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Negro A, Cesarani A, Cortellari M, Bionda A, Fresi P, Macciotta NPP, Grande S, Biffani S, Crepaldi P. A comparison of genetic and genomic breeding values in Saanen and Alpine goats. Animal 2024; 18:101118. [PMID: 38508133 DOI: 10.1016/j.animal.2024.101118] [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: 09/08/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Nowadays, several countries are developing or adopting genomic selection in the dairy goat sector. The most used method to estimate breeding values is Single-Step Genomic Best Linear Unbiased Prediction (ssGBLUP) which offers several advantages in terms of computational process and accuracy of the estimated breeding values (EBVs). Saanen and Alpine are the predominant dairy goat breeds in Italy, and both have similar breeding programs where EBVs for productive traits are currently calculated using BLUP. This work describes the implementation of genomic selection for these two breeds in Italy, aligning with the selection practices already carried out in the international landscape. The available dataset included 3 611 genotyped animals, 11 470 lactation records, five traits (milk, protein and fat yields, and fat and protein percentages), and three-generation pedigrees. EBVs were estimated using BLUP, GBLUP, and ssGBLUP both with single and multiple trait approaches. The methods were compared in terms of correlation between EBVs and genetic trends. Results were also validated with the linear regression method excluding part of the phenotypic data. In both breeds, EBVs and GEBVs were strongly correlated and the trend of each trait was similar comparing the three methods. The average increase in accuracy across traits and methods amounted to +13 and +10% from BLUP to ssGBLUP for Alpine and Saanen breeds, respectively. Results indicated higher prediction accuracy and correlation for GBLUP and ssGBLUP compared to BLUP, implying that the use of genotypes increases the accuracy of EBVs, particularly in the absence of phenotypic data. Therefore, ssGBLUP is likely to be the most effective method to enhance genetic gain in Italian Saanen and Alpine goats.
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Affiliation(s)
- A Negro
- Ufficio Studi, Associazione Nazionale della Pastorizia, 00187 Rome, Italy; Dipartimento di Scienze Agrarie e alimentari, Università degli studi di Milano, 20133 Milan, Italy
| | - A Cesarani
- Dipartimento di Scienze Agrarie, Università degli Studi di Sassari, 07100 Sassari, Italy; Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - M Cortellari
- Dipartimento di Scienze Agrarie e alimentari, Università degli studi di Milano, 20133 Milan, Italy
| | - A Bionda
- Dipartimento di Scienze Agrarie e alimentari, Università degli studi di Milano, 20133 Milan, Italy.
| | - P Fresi
- Ufficio Studi, Associazione Nazionale della Pastorizia, 00187 Rome, Italy
| | - N P P Macciotta
- Dipartimento di Scienze Agrarie, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - S Grande
- Ufficio Studi, Associazione Nazionale della Pastorizia, 00187 Rome, Italy
| | - S Biffani
- Istituto di Biologia e Biotecnologia, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy
| | - P Crepaldi
- Dipartimento di Scienze Agrarie e alimentari, Università degli studi di Milano, 20133 Milan, Italy
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Cardona SJC, García-Baccino CA, Escobar-Restrepo CS, Cadavid HC, Álvarez JDC, Duarte JLG, Rogberg-Muñoz A. Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information. Trop Anim Health Prod 2024; 56:109. [PMID: 38509383 DOI: 10.1007/s11250-024-03948-6] [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: 03/30/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.
