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Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle
Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference popul...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261042/ https://www.ncbi.nlm.nih.gov/pubmed/34248929 http://dx.doi.org/10.3389/fimmu.2021.620847 |
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author | Cardoso, Fernando Flores Matika, Oswald Djikeng, Appolinaire Mapholi, Ntanganedzeni Burrow, Heather M. Yokoo, Marcos Jun Iti Campos, Gabriel Soares Gulias-Gomes, Claudia Cristina Riggio, Valentina Pong-Wong, Ricardo Engle, Bailey Porto-Neto, Laercio Maiwashe, Azwihangwisi Hayes, Ben J. |
author_facet | Cardoso, Fernando Flores Matika, Oswald Djikeng, Appolinaire Mapholi, Ntanganedzeni Burrow, Heather M. Yokoo, Marcos Jun Iti Campos, Gabriel Soares Gulias-Gomes, Claudia Cristina Riggio, Valentina Pong-Wong, Ricardo Engle, Bailey Porto-Neto, Laercio Maiwashe, Azwihangwisi Hayes, Ben J. |
author_sort | Cardoso, Fernando Flores |
collection | PubMed |
description | Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference populations from multi-country beef cattle breeds to assess the possibility of improving host resistance through multi-trait genomic selection. Data consisted of tick counts or scores assessing the number of female ticks at least 4.5 mm length and derived from seven populations, with breed, country, number of records and genotyped/phenotyped animals being respectively: Angus (AN), Brazil, 2,263, 921/1,156, Hereford (HH), Brazil, 6,615, 1,910/2,802, Brangus (BN), Brazil, 2,441, 851/851, Braford (BO), Brazil, 9,523, 3,062/4,095, Tropical Composite (TC), Australia, 229, 229/229, Brahman (BR), Australia, 675, 675/675, and Nguni (NG), South Africa, 490, 490/490. All populations were genotyped using medium density Illumina SNP BeadChips and imputed to a common high-density panel of 332,468 markers. The mean linkage disequilibrium (LD) between adjacent SNPs varied from 0.24 to 0.37 across populations and so was sufficient to allow genomic breeding values (GEBV) prediction. Correlations of LD phase between breeds were higher between composites and their founder breeds (0.81 to 0.95) and lower between NG and the other breeds (0.27 and 0.35). There was wide range of estimated heritability (0.05 and 0.42) and genetic correlation (-0.01 and 0.87) for tick resistance across the studied populations, with the largest genetic correlation observed between BN and BO. Predictive ability was improved under the old-young validation for three of the seven populations using a multi-trait approach compared to a single trait within-population prediction, while whole and partial data GEBV correlations increased in all cases, with relative improvements ranging from 3% for BO to 64% for TC. Moreover, the multi-trait analysis was useful to correct typical over-dispersion of the GEBV. Results from this study indicate that a joint genomic evaluation of AN, HH, BN, BO and BR can be readily implemented to improve tick resistance of these populations using selection on GEBV. For NG and TC additional phenotyping will be required to obtain accurate GEBV. |
format | Online Article Text |
id | pubmed-8261042 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-82610422021-07-08 Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle Cardoso, Fernando Flores Matika, Oswald Djikeng, Appolinaire Mapholi, Ntanganedzeni Burrow, Heather M. Yokoo, Marcos Jun Iti Campos, Gabriel Soares Gulias-Gomes, Claudia Cristina Riggio, Valentina Pong-Wong, Ricardo Engle, Bailey Porto-Neto, Laercio Maiwashe, Azwihangwisi Hayes, Ben J. Front Immunol Immunology Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference populations from multi-country beef cattle breeds to assess the possibility of improving host resistance through multi-trait genomic selection. Data consisted of tick counts or scores assessing the number of female ticks at least 4.5 mm length and derived from seven populations, with breed, country, number of records and genotyped/phenotyped animals being respectively: Angus (AN), Brazil, 2,263, 921/1,156, Hereford (HH), Brazil, 6,615, 1,910/2,802, Brangus (BN), Brazil, 2,441, 851/851, Braford (BO), Brazil, 9,523, 3,062/4,095, Tropical Composite (TC), Australia, 229, 229/229, Brahman (BR), Australia, 675, 675/675, and Nguni (NG), South Africa, 490, 490/490. All populations were genotyped using medium density Illumina SNP BeadChips and imputed to a common high-density panel of 332,468 markers. The mean linkage disequilibrium (LD) between adjacent SNPs varied from 0.24 to 0.37 across populations and so was sufficient to allow genomic breeding values (GEBV) prediction. Correlations of LD phase between breeds were higher between composites and their founder breeds (0.81 to 0.95) and lower between NG and the other breeds (0.27 and 0.35). There was wide range of estimated heritability (0.05 and 0.42) and genetic correlation (-0.01 and 0.87) for tick resistance across the studied populations, with the largest genetic correlation observed between BN and BO. Predictive ability was improved under the old-young validation for three of the seven populations using a multi-trait approach compared to a single trait within-population prediction, while whole and partial data GEBV correlations increased in all cases, with relative improvements ranging from 3% for BO to 64% for TC. Moreover, the multi-trait analysis was useful to correct typical over-dispersion of the GEBV. Results from this study indicate that a joint genomic evaluation of AN, HH, BN, BO and BR can be readily implemented to improve tick resistance of these populations using selection on GEBV. For NG and TC additional phenotyping will be required to obtain accurate GEBV. Frontiers Media S.A. 2021-06-23 /pmc/articles/PMC8261042/ /pubmed/34248929 http://dx.doi.org/10.3389/fimmu.2021.620847 Text en Copyright © 2021 Cardoso, Matika, Djikeng, Mapholi, Burrow, Yokoo, Campos, Gulias-Gomes, Riggio, Pong-Wong, Engle, Porto-Neto, Maiwashe and Hayes https://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 | Immunology Cardoso, Fernando Flores Matika, Oswald Djikeng, Appolinaire Mapholi, Ntanganedzeni Burrow, Heather M. Yokoo, Marcos Jun Iti Campos, Gabriel Soares Gulias-Gomes, Claudia Cristina Riggio, Valentina Pong-Wong, Ricardo Engle, Bailey Porto-Neto, Laercio Maiwashe, Azwihangwisi Hayes, Ben J. Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title | Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title_full | Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title_fullStr | Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title_full_unstemmed | Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title_short | Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle |
title_sort | multiple country and breed genomic prediction of tick resistance in beef cattle |
topic | Immunology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261042/ https://www.ncbi.nlm.nih.gov/pubmed/34248929 http://dx.doi.org/10.3389/fimmu.2021.620847 |
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