Milk transcriptome biomarker identification to enhance feed efficiency and reduce nutritional costs in dairy ewes

In recent years, rising prices for high-quality protein-based feeds have significantly increased nutrition costs. Consequently, investigating strategies to reduce these expenses and improve feed efficiency (FE) have become increasingly important for the dairy sheep industry. This research investigates the impact of nutritional protein restriction (NPR) during prepuberty and FE on the milk transcriptome of dairy Assaf ewes (sampled during the first lactation). To this end, we first compared transcriptomic differences between NPR and control ewes. Subsequently, we evaluated gene expression differences between ewes with divergent FE, using feed conversion ratio (FCR), residual feed intake (RFI), and consensus classifications of high- and low-FE animals for both indices. Lastly, we assess milk gene expression as a predictor of FE phenotype using random forest. No effect was found for the prepubertal NPR on milk performance or FE. Moreover, at the milk transcriptome level, only one gene, HBB, was differentially expressed between the NPR (n = 14) and the control group (n = 14). Further, the transcriptomic analysis between divergent FE sheep revealed 114 differentially expressed genes (DEGs) for RFI index (high-FERFI = 10 vs low-FERFI = 10), 244 for FCR (high-FEFCR = 10 vs low-FEFCR = 10), and 1 016 DEGs between divergent consensus ewes for both indices (high-FEconsensus = 8 vs low-FEconsensus = 8). These results underscore the critical role of selected FE indices for RNA-Seq analyses, revealing that consensus divergent animals for both indices maximise differences in transcriptomic responses. Genes overexpressed in high-FEconsensus ewes were associated with milk production and mammary gland development, while low-FEconsensus genes were linked to higher metabolic expenditure for tissue organisation and repair. The best prediction accuracy for FE phenotype using random forest was obtained for a set of 44 genes consistently differentially expressed across lactations, with Spearman correlations of 0.37 and 0.22 for FCR and RFI, respectively. These findings provide insights into potential sustainability strategies for dairy sheep, highlighting the utility of transcriptomic markers as FE proxies.

Polymorphisms of the SCD1 Gene and Its Association Analysis with Carcass, Meat Quality, Adipogenic Traits, Fatty Acid Composition, and Milk Production Traits in Cattle

Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future.

Feed efficiency in dairy sheep: An insight from the milk transcriptome

Introduction

As higher feed efficiency in dairy ruminants means a higher capability to transform feed nutrients into milk and milk components, differences in feed efficiency are expected to be partly linked to changes in the physiology of the mammary glands. Therefore, this study aimed to determine the biological functions and key regulatory genes associated with feed efficiency in dairy sheep using the milk somatic cell transcriptome.

Material and methods

RNA-Seq data from high (H-FE, n = 8) and low (L-FE, n = 8) feed efficiency ewes were compared through differential expression analysis (DEA) and sparse Partial Least Square-Discriminant analysis (sPLS-DA).

Results

In the DEA, 79 genes were identified as differentially expressed between both conditions, while the sPLS-DA identified 261 predictive genes [variable importance in projection (VIP) > 2] that discriminated H-FE and L-FE sheep.

Discussion

The DEA between sheep with divergent feed efficiency allowed the identification of genes associated with the immune system and stress in L-FE animals. In addition, the sPLS-DA approach revealed the importance of genes involved in cell division (e.g., KIF4A and PRC1) and cellular lipid metabolic process (e.g., LPL, SCD, GPAM, and ACOX3) for the H-FE sheep in the lactating mammary gland transcriptome. A set of discriminant genes, commonly identified by the two statistical approaches, was also detected, including some involved in cell proliferation (e.g., SESN2, KIF20A, or TOP2A) or encoding heat-shock proteins (HSPB1). These results provide novel insights into the biological basis of feed efficiency in dairy sheep, highlighting the informative potential of the mammary gland transcriptome as a target tissue and revealing the usefulness of combining univariate and multivariate analysis approaches to elucidate the molecular mechanisms controlling complex traits.

Linear Mixed-Effects Model to Quantify the Association between Somatic Cell Count and Milk Production in Italian Dairy Herds

Milk production loss due to mastitis in dairy herds is economically important. Before estimating the economic impacts of mastitis, it is crucial to quantify the association between mastitis and milk production. The objective of this study was to estimate the association between somatic cell count (SCC, as an indicator of intramammary infection due to mastitis) and milk production for dairy cows in Lombardy, Italy. The test-day (TD) records data of 3816 dairy herds located in three different geographical areas of Lombardy from January 2016 to December 2018 were used. After data editing, the final dataset comprised 10,445,464 TD records from 2970 farms and 826,831 cows. The analysis was carried out by using a mixed-effects model with six fixed effects (geographical Area, Breed, Days in Milk, Parity, Season and Year) and nested random effects for each cow and herd. The results confirmed that the SCC had a negative association with milk production. On average, this study found that any two-fold increase of SCC resulted in a milk production loss of 0.830 (95% CI: -0.832, -0.828) kg/cow/day in the whole of Lombardy. These results can be used for economic calculations on the costs of mastitis.