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Affiliation(s)
- Samir Julián Calvo Cardona
- Universidad Tecnológica de Pereira, Facultad de Ciencias de La Salud, Programa de Medicina Veterinaria y Zootecnia, Grupo de Investigación BIOPEC, Carrera 27 # 10-02, Álamos, Pereira-Risaralda, Colombia
| | - Carolina Andrea García-Baccino
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Santiago Escobar-Restrepo
- Grupo de investigación en Agronomía y Zootecnia-GIAZ, Facultad de Ciencias Agropecuarias, Universidad Católica de Oriente, Sector 3, Carrera 46, no 40B-50, Rionegro, Colombia.
| | - Henry Cardona Cadavid
- Universidad de Antioquia UdeA, Facultad de Ciencias Agrarias, Grupo de Investigación Agrociencias, Biodiversidad y Territorio-GAMMA, Cl. 70 # 52-21, 050010, Medellín, Colombia
| | | | - José Luis Gualdrón Duarte
- Unit of Animal Genomics, GIGA-R, University of Liège, 11 Avenue de L'Hôpital (B34), 4000, Liège, Belgium
| | - Andres Rogberg-Muñoz
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires. Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
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Ziadi C, Sánchez JP, Sánchez M, Morales R, Molina A. Survival analysis of productive life in Florida dairy goats using a Cox proportional hazards model. J Anim Breed Genet 2023. [PMID: 36932904 DOI: 10.1111/jbg.12769] [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: 11/10/2022] [Accepted: 02/22/2023] [Indexed: 03/19/2023]
Abstract
Longevity is an economically important trait, since extending the functional life of a doe would allow us to keep the most productive females in the herd as long as possible, and this could result in the increased profitability of dairy farms. Thus, the objectives of this study were to determine the most important factors that influence the length of productive life (LPL) of female Florida goats and to estimate its genetic additive variance using a Cox proportional hazards model. The data consisted of 70,695 productive life records from 25,722 Florida females kidding between 2006 and 2020. A total of 19,495 does had completed their productive life while 6227 (24.2%) does had censored information. The pedigree contained information on 56,901 animals. The average censoring age and average failure age after first kidding for LPL were 36 and 47 months respectively. The model included, as time-independent effects, the age at first kidding and the interaction between herd, year and season of birth of the doe, and as time-dependent effects, the age at kidding, the interaction between herd, year and season of kidding, the within-herd class of milk production deviation, and the interaction between the lactation number and the stage of lactation. All fixed effects had a significant effect on LPL (p < 0.05). Does with older ages at the first kidding and an earlier age at kidding were at higher risk of being culled. A large difference among herds was observed in terms of culling risk, which highlighted the importance of adequate management practices. Also, high-producing does were less likely to be culled. The estimate of the additive genetic variance was 1.844 (in genetic standard deviation), with a heritability estimate of 0.58 ± 0.012. The results of this study are expected to contribute to the development of a genetic model for genetic evaluation of the length of the productive life of Spanish dairy goat breeds.
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Affiliation(s)
- C Ziadi
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel. Campus de Rabanales, Córdoba, Spain
| | - J P Sánchez
- Departamento de Genética y Mejora Animal, IRTA. Torre Marimon, Caldes de Montbui, Barcelona, Spain
| | - M Sánchez
- Departamento de Producción Animal, Universidad de Córdoba. Campus de Rabanales, Córdoba, Spain
| | - R Morales
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel. Campus de Rabanales, Córdoba, Spain
| | - A Molina
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel. Campus de Rabanales, Córdoba, Spain
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Cruz A, Sedano J, Burgos A, Gutiérrez JP, Wurzinger M, Gutiérrez-Reynoso G. Genomic selection improves genetic gain for fiber traits in a breeding program for alpacas. Livest Sci 2023. [DOI: 10.1016/j.livsci.2023.105195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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Selionova M, Aibazov M, Mamontova T, Malorodov V, Sermyagin A, Zinovyeva N, Easa AA. Genome-wide association study of live body weight and body conformation traits in young Karachai goats. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Genetic Parameters of Somatic Cell Score in Florida Goats Using Single and Multiple Traits Models. Animals (Basel) 2022; 12:ani12081009. [PMID: 35454255 PMCID: PMC9025430 DOI: 10.3390/ani12081009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
A total of 1,031,143 records of daily dairy control test of Spanish Florida goats were used for this study. The database was edited, and only the records of the first three lactations were kept. The final database contained 340,654 daily-test somatic cell counts from 27,749 daughters of 941 males and 16,243 goats. The evolution of this count in the last 14 years was analyzed following French and American international associations’ criteria for the risk of mastitis in goats, and confirmed the slight increase in SCS in the last years and the importance of this problem (50% of dairy control tests show a risk of suffering mastitis). For the genetic analysis, the SCS records were log-transformed to normalize this variable. Two strategies were used for the genetic analysis: a univariate animal model for the SCS assuming that SCS does not vary throughout the parities, and a multi-character animal model, where SCS is not considered as the same character in the different parities. The heritabilities (h2) were higher in the multiple traits models, showings an upward trend from the first to the third parity (h2 between 0.245 to 0.365). The genetic correlations of the same trait, as well as between breeding values (GVs) between different parities, were different from unity. The breeding values (EBVs) obtained for both models were subjected to a PCA: the first eigenvector (λ1) explained most of the variations (between 74% to 90%), while the second λ2 accounted for between 9% to 20% of the variance, which shows that the selection will be proportionally favorable but not equivalent in all parities and that there are some variations in the type of response.
