Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations

Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats.

Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield

This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype.

Review: Genetic and protein variants of milk caseins in goats

The milk casein genes in goats, are highly polymorphic genes with numerous synonymous and non-synonymous mutations. So far, 20 protein variants have been reported in goats for alpha-S1-casein, eight for beta-casein, 14 for alpha-S2-casein, and 24 for kappa-casein. This review provides a comprehensive overview on identified milk casein protein variants in goat and non-coding DNA sequence variants with some affecting the expression of the casein genes. The high frequency of some casein protein variants in different goat breeds and geographical regions might reflect specific breeding goals with respect to milk processing characteristics, properties for human nutrition and health, or adaptation to the environment. Because protein names, alongside the discovery of protein variants, go through a historical process, we linked old protein names with new ones that reveal more genetic variability. The haplotypes across the cluster of the four genetically linked casein genes are recommended as a valuable genetic tool for discrimination between breeds, managing genetic diversity within and between goat populations, and breeding strategies. The enormous variation in the casein proteins and genes is crucial for producing milk and dairy products with different properties for human health and nutrition, and for genetic improvement depending on local breeding goals.

Proteomics analysis reveals promotion effect of 1α,25-dihydroxyvitamin D3 on mammary gland development and lactation of primiparous sows during gestation

1α,25(OH)₂VD₃ is the most active form of vitamin D₃ in animals, and it plays an important role in regulating mineral metabolism and reproduction. In this study, 140 crossbred gilts (Landrace × Yorkshire) were selected, randomly divided into four groups, and fed with a commercial diet supplemented with 0, 1, 2, and 4 μg/kg of 1α,25(OH)₂VD₃ in the form of 1α,25(OH)₂VD₃-glycosides. The mammary gland tissues were sampled from sows on day 114 of gestation. The production data of sows in each group were analyzed, and the colostrum quality was evaluated. Differentially abundant proteins (DAPs) in the mammary tissues were identified by tandem mass tag (TMT) technique and were verified by Western blot and parallel reaction monitoring (PRM). The results showed that 4 μg/kg 1α,25(OH)₂VD₃-glycosides significantly promoted the piglet birth weight, weaning weight, colostrum quality, and lactation ability of primiparous sows. The proteomics analysis showed that of the identified 53,118 peptides, 48,868 were unique peptides. A total of 5029 DAPs were identified, of which 4292 DAPs contained quantitative information. Our data indicated that 1α,25(OH)₂VD₃ was involved in the regulation of the mammary gland development and lactation in a dose-dependent manner through multiple pathways during gestation of primiparous sows. SIGNIFICANCE: The mammary gland is an important lactation organ of female mammals. Our research aims to reveal the effect of dietary supplementation with 1α,25(OH)₂VD₃ on mammary gland development and lactation of primiparous sow. This study identified potential signaling pathways and DAPs involved in regulating the mammary gland development and lactation in sows. Our findings provides theoretical basis for improving the fecundity of sows.

Detecting the footprint of selection on the genomes of Murciano-Granadina goats

Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80-49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76-37.67 Mb), 22 (31.75 Mb), and 26 (26.69-31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

Background

In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats.

Results

The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins.

Conclusions

The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.

Does the Acknowledgement of αS1-Casein Genotype Affect the Estimation of Genetic Parameters and Prediction of Breeding Values for Milk Yield and Composition Quality-Related Traits in Murciano-Granadina?

Simple Summary

Genetic evaluations and the selection of breeding animals require the accurate estimation of genetic parameters for economically important traits. As a result, dairy livestock has evolved in response to the needs of producers and consumers. Genetic selection in goats has been mostly based on quantitative traits such as milk yield, fat, protein, and dry matter. However, as reported by the increased heritability values of these parameters after the inclusion of the different allelic variants of αS1 casein in evaluation models, the selection of animals carrying this gene could result in a more efficient genetic selection. High levels of genetic polymorphism (89.58% of polymorphic SNP—as only five out of the 48 SNPs assessed were monomorphic) that are related to greater production of coagulable proteins in milk, a fact that could be associated with a higher yield and improved curd firmness properties.

