Novel insight into the genomic architecture of feed and nitrogen efficiency measured by residual energy intake and nitrogen excretion in growing pigs

Abstract

BackgroundImprovement of feed efficiency in pigs is of great economical and environmental interest and contributes to use limited resources efficiently to feed the world population. Genome scans for feed efficiency traits are of importance to reveal the underlying biological causes and increase the rate of genetic gain. The aim of this study was to determine the genomic architecture of feed efficiency measured by residual energy intake (REI), in association with production, feed conversion ratio (FCR) and nitrogen excretion traits through the identification of quantitative trait loci (QTL) at different stages of growth using a three generation full-sib design population which originated from a cross between Pietrain and a commercial dam line.ResultsSix novel QTL for REI were detected explaining 2.7-6.1% of the phenotypic variance in REI. At growth from 60–90 kg body weight (BW), a QTL with a significant dominance effect was identified for REI on SSC14, at a similar location to the QTL for feed intake and nitrogen excretion traits. At growth from 90–120 kg BW, three QTL for REI were detected on SSC2, SSC4 and SSC7 with significant additive, imprinting and additive effects, respectively. These QTL (except for the imprinted QTL) were positionally overlapping with QTL for FCR and nitrogen excretion traits. During final growth (120–140 kg BW), a further QTL for REI was identified on SSC8 with significant additive effect, which overlapped with QTL for nitrogen excretion. During entire analysed growth (60–140 kg BW), a novel additive QTL for REI on SSC4 was observed, with no overlapping with QTL for any other traits considered.ConclusionsThe occurrence of only one overlapping QTL of REI with feed intake suggests that only a small proportion of the variance in REI was explained by change in feed intake, whereas four overlapping QTL of REI with those of nitrogen excretion traits suggests that mostly underlying factors of feed utilisation such as metabolism and protein turnover were the reason for change in REI. Different QTL for REI were identified at different growth stages, indicating that different genes are responsible for efficiency in feed utilisation at different stages of growth.

Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency in a Swiss large white pig population using chemical analysis

“…In contrast to other studies that reported heritabilities of ADG and FCR in pigs ranging from 0.05 to 0.48 and 0.22 to 0.40 for ADG and FCR, respectively (Kavlak & Uimari, 2019; Nascimento, Nascimento, Dekkers, & Serão, 2019; Saintilan et al, 2013; Shirali, Varley, & Jensen, 2018; Silva, Lopes, Lopes, & Gasparino, 2019), our heritability estimate of ADG was close to zero and the one of FCR was rather low. Several QTLs were identified for ADG (Shirali et al, 2013; Silva et al, 2019) and FCR (Reyer et al, 2017; Silva et al, 2019), indicating a genetic basis of these traits. One possible reason why our estimates for ADG and FCR were comparably low could be the relatively small sample size of our study.…”

“…Because of the costs involved in chemical analysis, the N and P contents in the empty body or the carcass are generally estimated. For instance, Saintilan et al (2013) used prediction equations that relate lean meat content during dissections to nitrogen or phosphorus excretion and Shirali et al (2013) used the deuterium dilution technique to estimate water content, from which lean meat content can be derived. Saintilan et al (2013) reported heritabilities of N and P retention between 36%–43% and 30%–41%, respectively, in a range of pig breeds.…”

Joint analysis of longitudinal feed intake and single recorded production traits in pigs using a novel Horizontal model

“…This suggests that different genes can be associated with RFI at different stages of growth. Shirali et al (2013) showed that different QTL influence RFI at different stages of growth in growing-finishing pigs. In addition, Shirali et al (2014) reported that RFI at 60 to 90 kg BW was lowly correlated with RFI at 90 to 120 kg BW and 120 to 140 kg BW, supporting the findings of this study.…”

Longitudinal analysis of residual feed intake and BW in mink using random regression with heterogeneous residual variance

“…This difference can be due to different definitions of feed efficiency and different methods of estimating correlations. Furthermore, feed efficiency has been shown to have different genetic backgrounds at different stages of growth in other species, for example in pigs (Shirali et al, 2014) and different genes responsible for efficiency of feed utilization at different stages of growth (Shirali et al, 2013). The phenotypic correlations between the growing and furring periods were positive and moderate to high and generally smaller than the genetic correlations, suggesting the effect of residual variance on the feed efficiency.…”