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Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.

International audience

International audience

International audience; The use of early biomarkers is an interesting approach to improve selection efficiency for traits that are difficult to measure. The aim of this study was to validate juvenile IGF1 and leptin as biomarkers of growth and feed efficiency in Large White (LW), Duroc and Piétrain purebred lines. To determine plasma concentrations of IGF1 and leptin, blood samples were obtained from 8-9-week-old piglets at the end of the post-weaning phase. After data curation, 337 LW, 192 Duroc and 189 Piétrain pigs had both plasma concentrations and production performance recorded during the growing-finishing phase, namely average daily gain (ADG), daily feed intake (DFI) and feed conversion ratio (FCR). Nested linear mixed models including successively the biomarker concentration and the weight at bleeding (BBW) as covariables in addition to the usual effects were compared using a likelihood ratio test. In the three lines, adding IGF1 concentration in prediction models of growth and feed efficiency traits increased the goodness-of-fit, with the covariable being significant (P < 0.001), except for FCR in the Piétrain line. Augmenting this model with BBW increased the model likelihood in the LW and Duroc breeds for any traits, as BBW was highly significant (P < 0.001) although IGF1 was not significant anymore. These results suggested that IGF1 is a biomarker of growth and feed efficiency that captured the same information as BBW. In the Piétrain line, IGF1 contributed to increase the likelihood of the model along with BBW for ADG and DFI. Hence, IGF1 seems to be a relevant biomarker for the Piétrain breed but to have limited utility for the LW and Duroc breeds if pigs can be weighed in the post-weaning phase. The same approach was applied to juvenile leptin, but it was found not to be a useful biomarker of growth or feed efficiency for the three lines.

National audience; One of the expected benefits of crossbreeding, a common practice in the pig industry, may be the increase in genetic variability, especially in a context of creation of synthetic populations. This increase in variability, related to the heterozygous status of individuals, remains difficult to specify when only genealogical information is available. It is now possible to characterize genetic variability in pig populations at a genome scale by analyzing genotypic data. One possible approach is to detect homozygous regions along the genome to quantify genomic consanguinity in an individual. These homozygous regions can be quantified at the genome or chromosome scale. It is then possible to characterize both overall genomic consanguinity of an individual or a local one in specific areas of the genome. In this study, we used genomic information to estimate inbreeding by detecting homozygous regions in the genomes of purebred Large White dams and Pietrain sires and their crossbred offspring. All individuals were genotyped using the IlluminaSNP60 porcine chip. As expected, fewer homozygous segments were detected in crossbr ed animals than in their parental populations. In addition, the total length of these segments was lower in crossbr ed animals. These observations can be interpreted as a decrease in consanguinity; however, the conservation of homozygous segments in crossbred offspring means that some haplotypes were shared between parental populations.; Un des bénéfices attendus du croisement entre lignées, pratique répandue dans la filière porcine, peut être l’accroissement de variabilité génétique, notamment dans un contexte de création de populations synthétiques. Cette augmentation de la variabilité, liée à l’état hétérozygote des individus, reste difficile à préciser lorsque seule l’information généalogique est disponible. Il est dorénavant possible de caractériser la variabilité génétique présente dans les populations porcines à une échelle génomique via l’analyse de données de génotypage. Une des approches possibles est la détection de régions homozygotes le long du génome, qui permet de quantifier la consanguinité génomique chez un individu. La quantification de ces régions homozygotes pouvant être réalisée à l’échelle du génome ou du chromosome, elle permet de caractériser à la fois la consanguinité génomique globale d’un individu ou une consanguinité locale en des zones plus ciblées du génome. Nous proposons dans cette étude d’utiliser l’information génomique afin d’estimer la consanguinité via la détection de régions homozygotes présentes dans les génomes de reproducteurs de races pures Large White et Piétrain et de leurs produits croisés. L’ensemble des individus a été génotypé sur la puce porcine IlluminaSNP60. Comme attendu, un nombre moins important de segments homozygotes est détecté chez les animaux croisés par rapport aux deux populations parentales. De plus, la longueur totale de ces segments est plus faible chez les animaux croisés. Même si ces observations peuvent être interprétées comme une diminution de la consanguinité, la conservation de segments homozygotes chez les descendants croisés signifie que certains haplotypes sont partagés entre les populations parentales.

International audience

51. Journées de la Recherche Porcine, 5 et 6 février 2019, Paris, p. 309-314,; Intérêt des performances de truies croisées pour la sélection en race pure de caractères de reproduction de la lignée maternelle Large-White. 51. Journées de la Recherche Porcine

National audience