as pseudo-SNP for milk production and udder type traits and SCS in French dairy goats. J Dairy Sci 2020; 103:11559-11573. [PMID: 33041034 DOI: 10.3168/jds.2020-18662] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]
Abstract
The development of statistical methods aiming to improve the accuracy of genomic predictions is of utmost value for dairy goat breeding programs. In this context, the use of haplotypes, instead of individual SNP, could improve the accuracy of genomic predictions by better capturing the effect of causal variants, instead of relying solely on linkage disequilibrium with individual SNP. Haplotypes can be included in genomic evaluation models in various ways, such as fitting them as pseudo-SNP (i.e., haplotypes converted into biallelic SNP format). This can be easily incorporated in the software already available for single-step genomic predictions (ssGBLUP). Therefore, the aim of this study was to compare the predictive performances of ssGBLUP and weighted ssGBLUP (WssGBLUP) based on individual SNP or on haplotypes fitted as pseudo-SNP. Performance was compared in terms of accuracy, bias, and weights for SNP versus pseudo-SNP. Genomic predictions were performed on 5 milk production traits, 5 udder type traits, and somatic cell score (SCS). The training population was formed by 307 Alpine and 247 Saanen progeny-tested bucks, genotyped using the Illumina Goat SNP50 BeadChip (Illumina, San Diego, CA). The validation population included 205 Alpine and 146 Saanen young bucks. The accuracy of genomic predictions was evaluated in the validation population as the Pearson correlation between genomic estimated breeding values (GEBV), predicted based on various methods, and daughter deviation (DD) based on the official genetic evaluation of January 2016. Haplotype-based models were shown to improve the performance of genomic predictions for some traits. Gains in accuracy of up to +19% (0.310 to 0.368 for fat yield) in Alpine and up to +3% (0.361 to 0.373 for udder shape) in Saanen were observed with ssGBLUP. The ssGBLUP accuracies averaged across all traits and methods were equal to 0.467 (SNP) versus 0.471 (pseudo-SNP) in Alpine and 0.528 (SNP) versus 0.523 (pseudo-SNP) in Saanen. With WssGBLUP, gains in accuracy of up to 24% (0.298 to 0.370 for fat yield) in Alpine and 14% (0.431 to 0.490 for SCS) in Saanen were observed with WssGBLUP. Accuracies of WssGBLUP averaged across all traits and methods were equal to 0.455 (SNP and pseudo-SNP) in Alpine and 0.542 (SNP) versus 0.528 (pseudo-SNP) in Saanen. The average (±SD) slope of the regression of DD on GEBV for the validation animals, across all breeds, traits and scenarios, were equal to 0.82 ± 0.20 (SNP) and 0.83 ± 0.18 (pseudo-SNP) for ssGBLUP and 0.67 ± 0.16 (SNP) and 0.65 ± 0.16 (pseudo-SNP) for WssGBLUP, which suggest that haplotype-based models and ssGBLUPSNP were similarly biased. However, WssGBLUP was more biased than ssGBLUP, and its gains in accuracies were limited to milk production traits. Despite the fact that genomic predictions based on haplotypes require additional steps and time, the observed gains in GEBV predictive performance indicate that haplotype-based methods could be recommended for some traits.
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Affiliation(s)
- Marc Teissier
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France.
