Milk Production Traits Research Articles

Genetic Evaluation of Monthly Test-Day Milk Yields of Jersey Crossbred Cattle Under Farmers' Production System in Tamil Nadu, India.

Tamil Nadu, a state in southern India, is bereft of any native dairy or dual-purpose cattle breeds, and the state depends chiefly on crossbred cattle for milk production. Jersey crossbred cattle account for 90% of the state's milk production. This genetic evaluation study aimed to assess milk production traits, including test-day milk yields (TDMYs), total lactation milk yield (TMY), and 305-day milk yield (305MY), in these cattle reared under farmers' conditions. Data on monthly TDMYs (TDMY1 to TDMY10) of Jersey crossbred cows (n = 75,627) reared by the farmers over 11 years (2012-2022) were collected for evaluation. The influence of non-genetic factors viz., location (agroclimatic zones), period and season of calving, and parity on TDMYs, TMY and 305MY were assessed, and the variance and covariance components for genetic parameters (heritability and genetic correlation) of the traits were estimated by the method of restricted maximum likelihood (REML) under a multivariate animal model and by a random regression model (RRM). The overall means of various TDMYs ranged from 4.98 (TDMY10) to 9.95 kg (TDMY2), and for TMY and 305MY, the means were 2480.33 and 2393.71 kg, respectively. The heritabilities estimated by the multivariate animal model for TDMYs were moderate and ranged from 0.26 ± 0.02 to 0.37 ± 0.02 and the estimates were less variable throughout lactation, while the estimates obtained by RRM were medium to high and ranged between 0.29 ± 0.01 and 0.67 ± 0.02 for milk yield on day 5 to 305 (DIM 5-DIM 305). The heritabilities estimated for TMY and 305MY were 0.43 ± 0.02 and 0.43 ± 0.02, respectively. The estimates of heritability for mid-lactation yields were comparatively less than those at the beginning and the end of lactation. The moderate to high estimates of heritabilities for TDMYs, TMY, and 305MY obtained in the present study offer ample scope for improving milk production through selective breeding. Genetic correlations between TDMYs estimated by the multivariate animal model were positive and high, with a range between 0.75 ± 0.03 and 0.99 ± 0.00. Considerably higher estimates (0.98-0.99) were observed between adjacent TDMYs showing strong genetic associations. By RRM, genetic correlations estimated between DIMs were positive (except for DIM 5 with DIM 125 to DIM 185 and DIM 125 with DIM 305), and the magnitude of genetic correlation decreased with an increase in the interval between the DIMs. The high genetic correlation observed between the TDMYs (in the early stage of lactation) and total lactation milk yield suggested that these test-day yields could be used favorably for the early selection of cows for milk production, which facilitates reduction in the generation interval and consequently increases the annual genetic gain for the milk production traits.

Association of SPP1 and NCAPG genes with milk production traits in Chinese Holstein cows: polymorphism and functional validation analysis.

Milk production traits play an important role in dairy cattle breeding, and single nucleotide polymorphisms can be used as effective molecular markers for milk production trait marker-assisted breeding in dairy cattle. Based on the results of the preliminary GWAS, candidate genes SPP1 and NCAPG associated with milk production traits were screened. In this study, the aim was to screen and characterize the SNPs of SPP1 and NCAPG genes about milk production traits. Two SNPs and one haplotype block of the SPP1 gene and four SNPs and one haplotype block of the NCAPG gene were obtained by amplification, sequencing and association analysis, and all six SNPs were located in the exon region. Association analysis showed that all six SNPs were significantly associated with milk protein percentage. Linkage disequilibrium analysis showed that 2 SNPs of SPP1 (g. 36,700,265 C > T and g. 36,693,596 C > A) constituted a haplotype that correlated with milk protein percentage, and the dominant haplotype was H2H2, which was CCTT. 4 SNPs of NCAPG (g. 37,342,705 C > A, g. 37,343,379 G > T, g. 37,374,314 C > A and g. 37,377,857 G > A) constituted a haplotype associated with milk protein percentage, 305-days milk protein yield and 305 days milk yield. Tissue expression profiling results revealed that SPP1 and NCAPG had the highest expression in mammary tissue. Interference with SPP1 and NCAPG inhibited the proliferation of Bovine mammary epithelial cells. (BMECs), down-regulated the expression of PCNA, CDK2 and CCND1, up-regulated the expression of BAX and BAD, and promoted apoptosis. Reduced triglyceride synthesis in BMECs, down-regulated the expression of DGAT1, DGAT2, LPIN1, and AGPAT6.SPP1 and NCAPG are involved in the synthesis of milk proteins, and interfering with SPP1 and NCAPG decreased the secretion of β-casein, κ-casein, and αs1-casein, as well as up-regulated the CSN2 and CSN3 expression. The above results indicate that the SNP loci of SPP1 and NCAPG can be used as potential molecular markers to improve milk production traits in dairy cows, laying the foundation for marker-assisted selection. It also proves that SPP1 and NCAPG can be used as candidate key genes for milk production traits in dairy cows, providing new insights into the physiological mechanisms of lactation regulation in dairy cows.

