How old are quantitative trait loci and how widely do they segregate?

Kemper, K. E., Hayes, B. J., Daetwyler, H. D. and Goddard, M. E. (2015) How old are quantitative trait loci and how widely do they segregate?. Journal of Animal Breeding and Genetics, 132 2: 121-134. doi:10.1111/jbg.12152

Author Kemper, K. E.
Hayes, B. J.
Daetwyler, H. D.
Goddard, M. E.
Title How old are quantitative trait loci and how widely do they segregate?
Journal name Journal of Animal Breeding and Genetics   Check publisher's open access policy
ISSN 1439-0388
Publication date 2015-04-01
Year available 2015
Sub-type Article (original research)
DOI 10.1111/jbg.12152
Open Access Status Not Open Access
Volume 132
Issue 2
Start page 121
End page 134
Total pages 14
Place of publication Berlin, Germany
Publisher Wiley-Blackwell Verlag GmbH
Language eng
Formatted abstract
The mutations that cause genetic variation in quantitative traits could be old and segregate across many breeds or they could be young and segregate only within one breed. This has implications for our understanding of the evolution of quantitative traits and for genomic prediction to improve livestock. We investigated the age of quantitative trait loci (QTL) for milk production traits identified as segregating in Holstein dairy cattle. We use a multitrait method and found that six of 11 QTL also segregate in Jerseys. Variants identified as Holstein-only QTL were fixed or rare [minor allele frequency (MAF) < 0.05] in Jersey. The age of the QTL mutations appears to vary from perhaps 2000 to 50 000 generations old. The older QTL tend to have high derived allele frequencies and often segregate across both breeds. Holstein-only QTL were often embedded within longer haplotypes, supporting the conclusion that they are typically younger mutations that have occurred more recently than QTL that segregate in both breeds. A reference population for genomic prediction using both Holsteins and Jersey cattle incorrectly predicted a QTL in Jersey cattle when the QTL only segregates in Holsteins. Overcoming this error should help to make genomic prediction more accurate in smaller breeds.
Keyword Dairy cattle
Genetic architecture
Genomic prediction
Genomic sequence variants
QTL mapping
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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