Florence Phocas

Developing a breeding objective for a French purebred beef cattle selection programme.

Abstract This paper presents a procedure for the development of a breeding objective for a beef cattle breed used in a range of production systems. The five main beef cattle production systems in France were first described and then equations of income and costs as a function of the 25 biological traits to be genetically improved for breeding and production were established. Economic values for individual systems were defined as the first derivative of the herd profit with respect to these 25 traits while the economic values for the overall breeding objective were taken as the average of economic values over the five production systems. An application is presented for the Limousin breed. Sensitivity of the breeding objective to variation in the economic or demographic context was also studied. Breeding traits, especially maternal effects on weaning weight and calving success, were identified as the most economically important traits requiring improvement. Relative economic values were very robust with respect to variations in system frequencies and replacement rates. A dramatic change in the market price for beef (−50%) increased the relative weighting of carcass quality traits to the detriment of breeding traits although a smaller change in beef price (−25%) had no significant effect on the relative economic values.

Regulation of anti-Müllerian hormone production in domestic animals

In mammals, anti-Müllerian hormone (AMH) expression is detected in the granulosa cells of all growing follicles and is highest in healthy small antral follicles, which contribute most significantly to AMH endocrine levels. AMH is a reliable endocrine marker of this population of gonadotrophin-responsive follicles in ruminants and, over the longer term, plasma AMH concentrations are characteristic of individual animals. In the cow, plasma AMH concentrations follow specific dynamic profiles throughout the prepubertal period, the oestrous cycle and the change from gestation to the post partum period, with the alterations most likely reflecting numerical changes in the population of high AMH-producing follicles. In granulosa cells, bone morphogenetic proteins (BMP) enhance AMH gene expression and AMH synthesis, with these effects antagonised by FSH. BMP could both support follicular growth and contribute significantly to the induction and/or maintenance of AMH expression in small growing follicles. AMH expression decreases sharply in large follicles when they become oestrogenic, suggesting a role for FSH and/or oestradiol in these changes, but the underlying mechanisms remain hypothetical. A better understanding of the factors and mechanisms regulating AMH production is needed to propose new strategies for managing the reserve of primordial and small growing follicles, as well as for improving embryo production.

High-density marker imputation accuracy in sixteen French cattle breeds

BackgroundGenotyping with the medium-density Bovine SNP50 BeadChip® (50K) is now standard in cattle. The high-density BovineHD BeadChip®, which contains 777 609 single nucleotide polymorphisms (SNPs), was developed in 2010. Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection. However, re-genotyping all animals with the high-density chip is not economically feasible. An alternative strategy is to genotype part of the animals with the high-density chip and to impute high-density genotypes for animals already genotyped with the 50K chip. Thus, it is necessary to investigate the error rate when imputing from the 50K to the high-density chip.MethodsFive thousand one hundred and fifty three animals from 16 breeds (89 to 788 per breed) were genotyped with the high-density chip. Imputation error rates from the 50K to the high-density chip were computed for each breed with a validation set that included the 20% youngest animals. Marker genotypes were masked for animals in the validation population in order to mimic 50K genotypes. Imputation was carried out using the Beagle 3.3.0 software.ResultsMean allele imputation error rates ranged from 0.31% to 2.41% depending on the breed. In total, 1980 SNPs had high imputation error rates in several breeds, which is probably due to genome assembly errors, and we recommend to discard these in future studies. Differences in imputation accuracy between breeds were related to the high-density-genotyped sample size and to the genetic relationship between reference and validation populations, whereas differences in effective population size and level of linkage disequilibrium showed limited effects. Accordingly, imputation accuracy was higher in breeds with large populations and in dairy breeds than in beef breeds. More than 99% of the alleles were correctly imputed if more than 300 animals were genotyped at high-density. No improvement was observed when multi-breed imputation was performed.ConclusionIn all breeds, imputation accuracy was higher than 97%, which indicates that imputation to the high-density chip was accurate. Imputation accuracy depends mainly on the size of the reference population and the relationship between reference and target populations.