Abstract

A total of 2090 lactation records for 710 Murciano-Granadina goats were collected during the years 2005–2016 and analyzed to investigate the influence of the αS1-CN genotype on milk yield and components (protein, fat, and dry matter). Goats were genetically evaluated, including and excluding the αS1-CN genotype, in order to assess its repercussion on the efficiency of breeding models. Despite no significant differences being found for milk yield, fat and dry matter heritabilities, protein production heritability considerably increased after aS1-CN genotype was included in the breeding model (+0.23). Standard errors suggest that the consideration of genotype may improve the model’s efficiency, translating into more accurate genetic parameters and breeding values (PBV). Genetic correlations ranged from −0.15 to −0.01 between protein/dry matter and milk yield/protein and fat content, while phenotypic correlations were −0.02 for milk/protein and −0.01 for milk/fat or protein content. For males, the broadest range for reliability (R_AP) (0.45–0.71) was similar to that of females (0.37–0.86) when the genotype was included. PBV ranges broadened while the maximum remained similar (0.61–0.77) for males and females (0.62–0.81) when the genotype was excluded, respectively. Including the αS1-CN genotype can increase production efficiency, milk profitability, milk yield, fat, protein and dry matter contents in Murciano-Granadina dairy breeding programs.

Genomic analysis of the origins of extant casein variation in goats

The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.

Longitudinal data analysis of polymorphisms in the κ-casein and β-lactoglobulin genes shows differential effects along the trajectory of the lactation curve in tropical dairy goats

The κ-casein (CSN-3) and β-lactoglobulin (BLG) genes are extensively polymorphic in ruminants. Several association studies have estimated the effects of polymorphisms in these genes on milk yield, milk composition, and cheese-manufacturing properties. Usually, these results are based on production integrated over the lactation curve or on cross-sectional studies at specific days in milk (DIM). However, as differential expression of milk protein genes occurs over lactation, the effect of the polymorphisms may change over time. In this study, we fitted a mixed-effects regression model to test-day records of milk yield and milk quality traits (fat, protein, and total solids yields) from Colombian tropical dairy goats. We used the well-characterized A/B polymorphisms in the CSN-3 and BLG genes. We argued that this approach provided more efficient estimators than cross-sectional designs, given the same number and pattern of observations, and allowed exclusion of between-subject variation from model error. The BLG genotype AA showed a greater performance than the BB genotype for all traits along the whole lactation curve, whereas the heterozygote showed an intermediate performance. We observed no such constant pattern for the CSN-3 gene between the AA homozygote and the heterozygote (the BB genotype was absent from the sample). The differences among the genotypic effects of the BLG and the CSN-3 polymorphisms were statistically significant during peak and mid lactation (around 40-160 DIM) for the BLG gene and only for mid lactation (80-145 DIM) for the CSN-3 gene. We also estimated the additive and dominant effects of the BLG locus. The locus showed a statistically significant additive behavior along the whole lactation trajectory for all quality traits, whereas for milk yield the effect was not significant at later stages. In turn, we detected a statistically significant dominance effect only for fat yield in the early and peak stages of lactation (at about 1-45 DIM). The longitudinal analysis of test-day records allowed us to estimate the differential effects of polymorphisms along the lactation curve, pointing toward stages that could be affected by the gene.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

Goat casein genotypes are associated with milk production traits in the Sarda breed

The aim of the current work was to analyze, in the Sarda breed goat, genetic polymorphism within the casein genes and to assess their influence on milk traits. Genetic variants at the CSN1S1, CSN2, CSN1S2 and CSN3 gene loci were investigated using PCR-based methods, cloning and sequencing. Strong alleles prevailed at the CSN1S1 gene locus and defective alleles also were revealed. Null alleles were evidenced at each calcium-sensitive gene locus. At the CSN3 gene locus, we observed a prevalence of the CSN3 A and B alleles; the occurrence of rare alleles such as CSN3 B'', C, C', D, E and M; and the CSN3 S allele (GenBank KF644565) described here for the first time in Capra hircus. Statistical analysis showed that all genes, except CSN3, significantly influenced milk traits. The CSN1S1 BB and AB genotypes were associated with the highest percentages of protein (4.41 and 4.40 respectively) and fat (5.26 and 5.34 respectively) (P < 0.001). A relevant finding was that CSN2 and CSN1S2 genotypes affected milk protein content and yield. The polymorphism of the CSN2 gene affected milk protein percentage with the highest values recorded in the CSN2 AA goats (4.35, at P < 0.001). The CSN1S2 AC goats provided the highest fat (51.02 g/day) and protein (41.42 g/day) (P < 0.01) production. This information can be incorporated into selection schemes for the Sarda breed goat.

