Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake

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

A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs

International audienceAbstractBackgroundCrossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace–Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set.ResultsAdditive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG.ConclusionsMethodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system

Changes in the relative thickness of individual subcutaneous adipose tissue layers in growing pigs

<p>Abstract</p> <p>Background</p> <p>The thickness of the subcutaneous fat layer is an important parameter at all stages of pig production. It is used to inform decisions on dietary requirements to optimize growth, in gilts to promote longevity and finally to assist in the calculation of payments to producers that allow for general adiposity. Currently for reasons of tradition and ease, total adipose thickness measurements are made at one or multiple sites although it has been long recognized that up to three well defined layers (outer (L1), middle (L2), and inner (L3)) may be present to make up the total. Various features and properties of these layers have been described. This paper examines the contribution of each layer to total adipose thickness at three time points and describes the change in thickness of each layer per unit change in body weight in normal growing pigs.</p> <p>Methods</p> <p>A group of nine pigs was examined using 14 MHz linear array transducer on three separate occasions. The average weight was 51, 94 and 124 kg for each successive scan. The time between scanning was approximately 4 weeks. The proportion of each layer to total thickness was modeled statistically with scan session as a variable and the change in absolute thickness of each layer per unit change in body weight was modeled in a random regression model.</p> <p>Results</p> <p>There was a significant change in ratios between scans for the middle and inner layers (<it>P </it>< 0.001). The significant changes were seen between the first and second, and between the first and final, scan sessions. The change in thickness per unit change in body weight was greatest for L2, followed by L1 and L3.</p> <p>Conclusion</p> <p>These results demonstrate that subcutaneous adipose layers grow at different rates relative to each other and to change in body weight and indicate that ultrasound can be used to track these differences.</p

Animal production for efficient phosphate utilization: from optimized feed to high efficiency livestock

Phosphorus (P) is an essential nutrient for livestock but its efficiency of utilization is below 40%, contributing to environmental issues. In this review, we summarize recent approaches to optimize P availability in livestock diets and improve its utilization efficiency. Phase feeding could potentially reduce P excretion by 20%. Addition of phytase enzymes to diets increased P availability from 42 to 95%. Low phytate transgenic plants and transgenic animals increased P availability by 14% and 52-99%, respectively. In practice, a combination of phase feeding and enzymes has the highest potential for P reduction but legislation and ethics implications will prevent using transgenic animals in the short term. Functional and nutritional genomics may provide tools to improve efficiency in the future