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Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo

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 ped...

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Autores principales: Gómez, Mayra, Rossi, Dario, Cimmino, Roberta, Zullo, Gianluigi, Gombia, Yuri, Altieri, Damiano, Di Palo, Rossella, Biffani, Stefano
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901897/
https://www.ncbi.nlm.nih.gov/pubmed/33633785
http://dx.doi.org/10.3389/fgene.2021.625335
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author Gómez, Mayra
Rossi, Dario
Cimmino, Roberta
Zullo, Gianluigi
Gombia, Yuri
Altieri, Damiano
Di Palo, Rossella
Biffani, Stefano
author_facet Gómez, Mayra
Rossi, Dario
Cimmino, Roberta
Zullo, Gianluigi
Gombia, Yuri
Altieri, Damiano
Di Palo, Rossella
Biffani, Stefano
author_sort Gómez, Mayra
collection PubMed
description 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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spelling pubmed-79018972021-02-24 Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo Gómez, Mayra Rossi, Dario Cimmino, Roberta Zullo, Gianluigi Gombia, Yuri Altieri, Damiano Di Palo, Rossella Biffani, Stefano Front Genet Genetics 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. Frontiers Media S.A. 2021-02-04 /pmc/articles/PMC7901897/ /pubmed/33633785 http://dx.doi.org/10.3389/fgene.2021.625335 Text en Copyright © 2021 Gómez, Rossi, Cimmino, Zullo, Gombia, Altieri, Di Palo and Biffani. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Gómez, Mayra
Rossi, Dario
Cimmino, Roberta
Zullo, Gianluigi
Gombia, Yuri
Altieri, Damiano
Di Palo, Rossella
Biffani, Stefano
Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title_full Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title_fullStr Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title_full_unstemmed Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title_short Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo
title_sort accounting for genetic differences among unknown parents in bubalus bubalis: a case study from the italian mediterranean buffalo
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901897/
https://www.ncbi.nlm.nih.gov/pubmed/33633785
http://dx.doi.org/10.3389/fgene.2021.625335
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