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Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population
Purfield, D. C. Evans, R. D. Berry, Donagh
Purfield, D. C.
Evans, R. D.
Berry, Donagh
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2019-09-18
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Purfield, D.C., Evans, R.D. & Berry, D.P. Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population. BMC Genomics 20, 720 (2019). https://doi.org/10.1186/s12864-019-6071-9
Abstract
Background: The high narrow sense heritability of carcass traits suggests that the underlying additive genetic
potential of an individual should be strongly correlated with both animal carcass quality and quantity, and
therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions
associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole
genome sequence in 28,470 dairy and beef sires from six breeds with a total of 2,199,926 phenotyped progeny.
Results: Major genes previously associated with carcass performance were identified, as well as several putative
novel candidate genes that likely operate both within and across breeds. The role of MSTN in carcass performance
was re-affirmed with the segregating Q204X mutation explaining 1.21, 1.11 and 5.95% of the genetic variance in
carcass weight, fat and conformation, respectively in the Charolais population. In addition, a genomic region on
BTA6 encompassing the NCAPG/LCORL locus, which is a known candidate locus associated with body size, was
associated with carcass weight in Angus, Charolais and Limousin. Novel candidate genes identified included ZFAT in
Angus, and SLC40A1 and the olfactory gene cluster on BTA15 in Charolais. Although the majority of associations
were breed specific, associations that operated across breeds included SORCS1 on BTA26, MCTP2 on BTA21 and
ARL15 on BTA20; these are of particular interest due to their potential informativeness in across-breed genomic
evaluations. Genomic regions affecting all three carcass traits were identified in each of the breeds, although these
were mainly concentrated on BTA2 and BTA6, surrounding MSTN and NCAPG/LCORL, respectively. This suggests that
although major genes may be associated with all three carcass traits, the majority of genes containing significant
variants (unadjusted p-value < 10− 4
) may be trait specific associations of small effect.
Conclusions: Although plausible novel candidate genes were identified, the proportion of variance explained by
these candidates was minimal thus reaffirming that while carcass performance may be affected by major genes in
the form of MSTN and NCAPG/LCORL, the majority of variance is attributed to the additive (and possibly
multiplicative) effect of many polymorphisms of small effect.