| | - Hélène Larroque
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Ge F, Jia C, Bao P, Wu X, Liang C, Yan P. Accuracies of Genomic Prediction for Growth Traits at Weaning and Yearling Ages in Yak. Animals (Basel) 2020; 10:E1793. [PMID: 33023134 PMCID: PMC7650705 DOI: 10.3390/ani10101793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Genomic selection is a promising breeding strategy that has been used in considerable numbers of breeding projects due to its highly accurate results. Yak are rare mammals that are remarkable because of their ability to survive in the extreme and harsh conditions predominantly at the so-called "roof of the world"-the Qinghai-Tibetan Plateau. In the current study, we conducted an exploration of the feasibility of genomic evaluation and compared the predictive accuracy of early growth traits with five different approaches. In total, four growth traits were measured in 354 yaks, including body weight, withers height, body length, and chest girth in two early stages of development (weaning and yearling). Genotyping was implemented using the Illumina BovineHD BeadChip. The predictive accuracy was calculated through five-fold cross-validation in five classical statistical methods including genomic best linear unbiased prediction (GBLUP) and four Bayesian methods. Body weights at 30 months in the same yak population were also measured to evaluate the prediction at 6 months. The results indicated that the predictive accuracy for the early growth traits of yak ranged from 0.147 to 0.391. Similar performance was found for the GBLUP and Bayesian methods for most growth traits. Among the Bayesian methods, Bayes B outperformed Bayes A in the majority of traits. The average correlation coefficient between the prediction at 6 months using different methods and observations at 30 months was 0.4. These results indicate that genomic prediction is feasible for early growth traits in yak. Considering that genomic selection is necessary in yak breeding projects, the present study provides promising reference for future applications.
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Affiliation(s)
| | | | | | | | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.G.); (C.J.); (P.B.); (X.W.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.G.); (C.J.); (P.B.); (X.W.)
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Ross EM, Hayes BJ, Tucker D, Bond J, Denman SE, Oddy VH. Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries). J Anim Sci 2020; 98:5894828. [PMID: 32815548 DOI: 10.1093/jas/skaa262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
Methane production from rumen methanogenesis contributes approximately 71% of greenhouse gas emissions from the agricultural sector. This study has performed genomic predictions for methane production from 99 sheep across 3 yr using a residual methane phenotype that is log methane yield corrected for live weight, rumen volume, and feed intake. Using genomic relationships, the prediction accuracies (as determined by the correlation between predicted and observed residual methane production) ranged from 0.058 to 0.220 depending on the time point being predicted. The best linear unbiased prediction algorithm was then applied to relationships between animals that were built on the rumen metabolome and microbiome. Prediction accuracies for the metabolome-based relationships for the two available time points were 0.254 and 0.132; the prediction accuracy for the first microbiome time point was 0.142. The second microbiome time point could not successfully predict residual methane production. When the metabolomic relationships were added to the genomic relationships, the accuracy of predictions increased to 0.274 (from 0.201 when only the genomic relationship was used) and 0.158 (from 0.081 when only the genomic relationship was used) for the two time points, respectively. When the microbiome relationships from the first time point were added to the genomic relationships, the maximum prediction accuracy increased to 0.247 (from 0.216 when only the genomic relationship was used), which was achieved by giving the genomic relationships 10 times more weighting than the microbiome relationships. These accuracies were higher than the genomic, metabolomic, and microbiome relationship matrixes achieved alone when identical sets of animals were used.
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Affiliation(s)
- Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Australia
| | - David Tucker
- New South Wales Department of Primary Industries, Livestock Industries Centre, University of New England, Armidale, Australia
| | - Jude Bond
- New South Wales Department of Primary Industries, Livestock Industries Centre, University of New England, Armidale, Australia
| | - Stuart E Denman
- Department of Animal Food and Health Sciences, CSIRO, Brisbane, St Lucia, Australia
| | - Victor Hutton Oddy
- New South Wales Department of Primary Industries, Livestock Industries Centre, University of New England, Armidale, Australia
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24
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Genetic evaluation of tropical climate-adapted sheep for carcass traits including genomic information. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lillehammer M, Sonesson AK, Klemetsdal G, Blichfeldt T, Meuwissen THE. Genomic selection strategies to improve maternal traits in Norwegian White Sheep. J Anim Breed Genet 2020; 137:384-394. [PMID: 32236991 DOI: 10.1111/jbg.12475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 01/16/2023]
Abstract
This study tested and compared different implementation strategies for genomic selection for Norwegian White Sheep, aiming to increase genetic gain for maternal traits. These strategies were evaluated for their genetic gain ingrowth, carcass and maternal traits, total genetic gain, a weighted sum of the gain in each trait and rates of inbreeding through a full-scale stochastic simulation. Results showed genomic selection schemes to increase genetic gain for maternal traits but reduced genetic gain for other traits. This could also be obtained by selecting rams for artificial selection at a higher age. Implementation of genomic selection in the current breeding structure increased genetic gain for maternal traits up to 57%, outcompeted by reducing the generation interval for artificial insemination rams from current 3 to 2 years. Then, total genetic gain for maternal traits increased by 65%-77% and total genetic gain by18%-20%, but at increased rates of inbreeding.