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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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Ziadi C, Muñoz-Mejías E, Sánchez M, López MD, González-Casquet O, Molina A. Genetic analysis of reproductive efficiency in Spanish goat breeds using a random regression model as a strategy for improving female fertility. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1979900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Chiraz Ziadi
- Departamento de Genética, University of Córdoba, Rabanales Campus, Córdoba, Spain
| | - Eva Muñoz-Mejías
- Departamento de Patología Animal, Producción Animal, Bromatología y Tecnología de los Alimentos, Cardones de Arucas Campus of Las Palmas de Gran Canaria, Cardones de Arucas University Campus, Arucas, Spain
| | - Manuel Sánchez
- Departamento de Producción Animal, University of Córdoba, Rabanales Campus, Córdoba, Spain
| | | | | | - Antonio Molina
- Departamento de Genética, University of Córdoba, Rabanales Campus, Córdoba, Spain
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10
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Selection Criteria for Improving Fertility in Spanish Goat Breeds: Estimation of Genetic Parameters and Designing Selection Indices for Optimal Genetic Responses. Animals (Basel) 2021; 11:ani11020409. [PMID: 33562683 PMCID: PMC7915267 DOI: 10.3390/ani11020409] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to estimate genetic parameters for several female fertility criteria and to choose the most suitable selection index in Spanish Florida and Payoya goat breeds. In this study, we analyzed as fertility traits, the age at first kidding (AgFiKid), and the interval between the first and second kiddings (Int12Kid), between the second, third, and remaining kiddings (Int3toKid), and between all kiddings (IntAllKid) in 51,123 and 22,049 Florida and Payoya females, respectively. Genetic parameters were estimated by fitting animal models using restricted maximum likelihood (REML) methodology. We proposed six selection indices to compare the genetic responses for all traits included, based on a new selection index theory. The heritability and repeatability estimates of the traits were low, as expected. The genetic correlations among fertility traits covered a wide range of values from 0.07 (AgFiKid-Int12Kid) to 0.71 (Int3toKid-IntAllKid) in Florida and from -0.02 (AgFiKid-Int12Kid) to 0.82 (Int3toKid-IntAllKid) in Payoya. Overall, the results of this study indicate that IntAllKid gives the highest genetic responses in both breeds but is expressed late in a female's life. However, AgFiKid and Int12Kid could be recommended as early selection criteria for female fertility in both breeds.