Lipogenic Gene Single Nucleotide Polymorphic DNA Markers Associated with Intramuscular Fat, Fat Melting Point, and Health-Beneficial Omega-3 Long-Chain Polyunsaturated Fatty Acids in Australian Pasture-Based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu Beef Cattle

This study used targeted sequencing aimed at identifying single nucleotide polymorphisms (SNP) in lipogenic genes and their associations with health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP) of the M. longissimus dorsi muscle in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu cattle. It was hypothesized that SNP encoding for the fatty acid-binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and fatty acid synthase (FASN) genes will be significantly associated with health-beneficial n-3 LC-PUFA and the meat eating quality traits of IMF and FMP in an Australian pasture-based beef production system. Two SNP mutations, g.21267406 T>C and g.21271264 C>A, in the SCD gene were significantly (p < 0.05) associated with IMF, FMP, oleic acid (18:1n-9), linoleic acid (LA) 18:2n-6, alpha-linolenic acid (ALA) 18:3n-3, eicosapentaenoic acid (EPA) 20:5n-3, docosahexaenoic acid (DHA) 22:6-n-3, and docosapentaenoic acid (DPA) 22:5n-3. Significant positive correlations (p < 0.05) between FASN SNP g. 50787138 A>G and FMP, 18:1n-9, ALA, EPA, DHA, DPA, and total n-3 LC-PUFA were also detected. An SNP (g.44678794 G>A) in the FABP4 gene was associated with FMP. These results provide significant insights into the contributions of lipogenic genes to intramuscular fat deposition and the biosynthesis of health-beneficial n-3 LC-PUFA. The findings also unravel the potential use of lipogenic gene polymorphisms in marker-assisted selection to improve the content of health-promoting n-3 LC-PUFA and meat eating quality traits in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu beef cattle.

Performance and muscle lipogenesis of calves born to Nellore cows with different residual feed intake classification

This study aimed to evaluate relationships among maternal residual feed intake (RFI) with growth performance and expression of genes involved in lipid metabolism in offspring of Nellore cattle. Fifty-three cows classified as negative or positive RFI by genomic prediction were exposed to fixed-time artificial insemination (FTAI) protocols at 2 and 3 years of age using semen from the same bull. In the first year, cows gestated under grazing conditions and nursed their calves in the feedlot. In the second year, the opposite occurred. Cows were weighed every 28 days during pregnancy and calves were weighed at birth and every 28 days until weaning. Ultrasound images were collected from the carcass of cows and calves. Muscle gene expression was evaluated in calves at birth and weaning. Data were analyzed by year considering the fixed effects of RFI class and FTAI protocol for variables measured in cows, and RFI class, FTAI protocol and sex for variables measured in calves. There was no effect of maternal RFI on calves performance in the first year. Lower expression of FABP4 gene and trend towards lower expression of SREBF1 and LPL genes were detected in samples collected after birth from calves born to negative RFI cows, indicating that adipogenesis was reduced during the fetal and neonatal period. In the second year, negative RFI cows had greater subcutaneous fat thickness than positive RFI cows, and their calves tended to be heavier at birth and to have less rump fat thickness at weaning. No significant differences in expression of genes studied were detected between cow RFI classes. Nellore cows classified as negative RFI consume less feed and produce calves whose growth potential is similar to that of calves produced by positive RFI cows.

Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions

Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.

CircEZH2 Regulates Milk Fat Metabolism through miR-378b Sponge Activity

Simple Summary

Heat stress has seriously threatened the performance and health of dairy cows and has become one of the most important factors restricting the development of the dairy industry. In our previous study, we found that heat stress markedly altered the expression patterns of circRNAs in dairy cow’s mammary gland tissue, and heat-induced circRNAs participated in the regulation of milk fat metabolism through competing endogenous RNA (ceRNA) networks. Therefore, we evaluated the roles of heat-induced circEZH2 in the regulation of milk fat metabolism in this study. In more detail, we found that circEZH2 affects the proliferation, apoptosis, and lipid metabolism of mammary gland epithelial cells, and successfully verified the targeting relationship of circEZH2-bta-miR378b-LPL and circEZH2-bta-miR378b-CD36. This experiment expands the basic data on the role of circRNA in milk fat regulation, and provides a theoretical basis for alleviating heat stress in dairy cows.

Abstract

In this study, we evaluated the roles of heat-induced circEZH2 in the regulation of milk fat metabolism. CircEZH2 overexpression increased HC11 cell proliferation and decreased apoptosis. These changes were accompanied by increased expression of proliferation marker proteins (PCNA, Cyclin D, and Cyclin E) and the anti-apoptotic protein Bcl2, while expression of the pro-apoptotic proteins Bax and cleaved-caspase was reduced. SiRNA-mediated silencing of EZH2 in HC11 cells had the opposite effects. CircEZH2 overexpression promoted the uptake of a fluorescent fatty acid (Bodipy) as well as expression of the fatty acid transport-related protein CD36, lipolysis-related protein LPL, and unsaturated fatty acid metabolism-related proteins FADS1 and SCD1. Dual luciferase reporter assays verified the targeting relationship of the two ceRNA networks, circEZH2-miR378b-LPL and circEZH2-miR378b-CD36. This information provides further clarification of the role of circRNAs in milk fat regulation in addition to a theoretical basis for alleviating the effects of heat stress on milk production by dairy cows.

Multi-Omics Analysis of Mammary Metabolic Changes in Dairy Cows Exposed to Hypoxia

Hypoxia exposure can cause a series of physiological and biochemical reactions in the organism and cells. Our previous studies found the milk fat rate increased significantly in hypoxic dairy cows, however, its specific metabolic mechanism is unclear. In this experiment, we explored and verified the mechanism of hypoxia adaptation based on the apparent and omics results of animal experiments and in vitro cell model. The results revealed that hypoxia exposure was associated with the elevation of AGPAT2-mediated glycerophospholipid metabolism. These intracellular metabolic disorders consequently led to the lipid disorders associated with apoptosis. Our findings update the existing understanding of increased adaptability of dairy cows exposure to hypoxia at the metabolic level.

