Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. Genome-wide association analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as XIRP2, TTC29, SOGA1, MAS1, GRK5, PROX1, GPR155 and ZFYVE26 were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kilo base pairs of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher’s exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important pathways for RFI. Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs.

Bovine maternal behavior is known to be influenced by a variety of factors including hormonal mediation, breed, age, parity, host genetics and general management practices. Following centuries of varying levels of domestication processes, the behavior of the bovine cow has altered from that of her original wild ungulate ancestors, although many maternal instincts have remained unchanged. The influence of maternal behavior on calf health and performance is of interest to cow-calf beef production operations, as in most instances, the cow is solely responsible for rearing the calf until weaning. However, investigating the magnitude of this influence is challenging, in part because objective measurement of behavioral traits is difficult, particularly in extensive settings. In recent years, while a number of remote monitoring devices have been developed that afford opportunities for objective measurement of behavioral traits in livestock, characterization of physiological mechanisms that underlie superior maternal behavior, including identification of potential biomarkers remains elusive in cattle. Hormonal profiles during the periparturient period have been shown to influence behavioral patterns in both current and future generations in other mammalian species and may provide insights into the physiology of bovine maternal behavior. Therefore, the aim of this review is to describe general characteristics of bovine maternal behavior and the factors known to influence it, including hormonal drivers, through which cross-reference to other species is made. Current methods of measuring and assessing behavior that may also be applicable to most production settings have also been reviewed. At present, there is no known hormonal assay that can be used to measure and/or reliably predict bovine maternal behavior post-calving or across generations. Being able to objectively assess superior maternal behavior, whether that be through remote monitoring, hormonal profiling or indirectly through measuring calf performance will be beneficial to livestock industries in the future.

Background: Johne's disease is a chronic inflammatory bowel disease (IBD) of ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP). Since this pathogen has been implicated in the pathogenesis of human IBDs, the goal of this study was to assess whether single nucleotide polymorphism (SNPs) in several well-known candidate genes for human IBD are associated with susceptibility to MAP infection in dairy cattle. Methods: The bovine candidate genes, interleukin-10 (IL10), IL10 receptor alpha/beta (IL10RA/B), transforming growth factor beta 1 (TGFB1), TGFB receptor class I/II (TGFBR1/2), and natural resistance-associated macrophage protein 1 (SLC11A1) were sequenced for SNP discovery using pooled DNA samples, and the identified SNPs were genotyped in a case-control association study comprised of 242 MAP negative and 204 MAP positive Holstein dairy cattle. Logistic regression was used to determine the association of SNPs and reconstructed haplotypes with MAP infection status. Results: A total of 13 SNPs were identified. Four SNPs in IL10RA (984G > A, 1098C > T, 1269T > C, and 1302A > G) were tightly linked, and showed a strong additive and dominance relationship with MAP infection status. Haplotypes AGC and AAT, containing the SNPs IL10RA 633C > A, 984G > A and 1185C > T, were associated with an elevated and reduced likelihood of positive diagnosis by serum ELISA, respectively. Conclusions: SNPs in IL10RA are associated with MAP infection status in dairy cattle. The functional significance of these SNPs warrants further investigation.