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Ziadi C, Muñoz-Mejías E, Sánchez Rodríguez M, López MD, González-Casquet O, Molina Alcalá A. Genetic analysis of litter size and number of kids born alive across parities in Spanish goat breeds using a random regression model. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2020.1869601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Chiraz Ziadi
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel. Campus de Rabanales. Ctra, Madrid-Cádiz, Córdoba, España
| | - Eva Muñoz-Mejías
- Departamento de Patología Animal, Producción Animal, Bromatología y Tecnología de los Alimentos de la Universidad de Las Palmas de Gran Canaria. Campus Universitario Cardones de Arucas, Arucas, España
| | - Manuel Sánchez Rodríguez
- Departamento de Producción Animal, Universidad de Córdoba. Campus de Rabanales. Ctra, Madrid-Cádiz, Córdoba, España
| | - María Dolores López
- ACRIFLOR. Edificio de Producción Animal. Campus de Rabanales. Ctra, Madrid-Cádiz, Córdoba, España
| | | | - Antonio Molina Alcalá
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel. Campus de Rabanales. Ctra, Madrid-Cádiz, Córdoba, España
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Advantage of including Genomic Information to Predict Breeding Values for Lactation Yields of Milk, Fat, and Protein or Somatic Cell Score in a New Zealand Dairy Goat Herd. Animals (Basel) 2020; 11:ani11010024. [PMID: 33375575 PMCID: PMC7823755 DOI: 10.3390/ani11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary The objective of this study was to quantify the benefit from the inclusion of genomic information in the estimation of breeding values for lactation yields of milk, fat, and protein or somatic cell score in a New Zealand dairy goat herd. The dataset included lactation yields of milk, fat, and protein and average somatic cell score of 839 does and genotypes from 388 does. A prototype single-step BayesC model was developed to predict genomic breeding values and demonstrated that including genomic information into the evaluation can increase the accuracy of predictions compared with the traditional best linear unbiased prediction methods based on pedigrees alone, which is currently implemented in the New Zealand dairy goat industry. Abstract Selection on genomic breeding values (GBVs) is now readily available for ranking candidates in improvement schemes. Our objective was to quantify benefits in terms of accuracy of prediction from including genomic information in the single-trait estimation of breeding values (BVs) for a New Zealand mixed breed dairy goat herd. The dataset comprised phenotypic and pedigree records of 839 does. The phenotypes comprised estimates of 305-day lactation yields of milk, fat, and protein and average somatic cell score from the 2016 production season. Only 388 of the goats were genotyped with a Caprine 50K SNP chip and 41,981 of the single nucleotide polymorphisms (SNPs) passed quality control. Pedigree-based best linear unbiased prediction (PBLUP) was used to obtain across-breed breeding values (EBVs), whereas a single-step BayesC model (ssBC) was used to estimate across-breed GBVs. The average prediction accuracies ranged from 0.20 to 0.22 for EBVs and 0.34 to 0.43 for GBVs. Accuracies of GBVs were up to 103% greater than EBVs. Breed effects were more reliably estimated in the ssBC model compared with the PBLUP model. The greatest benefit of genomic prediction was for individuals with no pedigree or phenotypic records. Including genomic information improved the prediction accuracy of BVs compared with the current pedigree-based BLUP method currently implemented in the New Zealand dairy goat population.
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Wei C, Luo H, Zhao B, Tian K, Huang X, Wang Y, Fu X, Tian Y, Di J, Xu X, Wu W, Tulafu H, Yasen M, Zhang Y, Zhao W. The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep. Animals (Basel) 2020; 10:ani10040569. [PMID: 32231053 PMCID: PMC7222387 DOI: 10.3390/ani10040569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Genetic improvement of wool production and quality traits in fine-wool sheep is an appealing option for enhancing the market value of wool products. We estimated genetic parameters and the accuracies of estimated breeding values for various wool production and quality traits in fine-wool sheep using pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) strategies. ssGBLUP performed slightly better than PBLUP for the studied traits. Therefore, the single-step genetic evaluation method could be successfully implemented in genomic evaluations of fine-wool sheep and the prediction of future breeding values in young Merino sheep as part of an early preselection strategy in the near future. Abstract Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h2 values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP.
