Sequence-based GWAS meta-analyses for beef production traits.

Background: Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations.

Genetic relationships between weight loss in early lactation and daily milk production throughout lactation in Holstein cows.

After calving, high-yielding dairy cows mobilize body reserves for energy, sometimes to the detriment of health and fertility. This study aimed to estimate the genetic correlation between body weight loss until nadir and daily milk production (MY24) in first- (L1) and second-lactation (L2) Holstein cows. The data set included 859,020 MY24 records and 570,651 daily raw body weight (BWr) phenotypes from 3,989 L1 cows, and 665,361 MY24 records and 449,449 BWr phenotypes from 3,060 L2 cows, recorded on 36 French commercial farms equipped with milking robots that included an automatic weighing platform.

Association between body condition genomic values and feed intake, milk production, and body weight in French Holstein cows.

Body condition score (BCS) offers a good estimate of the amount of stored fat on the body, and its variations can be used as a proxy for energy balance. Many countries have implemented a genomic evaluation of BCS, including France, where estimated breeding values are based on an individual BCS determination during the first lactation. In this article, we investigate the degree to which this genomic estimated breeding value based on a single phenotype record per cow might reflect different profiles of body reserves throughout lactation and be used to predict, and perhaps limit, their mobilization during early lactation.

New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation.

Background: Bovine paratuberculosis, or Johne's disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences.

Correcting for base-population differences and unknown parent groups in single-step genomic predictions of Norwegian Red cattle.

Bias and inflation in genomic evaluation with the single-step methods have been reported in several studies. Incompatibility between the base-populations of the pedigree-based and the genomic relationship matrix (G) could be a reason for these biases. Inappropriate ways of accounting for missing parents could be another reason for biases in genetic evaluations with or without genomic information.

Opportunities for genomic selection of cheese-making traits in Montbéliarde cows.

As part of the From'MIR project, traits related to the composition and cheese-making properties (CMP) of milk were predicted from 6.6 million mid-infrared spectra taken from 410,622 Montbéliarde cows (19,862 with genotypes). Genome-wide association studies of imputed whole-genome sequences highlighted candidate SNPs that were then added to the EuroG10K BeadChip, which is routinely used in genomic selection.

In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets.

MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. Some polymorphisms have been studied in various livestock species from the perspective of pathology or production traits. To target variants that could be the causal variants of dairy traits, genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy quantitative trait loci (QTLs) were investigated in bovine, caprine, and ovine species.

Exploring simultaneous perturbation profiles in milk yield and body weight reveals a diversity of animal responses and new opportunities to identify resilience proxies.

Livestock husbandry aims to manage the environment in which animals are reared to enable them to express their production potential. However, animals are often confronted with perturbations that affect their performance. Evaluating effects of these perturbations on animal performance could provide metrics to quantify and understand how animals cope with their environment, and therefore to better manage them.

Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds.

Background: Sequence-based genome-wide association studies (GWAS) provide high statistical power to identify candidate causal mutations when a large number of individuals with both sequence variant genotypes and phenotypes is available. A meta-analysis combines summary statistics from multiple GWAS and increases the power to detect trait-associated variants without requiring access to data at the individual level of the GWAS mapping cohorts. Because linkage disequilibrium between adjacent markers is conserved only over short distances across breeds, a multi-breed meta-analysis can improve mapping precision.

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals.

Stature is affected by many polymorphisms of small effect in humans . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs.

Estimation of the effects of selection on French Large White sow and piglet performance during the suckling period.

The effects of 21 yr of selection were estimated for sow and piglet performance during the suckling period in a French Large White (LW) pig population using frozen semen. Two experimental groups (EXP = L77 and L98) were produced by inseminating LW sows with either stored frozen semen from 17 LW boars born in 1977 (EXP = L77) or with fresh semen from 23 LW boars born in 1998 (EXP = L98). Seventy-four L77 and 89 L98 randomly chosen females were mated to 15 L77 and 15 L98, respectively, randomly chosen boars for 6 successive parities.

