Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle

H.A. Mulder, M. Lidauer, J.H. Vilkki, I. Strandén, R.F. Veerkamp

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

Abstract

Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.
LanguageEnglish
Pages4164-4173
JournalJournal of Dairy Science
Volume94
Issue number8
DOIs
Publication statusPublished - 2011

Fingerprint

Ayrshire (cattle breed)
Mastitis
breeding value
Haplotypes
mastitis
Breeding
haplotypes
cattle
Quantitative Trait Loci
quantitative trait loci
genetic variance
somatic cells
bulls
Pedigree
Genetic Markers
pedigree
heritability

Keywords

  • quantitative trait loci
  • somatic-cell score
  • dairy-cattle
  • genetic evaluations
  • clinical mastitis
  • count traits
  • prediction
  • selection
  • haplotypes
  • conformation

Cite this

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title = "Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle",
abstract = "Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20{\%} or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.",
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author = "H.A. Mulder and M. Lidauer and J.H. Vilkki and I. Strand{\'e}n and R.F. Veerkamp",
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language = "English",
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Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle. / Mulder, H.A.; Lidauer, M.; Vilkki, J.H.; Strandén, I.; Veerkamp, R.F.

In: Journal of Dairy Science, Vol. 94, No. 8, 2011, p. 4164-4173.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle

AU - Mulder, H.A.

AU - Lidauer, M.

AU - Vilkki, J.H.

AU - Strandén, I.

AU - Veerkamp, R.F.

PY - 2011

Y1 - 2011

N2 - Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.

AB - Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.

KW - quantitative trait loci

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KW - dairy-cattle

KW - genetic evaluations

KW - clinical mastitis

KW - count traits

KW - prediction

KW - selection

KW - haplotypes

KW - conformation

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SN - 0022-0302

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