Genomic Prediction and Genome-Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows.

Genomic selection (GS) and genome-wide association studies (GWAS) have not been investigated in Vietnamese dairy cattle, even for basic milk production traits, largely due to the scarcity of individual phenotype recording in smallholder dairy farms (SDFs). This study aimed to estimate heritability (h2) and test the applicability of GS and GWAS for milk production, body conformation and novel heat tolerance traits using single test day phenotypic data. Thirty-two SDFs located in either the north (a lowland vs. a highland) or the south (a lowland vs. a highland) of Vietnam were each visited for an afternoon and the next morning to collect phenotype data of all lactating cows (n = 345). Tail hair from each cow was sampled for subsequent genotyping with a 50K SNP chip at that same visit. Milk production traits (single-test day) were milk yield (MILK, kg/cow/day), energy corrected milk yield adjusted for body weight (ECMbw, kg/100 kg BW/day), fat (mFA, %), protein (mPR, %) and dry matter (mDM, %). Conformation traits were body weight (BW, kg) and body condition score (BCS, 1 = thin to 5 = obese). Heat tolerance traits were panting score (PS, 0 = normal to 4.5 = extremely heat-stressed) and infrared temperatures (IRTs, °C) at 11 areas on the external body surface of the cow (inner vulval lip, outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof and hind hoof), assessed by an Infrared Camera. Univariate linear mixed models and a 10-fold cross-validation approach were applied for GS. Univariate single SNP mixed linear models were applied for the GWAS. Estimated h2 (using the genotype information to build relationships among animals) were moderate (0.20-0.37) for ECMbw, mFA, mPR, mRE, BW, BCS and IRT at rear udder; low (0.08-0.19) for PS and other IRTs; and very low (≤ 0.07) for MILK, ECM and mDM. Accuracy of genomic estimated breeding values (GEBVs) was low (≤ 0.12) for MILK, ECM, mDM and IRT at hind hoof; and moderate to high (0.32-0.46) for all other traits. The most significant regions on chromosomes (BTA) associated with milk production traits were 0.47-1.18 Mb on BTA14. Moderate to high h2 and moderate accuracies of GEBVs for mFA, mPR, ECMbw, BCS, BW, PS and IRTs at rear udder and outer vulval surface suggested that GS using single test day phenotypic data could be applied for these traits. However, a greater sample size is required to decrease the bias of GEBVs by GS and increase the power of detecting significant quantitative trait loci (QTLs) by GWAS.

Effects of the Prenatal Maternal Health Status on Calf Disease Prevalences and Respective Genetic Parameter Estimates in German Holstein Cattle.