Variation in the stearoyl-CoA desaturase gene (SCD) and its influence on milk fatty acid composition in late-lactation dairy cattle grazed on pasture

Gene markers have become useful tools for improving animal genetics and breeding since they improve the accuracy of selection for superior breeding stock. In this study, the stearoyl-CoA desaturase (Δ-9-desaturase) gene (SCD) was investigated in New Zealand pasture-grazed Holstein–Friesian × Jersey cows. Three nucleotide substitutions were identified in exon 5 of the gene (c.702A/G, c.762T/C and c.878C/T), and a single nucleotide substitution was identified in intron 5 (c.880+105A/G). The c.878C/T substitution would, if expressed, result in the amino acid substitution p.A293V. Four nucleotide substitutions (c.*1783A/G, c.*1883C/T, c.*1984G/A and c.*2066T/C/G) were identified in the 3′-untranslated region (3′-UTR), and these resulted in three nucleotide sequence variants (named a, b and c). The sequence that would encode valine (V) at position 293 of SCD was linked to 3′-UTR variant a, and the sequence that would encode alanine (A) was linked to variants b and c. The frequency of the genotypes was as follows: VV (equivalent to aa: 15.1 %), VA (equivalent to ab+ac: 50.0 %) and AA (equivalent to bb+cc+bc: 34.9 %). The cows with the V variant produced less C10:1, C12:1 and C14:1 fatty acid (FA) but more C10:0, C11:0, C14:0, C16:1 and C18:2 FA than the A variant cows (P<0.001). Effects of c.*1783A/G and c.*2066T/C/G on milk fat composition were also found for the AA cows. The presence of c was associated with decreased levels of C16:1 (P<0.001), C17:1 (P=0.001), C18:2 cis-9, trans-13 (P=0.045), C18:2 cis-9, trans-12 (P=0.018) FA and C16:1 FA index (P<0.001). The presence of b was associated with increased levels of C13:0 iso FAs (P<0.001), monounsaturated FA (MUFA; P=0.002) and C12:1 (P<0.001).

Small RNA deep sequencing reveals the expressions of microRNAs in ovine mammary gland development at peak-lactation and during the non-lactating period

MicroRNAs (miRNAs) are small non-coding RNAs that are involved in mammary gland development and lactation in livestock. Little is known about the roles of miRNAs in ovine mammary gland development, hence in this study the expression profiles of miRNAs of the mammary gland tissues of ewes at peak-lactation and during the non-lactating period were investigated using RNA sequencing. A total of 147 mature miRNAs were expressed in the two periods. Compared with peak-lactation, eight miRNAs in the non-lactating ewe mammary gland were significantly up-regulated, whereas fifteen miRNAs were down-regulated. A KEGG analysis revealed that the target genes of the up-regulated miRNAs were significantly enriched in lysosome, Wnt and MAPK signaling pathways, while the target genes of down-regulated miRNAs were significantly enriched in the PI3K-Akt signaling pathway, protein processing in endoplasmic reticulum and axon guidance. These results suggest that further study of the differentially expressed miRNAs could provide a better understanding of the molecular mechanisms of mammary development and lactation in sheep.

Identification of circRNA-Associated-ceRNA Networks Involved in Milk Fat Metabolism under Heat Stress

Summer temperatures are generally high in Southern China, and cows are likely to suffer a heat stress reaction. Heat stress will have a negative impact on the performance of dairy cows; however, the mechanism by which high temperature affects lactation is not clear. CircRNA is a type of non-coding RNA discovered in recent years, which performs a crucial function in many biological activities. However, the effects of circRNA on lactation function of dairy cows under heat stress is unknown. The present study aimed to explore the expression levels of circRNA in the mammary gland tissue of cows under heat stress. Firstly, we collected blood and milk samples of summer and winter cows and evaluated lactation performance using serum indicators, milk production, and milk composition. Incorporating the calculation of the temperature and humidity index, we conformed the heat stress status of cows in summer. Heat stress increased the concentration of HSP70 and decreased the concentration of SOD and PRL. Heat stress not only reduced milk yield but also affected milk quality, with milk lactose and milk protein decreasing with increased temperature. The analysis of the fatty acid composition in summer milk found significantly reduced concentrations of unsaturated fatty acids, especially long-chain unsaturated fatty acids. Sequencing of the cow's mammary gland transcriptome revealed that compared to the appropriate temperature (ST) group, the heat stress (HS) group had a total of 2204 upregulated and 3501 downregulated transcripts. GO enrichment and KEGG pathway analysis showed that these genes were mainly related to milk fat metabolism. In addition, 19 upregulated and 19 downregulated circRNA candidates were found in response to heat stress. We used Pearson's test to establish the correlation of circRNA-mRNA and identified four pairs of circRNA-miRNA networks between four circRNAs, six miRNAs, and the CD36 gene. In this study, we revealed the possible role of circRNAs in lactation of dairy cows and identified that circRNA-miRNA-mRNA networks might exist in the cow's mammary glands, providing valuable experience for dairy lactation and milk quality.

Polymorphisms in Fatty Acid Desaturase 2 Gene are Associated with Milk Production Traits in Chinese Holstein Cows

Simple Summary

Searching for causative polymorphisms underlying the variability of milk production traits and then incorporating them into breeding programs are very effective ways to improve the efficiency and reliability of conventional dairy cattle breeding. Fatty acid desaturase 2 (FADS2) plays a pivotal role in the biosynthesis of polyunsaturated fatty acids. Previous studies provided evidence that FADS2 was one of the most downregulated genes during negative energy balance in the liver of postpartum dairy cattle. Genes involved in the energetic pathways may influence other production traits, such as protein, fat and milk yields. Therefore, in the present study, we investigated the common genetic variants of the FADS2 gene in Chinese Holstein cows. Our results provided direct evidence that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis.

