Uncovering Molecular Mechanisms of Milk Production in Indigenous Cattle through Transcriptome Profiling
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ABSTRACT:
ORGANISM(S): Bos indicus
PROVIDER: GSE312970 | GEO | 2025/12/23
REPOSITORIES: GEO
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Project description:Uncovering Molecular Mechanisms of Milk Production in Indigenous Cattle through Transcriptome Profiling
| PRJNA1377680 | ENA
Project description:The objective of this study was to evaluate the proportion of genetic variance explained by single nucleotide polymorphism markers, individually or clustered in 1, 2, and 5 Mb windows, for milk yield, fat yield, protein yield, fat content, protein content, and somatic cell score in Mexican Holstein cattle. The analysis included data from 640,746 lactation records of 358,857 cows born between 1979 and 2019, distributed in 353 herds in 18 states of Mexico. The analysis included genotypic data on 7,713 cows and 577 sires, with information on 88,911 markers previously imputed and filtered by quality control. Genomic scans via the single-step genomic best linear unbiased prediction method were performed using BLUPF90 software. A total of 162 markers were significantly associated (p<0.01) with the phenotypic traits evaluated, and the SNP markers were distributed across chromosomes 1, 3, 5, 6, 10, 12, 14, 16, 18, 20, 22, and 29. When the size of the genomic windows was increased from 1 to 5 Mb, a greater proportion of genetic variance was explained by the SNPs within the window, and a greater number of windows explained more than 1% of the genetic variance. The most significant regions were associated with two or more phenotypic traits, such as one region on chromosome 14 that harbors the DGAT1, EXOSC4, PPP1R16A, and FOXH1 genes, which affect all the traits under study. In general, the utilization of genomic windows resulted in a greater proportion of genetic variance explained by milk production traits.
| S-EPMC11790082 | biostudies-literature
Project description:Malnad Gidda is one among the 43 registered cattle breeds of India with unique traits and spread over Western Ghats and coastal regions of Karnataka state in India. Selection of highly elite fertile bulls for the breeding purpose is a critical control point in animal breeding programmes. Therefore, to characterize the semen proteome and to understand the semen biology of this breed, a comprehensive proteomic analysis of spermatozoa and seminal plasma has been carried out by employing SCX and bRPLC fractionation strategies in a mass-spectrometry platform. The semen samples from three Malnad Gidda bulls maintained at Southern Regional Station of ICAR-NDRI under standard managemental conditions were used in the study. The proteomic characterisation of semen from Malnad Gidda breed resulted in the identification of 5, 84,520 PSMs, from 24,467 peptides from 2,815 proteins in spermatozoa and identification of 2, 77,583 PSMs from 12,047 peptides, which resulted in 1,974 proteins from seminal plasma. Out of 2,815 proteins in spermatozoa and 1,974 proteins from seminal plasma, 969 proteins were common to both seminal plasma and spermatozoa. The biological processes and cellular localization of spermatozoa proteins were studied using DAVID tool and were further enriched the identical GO terms using REVIGO online tool. The functional enrichment analysis of identified proteins indicated their roles in the biological processes like sperm motility, spermatid development, spermatogenesis, and so on. GO studies showed the commonalities and differences in the molecular functions of the proteins exclusively identified in spermatozoa, seminal plasma and common proteins. This is the first proteomic investigation conducted on the semen samples of an Indian indigenous breed; therefore, we believe that our preliminary data should significantly advance our understanding of semen proteome of Indian cattle.
2020-06-12 | PXD014172 | Pride
Project description:This study investigated polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. Considering 67 animals, DNA sequencing of the genes' exons, flanking regions and parts of the 5'-upstream regions identified 1058 genetic variants including 731 previously unknown. In addition, four novel milk protein variants were detected, including CSN3K (p.Ala66Val), LALBAF (p.Arg58Trp), LGBB1 (p.Ala134Val) and LGBK (p.Thr92Asnfs*13). CSN3K is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas LALBAF and LGBB1 are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding LGBK, a frameshift insertion of one adenine residue at BTA11:103257980 (exon 3) induces a premature translation termination resulting in a 46% reduction of the reference protein sequence. The casein polymorphisms formed five main CSN1S1-CSN2-CSN1S2-CSN3 haplotypes including B-A1-A-B, B-A1-A-A and C-A2-A-B which are predominant in the investigated cattle breeds. Moreover, in silico analyses of polymorphisms within the 5'- and 3'- untranslated regions of all six milk proteins revealed effects on microRNA and transcription factor binding sites. This study suggests a large genetic variation of milk protein genes in Beninese cattle, which should be investigated in further studies for their effects on milk production, including quality and yield traits.