The aim of the present study was to infer phenotypic responses and genetic parameters of the F1 calf diseases diarrhoea (DIAR) and pneumonia (PNEU) in dependency of the prenatal maternal health status (PMHS) of the dam and of the herd-calving year. The PMHS considered diagnoses for the cow disease mastitis (MAST) and claw disorders (CD) during gestation of F0 dams. Furthermore, 305-d milk production traits of F1 offspring from either healthy or diseased dam groups were compared. The study comprised 20,045 female calves (F1 = generation 1) and their corresponding dams (F0 = parental generation 0), kept in 41 large-scale herds. All F1 calves were from their dams' 2nd parity, implying that all dam (maternal) diseases were recorded during the first lactation and dry period of the dams. The F1 calves were phenotyped for DIAR up to 30 days post-partum, and for PNEU up to 180 days of age. At least one entry for the respective disease implied a score = 1 = sick, otherwise, a score = 0 = healthy, was assigned. Production records of the 10,129 F1 cows comprised 305-d records in first lactation for milk yield (MY), protein yield (PY) and fat yield (FY). Linear and generalised linear mixed models were applied to infer phenotypic responses of F1 traits in dependency of the PMHS for CD and MAST. A diagnosis for MAST or CD in F0 cows during gestation was significantly (p ≤ 0.05) associated with an increased prevalence for DIAR and PNEU, with pairwise differences of least-squares-means between calves from healthy and diseased cow groups up to 3.61%. The effects of PMHS on 305-d production traits in offspring were non-significant (p > 0.05). In bivariate genetic analyses, DIAR and PNEU were defined as different traits according to the PMHS, i.e., DIAR-MASThealthy and DIAR-MASTdiseased, DIAR-CDhealthy and DIAR-CDdiseased, PNEU-MASThealthy and PNEU-MASTdiseased, and PNEU-CDhealthy and PNEU-CDdiseased. The direct heritabilities for DIAR and PNEU were quite similar in the healthy and respective diseased dam group. Slightly larger direct heritabilities in the diseased dam groups were due to increased genetic variances. Maternal heritabilities were quite stable and smaller than the direct heritabilities. In random regression models, genetic parameters for DIAR and PNEU were estimated along the continuous herd-calving-year prevalence scale, considering a prevalence for MAST and CD (based on the 20,045 dam records plus 16,193 herd contemporary records) in the range from 0% to 30%. Direct heritabilities for PNEU were quite stable along the herd-calving-year gradient for MAST and CD. For DIAR, we observed stronger estimate fluctuations, especially increasing direct heritabilities in dependency of the herd-calving-year prevalence for MAST from 0.13 (at a MAST prevalence of 0%) to 0.30 (at a MAST prevalence of 30%). Consequently, obvious genotype x herd-calving-year PMHS interactions were observed for DIAR on the prenatal MAST scale, with a minimal correlation of 0.48 between direct genetic effects at 0% MAST prevalence and at 30% MAST prevalence. The correlations between direct genetic and maternal genetic effects were antagonistic at all herd-calving-year prevalence levels, displaying strongest fluctuations for "DIAR-MAST." The genotype x herd-calving-year PMHS interactions for DIAR suggest consideration of specific sires according to the herd health status for CD and for MAST.

Milk traits characterization and association studies with DGAT1 polymorphisms in Bagnolese sheep.

The Bagnolese sheep is an authochtonous dual-purpose breed (milk and meat) reared in the Campania region, whose milk is used to produce Pecorino Bagnolese cheese. Genetic information on this sheep is extremely limited, especially regarding genes affecting productions. The aim of this study was to investigate milk production traits in Bagnolese sheep and the variability of diacylglycerol acyltransferase 1 (DGAT1) gene and its effects on milk production. Milk quantity was recorded during the morning milking, while Kjeldahl and Gerber methods were used to assess protein and fat percentage (w/v) of collected milk samples. Two PCR-RFLP protocols using BamHI and MspI endonucleases for genotyping of g.5553C>T and g.8539C>T at DGAT1 locus, respectively, were set up. Bagnolese sheep milk shows high fat and protein concentrations. Genotyping revealed a high frequency of the g.5553C and g.8539C alleles (0.56 and 0.95, respectively). The association study between the SNP g.5553C>T and milk traits showed that animals with the CT genotype had a higher percentage of fat produced per milking than those with the CC and TT genotypes (p<0.01). Similar results were found for protein yield percentage, with CT individuals being more productive than CC individuals (p<0.01). Bagnolese sheep milk parameters found are associated with high yields in the resulting dairy products. CT genotype at the SNP g.5553 of DGAT1 has shown a positive association with fat and protein milk yield percentage suggesting it could be considered a marker to improve productions of this breed. Finally, the new genotyping techniques used for this study enable a cheap and reliable characterization of two DGAT1 SNPs in sheep.