Identification of an intronic regulatory mutation at the buffalo αS1-casein gene that triggers the skipping of exon 6

The characterization of casein polymorphism is an essential step in order to understand the genetic basis of milk quality in dairy ruminants. In this work, we report the identification of a regulatory mutation at the buffalo αs1-casein (CSN1S1) gene that alters the normal processing of the primary transcript. Sequencing of CSN1S1 cDNA from individuals harbouring this new variant revealed that its most distinctive feature is the loss of exon 6 that encodes eight amino acids between positions 35-42 of mature protein. In an effort to map the causal mutation, we sequenced a genomic region spanning exons 5-7 of the buffalo CSN1S1 gene. This experiment allowed us to establish that exon 6-skipping is produced by a G to C substitution at the first position of intron 6 that inactivates the donor splice site. This mutation can be typed by PCR-RFLP by using either TaaI or Bpu10I diagnostic restriction enzymes, and it has a frequency of 0.18 in Romanian buffaloes. This exon skipping phenomenon is the first one described in buffalo CSN1S1 locus.

Effect of CSN1S1 gene polymorphism and stage of lactation on milk yield and composition of extensively reared goats

The effect of CSN1S1 genotype and lactation stage on milk yield and composition were investigated in 80 extensively reared goats. Milk yield was recorded in early, mid and late lactation and individual milk samples were collected to determine: fat, protein, lactose and casein content, pH, freezing point, somatic cell count (SCC) and total microbic mesophilic count (TMC). Relative casein composition and amino acid profile were quantified by HPLC. Fatty acid profile was measured by gas-chromatography. Genotype did not affect milk yield, while this trait was significantly affected by lactation stage (P < 0·01). CSN1S1 BB goats produced significantly higher protein and casein percentages (P < 0·05). αs1-casein (CN) was significantly higher in BB and AB goats than AF and BF, showing intermediate values in AA goats (P < 0·01). The protein percentage and the αs1 and αs2-CN fractions were not affected by lactation stage, while the casein content and the β and κ-CN significantly increased throughout lactation (P < 0·01). C4 : 0 and C6 : 0 were not affected by genotype, while C8 : 0 and C10 : 0 were higher in the AA goats than BB; most of the long chain FA were higher in BB than AA goats. MUFA and PUFA increased in late lactation. In addition, BB goats showed higher essential amino acids, resulting in an optimal composition from the nutritional point of view, when compared with AA goats. The increase of MUFA, PUFA, essential and cis-FA in late lactation indicate that the lipid composition of goat's milk, with the progress of lactation, tends to improve its nutritional value.

Identification of two paralogous caprine CD36 genes that display highly divergent mRNA expression profiles

The CD36 molecule plays a pivotal role in a variety of immunological and cellular processes, including pathogen recognition, inflammation and apoptosis. Herein, we demonstrate that this gene is duplicated in goats, with two copies (CD36 and CD36-like) that display highly divergent mRNA expression profiles. In this way, CD36 mRNA is mostly expressed in the adipose tissue and heart whilst CD36-like mRNA shows a high expression in the liver. We have also found evidence of the presence of two paralogous CD36 and CD36-like genes in the bovine genome, suggesting that CD36 duplication took place before goat-cattle radiation, i.e. at least 20 MYR ago. Finally, we have characterized the polymorphism of the coding regions of the goat CD36 and CD36-like genes. In doing so, we have identified one synonymous polymorphism at the CD36-like gene (c.390A>C) that displays a significant association (P=0.04) with milk somatic cell count, a parameter often used to diagnose mastitis in domestic ruminants.

Casein SNP in Norwegian goats: additive and dominance effects on milk composition and quality

Background

The four casein proteins in goat milk are encoded by four closely linked casein loci (CSN1S1, CSN2, CSN1S2 and CSN3) within 250 kb on caprine chromosome 6. A deletion in exon 12 of CSN1S1, so far reported only in Norwegian goats, has been found at high frequency (0.73). Such a high frequency is difficult to explain because the national breeding goal selects against the variant's effect.

