Additional file 2: Table S2. Additive (a), dominant (d) and allele substitution (α) effects of 17 SNPs on milk fatty acid traits of AGPAT3 gene in Chinese Holstein cows
Abstract Background People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids (FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study (GWAS) on milk FAs in dairy cattle, 83 genome-wide significant single nucleotide polymorphisms (SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18index ( P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3 ( AGPAT3 ) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle. Results Through re-sequencing the complete coding region, and 3000 bp of 5′ and 3′ regulatory regions of the AGPAT3 gene, a total of 17 SNPs were identified, including four in 5′ regulatory region, one in 5′ untranslated region (UTR), three in introns, one in 3′ UTR, and eight in 3′ regulatory region. By the linkage disequilibrium (LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs, respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1065 Chinese Holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0 ( P < 0.0001–0.0384). Further, with Genomatix, we predicted that four SNPs in 5′ regulatory region (g.146702957G > A, g.146704373A > G, g.146704618A > G and g.146704699G > A) changed the transcription factor binding sites (TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the alleles A of both SNPs, g.146704373A > G and g.146704618A > G, increased the transcriptional activities of AGPAT3 promoter compared with alleles G ( P = 0.0004). Conclusions In conclusion, our findings first demonstrated the significant genetic associations of the AGPAT3 gene with milk FAs in dairy cattle, and two potential causal mutations were detected.
Abstract Background: People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids (FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study (GWAS) on milk FAs in dairy cattle, 83 genome-wide significant single nucleotide polymorphisms (SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18index ( P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3 ( AGPAT3 ) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle. Results: Through re-sequencing the complete coding region, and 3,000bp of 5' and 3' regulatory regions of the AGPAT3 gene, a total of 17 SNPs were identified, including four in 5' regulatory region, one in 5' untranslated region (UTR), three in introns, one in 3' UTR, and eight in 3' regulatory region. By the linkage disequilibrium (LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs, respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1,065 Chinese Holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0 ( P < 0.0001~ 0.0384). Further, with Genomatix, we predicted that four SNPs in 5' regulatory region (g.146702957G>A, g.146704373A>G g.146704618A>G and g.146704699G>A) changed the transcription factor binding sites (TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the alleles A of both SNPs, g.146704373A>G and g.146704618A>G, increased the transcriptional activities of AGPAT3 promoter compared with alleles G ( P = 0.0004). Conclusions: In conclusion, our findings first demonstrated the significant genetic associations of the AGPAT3 gene with milk FAs in dairy cattle, and two potential causal mutations were detected.
Abstract Background: People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids (FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study (GWAS) on milk FAs in dairy cattle, 83 genome-wide significant single nucleotide polymorphisms (SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18index ( P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3 ( AGPAT3 ) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle. Results: Through re-sequencing the complete coding region, and 3,000bp of 5' and 3' regulatory regions of the AGPAT3 gene, a total of 17 SNPs were identified, including four in 5' regulatory region, one in 5' untranslated region (UTR), three in introns, one in 3' UTR, and eight in 3' regulatory region. By the linkage disequilibrium (LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs, respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1,065 Chinese Holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0 ( P < 0.0001~ 0.0384). Further, with Genomatix, we predicted that four SNPs in 5' regulatory region (g.146702957G>A, g.146704373A>G g.146704618A>G and g.146704699G>A) changed the transcription factor binding sites (TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the alleles A of both SNPs, g.146704373A>G and g.146704618A>G, increased the transcriptional activities of AGPAT3 promoter compared with alleles G ( P = 0.0004). Conclusions: In conclusion, our findings first demonstrated the significant genetic associations of the AGPAT3 gene with milk FAs in dairy cattle, and two potential causal mutations were detected.
Abstract Background The rumen is the main digestive and absorption organ of dairy cows that contains abundant microorganisms and effectively utilizes human-indigestible plant mass. Investigation on microbiome in the rumen from lactating dairy cows using metagenomic sequencing is reasonable for identifying ruminal microorganisms that contribute to milk composition traits. Results We used the Illumina HiSeq platform to generate the rumen microbiome of the six lactating Holstein cows with extremely high and low milk protein and fat percentages (high and low groups of PP and FP). In total, 6977 microorganism species were detected in which Bacteroidetes (51.4%) and Prevotella (38.48%) was the most predominant phylum and genus, respectively. Between high and low groups, we observed significantly differential microorganism abundances in genus and species levels. By performing LEfSe and Metastats analyses, we identified 38 top abundant species displaying differential richness between two groups in common (LDA > 3, p < 0.05, q = 0.037 ~ 0.048), in which Prevotella accounted for 68.8% of the species with higher abundance in high group. Function annotation with KEGG, eggnog and CAZy databases showed the species with significantly higher abundance in high group were enriched in carbohydrate, amino acid, pyruvate, insulin and lipid metabolism and transportation, indicating their higher capability of digesting feed and subsequently providing substrate for milk composition synthesis in mammary gland. In addition, a kind of anaerobic fungi, Neocallimastix californiae , was identified in high group that could coexist with rumen microbes and promote cellulose digestion. Conclusion This study investigated the rumen microbiome in lactating Holstein cows using metagenomic sequencing. Significant differential bacterial richness were observed between the cows with extremely high and low PP and FP. Function annotation showed the abundant species in high group were involved in carbohydrate, amino acid, pyruvate, insulin and lipid metabolism and transportation, indicating the significant correlation between rumen microbiota and milk compositions formation in dairy cattle.
Slaughtered meat has been identified as one of the major vehicles for forming antimicrobial resistance (AMR). It is still believed that AMR pathogens introduced by overusing antimicrobials in the breeding industry are directly brought in from farm animals. This disregards however the fact that many gut pathogens do not settle on muscle parts; the presence of gut pathogens on muscle products does not directly correlate to farm feeding. To investigate whether the source of AMR bacteria on slaughtered meat was cross-contamination or self-contamination, many peer-reviewed publications were studied to assess if the observational studies focused on AMR pathogenic bacteria association between farms and slaughterhouses or the contamination on the slaughter line. Using PubMed, 1919 publications on AMR bacteria in farms and slaughterhouses were collected. The 1650 papers were assembled (269 of them being repeated). From these, 92 were included in the study: 29 surveillance studies reported that AMR bacteria in slaughtered products were related to farm sources; 63 papers reported cross-contamination in the slaughter process at a significant level. Several crucial points were highlighted, including 1) the scalding, de-feathering and evisceration in the broiler slaughter line; 2) residential flora, evisceration, inappropriate meat inspection, conveyor belts, splitting, equipment in the boning hall, holding, chilling, and lairage contamination in the pig slaughter line. In this study, AMR bacteria of the two sources were genetically related. However, the majority of cases still resulted from cross-contamination (29% to 98.48%). This means that major sources of gut AMR bacteria on slaughtered meat were cross contaminated during the slaughter process.
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