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.

Efficiency of genomic selection in a purebred pig male line

Stochastic simulation was used to compare the efficiency of 3 pig breeding schemes based on either traditional genetic evaluation or genomic evaluation. The simulated population contained 1,050 female and 50 male breeding animals. It was selected for 10 yr for a synthetic breeding goal that included 2 traits with equal economic weights and heritabilities of 0.2 or 0.4. The reference breeding scheme, named BLUP-AM, was based on the phenotyping of all candidates (13,770 animals/yr) for Trait 1 and of relatives from 10% of the litters (270 animals/yr) for Trait 2 and on BLUP-Animal Model genetic evaluations. Under the first alternative scenario, named GE-1TP, selection was based on genomic breeding values (GBV) estimated with one training population (TP) made up of candidate relatives phenotyped for both traits, with a size increasing from 1,000 to 3,430 over time. Under the second alternative scenario, named GE-2TP, the GBV for Trait 2 were estimated using a TP identical to that of GE-1TP, but the GBV for Trait 1 were estimated using a large TP made up of candidates that increased in number from 13,770 to 55,080 over time. Over the simulated period, both genomic breeding schemes generated 39 to 58% more accurate EBV for Trait 2 than the reference scheme, resulting in 78 to 128% (GE-1TP) and 63 to 84% (GE-2TP) greater average annual genetic trends for this trait. For Trait 1, GE-1TP was 18 to 24% less accurate than BLUP-AM, reducing average annual genetic trends by 27 to 44%. By contrast, GE-2TP generated 35 to 43% more accurate EBV and 8 to 22% greater average annual genetic trends for Trait 1 than the reference scheme. Consequently, GE-2TP was 27 to 33% more efficient in improving the global breeding goal than BLUP-AM whereas GE-1TP was globally as efficient as the reference scheme. Both genomic schemes reduced the inbreeding rate, the greatest decrease being observed for GE-2TP (-49 to -60% compared with BLUP-AM). In conclusion, genomic selection could substantially and durably improve the efficiency of pig breeding schemes in terms of reliability, genetic trends, and inbreeding rate without any need to modify their current structure. Even though it only generates a small TP, limited annual phenotyping capacity for traits currently only recorded on relatives would not be prohibitive. A large TP is, however, required to outperform the current schemes for traits recorded on the candidates in the latter.

Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population

Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds.

Assessment of different on-farm measures of beef cattle temperament for use in genetic evaluation

The aim of this study was to find a simple measure for calf temperament discrimination, which can be useful as a selection criterion for on-farm French beef cattle breeding schemes. Behavioral records were registered at an average age of 5 and 7 mo, respectively, for 1,282 and 1,440 Limousin calves born in 24 French farms between August 2007 and April 2008. Measures were repeated for 810 calves at the 2 ages. The test procedure consisted of individually restraining the calves in a chute, then exposing them to a stationary human situated in front of the chute for 10 s. For every calf and each period of the test, the number of rush movements and the total number of movements were scored by visual appraisal using a continuous scale ranging from 0 (no movements) to 60 (continuous movements). Initial scores were also transformed to categorical scores and analyzed. Genetic correlation across ages were very high for all the traits (above 0.84 ± 0.20) suggesting that these traits are governed by the same pool of genes at the 2 ages. The corresponding phenotypic correlations were about 0.3 for all the measures. Heritabilities were moderate for all measures (from 0.11 to 0.31) with the total number of movements during weighing measured at 7 mo being the greatest. All the measures were highly correlated (from 0.73 ± 0.26 to 0.99 ± 0.02). Genetic correlation across sexes was not statistically different from 1. However, traits measured during weighing showed different genetic variance estimates for females and males. Similar results were obtained for the transformed categorical scores. According to these results, the total number of movements during weighing seems to be the most promising trait for on-farm genetic evaluation of French beef cattle temperament.

