Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information

Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2012) Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science, 95 1: 377-388. doi:10.3168/jds.2011-4254


Author Pryce, J. E.
Hayes, B. J.
Goddard, M. E.
Title Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information
Journal name Journal of Dairy Science   Check publisher's open access policy
ISSN 0022-0302
1525-3198
Publication date 2012-01
Sub-type Article (original research)
DOI 10.3168/jds.2011-4254
Open Access Status Not yet assessed
Volume 95
Issue 1
Start page 377
End page 388
Total pages 12
Place of publication New York, United States
Publisher Elsevier
Language eng
Abstract In this study, 3 strategies for controlling progeny inbreeding in mating plans were compared. The strategies used information from pedigree inbreeding coefficients, genomic relationships, or shared runs of homozygosity. The strategies were compared for the reduction in genetic gain and progeny inbreeding that would be expected from selected matings, and for the decrease of homozygosity of deleterious recessive alleles. Using real pedigree, genotype [43,115 single nucleotide polymorphism (SNP) markers], and estimated breeding value data from Holstein cattle, mating plans were derived for herds of 300 cows with 20 sires available for mating, replicated 50 times. Each of the 300 individuals allocated as dams were matched to 1 of 20 sires to maximize genetic merit minus the penalty for estimated progeny inbreeding, and given the restriction that the sire could not be mated to more than 10% of the cows. The strategy that used a genomic relationship matrix (GRM) was the most effective in reducing average progeny inbreeding; this strategy also resulted in fewer homozygous SNP out of 1,000 low-frequency SNP compared with the strategy using pedigree information. In the future, large numbers of cattle may be genotyped for low-density SNP panels. A GRM constructed using 3,123 SNP produced results similar to a GRM constructed using the full 43,115 SNP. These results demonstrate that using GRM information, a 1% reduction in progeny inbreeding (valued at around $5 per cow) can be made with very little compromise in the overall breeding objective. These results and the availability of low-cost, low-density genotyping make it attractive to apply mating plans that use genomic information in commercial dairy herds.
Keyword Genomic
Inbreeding
Mating plan
Runs of homozygosity
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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