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Affiliation(s)
- Marie Lillehammer
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Anna K Sonesson
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Gunnar Klemetsdal
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Thor Blichfeldt
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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Mortimer SI, Jacob RH, Kearney G, Hopkins DL, Warner RD. Genetic variation in colour stability traits of lamb cuts under two packaging systems. Meat Sci 2019; 157:107870. [PMID: 31252375 DOI: 10.1016/j.meatsci.2019.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 10/26/2022]
Abstract
Data from samples of longissmus lumborum (LL) and semimembranosus (SM) muscles from 391 lamb carcasses, which had been packaged in overwrap (OW) or high oxygen modified atmosphere packaging (MAPO2) systems and then subjected to simulated retail display, were used to estimate genetic variation for colour stability traits of lamb meat as a step in identifying a trait for genetic evaluation. Traits included the ratio of the reflectance of light at wavelengths of 630 nm and 580 nm (oxy/met) measured at a single time point at the end of the display period (day 3 under OW; day 8 under MAPO2) and the predicted time for oxy/met to reach a benchmark value. Under OW and MAPO2, the measures of meat colour stability of the LL tended to be of moderate heritability (0.09-0.29), but for the SM were of low heritability (0-0.10). Improving retail colour stability of lamb loins through selection of genetically superior animals may be better based on measurement of oxy/met.
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Affiliation(s)
- S I Mortimer
- NSW Department of Primary Industries, Trevenna Road, Armidale, NSW 2351, Australia.
| | - R H Jacob
- Department of Primary Industries & Regional Development, Baron Hay Court, South Perth, WA 6151, Australia
| | - G Kearney
- 36 Paynes Road, Hamilton, VIC 3300, Australia
| | - D L Hopkins
- NSW Department of Primary Industries, Centre for Red Meat and Sheep Development, Cowra, NSW 2794, Australia
| | - R D Warner
- The University of Melbourne, Parkville, VIC 3010, Australia
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de Oliveira HR, Brito LF, Sargolzaei M, E Silva FF, Jamrozik J, Lourenco DAL, Schenkel FS. Impact of including information from bulls and their daughters in the training population of multiple-step genomic evaluations in dairy cattle: A simulation study. J Anim Breed Genet 2019; 136:441-452. [PMID: 31161635 DOI: 10.1111/jbg.12407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
The objective of this study was to investigate the impact of accounting for parent average (PA) and genotyped daughters' average (GDA) on the estimation of deregressed estimated breeding values (dEBVs) used as pseudo-phenotypes in multiple-step genomic evaluations. Genomic estimated breeding values (GEBVs) were predicted, in eight different simulated scenarios, using dEBVs calculated based on four methods. These methods included PA and GDA in the dEBV (VR) or only GDA (VRpa) and excluded both PA and GDA from the dEBV with either all information or only information from PA and GDA (JA and NEW, respectively). In general, VR and NEW showed the lowest and highest GEBV reliabilities across scenarios, respectively. Among all deregression methods, VRpa and NEW provided the most consistent bias estimates across the majority of scenarios, and they significantly yielded the least biased GEBVs. Our results indicate that removing PA and GDA information from dEBVs used in multiple-step genomic evaluations can increase the reliability of GEBVs, when both bulls and their daughters are included in the training population.