Genome-wide association studies for milk production traits and persistency of first calving Holstein cattle in Türkiye.

The study presents a comprehensive investigation into the genetic determinants of 100-day milk yield (100DMY), 305-day milk yield (305DMY), total milk yield (TMY), and persistency using first lactation records of 374 Holstein heifers reared in a private farm at Çanakkale province of Türkiye, employing a genome-wide association study (GWAS) approach. The research underscores the substantial genetic component underlying these economically important traits through detailed descriptive statistics and heritability estimations. The estimated moderate to high heritabilities (0.32-0.54) for milk production traits suggest the feasibility of targeted genetic improvement strategies. By leveraging GWAS, the study identifies many significant and suggestively significant single nucleotide polymorphisms (SNP) associated with studied traits. Noteworthy genes have identified in this analysis include BCAS3, MALRD1, CTNND2, DOCK1, TMEM132C, NRP1, CNTNAP2, GPRIN2, PLEKHA5, GLRA1, SCN7A, HHEX, KTM2C, RAB40C, RAB11FIP3, and FXYD6. These findings provide valuable understandings of the genetic background of milk production and persistency in Holstein cattle, shedding light on specific genomic regions and candidate genes playing pivotal roles in these traits. This research contributes valuable knowledge to the field of dairy cattle genetics and informs future breeding efforts to improve milk production sustainability and efficiency in Holstein cattle populations.

A transgenerational study on the effect of granddam conception month on granddaughter test day records for milk production traits in Italian Simmental cattle

The consequences of climate change are becoming a relevant issue also for the livestock industry in temperate countries. Transgenerational studies outlined the effect of the ancestors’ calving season, considered as an indicator of the period during which pregnancy occurs, on their female progeny performance. The aim of this study was to evaluate the effect of great granddam (F0) calving month on their great granddaughters (F3) Test Day (TD) records for milk production. A total of 414,069 TD records of milk, fat, and protein yields from 27,224 Italian Simmental F3 cows was analysed with a mixed linear model with year of calving, parity, age at parity, F0 calving month, days in milk class, the interactions between DIM and F0 calving month and between parity and F0 calving month, F3 calving date and the random effects of herd-test date and animal. The F0 calving month significantly influenced F3 performance for the three considered traits; largest F3 TD records were obtained for F0 calvings occurring in October, smallest for February. The largest milk production of F3 cows were observed when their F1 conceptions occurred in winter. Results were confirmed by a further analysis considering the calving seasons of F0, F1 and F2. The effect of F0 calving month (associated with the conception of F1) on milk production decreased as F3 parity increased. Results of this study suggest that the period of ancestor pregnancy and conception affects milk production traits of further generations also in temperate climates.

A comprehensive analysis of the effects of DGAT1 K232A polymorphism on milk production and fertility traits in Holstein Friesian and Jersey cows reared in Türkiye

Abstract. Research on the diacylglycerol acyltransferase 1 (DGAT1) K232A marker in cattle shows inconsistent results across regions, largely due to small sample sizes, limited genetic variation, and data restricted to few lactations, which complicates establishing a reliable genotype–phenotype correlation. This research aimed to determine the effect of the K232A polymorphism of the bovine DGAT1 gene on milk production and quality traits in dairy cattle. We used 1104 cattle, including 828 Holstein Friesian and 276 Jersey cows. The analysis utilized extensive data from six lactations of cows raised on four commercial dairy farms. We genotyped the population using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) technique and Sanger sequencing for verification. We then evaluated the 305 d and test-day milk yields as well as fat and protein yields and percentages. The number of inseminations per conception and calving ease were also assessed as reproduction indices. Genotype–phenotype associations were quantified using linear mixed models. The AA genotype was absent in Jersey cows, and the heterozygous genotype was predominant in both breeds. The K232A marker was significantly associated with test-day milk yield, fat, and protein content in Jersey cows. Further, it substantially affected the fat percentage of milk in Holstein Friesian cows (p&lt;0.001). We found that the KK genotype is highly desirable for milk quality and especially fat content. This comprehensive assessment demonstrated that the KK genotype of the DGAT1 K232A polymorphism significantly influenced fat and protein contents in dairy cattle.

