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How old are quantitative trait loci and how widely do they segregate?
Author(s) -
Kemper K.E.,
Hayes B.J.,
Daetwyler H.D.,
Goddard M.E.
Publication year - 2015
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12152
Subject(s) - quantitative trait locus , biology , family based qtl mapping , genetics , allele , trait , breed , population , inclusive composite interval mapping , gene , gene mapping , chromosome , sociology , computer science , programming language , demography
Summary 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 J erseys. 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 J ersey cattle incorrectly predicted a QTL in J ersey cattle when the QTL only segregates in H olsteins. Overcoming this error should help to make genomic prediction more accurate in smaller breeds.