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Affiliation(s)
- Hinayah Rojas de Oliveira
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Luiz Fernando Brito
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - Mehdi Sargolzaei
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,HiggsGene Solutions Inc., Guelph, Ontario, Canada
| | | | - Janusz Jamrozik
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,Canadian Dairy Network, Guelph, Ontario, Canada
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Gienapp P, Calus MPL, Laine VN, Visser ME. Genomic selection on breeding time in a wild bird population. Evol Lett 2019; 3:142-151. [PMID: 31289689 PMCID: PMC6591552 DOI: 10.1002/evl3.103] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Artificial selection experiments are a powerful tool in evolutionary biology. Selecting individuals based on multimarker genotypes (genomic selection) has several advantages over phenotype-based selection but has, so far, seen very limited use outside animal and plant breeding. Genomic selection depends on the markers tagging the causal loci that underlie the selected trait. Because the number of necessary markers depends, among other factors, on effective population size, genomic selection may be in practice not feasible in wild populations as most wild populations have much higher effective population sizes than domesticated populations. However, the current possibilities of cost-effective high-throughput genotyping could overcome this limitation and thereby make it possible to apply genomic selection also in wild populations. Using a unique dataset of about 2000 wild great tits (Parus major), a small passerine bird, genotyped on a 650 k SNP chip we calculated genomic breeding values for egg-laying date using the so-called GBLUP approach. In this approach, the pedigree-based relatedness matrix of an "animal model," a special form of the mixed model, is replaced by a marker-based relatedness matrix. Using the marker-based relatedness matrix, the model seemed better able to disentangle genetic and permanent environmental effects. We calculated the accuracy of genomic breeding values by correlating them to the phenotypes of individuals whose phenotypes were excluded from the analysis when estimating the genomic breeding values. The obtained accuracy was about 0.20, with very little effect of the used genomic relatedness estimator but a strong effect of the number of SNPs. The obtained accuracy is lower than typically seen in domesticated species but considerable for a trait with low heritability (∼0.2) as avian breeding time. Our results show that genomic selection is possible also in wild populations with potentially many applications, which we discuss here.
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Affiliation(s)
- Phillip Gienapp
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Mario P. L. Calus
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Veronika N. Laine
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
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Karimi K, Sargolzaei M, Plastow GS, Wang Z, Miar Y. Opportunities for genomic selection in American mink: A simulation study. PLoS One 2019; 14:e0213873. [PMID: 30870528 PMCID: PMC6417779 DOI: 10.1371/journal.pone.0213873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/01/2019] [Indexed: 12/25/2022] Open
Abstract
Genomic selection can be considered as an effective tool for developing breeding programs in American mink. However, the genetic gains for economically important traits can be influenced by the accuracy of genomic predictions. The objective of this study was to investigate the prediction accuracies of traditional best linear unbiased prediction (BLUP), multi-step genomic BLUP (GBLUP) and single-step GBLUP (ssGBLUP) methods in American mink using simulated data with different levels of heritability, marker density, training set (TS) sizes and selection designs based on either phenotypic performance or estimated breeding values (EBVs). Under EBV selection design, the accuracy of BLUP predictions was increased by 38% and 44% for h2 = 0.10, 27% and 29% for h2 = 0.20, and 5.8% and 6% for h2 = 0.50 using GBLUP and ssGBLUP methods, respectively. Under phenotypic selection design, the accuracies of prediction by ssGBLUP method were 11.8% and 15.4% higher than those obtained by GBLUP for heritability of 0.10 and 0.20, respectively. However, the efficiency of ssGBLUP and GBLUP was not influenced by selection design at higher level of heritability (h2 = 0.50). Furthermore, higher selection