Methods

In this study, 575 goats were genotyped for 38 Single Nucleotide Polymorphisms (SNP) located within the four casein genes. Milk production records of these goats were obtained from the Norwegian Dairy Goat Control. Test-day mixed models with additive and dominance fixed effects of single SNP were fitted in a model including polygenic effects.

Results

Significant additive effects of single SNP within CSN1S1 and CSN3 were found for fat % and protein %, milk yield and milk taste. The allele with the deletion showed additive and dominance effects on protein % and fat %, and overdominance effects on milk quantity (kg) and lactose %. At its current frequency, the observed dominance (overdominance) effects of the deletion allele reduced its substitution effect (and additive genetic variance available for selection) in the population substantially.

Conclusions

The selection pressure of conventional breeding on the allele with the deletion is limited due to the observed dominance (overdominance) effects. Inclusion of molecular information in the national breeding scheme will reduce the frequency of this deletion in the population.

Effects of αs1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk coagulation properties in Murciano-Granadina goats

The effects of the caprine αs1-casein (CSN1S1) polymorphisms on milk quality and cheese yield have been widely studied in French and Italian goat breeds. Much less is known about the consequences of κ-casein (CSN3) genotype on the technological and coagulation properties of goat milk. In the current study, we have performed an association analysis between polymorphisms at the goat CSN1S1 and CSN3 genes and milk coagulation (rennet coagulation time, curdling rate and curd firmness) and technological (time to cutting of curd and cheese yield) properties. In this analysis, we have included 193 records from 74 Murciano-Granadina goats (with genotypes constituted by different combinations of alleles B, E and F of the gene CSN1S1 and alleles A and B of the gene CSN3) distributed in three herds, which were collected bimonthly during a whole lactation. Data analysis, using a linear mixed model for repeated observations, revealed significant associations between CSN1S1 genotypes and the rate of the curdling process. In this way, milk from EE goats had a significantly higher curdling rate than milk from BB individuals (P<0·05). Contrary to previous experiments performed in French breeds, cheese yield was not significantly different in BB, EE and EF goats. Moreover, we have shown that CSN3 genotype has a significant effect on the rennet coagulation time (BB>AB, P<0·05) but not on cheese yield. No interaction between the CSN1S1 and CSN3 genotypes was observed.

Effect of prolactin, beta-lactoglobulin, and kappa-casein genotype on milk yield in East Friesian sheep

The effect of prolactin (PRL), beta-lactoglobulin (beta-LG), and kappa-casein (CSN3) on milk yield was estimated in an East Friesian dairy sheep population from Old Chatham Sheepherding Company, New York. Genotypes were determined by PCR amplification followed by digestion with HaeIII and RsaI for PRL and beta-LG, respectively, and by PCR amplification for CSN3. Monthly milking records and pedigree information were used to evaluate the effect of each polymorphism on milk yield. Results indicated that PRL genotype had a significant effect on milk yield. Ewes carrying one A allele produced 110.6g more milk per day than ewes with no A alleles. There was no statistical difference between ewes with only one A allele and ewes with 2 A alleles. No association among polymorphisms at the beta-LG and CSN3 loci and milk yield was found. The results presented in this study indicate that the PRL gene is a potential marker that could be used in selection programs for improving milk yield in dairy sheep.

Short communication: genetic variability in the predicted microRNA target sites of caprine casein genes

The main goal of the current work was to identify single nucleotide polymorphisms (SNP) that might create or disrupt microRNA (miRNA) target sites in the caprine casein genes. The 3' untranslated regions of the goat alpha(S1)-, alpha(S2)-, beta-, and kappa-casein genes (CSN1S1, CSN1S2, CSN2, and CSN3, respectively) were resequenced in 25 individuals of the Murciano-Granadina, Cashmere, Canarian, Saanen, and Sahelian breeds. Five SNP were identified through this strategy: c.175C>T at CSN1S1; c.109T>C, c.139G>C, and c.160T>C at CSN1S2; and c.216C>T at CSN2. Analysis with the Patrocles Finder tool predicted that all of these SNP are located within regions complementary to the seed of diverse miRNA sequences. These in silico results suggest that polymorphism at miRNA target sites might have some effect on casein expression. We explored this issue by genotyping the c.175C>T SNP (CSN1S1) in 85 Murciano-Granadina goats with records for milk CSN1S1 concentrations. This substitution destroys a putative target site for miR-101, a miRNA known to be expressed in the bovine mammary gland. Although TT goats had higher levels (6.25 g/L) of CSN1S1 than their CT (6.05 g/L) and CC (6.04 g/L) counterparts, these differences were not significant. Experimental confirmation of the miRNA target sites predicted in the current work and performance of additional association analyses in other goat populations will be an essential step to find out if polymorphic miRNA target sites constitute an important source of variation in casein expression.

