The shape of the lactation curve is linked to an animal's health, feed requirements, and milk production throughout the year. Random regression models (RRM) are widely used for genetic evaluation of ...total milk production throughout the lactation and for milk yield persistency. Genomic information used with the single-step genomic BLUP method (ssGBLUP) substantially improves the accuracy of genomic prediction of breeding values in the main dairy cattle breeds. The aim of this study was to implement an RRM using ssGBLUP for milk yield in Saanen dairy goats in France. The data set consisted of 7,904,246 test-day records from 1,308,307 lactations of Saanen goats collected in France between 2000 and 2017. The performance of this type of evaluation was assessed by applying a validation step with data targeting candidate bucks. The model was compared with a nongenomic evaluation and a traditional evaluation that use cumulated performance throughout the lactation model (LM). The incorporation of genomic information increased correlations between daughter yield deviations (DYD) and estimated breeding values (EBV) obtained with a partial data set for candidate bucks. The LM and the RRM had similar correlation between DYD and EBV. However, the RRM reduced overestimation of EBV and improved the slope of the regression of DYD on EBV obtained at birth. This study shows that a genomic evaluation from a ssGBLUP RRM is possible in dairy goats in France and that RRM performance is comparable to a LM but with the additional benefit of a genomic evaluation of persistency. Variance of adjacent SNPs was studied with LM and RRM following the ssGBLUP. Both approaches converged on approximately the same regions explaining more than 1% of total variance. Regions associated with persistency were also found.
Genomic evaluation of French dairy goats is routinely conducted using the single-step genomic BLUP (ssGBLUP) method. This method has the advantage of simultaneously using all phenotypes, pedigrees, ...and genotypes. However, ssGBLUP assumes that all SNP explain the same amount of genetic variance, which is unlikely in the case of traits whose major genes or QTL are segregating. In this study, we investigated the effect of weighted ssGBLUP and its alternatives, which give more weight to SNP associated with the trait, on the accuracy of genomic evaluation of milk production, udder type traits, and somatic cell scores. The data set included 2,955 genotyped animals and 2,543,680 pedigree animals. The number of phenotypes varied with the trait. The accuracy of genomic evaluation was assessed on 205 genotyped Alpine and 146 genotyped Saanen goats born between 2009 and 2012. For traits with unknown QTL, weighted ssGBLUP was less accurate than, or as accurate as, ssGBLUP. For traits with identified QTL (i.e., QTL only present in the Saanen breed), weighted ssGBLUP outperformed ssGBLUP by between 2 and 14%.
A high level of production at the peak of lactation may be associated with animal health disorders, high feeding costs, and reduced milk supply throughout the year. The objective of this study was to ...typologize the lactation curves in French dairy goats and analyze the influence of environmental and genetic factors on these curves. The data set consisted of 2,231,720 monthly test-day records of 213,534 French Saanen and Alpine goats recorded between September 2008 and June 2012. First, principal component analysis classified the shape of the lactation curves into 3 principal components: the first component accounted for milk yield level throughout lactation, the second component accounted for lactation persistency, and the third component accounted for milk yield in mid-lactation. Then, from the principal component scores, the lactations were clustered into 5 different groups. Most lactations had a similar shape to the mean curve, except 30% of the lactations that fell into 3 clusters that had a high production level at the peak and then a different persistency according to cluster. Estimated breeding value for milk yield and home region of breeding were the factors most related to lactation production level. Month of kidding, breed, and gestation stage had the biggest effect on persistency. Month of kidding was the factor most strongly linked to mid-lactation production. A herd effect was observed on all 3 principal components.
•Effect of feed restriction on milk lipolysis is reported for the first time in ewes.•Feed restriction reduced by more than 50% milk lipolysis in sheep milk.•Decreased lipolysis was not associated ...with a decrease in milk lipase activity.•Feed restriction increased milk fat globules diameters in sheep milk.•Our data should be confirmed in other sheep breeds.
Spontaneous lipolysis results in the breakdown of milk fat by the lipoprotein lipase (EC: 3.1.1.34), an enzyme present in milk. Free fatty acids (FFAs) and by-products released in milk during lipolysis can alter both the organoleptic value of milk (off-flavors release) and technological properties of dairy products (decrease in creaming capabilities). Current climate change is having significant impacts on the feeding of grazing animals, with negative consequences on the availability and quality of grass. We and others have demonstrated that dietary restriction increases milk lipolysis in the cow species. However, no data about the impact of feed restriction on milk lipolysis is available in the ewe species. Thus, this paper aims to investigate the effect of feed restriction on milk characteristics with regard to lipolysis values in dairy ewes. Two groups of 24 multiparous Lacaune ewes in mid-lactation received a “non-restricted” control diet (100% of ad libitum DM intake) or a “restricted” (RESTR) diet (65% of ad libitum DM intake) according to a 2 × 2 crossover design. Milk gross composition together with lipolysis analyses were performed. Blood samples were also screened for metabolites or hormone concentrations. The RESTR treatment induced a decrease in milk production (− 21% compared with control treatment) and a modification of the metabolism of dairy ewes characterized by an increase in plasma non-esterified fatty acids (NEFAs), which represents the balance between adipose tissue mobilization and the use of NEFA by other tissues (+153%), cholesterol (+17%) and β-hydroxybutyrate (+4 %) levels. As a result, a decrease in BW of dairy ewes was observed (−7%). Feed restriction also resulted in a decrease in milk lipolysis estimated by the milk FFA measured by the copper-soap method (−63 and −62%, respectively, for morning and evening milking) or by the reference Bureau of Dairy Industry method (−51 and –57%, respectively, for morning and evening milking). The decrease in milk spontaneous lipolysis under feed restriction was not associated with a decrease in lipoprotein lipase activity in ewes. These results will be completed with proteomic and lipidomic studies in milk samples to better understand mechanisms initiated in the ewe species specifically with regard to lipolysis in milk.