Abstract

This study investigated the single nucleotide polymorphisms (SNPs) of Fatty acid desaturase 2 (FADS2) gene and further explored their genetic effects on conventionally collected milk production traits in Chinese Holstein cows using 18,264 test-day records of 841 cows. One missense mutation c. 908 C > T (SNP site in the complementary DNA sequence), which caused an amino acid change from alanine to valine (294Ala > Val), and two 3’ untranslated region (UTR) SNPs, c.1571 G > A and c.2776 A > G were finally identified. The SNP c.908 C > T was significantly associated with test-day milk yield, fat percentage and 305-day milk, fat and protein yield. In particular, the T allele of the SNP c.908 C > T showed a significant association with decreased somatic cell score (SCS) in the investigated population. Significant relationship between the SNP c.1571 G > A and 305-day milk yield showed that genotype GG was linked to the highest milk yield. Substituting the allele G for A at the c.2776 A > G locus resulted in a decrease of protein percentage. Our results demonstrated that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis.

Characteristics of dairy productivity of Holstein heifers depending on their genetic potential

The study presents the results obtained in DNA testing of allelic polymorphism by PCR-RFLP based methods for the leptin and stearoyl-coenzyme A desaturase genes and the interaction of their complex genotypes on the milk productivity indicators of Holstein heifers of Tatarstan population. The study was carried out among 471 Holstein cow-heifers by Integrated Agricultural Production Centre “Stud farm named after Lenin” of Atninsky district of the Republic of Tatarstan in 2016–2018. All complex LEP/SCD1 genotypes were identified through the study. The maximum frequency was observed in the combination of heterozygous genotypes LEPTCSCD1TC 149 animals (31.5 %). Milk productivity test, based on the complex genotypes LEP and SCD1, showed that a significantly high level of productivity for 305 days of lactation was 7314.4 kg, and in heifers with a complex genotype LEPTTSCD1CC was minimal (6337.4 kg) in comparison with indicators of milk yield of heifers with other complex genotypes. According to the content of the mass fraction of fat, reliably the best indicators were established in a subpopulation of animals with a complex TT/TC genotype 3.87 %. The content of the mass fraction of protein was maximal for animals with a complex CC/CC genotype.

LEP and SCD polymorphisms are associated with milk somatic cell count, electrical conductivity and pH values in Holstein cows

This study was conducted to determine LEP-Sau3AI, SCD-Fnu4HI, NR1H3-HpyCH4IV and FABP4-HinII gene polymorphisms and to investigate the association between these SNPs and somatic cell count (SCC), electrical conductivity (EC) and pH in Holstein cow milk. LEP-Sau3AI polymorphism found associated with SCC (p < 0.01), EC (p < 0.01) and pH (p < 0.05). LEP-Sau3AI-BB genotype resulted with higher SCC, EC and pH compared to other genotypes. SCD-Fnu4HI polymorphism showed differences in genotypes for EC (p < 0.05) and pH (p ≤ 0.05) traits. While the highest EC value was found in SCD-Fnu4HI-CT genotype, the highest milk pH was found in genotype TT. In addition, NR1H3-HpyCH4IV genotypes was found the only associated with pH (p < 0.05) among all studied phenotypes. Based on the present findings, it was concluded that LEP and SCD genes could be used in breeding programs for improved SCC, EC and pH values in Holstein dairy cows.

Genetic polymorphisms at candidate genes affecting fat content and fatty acid composition in Modicana cows: effects on milk production traits in different feeding systems

Feeding greatly affects milk yield and composition. The research is highlighting the potential of genetic polymorphism at some loci to affect milk yield and quality traits. These loci can be up/down regulated depending on the production environment; therefore, we hypothesized that milk yield and composition could differ when cows with different genotype at SCD, DGAT1 and ABCG2 loci are reared in different feeding systems. The polymorphisms of SCD, DGAT1 and ABCG2 genes were investigated in Modicana breed. In all, three polymorphic sites, responsible for the genetic variation of quantitative trait loci and therefore defined quantitative trait nucleotides, were genotyped: the transition g.10329C&gt;T in 5th exon determines a substitution p.A293V in the SCD, the dinucleotide mutation g.10433-10434AA&gt;GC in 8th exon responsible for p.K232A substitution in the DGAT1 and the transition g.62569A&gt;C in the 14th exon responsible for p.Y581S substitution in the ABCG2 gene. In the sample of 165 Modicana cows, SCD and DGAT1 genes resulted polymorphic; the alleles g.10329T and g.10433-10434GC were the most frequent in SCD and DGAT1 (0.73 and 0.91) respectively, whereas ABCG2 locus was monomorphic for allele A (p.581Y). Sequencing analysis was carried out on 14 samples with different genotypes to confirm the results of the PCR-RFLP protocols. Based on the genotypes at SCD locus, 47 Modicana cows were selected for the nutritional trial: 24 cows in a semi-intensive farm, with 2 h/day grazing on natural pasture, and 23 cows in an extensive farm, with 8 h/day grazing on natural pasture. Monthly, milk yield and composition were evaluated and individual milk samples were analyzed for fatty acids composition by gas chromatography. No differences in milk yield, fat, protein, lactose, casein and urea were associated to SCD genotype. Feeding systems affected milk yield and composition. No significant genotype×feeding system interaction was observed for milk yield and composition. Fatty acids composition was significantly affected only by the feeding system. Significant interactions were found between SCD genotype and feeding system for six fatty acids: 4:0, 6:0, 8:0, 10:0, 12:0 and t11 18:1. We concluded that the feeding system was the factor that mostly affected milk production and composition; moreover, our results do not confirm what reported in literature as regard the effect of the SCD polymorphism on milk fatty acid composition. The high amount of pasture seemed to have resized the SCD polymorphism effects because of the different fatty acids composition of the diet.

