QTL region–specific microarrays reveal differential expression of positional candidate genes of signaling pathways associated with the liability for the inverted teat defect

Abstract

The inverted teat defect is the most common disorder of the mammary complex in pigs. It is characterized by the failure of teats to protrude from the udder surface, preventing normal milk flow and thus limiting the rearing capacity and increasing the risk of mastitis. The inverted teat defect is a liability trait with a complex mode of inheritance. We previously identified QTL for inverted teats. As a complementary approach that integrates map-based efforts to identify candidate genes for the inverted teat defect with function-driven expression analysis, application-specific microarrays were constructed that cover 1525 transcripts mapping in QTL regions on pig chromosomes 2, 3, 4, 6 and 11. About 950 transcripts were expressed in epithelial and mesenchymal teat tissue. The expression of three categories of teats was compared: normal teats of both non-affected and affected animals and inverted teats of affected animals. In epithelium and mesenchyme, 62 and 24 genes respectively were significantly differentially expressed (DE). The majority of biofunctions to which a significant number of DE genes were assigned are related to the following: (1) cell maintenance, proliferation, differentiation and replacement; (2) organismal, organ and tissue development; or (3) genetic information and nucleic acid processing. Moreover, the DE genes belong almost exclusively to canonical pathways related to signaling rather than metabolic pathways. This is in line with findings obtained by genome-wide catalogue microarrays. This study adds another piece to the puzzle of the etiology of inverted teats by indicating that causal genetic variation leading to the disorder is likely among the genes encoding for members of the signaling cascades of growth factors.

Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle

“…FUK has been reported by Ibeagha-Awemu et al [4] as a candidate gene for milk traits because of its association with butyric acid levels (C4:0). DDX19B is involved in molecular transport in human [17] and has been associated with organismal, organ and tissue development in pigs [18]. While our results show evidence for eQTL for both FUK and DDX19B expression in the region, it is not clear whether there is one eQTL affecting both genes or two different eQTL.…”

Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs

“…The ATXN3 also shares the cysteine-type peptidase activity molecular function with TINAGL1 gene on the network analyzed here. This gene is also known as tubulointerstitial nephritis antigen-like 1 and was cited to be differentially expressed in epithelial teat tissue of pigs in studies of QTL region-specific of positional candidate genes associated with the inverted teat defect (Chomwisarutkun et al 2013). The other genes of the network analyzed here did not have features in common with each other but they entered at the net to be related with the trait analyzed.…”

Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs

“…The formation of vertebrae arises from the somites, while the initiation of mammary gland formation is influenced by factors in the dermal mesenchyme, which also originates from the somites. Moreover, each individual mammary gland is believed to be governed by specific genetic components that dictate whether its development will be initiated and sustained [29][30][31][32].…”