Genetic control of multiple births in low ovulating mammalian species

In mammals, litter size is a highly variable trait. Some species such as humans or cattle are monotocous, with one or sometimes two newborns per birth, whereas others, the polytocous species such as mice or pigs, are highly prolific and often produce a dozen newborns at each farrowing. In monotocous species, however, two or three newborns per birth may sometime be unwanted. In more polytocous species such as sheep or pigs, litter size is studied in order to increase livestock prolificacy. By contrast, twinning rates in humans or cattle may increase birth difficulties and health problems in the newborns. In this context, the aim of our review was to provide a clearer understanding of the genetic and physiological factors that control multiple births in low-ovulating mammalian species, with particular focus on three species: sheep, cattle, and humans, where knowledge of the ovulation rate in one may enlighten findings in the others. This article therefore reviews the phenotypic and genetic variability observed with respect to ovulation and twinning rates. It then presents the QTL and major genes that have been identified in each species. Finally, we draw a picture of the diversity of the physiological mechanisms underlying multiple ovulation. Although several major genes have been discovered in sheep, QTL detection methods in humans or cattle have suggested that the determinism of litter size is complex and probably involves several genes in order to explain variations in the number of ovulations.

Genetic analysis of breeding traits in a Charolais cattle population segregating an inactive myostatin allele

The objective of this study was to quantify the effects of the Charolais-specific inactive myostatin allele on phenotypic means and genetic parameters of heifer breeding traits. Records were registered from 1996 to 2006 in 282 herds dedicated to the on-farm French Charolais purebred progeny test. Data consisted of 36,867 female calf records, including 17,518 inseminated heifers that were bred by 186 genotyped sires, of which 43 were heterozygous and 6 were double muscled bulls. Six traits were analyzed under a univariate animal model accounting for maternal effects and myostatin sire genotype: calving difficulty, birth and weaning weights, muscle and skeleton scores at weaning, and fertility of artificially inseminated heifers. The inactive myostatin allele had a large positive effect on weaned heifer muscle score, unfavorable effects on calving difficulty and skeleton score, and small effects on birth and weaning weight. This allele did not induce an adverse effect on heifer fertility. Univariate estimates of polygenic variance parameters were almost unaffected by the estimation of the myostatin sire genotype, except for heifer morphology traits. Direct and maternal genetic variances and covariances were significantly reduced under a model accounting for the myostatin sire genotype effect on muscle score. The myostatin genotype explained 45% of the direct genetic variance and had a pleiotropic action across both direct and maternal effects on muscle score. Because the myostatin sire genotype had no significant effect on birth weight, the multitrait sire analysis concerned only the 5 other traits. Accounting for the myostatin sire genotype, estimates of polygenic correlation between skeleton score and muscle score, on the one hand, and calving difficulty on the other hand, were largely modified: from a negative estimate of -0.3 to 0.0 and from a positive estimate of 0.4 to 0.7, respectively.

Genetics of behavioural adaptation of livestock to farming conditions

Behavioural adaptation of farm animals to environmental changes contributes to high levels of production under a wide range of farming conditions, from highly controlled indoor systems to harsh outdoor systems. The genetic variation in livestock behaviour is considerable. Animals and genotypes with a larger behavioural capacity for adaptation may cope more readily with varying farming conditions than those with a lower capacity for adaptation. This capacity should be exploited when the aim is to use a limited number of species extensively across the world. The genetics of behavioural traits is understood to some extent, but it is seldom accounted for in breeding programmes. This review summarizes the estimates of genetic parameters for behavioural traits in cattle, pigs, poultry and fish. On the basis of the major studies performed in the last two decades, we focus the review on traits of common interest in the four species. These concern the behavioural responses to both acute and chronic stressors in the physical environment (feed, temperature, etc.) and those in the social environment (other group members, progeny, humans). The genetic strategies used to improve the behavioural capacity for adaptation of animals differ between species. There is a greater emphasis on responses to acute environmental stress in fish and birds, and on responses to chronic social stress in mammals.