intensity increased the bias of predictions in both pedigree-based and genomic evaluations. Regardless of selection design, TS sizes for GBLUP and ssGBLUP methods should be at least 3000 to achieve more accuracy than using BLUP for heritability of 0.50 and marker density of 10k and 50k. Overall, more accurate predictions were obtained using ssGBLUP method particularly for lowly heritable traits and low density of markers. Our results indicated that TS sizes should be optimized in accordance with heritability level, marker density, selection design and prediction method for genomic selection in American mink. The results provided an initial framework for designing genomic selection in mink breeding programs.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- Select Sires Inc., Plain City, Ohio, United States of America
| | - Graham Stuart Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
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Teissier M, Larroque H, Robert-Granie C. Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits, udder type traits, and somatic cell scores in French dairy goats. J Dairy Sci 2019; 102:3142-3154. [PMID: 30712939 DOI: 10.3168/jds.2018-15650] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/05/2018] [Indexed: 01/17/2023]
Abstract
Genomic evaluation of French dairy goats is routinely conducted using the single-step genomic BLUP (ssGBLUP) method. This method has the advantage of simultaneously using all phenotypes, pedigrees, and genotypes. However, ssGBLUP assumes that all SNP explain the same amount of genetic variance, which is unlikely in the case of traits whose major genes or QTL are segregating. In this study, we investigated the effect of weighted ssGBLUP and its alternatives, which give more weight to SNP associated with the trait, on the accuracy of genomic evaluation of milk production, udder type traits, and somatic cell scores. The data set included 2,955 genotyped animals and 2,543,680 pedigree animals. The number of phenotypes varied with the trait. The accuracy of genomic evaluation was assessed on 205 genotyped Alpine and 146 genotyped Saanen goats born between 2009 and 2012. For traits with unknown QTL, weighted ssGBLUP was less accurate than, or as accurate as, ssGBLUP. For traits with identified QTL (i.e., QTL only present in the Saanen breed), weighted ssGBLUP outperformed ssGBLUP by between 2 and 14%.
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Affiliation(s)
- M Teissier
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France.
| | - H Larroque
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France
| | - C Robert-Granie
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France
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Piccoli ML, Brito LF, Braccini J, Brito FV, Cardoso FF, Cobuci JA, Sargolzaei M, Schenkel FS. A comprehensive comparison between single- and two-step GBLUP methods in a simulated beef cattle population. CANADIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1139/cjas-2017-0176] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The statistical methods used in the genetic evaluations are a key component of the process and can be best compared by using simulated data. The latter is especially true in grazing beef cattle production systems, where the number of proven bulls with highly reliable estimated breeding values is limited to allow for a trustworthy validation of genomic predictions. Therefore, we simulated data for 4980 beef cattle aiming to compare single-step genomic best linear unbiased prediction (ssGBLUP), which simultaneously incorporates pedigree, phenotypic, and genomic data into genomic evaluations, and two-step GBLUP (tsGBLUP) procedures and genomic estimated breeding values (GEBVs) blending methods. The greatest increases in GEBV accuracies compared with the parents’ average estimated breeding values (EBVPA) were 0.364 and 0.341 for ssGBLUP and tsGBLUP, respectively. Direct genomic value and GEBV accuracies when using ssGBLUP and tsGBLUP procedures were similar, except for the GEBV accuracies using Hayes’ blending method in tsGBLUP. There was no significant or slight bias in genomic predictions from ssGBLUP or tsGBLUP (using VanRaden’s blending method), indicating that these predictions are on the same scale compared with the true breeding values. Overall, genetic evaluations including genomic information resulted in gains in accuracy >100% compared with the EBVPA. In addition, there were no significant differences between the selected animals (10% males and 50% females) by using ssGBLUP or tsGBLUP.
