A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches. A GWAS was performed using a Bayesian sparse linear mixed model, based on 51 curly and 19 straighthaired French and North American horses from 13 paternal families genotyped on the Illumina EquineSNP50 Bead-Chip. A single strong signal was observed on equine chromosome 11, in a region that encompasses the type I keratin gene cluster. This region was refined by haplotype analysis to a segment including 36 genes, among which are 10 keratin genes (KRT-10, -12, -20, -23, -24, -25, -26, -27, -28, -222). To comprehensively identify candidate causal variants within all these genes, whole-genome sequences were obtained for one heterozygous curly stallion and its straighthaired son. Among the four non-synonymous candidate variants identified and validated in the curly region, only variant g. 21891160G> A in the KRT25 gene (KRT25:p.R89H) was in perfect agreement with haplotype status in the whole pedigree. Genetic association was then confirmed by genotyping a larger population consisting of 353 horses. However, five discordant curly horses were observed, which carried neither the variant nor the main haplotype associated with curliness. Sequencing of KRT25 for two discordant horses did not identify any other deleterious variant, which suggests locus rather than allelic heterogeneity for the curly phenotype. We identified the KRT25: p. R89H variant as responsible for the dominant curly trait, but a second dominant locus may also be involved in the shape of hairs within North American Curly horses

New approaches for feed efficiency selection in growing pig and opportunities to use them

L'amélioration de l'efficacité alimentaire est un enjeu économique et environnemental important pour la production porcine. L'aliment est le premier poste de dépenses en élevage porcin, et le restera vraisemblablement au vu de l'évolution du coût des matières premières. Historiquement, l'efficacité alimentaire a été améliorée en sélectionnant, avec succès, pour une diminution de l'indice de consommation (IC), qui représente l'efficacité de conversion de l'aliment en gain de poids. Dans un contexte d'évolution des objectifs de sélection, de nouvelles stratégies d'amélioration de l'efficacité alimentaire sont recherchées. Ce travail de thèse propose d'en explorer certaines en utilisant des données enregistrées en stations publiques de contrôle de performance entre 2000 et 2009 dans les quatre races porcines en sélection collective en France, deux races maternelles (Large White femelle et Landrace) et deux races paternelles (Large White mâle et Piétrain). L'approche privilégiée s'appuie sur la consommation moyenne journalière résiduelle (CMJR), qui est un critère d'efficacité alimentaire indépendant des performances des animaux, afin d'estimer ses relations génétiques avec les performances de production, ainsi qu'avec les quantités d'azote et de phosphore excrétées. Dans un premier temps, l'étude d'une population expérimentale Large White a montré que les corrélations génétiques entre sexes pour la CMJR étaient proches de 1, permettant par la suite de comparer les estimations de paramètres obtenues sur des femelles Piétrain à celles obtenues sur les mâles castrés des trois autres races. Nous montrons que ce caractère a une héritabilité (h²) comprise entre 0,21 et 0,33 selon les races, qu'il est un peu moins héritable que l'IC (h² entre 0,30 et 0,40), que ces deux caractères présentent des corrélations génétiques favorables (entre 0,52 et 0,85), et que si la CMJR est par définition phénotypiquement indépendante des caractères de croissance et de composition corporelle, elle l'est aussi au niveau génétique (corrélations inférieures à 0,16 en valeur absolue quelle que soit la race). En revanche, la CMJR, comme l'IC, a des relations génétiques antagonistes avec les caractères de qualité de la viande. Cependant, nous montrons que la CMJR, contrairement à l'IC, n'est pas affectée par le génotype halothane en ségrégation chez le Piétrain. Enfin, des corrélations génétiques très élevées avec l'IC (0,97 et plus), et plus modérées avec la CMJR (entre 0,38 et 0,86) ont été trouvées pour l'excrétion d'azote et de phosphore, suggérant la réduction attendue des rejets en réponse à la sélection sur l'efficacité alimentaire. Ces corrélations étaient globalement plus élevées dans les races paternelles que dans les races maternelles. Enfin, l'étude des cinétiques de croissance et d'ingestion des animaux en fonction de leur niveau d'efficacité alimentaire a montré qu'une sélection pour des animaux plus efficaces ne peut être réalisée qu'en adaptant la formulation des aliments, notamment leur concentration en acides aminés, de façon à permettre la pleine expression de leur potentiel génétique.Improvement of feed efficiency is a main economic and environmental goal for pig production. Feed is the first component of cost production for pig farmers, and this will remain the case due to the evolution of feedstuffs cost. Historically, feed efficiency has been improved through selection, with success, for a decrease of feed conversion ratio (FCR) representing efficiency of feed conversion into body weight gain. In a context of evolving breeding objectives, new strategies of feed efficiency improvement are investigated. This PhD work has studied some of them using data collected in the French central test stations between 2000 and 2009 for the four main pigs breeds used in collective selection, i.e. two dam breeds (Large White dam line and Landrace) and two sire breeds (Large White sire line and Piétrain). The main approach retained here deals with residual feed intake (RFI), which is a criterion of feed efficiency independent from animal's performance level, in order to estimate its genetic relationships with usual production traits, and also with nitrogen and phosphorus quantities excreted by the animals. In a first step, a study of an experimental Large White population showed that genetic correlations between the three sexes for RFI were very close to 1 for RFI. This result allowed the comparisons of the results obtained on Piétrain females with those obtained on castrated males in the three other breeds. We showed that RFI had an heritability (h²) ranging between 0.21 and 0.33 depending on the breed, slightly less heritable than FCR (h² between 0.30 and 0.40) and with a favourable genetic correlation between them (between 0.52 and 0.85). The RFI is, by definition, phenotypically independent from growth rate and carcass composition traits, and this was also the case at the genetic level (genetic correlations lower than 0.16 in absolute values whatever the breed). However, RFI, like FCR, did not display favourable genetic correlations with meat quality traits. Contrary to FCR, RFI was shown to be unaffected by the halothane genotype segregating in the Piétrain breed. Very high genetic correlations with FCR (0.97 and higher), and more moderate genetic correlations with RFI (between 0.38 and 0.86) were found for nitrogen and phosphorus excreted quantities, which indicates that the reduction of excreted quantities is expected in response to selection for a better feed efficiency. These genetic correlations were globally higher in sire lines than in dam lines. Finally, the study of growth and feed intake curves of animals classified according to their feed efficiency level (either RFI or FCR) suggested that breeding for more efficient animals could not be conducted without an adaptation of feed formulation (e.g. for amino acids concentration), in order to allow the full expression of their genetic potential