Взаємозв’язок поліморфізму генетико-біохімічних систем з показниками молочної продуктивності сучасних українських порід великої рогатої худоби

DNA typing technologies make it possible to detect alleles and their frequencies in biochemical systems of proteins and enzymes, including specific PCR sequences, restriction enzymes and actually single nucleotide polymorphisms. The development of breed-specific SNPs is necessary for genotyping and mapping of associations with milk productivity traits, which will make it possible to identify the most valuable genotypes for their further use in selection and breeding work. The purpose of the study is to determine the allelic and genotypic frequencies, genetic diversity and polymorphism of hemoglobin (HB), ceruloplasmin (CP), posttransferrin (pTf), amylase (Am-1) and the receptor for vitamin D (calcitriol) (GS) to identify the relationship breed-specific features of their genetic structure. The results of the research revealed the influence of the breed of cows on their genetic structure according to the genetic-biochemical systems pTf, GS, HB, CP and Am-1. A clear influence of the genotype factor at the posttransferrin locus was observed, among the studied breeds of cows, on the manifestation of the content and amount of protein in milk. In addition, a probable effect of ceruloplasmin on the parameters of fat and protein in milk was established, depending on the breed of cows. The assessment of the genetic-biochemical system based on the amylase locus established a clear influence of the genotype on the manifestation of milk yield, milk fat and the amount of protein in milk. Thus, the use of polymorphism of individual loci of proteins and blood enzymes in the conduct of selection and breeding work will not only contribute to the improvement of breeding work, but also to the improvement of dairy cattle in general. Therefore, the perspective of breeding work with Holstein cattle should be the assessment of the diversity of the allelogen according to the polymorphic system of proteins and enzymes, which will allow to identify the best genotypes not only in terms of productivity, but also in genetic terms.

Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges

Significant advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7115 milk production records (milk, fat and protein yield) from 3006 cows (first 5 lactations). Since little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) cytoplasmic model with maternal lineages (CYTO), (2) haplotypic model with mitogenome sequences (HAPLO), (3) amino acid model with unique amino acid sequences (AMINO), (4) evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.

Identification of Genetic Associations of IDH2, LDHA, and LDHB Genes with Milk Yield and Compositions in Dairy Cows.

Previous study revealed that isocitrate dehydrogenase (NADP (+)) 2, mitochondrial (IDH2), lactate dehydrogenase A (LDHA), and lactate dehydrogenase B (LDHB) genes were significantly differentially expressed in liver tissues of Holstein cows among different lactation periods and associated with lipid and protein metabolism; hence, they were considered as candidates for milk production traits. Herein, the genetic effects of the three genes on milk yield, fat, and protein traits were studied by association analysis using 926 Chinese Holstein cows from 45 sire families. As a result, five single nucleotide polymorphisms (SNPs) in IDH2, one in LDHA, and three in LDHB were identified by re-sequencing, and subsequently, they were genotyped in 926 Chinese Holstein cows by genotyping by target sequencing (GBTS). With the animal model, single-locus association analysis revealed that four SNPs in IDH2 and one SNP in LDHA were significantly associated with milk, fat, and protein yields (p ≤ 0.0491), and three SNPs in LDHB were associated with milk yield, milk fat yield, and fat percentage (p ≤ 0.0285). Further, four IDH2 SNPs were found to form a haplotype block significantly associated with milk yield, fat yield, protein yield, and protein percentage (p ≤ 0.0249). In addition, functional predictions indicated that one SNP in LDHA, g.26304153G>A, may affect transcription factor binding and two SNPs, g.88544541A>G and g.88556310T>C could alter LDHB mRNA secondary structure. In summary, this study profiled the significant genetic effects of IDH2, LDHA, and LDHB on milk yield and composition traits and provided referable genetic markers for genomic selection programs in dairy cattle.

Estimation of Genetic Parameters for Milk Production Rate and Its Stability in Holstein Population.

