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Duru S, Altınçekiç ŞÖ, Hanoğlu Oral H. Effectiveness of genetic grouping with different strategies for estimation of genetic parameters in growth traits in Merino lambs. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gómez M, Rossi D, Cimmino R, Zullo G, Gombia Y, Altieri D, Di Palo R, Biffani S. Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo. Front Genet 2021; 12:625335. [PMID: 33633785 PMCID: PMC7901897 DOI: 10.3389/fgene.2021.625335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
The use of genetic evaluations in the Water Buffalo by means of a Best Linear Unbiased Prediction (BLUP) animal model has been increased over the last two-decades across several countries. However, natural mating is still a common reproductive strategy that can increase the proportion of missing pedigree information. The inclusion of genetic groups in variance component (VC) and breeding value (EBV) estimation is a possible solution. The aim of this study was to evaluate two different genetic grouping strategies and their effects on VC and EBV for composite (n = 5) and linear (n = 10) type traits in the Italian Mediterranean Buffalo (IMB) population. Type traits data from 7,714 buffalo cows plus a pedigree file including 18,831 individuals were provided by the Italian National Association of Buffalo Breeders. VCs and EBVs were estimated for each trait fitting a single-trait animal model and using the official DNA-verified pedigree. Successively, EBVs were re-estimated using modified pedigrees with two different proportion of missing genealogies (30 or 60% of buffalo with records), and two different grouping strategies, year of birth (Y30/Y60) or genetic clustering (GC30, GC60). The different set of VCs, estimated EBVs and their standard errors were compared with the results obtained using the original pedigree. Results were also compared in terms of efficiency of selection. Differences among VCs varied according to the trait and the scenario considered. The largest effect was observed for two traits, udder teat and body depth in the GC60 genetic cluster, whose heritability decreased by -0.07 and increased by +0.04, respectively. Considering buffalo cows with record, the average correlation across traits between official EBVs and EBVs from different scenarios was 0.91, 0.88, 0.84, and 0.79 for Y30, CG30, Y60, and CG60, respectively. In bulls the correlations between EBVs ranged from 0.90 for fore udder attachment and udder depth to 0.96 for stature and body length in the GC30 scenario and from 0.75 for udder depth to 0.90 for stature in the GC60 scenario. When a variable proportion of missing pedigree is present using the appropriate strategy to define genetic groups and including them in VC and EBV is a worth-while and low-demanding solution.
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Affiliation(s)
- Mayra Gómez
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Dario Rossi
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Roberta Cimmino
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Gianluigi Zullo
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Yuri Gombia
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Damiano Altieri
- Italian National Association of Buffalo Breeders, Caserta, Italy
| | - Rossella Di Palo
- Department of Veterinary Medicine and Animal Production, University of Federico II, Naples, Italy
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology, National Research Council, Milan, Italy
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Raoul J, Elsen JM. The levels of artificial insemination and missing sire information make genomic selection not always beneficial in meat sheep. Animal 2021; 15:100040. [PMID: 33573971 DOI: 10.1016/j.animal.2020.100040] [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: 10/22/2019] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/01/2022] Open
Abstract
Numerous meat sheep breeding programs in developed and developing countries are characterized by incomplete sire information and a predominant use of natural matings. These two parameters potentially affect the benefit of genomic selection (GS), especially for the selection of a late-in-life trait. Using stochastic simulations, the genetic gains obtained using genomic and conventional strategies for a maternal trait were evaluated in meat sheep population. Natural mating and artificial insemination (AI)-based designs, inspired by the current diversity of designs used for French meat sheep breeds, were modeled and three genomic strategies were tested and compared with a conventional selection strategy: parentage assignment, GS based on a male or a male and female reference population. Genomic selection based on a male reference population did not always outperform conventional selection. Its benefit depended on the design, the level of missing information on dam sires, and the level of AI. Genomic selection based on a male and female reference population always outperformed the conventional selection strategy, even if only 25 % of the females in the nucleus were genotyped.
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Affiliation(s)
- J Raoul
- Institut de l'Elevage, Castanet-Tolosan, France; GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France.
| | - J M Elsen
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
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Definition of a SNP panel for paternity testing in ten sheep populations in Mexico. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Effect of the rate of artificial insemination and paternity knowledge on the genetic gain for French meat sheep breeding programs. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Talenti A, Palhière I, Tortereau F, Pagnacco G, Stella A, Nicolazzi EL, Crepaldi P, Tosser-Klopp G. Functional SNP panel for parentage assessment and assignment in worldwide goat breeds. Genet Sel Evol 2018; 50:55. [PMID: 30449282 PMCID: PMC6240953 DOI: 10.1186/s12711-018-0423-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 10/15/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs. RESULTS Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires. CONCLUSIONS In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Flavie Tortereau
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
| | - Ezequiel L. Nicolazzi
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - AdaptMap Consortium
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
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Amills M, Capote J, Tosser-Klopp G. Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim Genet 2017; 48:631-644. [PMID: 28872195 DOI: 10.1111/age.12598] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
Abstract
Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.
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Affiliation(s)
- M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna, 38108, Tenerife, Spain
| | - G Tosser-Klopp
- INRA-GenPhySE-Génétique, Physiologie et Systèmes d'Elevage-UMR1388, 24 Chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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Tortereau F, Moreno CR, Tosser-Klopp G, Servin B, Raoul J. Development of a SNP panel dedicated to parentage assignment in French sheep populations. BMC Genet 2017; 18:50. [PMID: 28549462 PMCID: PMC5446718 DOI: 10.1186/s12863-017-0518-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/17/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values. RESULTS In order to address this issue and offer an alternative strategy for obtaining parentage information, we designed a set of 249 SNPs for parentage assignment in French sheep breeds and tested its efficiency in one breed. The set was derived from the 54 K SNP chip that was used to genotype the thirty main French sheep populations. Only SNPs in Hardy-Weinberg equilibrium, displaying the highest Minor Allele Frequency across all the thirty populations and not associated with Mendelian errors in verified family trios were selected. The panel of 249 SNPs was successfully used in an on-farm test in the BMC breed and resulted in more than 95% of lambs being assigned to a unique sire. CONCLUSION In this study we developed a SNP panel for assignment that achieved good results in the on-farm testing. We also raised some conditions for optimal use of this panel: at least 180 SNPs should be used and a minute preparation of the list of candidate sires. Our panel also displays high levels of MAF in the SheepHapMap breeds, particularly in the South West European breeds.
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Affiliation(s)
- F Tortereau
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France.
| | - C R Moreno
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - G Tosser-Klopp
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - B Servin
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - J Raoul
- Institut de l'Elevage, DGEP, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
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