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

Genomic analyses of nitrogen utilization efficiency, its indicator trait blood urea nitrogen and the relationship to classical growth performance and feed efficiency traits in a Landrace × Piétrain crossbred population

Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was h2 = 0.293 in FP1 and h2 = 0.163 in FP2 and BUN had the by far highest heritability (h2 = 0.415 in FP1 and h2 = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlationsr g = - 0.631 $$ {r}_g=-0.631 $$ andr g = - 0.688 $$ {r}_g=-0.688 $$ between NUE and BUN measured in FP1 and FP2, respectively). The genetic correlations of NUE and BUN with important production traits suggest selecting pigs with high growth rates and low BUN levels to breed more efficient pigs in future breeding programs.

Phenotypic link between protein efficiency and pig welfare suggests no apparent trade-offs for mitigating nitrogen pollution

Pig manure contributes significantly to environmental pollution through nitrogen compounds. Reducing protein in feed can help, but it may lead to damaging behaviors if pigs' nutritional needs are not met. Breeding pigs for higher protein efficiency (PE) is a long-term solution to reduce nitrogen pollution, but concerns about pig welfare remain. We studied 95 pigs involved in a project on the genetic basis of PE on a 20% protein restricted diet to investigate the phenotypic connection between PE and welfare. These pigs represented natural PE variations in the population. At around 100 days, before their PE was known, we observed their behaviors. Only three pigs engaged in tail biting and manipulation of vulnerable regions, but this was not associated with PE. There was no clear link between PE and manipulating pen mates' less vulnerable regions. Such behaviors are normal but can cause stress and injury if carried out excessively due to boredom or stress. Overall, pigs with higher PE showed no major behavioral abnormalities in this study. Considering the lack of genetic knowledge, the risk of increased harmful behaviors when selecting for higher PE appears low when inferred from this purely phenotypic association.

Genetic analysis of protein efficiency and its association with performance and meat quality traits under a protein-restricted diet

BACKGROUND

An essential component in the development of sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to incomplete conversion to muscle tissue, excess nitrogen is excreted, resulting in environmental problems such as nitrate pollution and greenhouse gas emissions. Therefore, improving protein efficiency (PE), i.e., the proportion of dietary protein that remains in the carcass, is desirable. The aim of this study was to estimate the heritability (h²) of PE and its genetic correlations with phosphorus efficiency, three performance, seven meat quality and two carcass quality traits when pigs were fed a 20% protein-restricted diet, using 1071 Swiss Large White pigs. To determine PE, the intake of feed with known nutrient content was accurately recorded for each pig and the nitrogen and phosphorus content of the carcass was determined using dual-energy X-ray absorptiometry.

RESULTS

We found an average PE of 0.39 ± 0.04 and a heritability of 0.54 ± 0.10. PE showed a high genetic correlation with phosphorus efficiency (0.61 ± 0.16), moderate genetic correlations with feed conversion ratio (- 0.55 ± 0.14) and average daily feed intake (- 0.53 ± 0.14), and a low genetic correlation with average daily gain (- 0.19 ± 0.19). While PE has favourable genetic correlations with the performance traits and some meat quality traits, there is a potentially unfavourable correlation of PE with meat colour (redness [r_g = - 0.27 ± 0.17]; yellowness [r_g = - 0.31 ± 0.18]) and intra-muscular fat (IMF; r_g = - 0.39 ± 0.15). Feed conversion ratio (FCR) also showed unfavourable genetic correlations with meat lightness, redness yellowness, IMF and cooking loss.

CONCLUSIONS

PE is a heritable trait that can be considered in breeding programs to reduce the environmental impact of pig production. We found no strong negative correlation of PE with meat quality traits, and that there is potential to indirectly select for improved phosphorus efficiency. Selecting nutrient efficiencies might be a more suitable strategy to reduce nitrogen pollution from manure than focusing on FCR because the latter also shows genetic antagonism with some meat quality traits in our population.