Lactation curve shape can affect an animal's health, feed requirements, and milk production throughout the year. We implemented a random regression model for the genetic evaluation of lactation curve ...shapes of dairy traits in French Alpine goats for their first 3 parities. Milk, fat, and protein yields, fat and protein contents, somatic cell score, and fat/protein ratio were considered. The data consisted of test-day records from 49,849 first lactation Alpine goats during their first 3 lactations. The reference model used a Legendre polynomial of order 2 for each parity to describe the genetic and permanent environmental effects, and was compared with a model that combined the second and third parities. A rank reduction of the variance-covariance matrix was also performed using an eigenvalue decomposition for each parity from the 2 models. Genetic parameters were consistent between the models tested. With a reduction to rank 2 and combining the second and third parities, the first 2 principal components correctly summarized the genetic variability of milk yield level and persistency, with a near-nil correlation between the 2, and with a much shorter computation time than the reference model. A favorable correlation of +0.43 between milk yield persistency and fat/protein ratio persistency at the beginning of the lactation was found from buck estimated breeding values.
The collective economic and environmental interest of the whole dairy sheep sector is to reduce feedcosts and the negative impact of milk production on the environment. Thus, this study focused on ...thecharacterisation and genetic selection potential of feed efficiency in the Lacaune breed. Estimates for feedefficiency in dairy ewes are limited, mainly due to a lack of individual feed intake measurements in thesheepfold or in the pasture. We estimated the genetic parameters for two approximated (not entirelybased on individual data) feed efficiency traits (lactation feed conversion ratio (LFCR) and residual energyintake (REI)) and daily milk yield (DMY) at different stages of lactation and throughout lactation. Theaccuracy of the efficiency traits was first evaluated on samples from Lacaune dairy ewes that were mon-itored individually, especially for their feed intake. Then, feed efficiency estimation methods were appliedon eight commercial farms corresponding to 4 680 Lacaune dairy ewes over two milk lactations (30 854records). Animals were collectively (for a large part of feed intake) or individually (for milk performanceand dynamics of body fat reserves) monitored at different lactation stages. The heritabilities of LFCR andREI were estimated over lactations at 0.10 ± 0.01 and 0.11 ± 0.01, respectively. High genetic correlationswere observed between the two efficiency traits and milk production traits, with a genetic correlationbetween LFCR and DMY of 0.74 ± 0.04 and between REI and DMY of 0.79 ± 0.04. A strong influenceof environmental factors such as farm, year of milk production and lactation stage affected the geneticlink between REI and milk production traits. Efficiency values observed in early lactation when animalswere bred in the sheepfold were less genetically correlated with values obtained later in lactation whenanimals were grass-fed. However, individual characterisation of feed efficiency remains difficult due tothe collective feeding context in dairy ewe farms.
Mid-infrared (MIR) spectrometry was used to estimate the fatty acid (FA) composition in cow, ewe, and goat milk. The objectives were to compare different statistical approaches with wavelength ...selection to predict the milk FA composition from MIR spectra, and to develop equations for FA in cow, goat, and ewe milk. In total, a set of 349 cow milk samples, 200 ewe milk samples, and 332 goat milk samples were both analyzed by MIR and by gas chromatography, the reference method. A broad FA variability was ensured by using milk from different breeds and feeding systems. The methods studied were partial least squares regression (PLS), first-derivative pretreatment + PLS, genetic algorithm + PLS, wavelets + PLS, least absolute shrinkage and selection operator method (LASSO), and elastic net. The best results were obtained with PLS, genetic algorithm + PLS and first derivative + PLS. The residual standard deviation and the coefficient of determination in external validation were used to characterize the equations and to retain the best for each FA in each species. In all cases, the predictions were of better quality for FA found at medium to high concentrations (i.e., for saturated FA and some monounsaturated FA with a coefficient of determination in external validation >0.90). The conversion of the FA expressed in grams per 100mL of milk to grams per 100g of FA was possible with a small loss of accuracy for some FA.