The single nucleotide polymorphism g.133A>C in the stearoyl CoA desaturase gene (SCD) promoter affects gene expression and quali-quantitative properties of river buffalo milk

The stearoyl-CoA desaturase (SCD) gene has been investigated in depth in ruminants because of its effect on milk fat composition. In river buffalo, the single nucleotide polymorphism (SNP) g.133A>C in the gene promoter has been associated with milk quality and yield. However, the biological reason for such effects remains unexplored. In this study, we combined mRNA profile analysis, an electromobility shift assay, and quantitative PCR to elucidate the role of this SNP on gene transcription and its effects on milk fat traits. A preliminary genotyping of g.133A>C was carried out on a group of 303 river buffaloes to choose individuals for the downstream applications. Analysis of allele frequencies showed an increase in the minor allele C (0.25) compared with previous findings (0.16). Six animals (2 for each genotype) were chosen for cloning and 216 positive cDNA recombinant clones for SCD (72 per genotype) were analyzed by PCR. All clones showed the same length on agarose gel; therefore, random clones were chosen for sequencing. No qualitative differences were found and all gene transcripts assembled correctly. An electrophoretic mobility shift assay was performed to evaluate the binding of the transcription factor Sp1 to DNA sequences including g.133A>C. Genotype CC showed a higher binding (mean ± standard error of the mean) than genotype AA in 2 different conditions [Enzo buffer (EB), Enzo Life Science Inc., Farmingdale, NY: 201.77 ± 4.06 vs. 141.65 ± 3.77 band intensity values and Poletto buffer (PB): 95.90 ± 1.15 vs. 67.30 ± 2.14 band intensity values]. The subsequent quantitative PCR confirmed the upregulation of the CC genotype compared with the AA and AC genotypes. The association study with milk fat traits revealed a favorable effect of allele C. The heterozygous genotype had the highest values for monounsaturated fatty acids, oleic acid (C18:1 cis-9), polyunsaturated fatty acids, and odd- and branched-chain fatty acids, and the lowest values for saturated fatty acids and atherogenic and thrombogenic indices; the heterozygous genotype differed significantly from the AA genotype. The AC genotype has previously been associated with higher milk yield. Therefore, the g.133A>C SNP is a marker with dual effects and is an interesting candidate for assisted selection programs in river buffalo. These data clarified the biological role of the SNP g.133A>C in the SCD promoter and how it affects gene function, providing important knowledge on the genetic background of lipid metabolism, including the future possibility of selecting alleles with quantitatively or qualitatively favorable effects.

Fitting milk production curves through nonlinear mixed models

The aim of this work was to fit and compare three non-linear models (Wood, Milkbot and diphasic) to model lactation curves from two approaches: with and without cow random effect. Knowing the behaviour of lactation curves is critical for decision-making in a dairy farm. Knowledge of the model of milk production progress along each lactation is necessary not only at the mean population level (dairy farm), but also at individual level (cow-lactation). The fits were made in a group of high production and reproduction dairy farms; in first and third lactations in cool seasons. A total of 2167 complete lactations were involved, of which 984 were first-lactations and the remaining ones, third lactations (19 382 milk yield tests). PROC NLMIXED in SAS was used to make the fits and estimate the model parameters. The diphasic model resulted to be computationally complex and barely practical. Regarding the classical Wood and MilkBot models, although the information criteria suggest the selection of MilkBot, the differences in the estimation of production indicators did not show a significant improvement. The Wood model was found to be a good option for fitting the expected value of lactation curves. Furthermore, the three models fitted better when the subject (cow) random effect was considered, which is related to magnitude of production. The random effect improved the predictive potential of the models, but it did not have a significant effect on the production indicators derived from the lactation curves, such as milk yield and days in milk to peak.

Genetic effects of FASN, PPARGC1A, ABCG2 and IGF1 revealing the association with milk fatty acids in a Chinese Holstein cattle population based on a post genome-wide association study

Background

A previous genome-wide association study deduced that one (ARS-BFGL-NGS-39328), two (Hapmap26001-BTC-038813 and Hapmap31284-BTC-039204), two (Hapmap26001-BTC-038813 and BTB-00246150), and one (Hapmap50366-BTA-46960) genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk fatty acids were close to or within the fatty acid synthase (FASN), peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PPARGC1A), ATP-binding cassette, sub-family G, member 2 (ABCG2) and insulin-like growth factor 1 (IGF1) genes. To further confirm the linkage and reveal the genetic effects of these four candidate genes on milk fatty acid composition, genetic polymorphisms were identified and genotype-phenotype associations were performed in a Chinese Holstein cattle population.

Results

Nine SNPs were identified in FASN, among which SNP rs41919985 was predicted to result in an amino acid substitution from threonine (ACC) to alanine (GCC), five SNPs (rs136947640, rs134340637, rs41919992, rs41919984 and rs41919986) were synonymous mutations, and the remaining three (rs41919999, rs132865003 and rs133498277) were found in FASN introns. Only one SNP each was identified for PPARGC1A, ABCG2 and IGF1.

Association studies revealed that FASN, PPARGC1A, ABCG2 and IGF1 were mainly associated with medium-chain saturated fatty acids and long-chain unsaturated fatty acids, especially FASN for C10:0, C12:0 and C14:0. Strong linkage disequilibrium was observed among ARS-BFGL-NGS-39328 and rs132865003 and rs134340637 in FASN (D´ > 0.9), and among Hapmap26001-BTC-038813 and Hapmap31284-BTC-039204 and rs109579682 in PPARGC1A (D´ > 0.9). Subsequently, haplotype-based analysis revealed significant associations of the haplotypes encompassing eight FASN SNPs (rs41919999, rs132865003, rs134340637, rs41919992, rs133498277, rs41919984, rs41919985 and rs41919986) with C10:0, C12:0, C14:0, C18:1n9c, saturated fatty acids (SFA) and unsaturated fatty acids (UFA) (P = 0.0204 to P < 0.0001).

Conclusion

Our study confirmed the linkage between the significant SNPs in our previous genome-wide association study and variants in FASN and PPARGC1A. SNPs within FASN, PPARGC1A, ABCG2 and IGF1 showed significant genetic effects on milk fatty acid composition in dairy cattle, indicating their potential functions in milk fatty acids synthesis and metabolism. The findings presented here provide evidence for the selection of dairy cows with healthier milk fatty acid composition by marker-assisted breeding or genomic selection schemes, as well as furthering our understanding of technological processing aspects of cows’ milk.