Genetic analyses of nutrient digestibility measured by fecal near-infrared spectroscopy in pigs

Improved nutrient digestibility is an important trait in genetic improvement in pigs due to global resource scarcity, increased human population and greenhouse gas emissions from pork production. Further, poor nutrient digestibility represents a direct nutrient loss, which affects the profit of the farmer. The aim of this study was to estimate genetic parameters for apparent total tract digestibility of nitrogen (ATTDn), crude fat (ATTDCfat), dry matter (ATTDdm), and organic matter (ATTDom) and to investigate their genetic relationship to other relevant production traits in pigs. Near-infrared spectroscopy was used for prediction of total nitrogen content and crude fat content in feces. The predicted content was used to estimate apparent total tract digestibility of the different nutrients by using an indicator method, where acid insoluble ash was used as an indigestible marker. Average ATTDdm, ATTDom, ATTDn, and ATTDCfat ranged from 61% to 75.3%. Moderate heritabilities was found for all digestibility traits and ranged from 0.15 to 0.22. The genetic correlations among the digestibility traits were high (>0.8), except for ATTDCfat, which had no significant genetic correlation to the other digestibility traits. Significant genetic correlations were found between ATTDn and feed consumption between 40 and 120 kg live weight (F40120) (-0.54 ± 0.11) and ATTDdm and F40120 (-0.35 ± 0.12) and ATTDom and F40120 (-0.28 ± 0.13). No significant genetic correlations were found between digestibility traits and loin depth at 100 kg, nor backfat thickness at 100 kg (BF), except between BF and ATTDn (-0.31 ± 0.14). These results suggested that selection for improved feed efficiency through reduced feed intake within a weight interval, also has led to improved ATTDdm, ATTDom, and ATTDn. Further, the digestibility traits are heritable, but mainly related to feed intake and general function of the intestines, as opposed to allocation of feed resources to different tissues in the body.

A new direction for tackling phosphorus inefficiency in the UK food system

The UK food system is reliant on imported phosphorus (P) to meet food production demand, though inefficient use and poor stewardship means P is currently accumulating in agricultural soils, wasted or lost with detrimental impacts on aquatic environments. This study presents the results of a detailed P Substance Flow Analysis for the UK food system in 2018, developed in collaboration with industry and government, with the key objective of highlighting priority areas for system interventions to improve the sustainability and resilience of P use in the UK food system. In 2018 the UK food system imported 174.6 Gg P, producing food and exportable commodities containing 74.3 Gg P, a P efficiency of only 43%. Three key system hotspots for P inefficiency were identified: Agricultural soil surplus and accumulation (89.2 Gg P), loss to aquatic environments (26.2 Gg P), and waste disposal to landfill and construction (21.8 Gg P). Greatest soil P accumulation occurred in grassland agriculture (85% of total accumulation), driven by loadings of livestock manures. Waste water treatment (12.5 Gg P) and agriculture (8.38 Gg P) account for most P lost to water, and incineration ashes from food system waste (20.3 Gg P) accounted for nearly all P lost to landfill and construction. New strategies and policy to improve the handling and recovery of P from manures, biosolids and food system waste are therefore necessary to improve system P efficiency and reduce P accumulation and losses, though critically, only if they effectively replace imported mineral P fertilisers.