| S-EPMC8625544 | biostudies-literature
Project description: Not available
| S-EPMC11202589 | biostudies-literature
Project description:<p>Background: High-yield dairy cows are usually accompanied with lower milk fat (MF) rate, with huge variations in MF contents among individuals. The potential mechanisms of key microorganisms, their genes and metabolites participate in MF synthesis are still not well understood. By selecting 12 high-yielding (HIGH) and 12 low-yielding (LOW) cows from a large cohort of dairy cows, multi-omics technologies were applied to identify the hallmark microorganisms, metabolites, and metabolic pathways involved in MF synthesis.</p><p>Results: The LOW and HIGH cows under the same feeding and management conditions exhibited considerable phenotypic, microbial, functional, and metabolomic differences. The LOW and HIGH cows underwent acetic and propionic ruminal fermentation, respectively, with greater molar proportion of acetate and butyrate in the LOW cows, providing greater precursors for short-chain fatty acids (FAs) synthesis in mammary gland. The HIGH cows had greater molar proportion of propionate in rumen and contents of long-chain FAs and odd-chain FAs (OCFAs) in milk. Metagenomic analysis revealed that the HIGH and LOW cows possessed Prevotella- and Ruminococcus-driven enterotypes, respectively, associated with significantly lower abundances of Methanobacteriota and Methanobrevibacter_A in HIGH than that of the LOW cows. Moreover, 13 carbohydrate and 3 lipid metabolism pathways were greatly enhanced in HIGH cows, accompanied with greater abundances of CAZymes encoding genes and critical enzymes involved in fiber degradation and propionate synthetization. Metabolomic analysis revealed that the free FAs, glycerophospholipids and oxidized lipids in ruminal fluid, and bile acids, glycerides, and glycerophospholipids in serum were greater in HIGH cows; however, the contents of carnitines, being ubiquitously detected in ruminal fluid, serum, and milk, were consistently greater in LOW cows, suggesting the capability of being used as biomarkers for predicting the lactation potentiality.</p><p>Conclusions: The yield and MF composition between HIGH and LOW cows are microbiome-dependent, specifically greatly depend on the Prevotella- and Ruminococcus-driven enterotypes, respectively. The former enterotype is associated with higher milk efficiency and greater milk contents of OCFAs, which is more environmentally friend and healthier to human; whereas the later enterotype is characterized with greater methanogens and carnitines, which indicates a greater dietary energy loss and a poorer energy status of dairy cows.</p>
2025-10-28 | MTBLS13211 | MetaboLights
Project description:Peripheral blood mononuclear cells (PBMC) from cows with experimentally induced hypocalcaemia or spontaneous milk fever were subject of an oligo-microarray analysis following quantitative real-time reverse transcription PCR (q-PCR). In experimental hypocalcaemia induced by 10 % Na2EDTA infusion (n = 4), the microarray revealed that 32 genes were significantly up- or down-regulated compared to control treatment by 11 % CaEDTA infusion (n = 4). In milk fever cases (n = 8), the microarray demonstrated that 98 genes were expressed differentially higher or lower compared to healthy parturient cows (n = 5). From both data, five genes were selected to be strongly related to both experimental hypocalcaemia and milk fever. Additionally, another gene was judged to be specific for milk fever independent of hypocalcaemia. The mRNA expressions of these six genes in milk fever cases were verified by q-PCR, which were significantly higher or lower than those in healthy parturient cows.