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A post-GWAS confirming the SCD gene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population

The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.

The expression of the SCD1 gene and its correlation with fattening and carcass traits in sheep

Abstract. Stearoyl-CoA desaturase 1 (SCD1) is a critical enzyme that catalyzes the synthesis of monounsaturated fatty acids and is involved in several signaling pathways related to lipid metabolism. The objective of the present study was to estimate the expression of the SCD1 gene in three different ovine tissues strongly associated with lipid homeostasis. The SCD1 gene expression measurement was performed on three tissues (liver, subcutaneous fat, perirenal fat) originated from 15 old-type Polish Merino sheep. The SCD1 transcript abundance was evaluated based on the two most stable endogenous controls (RPS2 – ribosomal protein S2; ATP5G2 – H(+)-transporting ATP synthase). The highest expression of the SCD1 gene was observed in ovine subcutaneous fat compared to perirenal fat and liver. Furthermore, the present research indicated the significant correlation between ovine SCD1 transcript abundance and several important production traits. The expression of the SCD1 gene in liver and perirenal fat highly positively correlated with the feed : gain ratio, test of daily gain and age of the animals at slaughter. Moreover, in both tissues, the SCD1mRNA level positively correlated with weight and content of perirenal fat and subcutaneous fat (R =  0.64, 0.8, 0.6, respectively) and negatively with assessment of external fat content with the use of the EUROP scale (R = −0.64). The SCD1 expression in subcutaneous fat also corresponds with back fat of blade chop and thickness of longissimus dorsi muscles evaluated using USG (ultrasonography) (R =  −0.6 and 0.62, respectively). The significant correlation between SCD1 transcript abundance and fattening and slaughtering traits indicate the ability to improve important production traits in sheep via modification of expression of the SCD1 gene.

Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats

Dairy goats serve as an important source of milk and also fulfill agricultural and economic roles in developing countries. Understanding the genetic background of goat mammary gland is important for research on the regulatory mechanisms controlling tissue function and the synthesis of milk components. We collected tissue at four different stages of goat mammary gland development and generated approximately 25 GB of data from Illumina de novo RNA sequencing. The combined reads were assembled into 51,361 unigenes, and approximately 60.07 % of the unigenes had homology to other proteins in the NCBI non-redundant protein database (NR). Functional classification through eukaryotic Ortholog Groups of Protein (KOG), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the unigenes from goat mammary glands are involved in a wide range of biological processes and metabolic pathways, including lipid metabolism and lactose metabolism. The results of qPCR revealed that genes encoding FABP3, FASN, SCD, PLIN2, whey proteins (LALBA and BLG), and caseins (CSN1S1, CSN1S2, CSN2 and CSN3) at 100 and 310 days postpartum increased significantly compared with the non-lactating period. In addition to their role in lipid and protein synthesis, the higher expression at 310 days postpartum could contribute to mammary cell turnover during pregnancy. In conclusion, this is the first study to characterize the complete transcriptome of goat mammary glands and constitutes a comprehensive genomic resource available for further studies of ruminant lactation.

Associations between lipid metabolism and fertility in the dairy cow

Dairy cows mobilise body tissues to support milk production and, because glucose supplies are limited, lipids are used preferentially for energy production. Lipogenic activity is switched off and lipolytic mechanisms in adipose tissue increase through changes in the expression of several key enzymes. This results in a loss of body condition, together with high circulating concentrations of non-esterified fatty acids. Changes in the synthesis, secretion and signalling pathways of somatotrophic hormones (insulin, growth hormone, insulin-like growth factor 1) and adipokines (e.g. leptin) are central to the regulation of these processes. A high reliance on fatty acids as an energy source in the peripartum period causes oxidative damage to mitochondria in metabolically active tissues, including the liver and reproductive tract. The expression of genes involved in insulin resistance (PDK4, AHSG) is increased, together with expression of TIEG1, a transcription factor that can induce apoptosis via the mitochondrial pathway. Polymorphisms in TFAM and UCP2, two autosomal mitochondrial genes, have been associated with longevity in dairy cows. Polymorphisms in many other genes that affect lipid metabolism also show some associations with fertility traits. These include DGAT1, SCD1, DECR1, CRH, CBFA2T1, GH, LEP and NPY. Excess lipid accumulation in oocytes and the regenerating endometrium reduces fertility via reductions in embryo survival and increased inflammatory changes, respectively.

Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries

Genome-wide association studies for difficult-to-measure traits are generally limited by the sample size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein–Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with the feed utilisation complex: fat and protein corrected milk yield (FPCM), dry matter intake (DMI), body condition score (BCS) and live-weight (LW). Phenotypic data and 37 590 single nucleotide polymorphisms (SNPs) were available on up to 1629 animals. Genetic parameters of the traits were estimated using a linear animal model with pedigree information, and univariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. The variation in the phenotypes explained by the SNPs on each chromosome was related to the size of the chromosome and was relatively consistent for each trait with the possible exceptions of BTA4 for BCS, BTA7, BTA13, BTA14, BTA18 for LW and BTA27 for DMI. For LW, BCS, DMI and FPCM, 266, 178, 206 and 254 SNPs had a Bayes factor .3, respectively. Olfactory genes and genes involved in the sensory smell process were overrepresented in a 500 kbp window around the significant SNPs. Potential candidate genes were involved with functions linked to insulin, epidermal growth factor and tryptophan.