Evaluation of feeding behaviour traits to predict efficiency traits in pigs using partial least square regression

The improvement of efficiency traits, such as protein efficiency (PE), digestible energy efficiency (EnE) and lipid gain (LipG), are relevant given their associations with environmental pollution, cost of production, and the quality of meat. However, these traits are difficult to measure and usually require slaughtering of pigs. Efficiency traits are complex, and several factors, such as genetic predisposition, feed composition, but also individual feeding behaviour may contribute to efficiency. The objective of this study was therefore to evaluate the potential of using feeding behaviour traits to predict efficiency traits under dietary protein restriction. A total of 587 Swiss Large White pigs, consisting of 312 females and 275 castrated males, had ad libitum access to feed and water, and were fed a protein-reduced diet (80% of recommended digestible protein and essential amino acids) from 22.5 ± 1.6 to 106.6 ± 4.6 kg BW. Individual feed intake was monitored and carcass composition (lean and fat mass) at slaughter was determined by dual-energy X-ray absorptiometry. The PE and EnE were calculated as the ratio of protein or energy in the carcass (estimated by dual-energy X-ray absorptiometry) to the total protein or energy consumed. Feeding behaviour traits monitored were daily feed intake, feed intake per meal, number of daily meals, duration per meal, feeding rate, and feeder occupation. A partial least square (PLS) regression was used to predict PE, EnE and LipG from feeding behaviour traits, while including farrowing series (for PE only), age at slaughter and BW at slaughter. Accuracy of PLS regression was assessed based on RMSE and R² for calibration and validation sets, and on concordance correlation coefficient, which were estimated over 100 replicates of calibration and validation sets. Models with a number of latent variables of 5, 2 and 3 were identified as optimal for PE, EnE, and LipG, which explained 34.64%, 55.42% and 82.68% of the total variation in PE, EnE, and LipG, respectively. Significant concordance correlation coefficient was found between predicted and observed values for PE (0.50), EnE (0.70), and LipG (0.90). In conclusion, individual feeding behaviour traits can better predict EnE and LipG than for PE under dietary protein restriction when fed ad libitum.

Genetics of digestive efficiency in growing pigs fed a conventional or a high-fibre diet

The use of diets with increased dietary fibre content (HF) from alternative feedstuffs is a solution to limit the impact of increased feed costs on pig production. This study aimed at determining the impact of an alternative HF diet on pig digestibility and at estimating genetic parameters of this trait. Digestibility coefficients (DC) of energy, organic matter and nitrogen were predicted from faecal samples analysed with near infrared spectrometry for 1,242 samples, and it represented 654 Large White pigs fed a conventional (CO) diet and 588 fed a HF diet. Growth and feed efficiency traits, carcass composition and meat quality traits were recorded. Pigs fed the HF diet had significantly lower DC than pigs fed the CO diet (−4.5 to 6.0 points). The DC were moderately to highly heritable (about 0.26 ± 0.12 and 0.54 ± 0.15 in the CO and the HF diet, respectively). Genetic correlations were favourable with feed conversion ratio, daily feed intake and residual feed intake, but unfavourable with average daily gain (ADG) and carcass yield (CY). To conclude, DC could be an interesting trait to include in future breeding objectives if pigs were fed diet with HF diets, but adverse genetic trends with ADG and CY would have to be taken into account.

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

Pig production contributes to environmental pollution through excretion of phosphorus and nitrogenous compounds. European pig production requires annual imports of currently 36 million tons of soya bean, because domestic plant protein sources often do not meet the required protein quality. Most of the mineral phosphate sources are also imported. It is therefore desirable to improve nutrient deposition efficiency through selective breeding, that is to realise similar growth rates and carcass compositions as currently achieved but with a lower intake of dietary crude protein or phosphate. For a preliminary evaluation of the potential of selecting for increased nutrient deposition efficiency, we estimated genetic parameters for nitrogen and phosphorus efficiencies in a Swiss Large White pig population including 294 individuals. Nutrient efficiency phenotypes were obtained from wet‐chemistry analyses of pigs of various live weights. Heritability of nitrogen efficiency was estimated at 41%. Heritability of phosphorus efficiency was very low (0.3%), but positive genetic correlations with nitrogen efficiency suggest that breeding for nitrogen efficiency would positively affect phosphorus efficiency. Further studies are needed to improve the quality of estimates and to obtain accurate high‐throughput measures of nutrient efficiency to be implemented on farms.