Genomic selection in Lacaune dairy sheep was investigated based on genotypes from the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). Historical artificial insemination progeny-tested rams formed ...a population of 2,892 genotyped rams. Additional ungenotyped rams and females were included by single-step genomic BLUP (ssGBLUP). Three prediction strategies were tried: pseudo-BLUP (using all rams and daughter yield deviations), pseudo-ssGBLUP (using all rams and daughter yield deviations), and regular ssGBLUP (using all phenotypes and pedigree in an animal model). The population linkage disequilibrium was determined, with an average squared correlation coefficient of 0.11 for markers closer than 0.1cM (lower than in dairy cattle). The estimated effective population is 370 individuals. Gain in accuracy of genomic selection over parent averages ranged from 0.10 to 0.20. Highest accuracies and lowest bias were found using regular ssGBLUP. Transition to a genomic breeding scheme is possible but costs need to be carefully evaluated.
Fertility is of primary economic importance in dairy cattle and the most common reason for involuntary culling. However, standard fertility traits have very low heritability that renders genetic ...selection slow and difficult. In this study, we explored fertility from an endocrine standpoint. A total of 1,163 crossbred Holstein-Normande females in a 3-generation familial design were studied for progesterone level measured every 10 d to determine age at puberty (PUB) and commencement of postpartum luteal activity (CPLA). Genetic parameters were estimated using REML with WOMBAT software. The heritability estimates were 0.38 ± 0.10 and 0.16 ± 0.07 for PUB and CPLA, respectively. Moreover, the 2 traits were genetically correlated (0.45 ± 0.23), suggesting a partially common determinism. Because of the family structure, a linkage disequilibrium and linkage analysis approach was preferred over standard genome-wide association study to map genomic regions associated with these traits. Ten quantitative trait loci (QTL) were detected for PUB on chromosomes 1, 3, 11, 13, 14, 21, and 29, whereas 3 QTL were associated with CPLA on chromosomes 21 and 26. Only the QTL on chromosome 21 was common to both traits. Four functional candidate genes (NCOA2, GAS2, OVOL1, and FOSL1) were identified in the detected regions. These findings will contribute to a clearer understanding of fertility determinism and enhance the value of introducing endocrinological data in fertility studies.
Milk somatic cell count (SCC) is commonly higher in goats than in cattle and sheep. Furthermore, the ability of milk SCC to predict mastitis is considered lower in goats than in cattle and sheep, and ...the relevance of somatic cell score (SCS)-based selection in this species has been questioned. To address this issue, we created 2 divergent lines of Alpine goats using artificially inseminated bucks with extreme estimated breeding values for SCS. A total of 287 goats, 158 in high- and 129 in low-SCS lines, were scrutinized for mastitis infections. We subjected 2,688 milk samples to conventional bacteriological analyses on agarose and bacterial counts were estimated for positive samples. The SCS, milk yield, fat content, and protein content were recorded every 3 wk. Clinical mastitis was systematically noted. A subset of 40 goats (20 from each line) was subsequently challenged with Haemonchus contortus and monitored for anemia (blood packed cell volume) and fecal egg counts to see if SCS-based selection had an indirect effect on resistance to gastrointestinal nematodes. Milk production traits, including milk quantity, fat content, and protein content, were similar in both goat lines. In contrast, the raw milk SCC almost doubled between the lines, with 1,542,000 versus 855,000 cells/mL in the high- and low-SCS lines, respectively. The difference in breeding value for SCS between lines was 1.65 genetic standard deviation equivalents. The Staphylococcus spp. most frequently isolated from milk were S. xylosus, S. caprae, S. epidermidis, and S. aureus. The frequency of positive bacteriology samples was significantly higher in the high-SCS line (49%) than in the low-SCS line (33%). The highest odds ratio was 3.49 (95% confidence interval: 11.95–6.25) for S. aureus. The distribution of bacterial species in positive samples between lines was comparable. The average quantity of bacteria in positive samples was also significantly higher in high-SCS goats (69 ± 80 growing colonies) than in low-SCS goats (38 ± 62 growing colonies). Clinical cases were rare and equally distributed between high- (n = 4; 2.5%) and low-SCS (n = 3; 2.3%) lines. Furthermore, the larger the amounts of bacteria in milk the higher the SCS level. Conversely, goats with repeatedly culture-negative udders exhibited the lowest SCC levels, with an average of below 300,000 cells/mL. We therefore confirmed that SCS is a relevant predictor of intramammary infection and hygienic quality of milk in goats and can be used for prophylactic purposes. After challenge with H. contortus, goats were anemic with high fecal egg counts but we found no difference between the genetic lines. This result provides initial evidence that resistance to mastitis or to gastrointestinal nematodes infections is under independent genetic regulation. Altogether, this monitoring of the goat lines indicated that SCS-based selection helps to improve udder health by decreasing milk cell counts and reducing the incidence of infection and related bacterial shedding in milk. Selection for low SCC should not affect a goat's ability to cope with gastrointestinal nematodes.
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