Milk production rate (MPR) refers to the rate of milk secretion per hour (kg/h), calculated from the harvested milk yield and milking interval, and it is considered an appropriate measure to evaluate the production potential of cows. The objective of this study was to estimate the phenotypic and genetic parameters of milk production rate traits. In this study, the milking records of 4760 Holstein cows were collected, and four milk yield traits and six milk production rate traits were defined. The MIXED procedure was used to detect the impacts of non-genetic effects on milk yield and milk production rate traits, including parity, measured season and lactation stage. Variance and covariance components for milk yield and milk production rate traits were estimated using a univariate linear repeatability model. Parity, measurement season and lactation stage had significant effects (p < 0.01) on milk yield, milk production rate and its stability. Milk yield and milk production traits had high heritability, and ranged from 0.25 to 0.39. The stability of milk production rate had low heritability (0.04~0.05). Milk production rate is beneficial for the devolving novel trait in dairy breeding and provides new insights for herd management and genetic selection of production performance of dairy cattle.

Genetic improvement and conservation of goats in tropic

Goats indeed have a significant historical and contemporary importance in human civilization, particularly in the realm of agriculture and food production. Their adaptability and widespread distribution have made them crucial for various societies across the world. Goats have played a central role in the Neolithic agricultural revolution, aiding in the spread of human civilization globally. Their adaptability allowed them to thrive in diverse environments, contributing to the sustenance and expansion of human settlements. Goats are highly adaptable and are found in a wide range of geographical regions. Their presence spans across continents, from tropical to temperate climates, showcasing their ability to thrive in various environmental conditions. There is diversity in the production performance of goats based on the region of the world and the specific breeds. Genetic improvement programs aim to enhance economically important traits such as milk production, growth rates and fiber production, thereby increasing productivity and income for goat farmers. Understanding the genetic parameters such as heritabilities and repeatabilities for various traits is crucial for designing effective breeding programs. These parameters provide insights into the genetic potential of goats for traits like milk production, growth and fiber quality. Heritability estimates for reproductive traits, body weight, daily gain and direct and maternal heritability are important for implementing selective breeding strategies aimed at improving overall productivity and efficiency in goat farming. Genetic improvement programs have been implemented in tropical environments to enhance milk production traits in goats. Genetic improvements have also targeted fiber production in goats, with a focus on traits such as grease fleece weight and average fiber diameter. These efforts aim to enhance the quality and quantity of fiber produced by goats for various commercial purposes. Despite the importance of conserving goat breeds with unique characteristics, planned conservation programs in tropical regions are often neglected. It’s emphasized that preserving indigenous goat breeds in their native habitats is essential for maintaining genetic diversity and ensuring future resilience in goat farming.

Deciphering genomic signatures in different Indian milch cattle breeds

In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, four statistical tools (Tajima’s D, CLR, ROH, and iHS) were used on four indigenous cattle breeds. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). Our findings serve as a foundation for identifying selective sweeps responsible for the genetic variation of traits. These sweeps could hold functional significance for multiple cattle breeds across various subcontinents. However, to enhance the robustness of the results, further studies with high-density arrays or whole-genome sequencing, employing greater resolution and larger sample sizes, are warranted.

Analysis of miRNAs in milk of four livestock species

BackgroundMilk is essential for mammalian nutrition because it provides vital nutrients for growth and development. Milk composition, which is influenced by genetic and environmental factors, supports lactation, a complex process crucial for milk production and quality. Recent research has focused on noncoding RNAs, particularly microRNAs (miRNAs), which are present in body fluids and regulate gene expression post-transcriptionally. This study comprehensively characterizes miRNAs in milk of four livestock species, namely Bubalus bubalis, Capra hircus, Equus asinus, and Ovis aries and identifies potential target genes.ResultsHigh-throughput sequencing of milk RNA resulted in distinct read counts across species: B. bubalis (8,790,441 reads), C. hircus (12,976,275 reads), E. asinus (9,385,067 reads), and O. aries (7,295,297 reads). E. asinus had the highest RNA mapping rate (94.6%) and O. aries the lowest (84.8%). A substantially greater proportion of miRNAs over other small RNAs was observed for the donkey milk sample (7.74%) compared to buffalo (0.87%), goat (1.57%), and sheep (1.12%). Shared miRNAs, which included miR-200a, miR-200b, miR-200c, and miR-23a among others, showed varying expression levels across species, confirmed by qPCR analysis. Functional annotation of predicted miRNA target genes highlighted diverse roles, with an enrichment in functions linked to metabolism and immunity. Pathway analysis identified immune response pathways as significant, with several miRNAs targeting specific genes across species, suggesting their regulatory function in milk.ConclusionsBoth conserved and species-specific miRNAs were detected in milk of the investigated species. The identified target genes of these miRNAs have important roles in neonatal development, adaptation, growth, and immune response. Furthermore, they influence milk and meat production traits in livestock.