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Affiliation(s)
- Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanpeng Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bingru Zhao
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Xinming Xu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Weiwei Wu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Maerziya Yasen
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yajun Zhang
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
| | - Wensheng Zhao
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
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14
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de Lima LG, de Souza NOB, Rios RR, de Melo BA, dos Santos LTA, Silva KDM, Murphy TW, Fraga AB. Advances in molecular genetic techniques applied to selection for litter size in goats (Capra hircus): a review. JOURNAL OF APPLIED ANIMAL RESEARCH 2020. [DOI: 10.1080/09712119.2020.1717497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Luciano Gomes de Lima
- Northeastern Network in Biotechnology (known as RENORBIO in Portuguese), the Federal University of Alagoas, Maceió, Brazil
| | | | - Raisa Rodrigues Rios
- Northeastern Network in Biotechnology (known as RENORBIO in Portuguese), the Federal University of Alagoas, Maceió, Brazil
| | - Breno Araújo de Melo
- Northeastern Network in Biotechnology (known as RENORBIO in Portuguese), the Federal University of Alagoas, Maceió, Brazil
| | - Lays Thayse Alves dos Santos
- Animal Science of the Graduation Program, Agrarian Science Center, Federal University of Alagoas, Rio Largo, Brazil
| | - Kleibe de Moraes Silva
- Research Scientist Brazilian Agricultural Research Corporation - Goats and Sheep, Sobral, Brazil
| | - Thomas Wayne Murphy
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA
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15
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Gipson TA. Recent advances in breeding and genetics for dairy goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1275-1283. [PMID: 31357268 PMCID: PMC6668855 DOI: 10.5713/ajas.19.0381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022]
Abstract
Goats (Capra hircus) were domesticated during the late Neolithic, approximately 10,500 years ago, and humans exerted minor selection pressure until fairly recently. Probably the largest genetic change occurring over the millennia happened via natural selection and random genetic drift, the latter causing genes to be fixed in small and isolated populations. Recent human-influenced genetic changes have occurred through biometrics and genomics. For the most part, biometrics has concentrated upon the refining of estimates of heritabilities and genetic correlations. Heritabilities are instrumental in the calculation of estimated breeding values and genetic correlations are necessary in the construction of selection indices that account for changes in multiple traits under selection at one time. Early genomic studies focused upon microsatellite markers, which are short tandem repeats of nucleic acids and which are detected using polymerase chain reaction primers flanking the microsatellite. Microsatellite markers have been very important in parentage verification, which can impact genetic progress. Additionally, microsatellite markers have been a useful tool in assessing genetic diversity between and among breeds, which is important in the conservation of minor breeds. Single nucleotide polymorphisms are a new genomic tool that have refined classical BLUP methodology (biometric) to provide more accurate genomic estimated breeding values, provided a large reference population is available.
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Affiliation(s)
- Terry A Gipson
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
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16
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Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Eenennaam AV, Tassell CPV, Wells K. Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027. Front Genet 2019; 10:327. [PMID: 31156693 PMCID: PMC6532451 DOI: 10.3389/fgene.2019.00327] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/26/2019] [Indexed: 11/15/2022] Open
Abstract
In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.
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Affiliation(s)
- Caird Rexroad
- Office of National Programs, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Jeffrey Vallet
- Office of National Programs, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Lakshmi Kumar Matukumalli
- National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United States
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Derek Bickhart
- Dairy Forage Research Center, Agricultural Research Service, United States Department of Agriculture, Madison, WI, United States
| | - Harvey Blackburn
- National Animal Germplasm Program, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
| | - Mark Boggess
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Hans Cheng
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, East Lansing, MI, United States
| | - Archie Clutter
- Agricultural Research Division, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Noelle Cockett
- President’s Office, Utah State University, Logan, UT, United States
| | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | | | - John Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
| | - Joan Lunney
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Holly Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Catherine Purcell
- Department of Commerce, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
| | - Timothy P. L. Smith
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Tad Sonstegard
- Acceligen, A Recombinetics Company, St. Paul, MN, United States
| | - Jerry Taylor
- Division of Animal Science, University of Missouri, Columbia, MO, United States
| | - Bhanu Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Alison Van Eenennaam
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kevin Wells
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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