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Project

Excelling in equality: A new method to improve life-long uniformity and resilience of livestock via precision livestock breeding

The Piétrain pig breed is the last native Belgian pig breed with a viable population size. The breed originated in the vicinity of the village Piétrain during the first half of the 20th century, and the breed is characterized by its black spots with a grey outline and superior muscularity. After the formation of the breed, Piétrain pigs were exported worldwide from the 1960s which led to the formation of various Piétrain subpopulations nowadays. Piétrain pigs used as a paternal sire in the typical three-way crossbreeding in commercial pig farming: Piétrain boars are mated with crossbred sows from maternal lines to generate slaughter pigs. In Flanders, for example, a relatively small number of ~800 Piétrain pigs sired more than five million finishing pigs in 2021. Because of this enormous multiplier effect, maintaining the genetic diversity and increasing the genetic value of Piétrain pigs is crucial. Therefore, this PhD-thesis first focused on the genetic diversity status of different Piétrain pig subpopulations. Second, we explored the use of new phenotypes to breed Piétrain pigs for an increased overall resilience.

Our genetic diversity study analysed data from five Piétrain subpopulations from Belgium, The Netherlands, France, Germany and the United States. This study showed that the level of genetic diversity within the different Piétrain subpopulations is still acceptable, with effective population size (Ne) estimates between 85 and 92 animals for different Piétrain subpopulations, and 105 animals for all subpopulations combined. Moreover, inbreeding estimates based on runs of homozygosity (Froh) were moderate to high (18-23%), but in the same range as other commercial pig populations such as Landrace, Large White and Duroc (19-26%). A major finding of this study was a large runs of homozygosity island on chromosome 8 (34-126Mb) which was present in nearly all Piétrain pigs over all subpopulations. Moreover, about 80% of all Piétrains had identical homozygous haplotypes on chromosome 8 from 50-70 Mb and from 90-105 Mb. These findings indicate that these large inbred regions must have emerged before breed formation in the 1960s. We believe that strong selection and inbreeding during breed formation nearly fixed these genomic regions in Piétrains. Our genetic diversity analyses also showed the existence of least three genetically distinct subgroups within the Piétrain breed, where the Piétrain subpopulations seem to be genetically diverging. Herein, the Belgian Piétrain population was genetically unique and it is crucial to maintain this genetic diversity. However, the Belgian Piétrain population is becoming increasingly at risk of extinction, with negative trends in the number of breeding animals and breeders over the past decades. Therefore, we argue that actions must be taken to conserve the Belgian Piétrain at a viable level, including a sufficient population size, genetic diversity and a strong breeding structure. Without any actions, the authentic Belgium Piétrain population might disappear, and Belgium will lose its last remaining, native pig breed.

Increasing pigs’ overall resilience has become paramount. The driving factors for more resilient pigs are the increasing intensification in pig farming, increasing societal concerns for more animal welfare and a reduced antibiotic usage and increasing environmental variability. As a result, pig farmers desire pigs who are genetically primed to be resilient and less labor intensive. To meet these desired features, this PhD-thesis investigated the genetics of new phenotypes to breed more resilient Piétrain pigs.

In a first study, we investigated if we can breed pigs that need less antibiotic treatments. Here, we derived new phenotypes from on-farm parenteral antibiotic records from commercially grown crossbred finishing pigs with a Piétrain sire. Our study found moderate heritability estimates (18-44%) for antibiotic usage phenotypes, with low to moderate genetic correlations with mortality (rg=0.08-0.60) and no strong adverse genetic correlations with production traits. These findings suggest that phenotypes derived from on-farm antibiotics records are promising for inclusion in future pig breeding programs to breed for a decrease in antibiotics usage and an increased overall resilience.

In a second study, we expanded routine pig weighing with an overhead camera to estimate pigs’ body dimensions and activity levels using an automated computer vision system. Furthermore, we were able to couple these data with pedigree information to estimate genetic parameters. Via this system, we showed that body parts could be tracked accurately with an average tracking error of 3.3 cm. Additionally, the body dimensions extracted from video images were highly heritable (61-74%), whereas activity traits were low to moderately heritable (22-35%). These findings show we can automatically phenotype new production and behavioral traits on an individual level for pig breeding.

In a third study, we quantified resilience from longitudinal data of body weight, feed intake and feeding behavior collected via automated feeding stations. The resilience hypothesis states that a challenge will lead to a deviation from a pig’s optimal production level, with resilient pigs being less affected by a challenge. As a result, deviations from longitudinal data can be used as a proxy for pigs’ overall resilience. Within this study, we analysed 324,207 records between the age of 95 and 155 days on 5,939 Piétrain pigs with known pedigree and genomic information. We showed that resilience traits were lowly to moderately heritable for deviations in body weight (h2=2.9-20.2%), in feed intake (h2=9.4-23.3%) and in feeding behaviour (h2=16.2-28.3%). Deviations in individual body weight and feed intake trajectories are highly correlated (rg= 0.78) with low to moderate favorable genetic correlations with feed conversion ratio (rg= 0.39-0.49). These findings are valuable for breeding organizations as they offer evidence that pigs’ overall resilience can be selected on with good accuracy. Moreover, this methodology can be extended to other species to quantify resilience based on longitudinal data.

In a fourth study, we investigated to which extent these new resilience traits are associated with traits related to pigs’ resilience, health and welfare, such as mortality, tail biting wounds and lameness. In our experiment, 1919 finishing pigs with known pedigree were weighed every two weeks and scored for physical abnormalities, such as lameness and ear and tail biting wounds. Resilience was assessed via deviations in body weight, which had moderate heritability estimates (h2 = 25.2 to 36.3%) in line with our previous study. Moreover, deviations in body weight were positively associated and genetically correlated with tail biting wounds (rg = 0.22 to 0.30), lameness (rg = 0.15 to 0.31) and mortality (rg = 0.19 to 0.33). These results indicate that events of tail biting, lameness and mortality are associated with deviations in pigs’ body weight evolution. These findings are valuable for pig breeders, as they offer evidence that these resilience traits are an indication of animals’ overall health, welfare and resilience.

This PhD thesis has assessed the genetic diversity of different Piétrain populations. Urgent action is advised to maintain the genetically valuable Belgian Piétrain population at a viable level in the future. Furthermore, this PhD thesis has shown the possibility to breed pigs for a decreased antibiotic usage, altered activity levels and an increased overall resilience. We advise pig breeders to implement our proposed resilience traits based on longitudinal deviations in body weight and/or feed intake in their breeding programs, as these traits are heritable and favorably associated with pigs’ health, welfare and resilience related traits. Selective breeding on these traits would thus result in more resilient pigs that are needed for future pig farming.

Date:16 Oct 2017 →  Today
Keywords:Uniformity, Genomic Selection, Livestock, Resilience
Disciplines:Bio-informatics, Modelling and simulation, Animal genetics, Agricultural animal production not elsewhere classified
Project type:PhD project