DOI: 10.5061/dryad.r8251
title: Data from: Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics

description: A major pleiotropic quantitative trait locus (QTL) located at ~25Mbp on
 bovine chromosome 14 affects a myriad of growth and developmental traits
 in Bos taurus and indicus breeds. These QTL have been attributed to two
 functional variants in the bidirectional promoter of PLAG1 and CHCHD7, and
 although PLAG1 is a good candidate for mediating these effects, its role
 remains uncertain given these variants are also associated with expression
 of five additional genes at the broader locus. In the current study, we
 conducted expression QTL (eQTL) mapping of this region using a large, high
 depth mammary RNAseq dataset representing 375 lactating cows. Here we show
 that of the seven previously implicated genes, only PLAG1 and LYN are
 differentially expressed by QTL genotype, and only PLAG1 bears the same
 association signature of the growth and body weight QTLs. For the first
 time, we also report significant association of PLAG1 genotype with milk
 production traits, including milk fat, volume, and protein yield.
 Collectively, these data confirm PLAG1 as the causative gene underlying
 this diverse range of physiological QTLs, and indicate new effects for the
 locus on lactation phenotypes.
description: Milk Composition
 Phenotype DataMilk composition records
 were measured as part of standard herd testing procedures. Abbreviations
 used: id = animal identification, sire = sire animal identification,
 pgsire = parternal sire animal identification, pmgsire = partern fr =
 friesian, je = jersey, hol = holestein, FxJ = freisian x jersey, FxH =
 freisian x holestein, JxH = jersey x holestein, fat = fat yield, fat_pct =
 fat percentage, milk = milk yield, prot = protein, prot_pct = protein
 percentage, ydlwt = liveweightmilkcompdata_forsubsmission.xlsxGene Expression DataGene expression data for genes at the chromosome 14 liveweight locus from lactating mammary tissue biopsies. RNAseq read counts have been normalised using variance-stabilisation transformation. Abbreviations used: id = animal identification, sire = sire animal identification, pgsire = parternal sire animal identification, pmgsire = partern fr = friesian, je = jersey, hol = holestein, FxJ = freisian x jersey, FxH = freisian x holestein, JxH = jersey x holestein,eQTLdata_for_papersubmission.xlsxAnimal Genotypes for eQTL analysis at liveweight locusAnimal genotypes for the 432 Illumina BovineHD BeadChip markers at the chromosome 14 liveweight locus. Animals were genotyped using this panel directly, apart from 29 animals which were genotyped using the Illumina BovineSNP50 and imputed up to the HDChip density using Beagle. These genotypes were used for association analysis with gene expression phenotypes from the lactating mammary tissue biospies. PLINK was used to recode the genotypes to 0,1,2 to represent the number of alternative allele copies for each marker. anml_id = anonymised animal identificationeQTLgens.xlsxAnimal Genotypes for milk production analysis at liveweight locusAnimal genotypes for the 432 Illumina BovineHD BeadChip markers at the chromosome 14 liveweight locus. Animals were genotyped either using this panel directly, or were genotyped using the Illumina BovineSNP50 and imputed to the HDChip markers using Beagle. These genotypes were used for association analysis with milk production phenotypes generated as part of standard herd test procedures. PLINK was used to recode the genotypes to 0,1,2 to represent the number of alternative allele copies for each marker. anml_id = anonymised animal identificationmilkcompgens.xlsx