Associations of acetyl-coenzyme A carboxylase α, stearoyl-coenzyme A desaturase, and lipoprotein lipase genes with dairy traits in Alpine goats

Milk yield and composition are of great economic importance for the dairy goat industry. The identification of genes associated with phenotypic differences for these traits could allow for the implementation of gene-assisted selection programs in goats. Associations between polymorphisms at 3 candidate genes and milk production traits in Alpine goats farmed in Italy were investigated in the present research. Considered genes were acetyl-coenzyme A carboxylase α (ACACA), the major regulatory enzyme of fatty acid biosynthesis; stearoyl-coenzyme A desaturase (SCD), involved in the biosynthesis of monounsaturated fatty acids in the mammary gland; and lipoprotein lipase (LPL), which plays a central role in plasma triglyceride metabolism. An approach somewhat similar to the granddaughter design for detecting quantitative trait loci in dairy cattle was followed. Effects of genotypes of a sample of 59 Alpine bucks on phenotypes of their 946 daughters raised in 75 flocks were investigated. Data comprised 13,331 daily records for milk yields (L/d), fat and protein yields (kg/d), and fat and protein contents (%) of 2,200 lactations. Population genetics parameters were calculated and associations between milk production traits and 10 single nucleotide polymorphisms (SNP) at the 3 genes were tested. Two markers at the ACACA, 1 for the SCD and 1 at the LPL locus, deviated significantly from the Hardy-Weinberg equilibrium, with an observed heterozygosity lower than expected. Flock, age of the goat, kidding season, and stage of lactation affected all traits considered, except fat percentage. Three SNP were found to be significantly associated with milk production traits. The SNP located on the ACACA gene showed an effect on milk yield, with daughters of TT bucks having an average test-day milk yield of about 0.3 to 0.25 L/d lower than the other 2 genotypes. The marker on the LPL locus was highly associated with milk yield, with the largest values for CC daughters (about 0.50L more than GG). The TGT deletion located on the untranslated region of the SCD gene showed significant effects on average milk and protein yields. The homozygote-deleted genotype had values about 0.5 L/d and 16 g/d lower for milk and protein daily yield, respectively, compared with the TGT/TGT genotype. Differences between genotypes were quite constant across most of the lactation. Associations found in the present study, which should be tested in a larger sample, especially for those markers that show rare genotypes, may offer useful indications for the genetic improvement of dairy traits in goats.

A single nucleotide polymorphism in the promoter region of river buffalo stearoyl CoA desaturase gene (SCD) is associated with milk yield

An association study between the milk yield trait and the stearoyl-CoA desaturase (SCD) polymorphism (g.133A > C) in Italian Mediterranean river buffalo was carried out. A full characterization of the river buffalo SCD promoter region was presented. Genotyping information was provided and a quick method for allelic discrimination was developed. The frequency of the C allele was 0·16. Test-day (TD) records (43 510) of milk production belonging to 226 lactations of 169 buffalo cows were analysed with a mixed linear model in order to estimate the effect of g.133A > C genotype, as well as the effect of parity and calving season. The SCD genotype was significantly associated with milk yield (P = 0·02). The genotype AC showed an over-dominance effect with an average daily milk yield approximately 2 kg/d higher than CC buffaloes. Such a difference represents about 28% more milk/d. The effect of the genotype was constant across lactation stages. The contribution of SCD genotype (r2SCD) to the total phenotypic variance in milk yield was equal to 0·12. This report is among the first indications of genetic association between a trait of economic importance in river buffalo. Although such results need to be confirmed with large-scale studies in the same and other buffalo populations, they might offer useful indications for the application of MAS programmes in river buffalo and in the future they might be of great economic interest for the river buffalo dairy industry.

Genetic effects of stearoyl-coenzyme A desaturase (SCD) polymorphism on milk production traits in the Chinese dairy population

Stearoyl-CoA desaturase (SCD) is a multifunctional complex enzyme important in the cellular biosynthesis of fatty acids. The present study was to investigate the association of the SCD gene with milk production traits in dairy cattle. Two single nucleotide polymorphisms (SNPs) (g.6926A>G and g.8646A>G) in introns 3 and 4, and three SNPs (g.10153A>G, g.10213T>C and g.10329C>T) in exon 5 were identified with pooled DNA sequencing and genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry assay in 752 Chinese Holstein cows. Polymorphism g.10329C>T was predicted to result in an amino acid replacement from alanine to valine in the SCD protein. With a mixed animal model, the significant associations of the five SNPs with 305-day milk, fat and protein yields and protein percentage were determined. We further demonstrated cows with heterozygous genotypes (A/G or C/T) had highest 305 day milk yield, fat yield, protein yield and lowest protein percentage. Heterozygous cows with genotype AG at the g.6926A>G locus showed the greatest milk yield (P < 0.0001), fat yield (P < 0.0001) and protein yield (P < 0.0001) among other heterozygous genotypes at any of the loci. Dominance effects of all identified SNPs on milk, fat and protein yields and protein percentage were significant. Moreover, significant allele substitution effects at g.6926A>G locus on milk yield and at g.10213T>C on protein yield were observed. Five-locus haplotypes and strong linkage disequilibrium (D' > 0.9) between the five SNPs were also observed. The results suggest that identified polymorphisms could be potential genetic markers to improve the production performance of Chinese Holstein.

An association analysis between OXT genotype and milk yield and flow in Italian Mediterranean river buffalo

The aim of this study was to evaluate possible associations between three SNPs at the oxytocin locus (AM234538: g.28C>T; g.204A>G and g.1627G>T) and two productive traits, milk yield and milkability, in Italian Mediterranean river buffaloes. Effects of parity, calving season and month of production were also evaluated. A total of 41 980 test-day records belonging to 219 lactations of 163 buffalo cows were investigated. The allele call rate was 98·8% and the major allele frequency for all the investigated loci was 0·76. The OXT genotype was significantly associated with milk yield (P=0·029). The TT genotype showed an average daily milk yield approximately 1·7 kg higher than GT buffaloes. Such a difference represents about 23% more milk/d. A large dominance effect (−1·17±0·43 kg) was estimated, whereas the contribution of OXT genotype (r2OXT) to the total phenotypic variance in milk yield was equal to 0·06. The TT genotype showed higher values also for the milk flow, even though the estimated difference did not reach a level of statistical significance (P=0·07). Such an association, among the first reported for the oxytocin locus in ruminants, should be tested on a population scale and possible effects on milk composition traits should be evaluated in order to supply useful indications for the application of marker-assisted selection programmes in river buffaloes.