Genetic parameters for carcass weight, age at slaughter and conformation of young bulls

Genetic parameters for carcass weight, age at slaughter and conformation of young bulls. 66. Annual Meeting of the European Federation of Animal Science (EAAP

Genome-wide scan for reproductive traits of beef heifers using high density SNP panels

Quantitative Trait Loci (QTL) detection for sexual precocity and fertility of beef heifers was performed by a Bayesian approach and based on performance recorded in French progeny test station of Blonde d’Aquitaine bulls. Heifer oestrus and fertility were observed on about 25 daughters for each of the 158 genotyped bulls. Genotyping was mainly carried out with the Bovine high density BeadChip®. A total of 78 QTL were identified with strong evidence for an effect on sexual precocity. Comparing these results with QTL previously reported in the literature, 2 unknown QTL were identified for sexual precocity among the 7 regions with major evidence for a QTL. Regarding heifer fertility, only 6 QTL were detected, 3 of them matched with previous studies on dairy cattle. Two common QTL regions were identified as playing a strong role on both reproductive traits

Imputation accuracy from a low density SNP panel in 5 dairy sheep breeds in France

In France, genomic selection (GS) has been implemented in dairy sheep in Lacaune breed (LA) and more recently in Pyrenean breeds: Red-Faced Manech (RFM), Black-Faced Manech (BFM) and Basco-Béarnaise (BB). Genomic estimated breeding values (GEBV) are calculated on the basis of SNP50 Bead-Chip (50K) genotypes. Compared to dairy cattle, the relatively higher cost of genotyping limits the cost-effectiveness of GS in dairy sheep. However, a significant reduction of genotyping cost is forecast with the design of a low density (LD) chip by the International Sheep Genomics Consortium. Use of this chip requires harmonizing genotypes on LD panel and those existing on 50K panel by imputing missing SNPs. The aim of the study was to evaluate quality of imputation in 5 French dairy sheep breeds (with Corsica breed: CO) and its impact on GEBV. Genotypes of rams available in each breed (5,792 in LA, 1,741 in RFM, 470 in BFM, 556 in BB and 609 in CO) were split in two sets: a training set with oldest rams and a validation set with youngest rams (1,144 in LA, 430 in RFM, 80 in BFM, 140 in BB and 117 in CO). The 50K genotypes of validation set, after quality control, were ‘pierced’ in order to mimic LD genotypes. Out of 16,331 SNPs from LD panel, 9,822 were located on 50K panel. These genotypes were then imputed to the 50K panel, from the training population, using the FImpute software. Comparison of 50K imputed and true genotypes permitted to assess imputation accuracy. Concordance rates (CR: percentage of alleles properly imputed) per animal or per SNP were high, ranging from 96.6% to 99.1%, depending on breed. The squared correlations (r2) between true and imputed genotypes ranged from 81.3% to 95%. On the 3 criteria, Lacaune breed had the higher scores followed by RFM, BB, BFM and finally CO breeds, in accordance with training population size. For validation rams, correlations between GEBV computed with true or imputed genotypes exceeded 0.99 for production and type traits whatever the breed. Consequently, the 4 breeds in GS have decided to use LD genotypes for pre-selection of young rams

Multi‑breed and multi‑trait co‑association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Background: Studies to identify markers associated with beef tenderness have focused on Warner–Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co‑associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d’Aquitaine beef cattle breeds. Results: Genome‑wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi‑trait approach was applied separately for each breed across 17 phenotypes and second, between‑ and across‑breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed‑specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well‑known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi‑breed co‑association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Conclusions: Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one‑dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi‑breed beef cattle context.info:eu-repo/semantics/publishedVersio

Systems biology approach provides novel insights into gene networks controlling tenderness and meat quality traits across French beef breeds

Systems biology approach provides novel insights into gene networks controlling tenderness and meat quality traits across French beef breeds. 35. Conference of the International Society for Animal Genetics (ISAG

Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Background[br/] Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds.[br/] Results[br/] Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle.[br/] Conclusions[br/] Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context