Abstract
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp 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. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that 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 strongly suggest PLAG1 as the causative gene underlying this diverse range of traits, and demonstrate new effects for the locus on lactation phenotypes.
Highlights
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds
The genetic signature of the LYN expression QTL (eQTL) appeared to differ from the PLAG1 eQTL, with a different lead SNP (P = 1.71 × 10−7; rs109116062; chr14:24909247; Fig. 1a,b and c; Table 1), and with the rs109815800 variant appearing lower in the association rankings for LYN
The rs109815800 SNP explained 46.6% of the genetic variance and 32.6% of the phenotypic variance in PLAG1 expression, and 45.2% and 9.6% respectively for expression of LYN (Table 2). This contrasted with 61.6% and 9.9% respectively for the lead LYN SNP rs109116062, again suggesting that the PLAG1 and LYN eQTLs might be being driven by different or overlapping effects
Summary
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp 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. Further functional and genetic analysis reduced the number of candidate variants to two polymorphisms in the bidirectional promoter of the PLAG1 and CHCHD7 genes; rs209821678, a (CCG) repeat of 9 or 11 copies and rs210030313 an A to G nucleotide substitution[3] In this analysis, both variants were associated with foetal expression of seven of the nine genes within a ~780 kilobase (kb) interval representing the stature QTL.
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