Short communication: influence of the muscle hypertrophy mutation of the myostatin gene on milk production traits and milk fatty acid composition in dual-purpose Belgian Blue dairy cattle

The objective of this study was to estimate genetic effects for the muscle hypertrophy mutation (mh) of the myostatin gene for conventional milk production traits and for milk fatty acid composition in dual-purpose Belgian Blue dairy cows. For the present study, only cows from a single herd, in which genotype frequencies were as balanced as possible (0.266 for +/+, 0.523 for mh/+, and 0.211 for mh/mh), were chosen to avoid confounding between herd and genotype effects. A total of 109 cows with 3,190 test-day records for fat, protein, and milk yields and 1,064 test-day records for saturated and monounsaturated fatty acids were used for the calculations. Variance component and gene effect estimations were performed via expectation-maximization REML and BLUP methods, respectively, using a multi-trait mixed test-day model with an additional fixed regression on the muscle hypertrophy genotype. Results showed that one copy of the wild-type "+" allele led to a significant additive effect of 26.35 g/d for fat yield. Significant dominance effects of 23.22 g/d for protein yield and 30.28 g/d for fat yield were also observed. In contrast, a nonsignificant trend was observed in favor of lower saturated fatty acid contents in milk for one copy of the mutant "mh" allele. Concerning milk, fat, and protein yields, our results confirmed literature results indicating a superior effect of the "+" allele compared with the mutant allele. Therefore, the selection of the "+" allele has the potential to increase conventional milk production traits in the dual-purpose Belgian Blue breed. However, when focus is given to milk fatty acid profile, a possible antagonistic effect between the benefit of the "+" allele for higher milk production and the "mh" allele for reduced saturated fatty acid content in milk should be confirmed in further studies.

Stearoyl-CoA desaturase (SCD) gene polymorphism in goat breeds

There is evidence that stearoyl-CoA desaturase (SCD) is a key enzyme for lipid metabolism. Changes in enzyme activity that depends on SCD gene polymorphism and regulation could cause variations of fatty acid composition of meat and milk. We investigated genetic variability in caprine SCD, analyzing 335 animals belonging to three goat breeds by single-strand conformation polymorphism and DNA sequencing. Six single nucleotide polymorphism were identified, in intron 3 (585T-->A and 601A-->G; Ref. AF422168), intron 4 (719T-->A; AF422169), and exon 6 (690 A-->G, 718 C-->G, and 802 A-->C; AF422171). The less polymorphic SNP 601A-->G displayed variability only in Xuhuai and Boer breeds. Across breeds, the average frequency for the least frequent alleles ranged from 0.1158 to 0.2532. The three SNPs in exon 6 resulted in variations of amino acids 313 tyr --> cys, 322 phe --> leu, and 350 arg --> ser. The allelic distribution in exon 6 of Xuhuai was significantly different from Boer and Haimen.

Novel SNPs in the caprine stearoyl-CoA desaturase (SCD) and decorin (DCN) genes that are associated with growth traits in Chinese goat breeds

Stearoyl-CoA desaturase (SCD) is an iron-containing enzyme involving in the biosynthesis of monounsaturated fatty acids (MUFA) in mammary gland and adipose tissue, while decorin (DCN) consists of a protein core and a single dermatan or chondroitin sulfate glycosaminoglycan chain, contributing multifunctionally to matrix assembly, modulation of the activity of growth factors and cell migration and proliferation. However, few studies have focused on the genetic variability of them in goat. Herein, five Chinese goat breeds (1229 animals) were analyzed. Based on DNA pooling and PCR-RFLP, three nucleotide substitutions, one of which caused a amino acid substitution, were detected in SCD gene and three haploids (A, B, C) were constructed. According to SSCP analysis and DNA sequencing methods, a 2-bp deletion and two other SNPs were found existing in another analyzed gene DCN, and three haploids (X, Y, Z) were built. Associations between the genotypes and the growth traits (body length, body height, chest circumference, cannon circumference) were also analyzed. For SCD gene, genotype CC individuals had significant greater body height in Guanzhong and body length in both Guanzhong and Xinong saanen than genotype BC individuals (P < 0.05). For DCN gene, individuals with genotype XX was obviously higher than that with genotype XY (P < 0.05). These results indicated that genotype CC of SCD gene and genotype XX of DCN gene could be used for the breeding of new breeds of goat in China.

Database of cattle candidate genes and genetic markers for milk production and mastitis

A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3'UTRs of candidate genes.

Effect of ABCG2, PPARGC1A, OLR1 and SCD1 gene polymorphism on estimated breeding values for functional and production traits in Polish Holstein-Friesian bulls

This study investigated the impact of 6 polymorphisms located in the ABCG2, PPARGC1A, OLR1 and SCD1 genes on estimated breeding values for milk production, longevity, somatic cell count and reproductive traits. The analysis was conducted on 453 Polish Holstein-Friesian bulls. Genotypes were identified using PCR-RFLP, and haplotype inferences were performed for 3 linked mutations of PPARGC1A. The most significant associations were found between the A/C polymorphism located in exon 14 of ABCG2 and milk fat production traits as well as calving-to-first insemination interval, and between the T/C substitution in intron 9 of the PPARGC1A and non-return rate in heifers.