2013-06-16 | GSE46901 | GEO
Project description:In this study we sought to establish changes within the mammary glands of lactating dairy cows (n=3-4) in response to a single dose of exogenous DEX by performing serial biopsies of alternating quarters of the udder Transcriptomic changes in the mammary glands in response to DEX were identified by RNA sequencing of mammary gland RNA at 0, 12, 24 and 72h post-DEX injection, followed by differential gene expression analysis Coincident with the milk yield and composition changes was the differential expression of 519 and 320 genes at 12 and 24 h after DEX, respectively, with return of all gene expression to baseline levels by 72 h.
2023-01-11 | GSE217369 | GEO
Project description:German Black Pied cattle (DSN) is an endangered population of about 2,550 dual-purpose cattle in Germany. Having a milk yield of about 2,500 kg less than the predominant dairy breed Holstein, the preservation of DSN is supported by the German government and the EU. The identification of the genomic loci affecting milk production in DSN can provide a basis for selection decisions for genetic improvement of DSN in order to increase market chances through the improvement of milk yield. A genome-wide association analysis of 30 milk traits was conducted in different lactation periods and numbers. Association using multiple linear regression models in R was performed on 1,490 DSN cattle genotyped with BovineSNP50 SNP-chip. 41 significant and 20 suggestive SNPs affecting milk production traits in DSN were identified, as well as 15 additional SNPs for protein content which are less reliable due to high inflation. The most significant effects on milk yield in DSN were detected on chromosomes 1, 6, and 20. The region on chromosome 6 was located nearby the casein gene cluster and the corresponding haplotype overlapped the CSN3 gene (casein kappa). Associations for fat and protein yield and content were also detected. High correlation between traits of the same lactation period or number led to some SNPs being significant for multiple investigated traits. Half of all identified SNPs have been reported in other studies, previously. 15 SNPs were associated with the same traits in other breeds. The other associated SNPs have been reported previously for traits such as exterior, health, meat and carcass, production, and reproduction traits. No association could be detected between DGAT1 and other known milk genes with milk production traits despite the close relationship between DSN and Holstein. The results of this study confirmed that many SNPs identified in other breeds as associated with milk traits also affect milk traits in dual-purpose DSN cattle and can be used for further genetic analysis to identify genes and causal variants that affect milk production in DSN cattle.
| S-EPMC7982544 | biostudies-literature
Project description:Our initial RNA sequencing work identified that lipin 1 (LPIN1) was differentially expressed during dry period, early lactation, and peak of lactation in dairy cows, and it was enriched into the fat metabolic Gene Ontology (GO) terms and pathways, thus we considered LPIN1 as the candidate gene for milk production traits. In this study, we detected the polymorphisms of LPIN1 and verified their genetic effects on milk yield and composition in a Chinese Holstein cow population. We found seven SNPs by re-sequencing the entire coding region and partial flanking region of LPIN1, including one in 5' flanking region, four in exons, and two in 3' flanking region. Of these, four SNPs, c.637T > C, c.708A > G, c.1521C > T, and c.1555A > C, in the exons were predicted to result in the amino acid replacements. With the Haploview 4.2, we found that seven SNPs in LPIN1 formed two haplotype blocks (D' = 0.98-1.00). Single-SNP association analyses showed that SNPs were significantly associated with milk yield, fat yield, fat percentage, or protein yield in the first or second lactation (p = < 0.0001-0.0457), and only g.86049389C > T was strongly associated with protein percentage in both lactations (p = 0.0144 and 0.0237). The haplotype-based association analyses showed that the two haplotype blocks were significantly associated with milk yield, fat yield, protein yield, or protein percentage (p = < 0.0001-0.0383). By quantitative real-time PCR (qRT-PCR), we found that LPIN1 had relatively high expression in mammary gland and liver tissues. Furthermore, we predicted three SNPs, c.637T > C, c.708A > G, and c.1521C > T, using SOPMA software, changing the LPIN1 protein structure that might be potential functional mutations. In summary, we demonstrated the significant genetic effects of LPIN1 on milk production traits, and the identified SNPs could serve as genetic markers for dairy breeding.
| S-EPMC6523124 | biostudies-literature