Genetic variation at the goat hormone-sensitive lipase (LIPE) gene and its association with milk yield and composition

Hormone-sensitive lipase (LIPE) plays a fundamental role in the regulation of energy balance by releasing free fatty acids from adipose triacylglycerol stores. These fatty acids can be subsequently transferred to other body compartments to be oxidized or employed in other biochemical reactions. This enzymic function is particularly important in lactating animals because the synthesis of milk components involves the mobilization of lipid depots to satisfy the large energy demands of the mammary gland. In the current study, we partially sequenced the goatLIPEgene in several individuals. In doing so, we identified two synonymous polymorphisms at exons 2 (c.327C>A>T, triallelic polymorphism) and 3 (c.558C>T). Moreover, we found a mis-sense polymorphism at exon 6 (c.1162G>T) that involves an alanine to serine substitution at position 388. Analysis with Polyphen and Panther softwares revealed that this amino acid replacement is expected to be neutral. Performance of an association analysis with a variety of milk traits revealed that goatLIPEgenotype has highly suggestive effects on milk yield (P=0·0032) as well as on C18:3 n-6g (P=0·0051),trans-10cis-12 CLA (P=0·007) and C12:0 (P=0·0084) milk contents. These associations are concordant with the preference of LIPE to selectively mobilize medium-chain and unsaturated fatty acids.

Effect of CSN1S1 genotype and its interaction with diet energy level on milk production and quality in Girgentana goats fed ad libitum

A study was carried out to evaluate how the energy level of the diet can affect milk production and quality in Girgentana lactating goats in relation to polymorphism at the αs1-casein (CSN1S1) genotype locus. Twenty-seven goats, homogeneous for milk production (1·5±0·3 kg/d), days of lactation (90±10 d) and body weight (35·8±5·5 kg) were selected on the basis of their CSN1S1 genotype, as follows: nine goats homozygous for strong (AA) alleles, nine goats homozygous for weak alleles (FF) and nine goats heterozygous (AF). The goats were used in a 3×3 factorial arrangement of treatments, with three genotypes (AA, FF, AF) and three diets at different energy levels (100%, 65% and 30% of hay inclusion). The experiment consisted of three simultaneous 3×3 Latin squares for the three genotypes, with one square for each level of hay inclusion in the diet. All the animals were housed in individual pens. Each experimental period lasted 23 d and consisted of 15 d for adaptation and 8 d for data and sample collection, during which the goats received the scheduled diet ad libitum. The animals were fed three different diets designed to have the same crude protein content (about 15%) but different energy levels: a pelleted alfalfa hay (H100) and two feeds including 65% (H65) and 30% (H30) of alfalfa hay (respectively 1099, 1386 and 1590 kcal NE for lactation/kg DM). All the diets were ground and pelleted (6 mm diameter). AA goats were more productive than AF and FF goats (respectively: 1419v. 1145 and 1014 g/d;P=0·002). Indeed the interaction energy level×genotype was significant (P=0·018): in fact AA goats showed their milk increase only when fed with concentrates. Differences in protein and in casein levels between the three genotypes were in line with results expected from the different allele contribution to αs1-casein synthesis. Milk urea levels were significantly lower in AA goats compared with AF and FF genotypes (respectively 32·7v. 40·4 and 40·4 mg/dl;P=0·049) and significantly lower when goats were fed with 65H and 30H diets than with 100H diet (respectively 37·4 and 34·3v. 41·7 mg/dl;P<0·001). Indeed, a significant interaction genotype×diet (P=0·043) occurred for milk urea, which was significantly lower in AA goats but only when fed with concentrates (65H and 30H). Blood concentrations of energy indicators (glucose, non-esterified fatty acids and beta-hydroxybutyric acid) were not influenced by genotype. The results confirm that strong alleles are associated with a greater efficiency of feed utilization and seem to show that a high energy level of the diet can further improve this efficiency.