Estimation of the effects of selection on French Large White reproductive performance using frozen semen.

Genetic trends for male and female sexual development and components of litter size and weight at birth (LB) as well as traits related to sow lifetime productivity were estimated in a French Large White (LW) pig population using frozen semen. Two experimental groups (EXP = L77 and L98) were produced by inseminating LW sows with either stored frozen semen from 17 LW boars born in 1977 (EXP = L77) or with semen from 23 LW boars born in 1998 (EXP = L98). In each group, about 100 males were measured for testicular development and bulbo-urethral gland development, and 90 gilts were checked for puberty, among which about 50 gilts were measured for their first ovulation rate at puberty (ORP).

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.

Background: Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle.

A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality.

Background: Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS).

Economic aspects of implementing genomic evaluations in a pig sire line breeding scheme.

Background: Replacing pedigree-based BLUP evaluations by genomic evaluations in pig breeding schemes can result in greater selection accuracy and genetic gains, especially for traits with limited phenotypes. However, this methodological change would generate additional costs. The objective of this study was to determine whether additional expenditures would be more profitably devoted to implementing genomic evaluations or to increasing phenotyping capacity while retaining traditional evaluations.

Genetics of residual feed intake in growing pigs: Relationships with production traits, and nitrogen and phosphorus excretion traits.

Residual feed intake (RFI) is defined as the difference between the observed ADFI and the ADFI predicted from production and maintenance requirements. The objectives of this study were to evaluate RFI as a selection criterion to improve feed efficiency and its potential to reduce N and P excretion in 4 pig breeds. Data were collected between 2000 and 2009 in French central test stations for 2 dam breeds [French Landrace (LR) and Large White (LWD)], and 2 sire breeds [Large White (LWS) and Piétrain (PP)].

Phenotypic prediction based on metabolomic data for growing pigs from three main European breeds.

Predicting phenotypes is a statistical and biotechnical challenge, both in medicine (predicting an illness) and animal breeding (predicting the carcass economical value on a young living animal). High-throughput fine phenotyping is possible using metabolomics, which describes the global metabolic status of an individual, and is the closest to the terminal phenotype. The purpose of this work was to quantify the prediction power of metabolomic profiles for commonly used production phenotypes from a single blood sample from growing pigs.

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.

Estimation of genetic trends in French Large White pigs from 1977 to 1998 for growth and carcass traits using frozen semen.

Genetic trends for growth, feed efficiency, composition, and morphometry of carcasses were estimated in a French Large White (LW) pig population using frozen semen. Two groups of pigs were produced by inseminating LW sows with either stored, frozen semen from 17 LW boars born in 1977 or with semen from 23 LW boars born in 1998. In each group, 15 males and 90 females were randomly chosen and mated to produce approximately 1,000 pigs/group.

Estimation of genetic trends from 1977 to 2000 for stress-responsive systems in French Large White and Landrace pig populations using frozen semen.

An experimental design aiming at analysing the consequences of genetic selection from 1977 to 1998-2000 on the evolution of stress-responsive systems in the French Large White (LW) and Landrace (LR) pig populations was conducted by INRA and IFIP-Institut du Porc. Large White sows were inseminated with semen from LW boars born in 1977 (frozen semen) or in 1998 and their second-generation offspring were station-tested. Landrace sows were inseminated with semen from LR boars born in 1977 (frozen semen) or in 1999 to 2000, and their progeny was station-tested.

Optimized management of genetic variability in selected pig populations.

Controlling the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed to breeding animals, given the current situation with regard to genetic diversity, and further, through optimal design of matings. The potential of such an approach for pig breeding was tested by retrospective optimization on the French Landrace population in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall estimated breeding value (EBV) should be the same as the observed one, for not decreasing short-term genetic gain.

Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations.

A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers.