Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis.

PloS One
Hubert PauschRuedi Fries

Abstract

Pigmentation patterns allow for the differentiation of cattle breeds. A dominantly inherited white head is characteristic for animals of the Fleckvieh (FV) breed. However, a minority of the FV animals exhibits peculiar pigmentation surrounding the eyes (ambilateral circumocular pigmentation, ACOP). In areas where animals are exposed to increased solar ultraviolet radiation, ACOP is associated with a reduced susceptibility to bovine ocular squamous cell carcinoma (BOSCC, eye cancer). Eye cancer is the most prevalent malignant tumour affecting cattle. Selection for animals with ACOP rapidly reduces the incidence of BOSCC. To identify quantitative trait loci (QTL) underlying ACOP, we performed a genome-wide association study using 658,385 single nucleotide polymorphisms (SNPs). The study population consisted of 3579 bulls of the FV breed with a total of 320,186 progeny with phenotypes for ACOP. The proportion of progeny with ACOP was used as a quantitative trait with high heritability (h(2) = 0.79). A variance component based approach to account for population stratification uncovered twelve QTL regions on seven chromosomes. The identified QTL point to MCM6, PAX3, ERBB3, KITLG, LEF1, DKK2, KIT, CRIM1, ATRN, GSDMC, MITF and NBEAL2 ...Continue Reading

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Citations

Apr 1, 2014·BMC Genomics·Kathryn E KemperMichael E Goddard
Feb 15, 2013·Genetics, Selection, Evolution : GSE·Hubert PauschRuedi Fries
Aug 18, 2012·Human Molecular Genetics·Kathryn E Kemper, Mike E Goddard
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Mar 4, 2014·PLoS Genetics·Saber QanbariHenner Simianer
Nov 9, 2017·Genetics, Selection, Evolution : GSE·Heidi Signer-HaslerChristine Flury
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Dec 30, 2018·Molecular Ecology·Laurence FloriMathieu Gautier
Nov 11, 2019·Genetics, Selection, Evolution : GSE·Swati JivanjiMathew D Littlejohn
Aug 4, 2019·Journal of Comparative Pathology·M SözmenB Özba
Oct 27, 2018·Experimental Eye Research·Eleonora MauriziC B Tara Moore

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Methods Mentioned

BETA
genotyping
not
Chip

Software Mentioned

GCTA
EMMAX
PLINK
findhapV2

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