Genome-wide association studies for milk production traits in two autochthonous Aosta cattle breeds

Genome-wide association studies (GWASs) are used to identify quantitative trait loci for phenotypic traits of interest. The use of multilocus mixed models allows to correct for population stratification and account for long-range linkage disequilibrium. In this study, GWASs were conducted to identify the genetic bases of milk production (milk yield, protein and fat composition, and yield) in two autochthonous dual-purpose cattle breeds from the Aosta Valley. Using either the breeding values or the deregressed proofs, common significative single nucleotide polymorphisms have been identified for milk yield, protein percentage, and fat percentage. Two major quantitative trait loci regions have been identified on the chromosomes 5 and 14 for the fat percentage, harbouring the MGST1, CYHR1, VPS28, and CPSF1 genes. For the protein percentage, a candidate region has been identified on BTA 6; in this region, the CSN1S1, CSN2, HSTN, CSN3, and RUFY3 genes are annotated. Most of the identified genes have already been associated with milk composition in other studies on cosmopolitan and local cattle. These results show that the genes involved in milk composition quantitative traits in the Aosta cattle are common also in other cattle breeds and they can be further investigated with the use of whole genome sequencing data.

Mitochondrial sequence variants: testing imputation accuracy and their association with dairy cattle milk traits

BackgroundMitochondrial genomes differ from the nuclear genome and in humans it is known that mitochondrial variants contribute to genetic disorders. Prior to genomics, some livestock studies assessed the role of the mitochondrial genome but these were limited and inconclusive. Modern genome sequencing provides an opportunity to re-evaluate the potential impact of mitochondrial variation on livestock traits. This study first evaluated the empirical accuracy of mitochondrial sequence imputation and then used real and imputed mitochondrial sequence genotypes to study the role of mitochondrial variants on milk production traits of dairy cattle.ResultsThe empirical accuracy of imputation from Single Nucleotide Polymorphism (SNP) panels to mitochondrial sequence genotypes was assessed in 516 test animals of Holstein, Jersey and Red breeds using Beagle software and a sequence reference of 1883 animals. The overall accuracy estimated as the Pearson’s correlation squared (R2) between all imputed and real genotypes across all animals was 0.454. The low accuracy was attributed partly to the majority of variants having low minor allele frequency (MAF < 0.005) but also due to variants in the hypervariable D-loop region showing poor imputation accuracy. Beagle software provides an internal estimate of imputation accuracy (DR2), and 10 percent of the total 1927 imputed positions showed DR2 greater than 0.9 (N = 201). There were 151 sites with empirical R2 > 0.9 (of 954 variants segregating in the test animals) and 138 of these overlapped the sites with DR2 > 0.9. This suggests that the DR2 statistic is a reasonable proxy to select sites that are imputed with higher accuracy for downstream analyses. Accordingly, in the second part of the study mitochondrial sequence variants were imputed from real mitochondrial SNP panel genotypes of 9515 Australian Holstein, Jersey and Red dairy cattle. Then, using only sites with DR2 > 0.900 and real genotypes, we undertook a genome-wide association study (GWAS) for milk, fat and protein yields. The GWAS mitochondrial SNP effects were not significant.ConclusionThe accuracy of imputation of mitochondrial genotypes from the SNP panel to sequence was generally low. The Beagle DR2 statistic enabled selection of sites imputed with higher empirical accuracy. We recommend building larger reference populations with mitochondrial sequence to improve the accuracy of imputing less common variants and ensuring that SNP panels include common variants in the D-loop region.