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Affiliation(s)
- Mario L. Piccoli
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
- GenSys Consultores Associados S/S, Porto Alegre, RS 90460-060, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Luiz F. Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - José Braccini
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, DF 71605-001, Brazil
| | - Fernanda V. Brito
- GenSys Consultores Associados S/S, Porto Alegre, RS 90460-060, Brazil
| | - Fernando F. Cardoso
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, DF 71605-001, Brazil
- Embrapa Pecuária Sul, Bagé, RS 96401-970, Brazil
| | - Jaime A. Cobuci
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- The Semex Alliance, Guelph, ON N1H 6J2, Canada
| | - Flávio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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Teissier M, Larroque H, Robert-Granié C. Weighted single-step genomic BLUP improves accuracy of genomic breeding values for protein content in French dairy goats: a quantitative trait influenced by a major gene. Genet Sel Evol 2018; 50:31. [PMID: 29907084 PMCID: PMC6003172 DOI: 10.1186/s12711-018-0400-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 05/30/2018] [Indexed: 12/21/2022] Open
Abstract
Background In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain the same fraction of genetic variance. However, ssGBLUP is not suitable for protein content, which is controlled by a major gene, i.e. αs1casein. This gene explains about 40% of the genetic variation in protein content. In this study, we evaluated the accuracy of genomic prediction using different genomic methods to include the effect of the αs1casein gene. Methods Genomic evaluation for protein content was performed with data from the official genetic evaluation on 2955 animals genotyped with the Illumina goat SNP50 BeadChip, 7202 animals genotyped at the αs1casein gene and 6,767,490 phenotyped females. Pedigree-based BLUP was compared with regular unweighted ssGBLUP and with three weighted ssGBLUP methods (WssGBLUP, WssGBLUPMax and WssGBLUPSum), which give weights to SNPs according to their effect on protein content. Two other methods were also used: trait-specific marker-derived relationship matrix (TABLUP) using pre-selected SNPs associated with protein content and gene content based on a multiple-trait genomic model that includes αs1casein genotypes. We estimated accuracies of predicted genomic estimated breeding values (GEBV) in two populations of goats (Alpine and Saanen). Results Accuracies of GEBV with ssGBLUP improved by + 5 to + 7 percent points over accuracies from the pedigree-based BLUP model. With the WssGBLUP methods, SNPs that are located close to the αs1casein gene had the biggest weights and contributed substantially to the capture of signals from quantitative trait loci. Improvement in accuracy of genomic predictions using the three weighted ssGBLUP methods delivered up to + 6 percent points of accuracy over ssGBLUP. A similar accuracy was obtained for ssGBLUP and TABLUP considering the 20,000 most important SNPs. Incorporating information on the αs1casein genotypes based on the gene content method gave similar results as ssGBLUP. Conclusions The three weighted ssGBLUP methods were efficient for detecting SNPs associated with protein content and for a better prediction of genomic breeding values than ssGBLUP. They also combined fast computing, simplicity and required ssGBLUP to be run only twice.
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Affiliation(s)
- Marc Teissier
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France.
| | - Hélène Larroque
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
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Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs. Animal 2018; 12:2235-2245. [PMID: 29706144 DOI: 10.1017/s175173111800085x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The uptake of genomic selection (GS) by the swine industry is still limited by the costs of genotyping. A feasible alternative to overcome this challenge is to genotype animals using an affordable low-density (LD) single nucleotide polymorphism (SNP) chip panel followed by accurate imputation to a high-density panel. Therefore, the main objective of this study was to screen incremental densities of LD panels in order to systematically identify one that balances the tradeoffs among imputation accuracy, prediction accuracy of genomic estimated breeding values (GEBVs), and genotype density (directly associated with genotyping costs). Genotypes using the Illumina Porcine60K BeadChip were available for 1378 Duroc (DU), 2361 Landrace (LA) and 3192 Yorkshire (YO) pigs. In addition, pseudo-phenotypes (de-regressed estimated breeding values) for five economically important traits were provided for the analysis. The reference population for genotyping imputation consisted of 931 DU, 1631 LA and 2103 YO animals and the remainder individuals were included in the validation population of each breed. A LD panel of 3000 evenly spaced SNPs (LD3K) yielded high imputation accuracy rates: 93.78% (DU), 97.07% (LA) and 97.00% (YO) and high correlations (>0.97) between the predicted GEBVs using the actual 60 K SNP genotypes and the imputed 60 K SNP genotypes for all traits and breeds. The imputation accuracy was influenced by the reference population size as well as the amount of parental genotype information available in the reference population. However, parental genotype information became less important when the LD panel had at least 3000 SNPs. The correlation of the GEBVs directly increased with an increase in imputation accuracy. When genotype information for both parents was available, a panel of 300 SNPs (imputed to 60 K) yielded GEBV predictions highly correlated (⩾0.90) with genomic predictions obtained based on the true 60 K panel, for all traits and breeds. For a small reference population size with no parents on reference population, it is recommended the use of a panel at least as dense as the LD3K and, when there are two parents in the reference population, a panel as small as the LD300 might be a feasible option. These findings are of great importance for the development of LD panels for swine in order to reduce genotyping costs, increase the uptake of GS and, therefore, optimize the profitability of the swine industry.