Milk Lipid Regulation in Dairy Goats: A Comprehensive Review.

The growth, development, and milk production traits of dairy goats, which are important sources of high-quality animal protein, are significantly influenced by a combination of genetic and environmental factors. It is imperative to identify key genetic loci that govern economically valuable traits in order to enhance breeding programs. Despite advancements in genomic technologies, there are still gaps in knowledge regarding the interplay between genetic factors and environmental influences, particularly in relation to the regulation of milk production and quality. Therefore, the aim of this paper was to synthesize advancements in the genetic and environmental factors affecting milk production and quality in dairy goats and identify key regulatory mechanisms. This review summarizes the recent progress on the identification of genes associated with milk production traits using whole-genome resequencing, the use of transcriptomic profiling to identify genes linked to milk production, the exploration of regulatory mechanisms of lipid metabolism in goat mammary epithelial cells, and the evaluation of the influence of nutritional factors on milk quality. A comprehensive understanding of these interactions is essential for enhancing breeding strategies and ensuring the sustainability of dairy goat farming. Future research should incorporate multi-omics approaches to unravel the intricate regulatory processes governing milk production and adapt practices to meet global demand while upholding economic and environmental sustainability.

Genetic parameters of milk mid-infrared spectra and their genetic relationships with milk production and feed efficiency traits in French Lacaune dairy sheep

In French dairy sheep, Fourier transform infrared (FTIR) milk spectral data routinely predict the major milk components used in national genetic evaluations. The direct influence of genetic and environmental factors on milk FTIR spectra has been widely studied in dairy cattle, and relatively little in dairy ewes. In this study, 36,873 milk test-day records were available for 4,712 French Lacaune ewes farmed on 8 commercial farms. Our main goals were to provide the first description of spectral data and estimate the genetic parameters of French Lacaune dairy sheep during lactation. Principal component analysis (PCA) results demonstrated the impact of the lactation period on specific wavenumbers, allowing the identification of FTIR spectra collected at early (mo 2-4) and late (mo 5-7) lactation stages. The average estimated heritability (±mean SE) of the FTIR milk spectra from 2,971 to 926 cm-1 (446 wavenumbers) was 0.29 ± 0.02, ranging from 0.13 ± 0.01 to 0.42 ± 0.02. Furthermore, the heritabilities of spectra collected at the beginning or end of lactation changed at each point of the spectrum. However, at each wavenumber, the genomic correlation of transmittance values between these 2 lactation periods was high (>0.77), indicating the absence of a genotype-environment interaction. The genomic correlations between spectral regions and milk production traits (i.e., daily milk yield, fat and protein content, somatic cell score) varied from moderate to high. The results suggested that the most heritable areas of the spectrum were also genetically associated with dairy traits. Finally, the genomic correlations observed between the ewes' feed efficiency traits and the FTIR spectrum were moderate to high, while the genomic correlations between the change in body condition score and spectral data were rather low to moderate. This study confirmed that spectral data from Lacaune ewe milk were heritable, evolved phenotypically and genetically during lactation and were genetically correlated with traits included in breeding goals or traits of interest to the dairy industry.

Influence of non-genetic factors on milk production traits of Gangatiri cattle in Varanasi district of Uttar Pradesh

Research was carried out to examine the influence of non-genetic factors on the milk production characteristics of Gangatiri cows. The study was analyzed from 1254 Gangatiri cows across three tehsils (Pindra, Rajatalab, and Sadar) in Varanasi, Uttar Pradesh. The objective was to ascertain the effects of a number of variables on lactation duration, daily milk production, and lactation milk production including the area, calving season, farmer's economic background, parity, and age at first calving. The overall average means for lactation milk production, daily production of milk, and lactation period were discovered to be 794.6413 kg, 3.956 kg, and 203.8327 days, respectively. The comparison of different parameters indicated that non-genetic factors had a significant impact on milk production. These factors include the region where the survey was conducted, the calving season, the financial context of the farmer, parity or lactation, and first calving age. By analyzing the mean of these parameters, we could determine their impact on milk yield potentials. Given the influence of external variables and differences in the qualities under investigation, the study indicates that significant improvements in the population of Gangatiri cattle can be accomplished by improved management.