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Wu S, Wang Y, Ning Y, Guo H, Wang X, Zhang L, Khan R, Cheng G, Wang H, Zan L. Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle. Int J Mol Sci 2018; 19:ijms19041035. [PMID: 29596388 PMCID: PMC5979584 DOI: 10.3390/ijms19041035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy-Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle.
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Affiliation(s)
- Sen Wu
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yaning Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yue Ning
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Le Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
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Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet 2017; 13:e1006997. [PMID: 28915238 PMCID: PMC5626511 DOI: 10.1371/journal.pgen.1006997] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/03/2017] [Accepted: 08/24/2017] [Indexed: 02/08/2023] Open
Abstract
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of 'guilt by association' was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.
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Affiliation(s)
- Emily L. Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Mary E. B. McCulloch
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Iseabail L. Farquhar
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rachel Young
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Clare Pridans
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Hiu G. Tsang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Cyrus Afrasiabi
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - C. Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Tom C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Kim M. Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Mater Research Institute and University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - David A. Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Mater Research Institute and University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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Prieur V, Clarke SM, Brito LF, McEwan JC, Lee MA, Brauning R, Dodds KG, Auvray B. Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps. BMC Genet 2017; 18:68. [PMID: 28732466 PMCID: PMC5521107 DOI: 10.1186/s12863-017-0534-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of N e can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and N e . Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503). RESULTS The estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower N e results and higher LD decay. The results suggest that N e has decreased since the development of sheep breeds in Europe and this reduction in Ne has been accelerated in the last three decades. The N e estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives. CONCLUSIONS M3 was considered the most accurate method to create genetic maps for the estimation of LD and Ne. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.
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Affiliation(s)
- Vincent Prieur
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053 New Zealand
- Current address: France Limousin Sélection, Pôle de Lanaud, 87220 Boisseuil, France
| | - Shannon M. Clarke
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053 New Zealand
| | - Luiz F. Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, N1G2W1, Guelph, Canada
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053 New Zealand
| | - Michael A. Lee
- Department of Mathematics and Statistics, University of Otago, Dunedin, 9058 New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053 New Zealand
| | - Ken G. Dodds
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053 New Zealand
| | - Benoît Auvray
- Department of Mathematics and Statistics, University of Otago, Dunedin, 9058 New Zealand
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Brito LF, McEwan JC, Miller SP, Pickering NK, Bain WE, Dodds KG, Schenkel FS, Clarke SM. Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip. BMC Genet 2017; 18:25. [PMID: 28288558 PMCID: PMC5348757 DOI: 10.1186/s12863-017-0492-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
Background Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources. Results Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r2 between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial. Conclusions This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Ne highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0492-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, N1G 2W1, Canada. .,AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Stephen P Miller
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, N1G 2W1, Canada.,AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | | | - Wendy E Bain
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, N1G 2W1, Canada
| | - Shannon M Clarke
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
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