scholarly journals A Post-GWAS Confirming the Genetic Effects and Functional Polymorphisms of AGPAT3 Gene on Milk Fatty Acids in Dairy Cattle

2020 ◽  
Author(s):  
Lijun Shi ◽  
Zhu Ma ◽  
Xiaoqing Lv ◽  
Lin Liu ◽  
Yanhua Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Regulatory Region ◽  
Genetic Effects ◽  
Luciferase Assay ◽  
Milk Fatty Acids ◽  
Medium Chain ◽  
Haplotype Blocks ◽  
Functional Polymorphisms ◽  
Genome Wide

Abstract Background: In our previous genome-wide association study (GWAS) on milk fatty acids (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 medium-chain saturated fatty acids (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 medium-chain saturated FAs in dairy cattle, and two potential causal mutations were detected.

scholarly journals A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lijun Shi ◽  
Xin Wu ◽  
Yuze Yang ◽  
Zhu Ma ◽  
Xiaoqing Lv ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Heart Diseases ◽  
Regulatory Region ◽  
Genetic Effects ◽  
Luciferase Assay ◽  
Milk Fatty Acids ◽  
Haplotype Blocks ◽  
Functional Polymorphisms ◽  
Genome Wide

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.

scholarly journals A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

2020 ◽  
Author(s):  
Lijun Shi ◽  
Xin Wu ◽  
Zhu Ma ◽  
Xiaoqing Lv ◽  
Lin Liu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Heart Diseases ◽  
Regulatory Region ◽  
Genetic Effects ◽  
Luciferase Assay ◽  
Milk Fatty Acids ◽  
Haplotype Blocks ◽  
Functional Polymorphisms ◽  
Genome Wide

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.

scholarly journals A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

2020 ◽  
Author(s):  
Lijun Shi ◽  
Xin Wu ◽  
Zhu Ma ◽  
Xiaoqing Lv ◽  
Lin Liu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Heart Diseases ◽  
Regulatory Region ◽  
Genetic Effects ◽  
Luciferase Assay ◽  
Milk Fatty Acids ◽  
Haplotype Blocks ◽  
Functional Polymorphisms ◽  
Genome Wide

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.

scholarly journals Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits

2020 ◽  
Author(s):  
Mingyue Cao ◽  
Lijun Shi ◽  
Peng Peng ◽  
Bo Han ◽  
Lin Liu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Dairy Cattle ◽  
Genetic Effects ◽  
Milk Fatty Acid ◽  
Milk Fatty Acids ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Exon 1 ◽  
Flanking Region

Abstract Background: Our previous genome-wide association study (GWAS) on milk fatty acid traits in Chinese Holstein cows revealed, the SNP, BTB-01556197, was significantly associated with C10:0 at genome-wide level (P = 0.0239). It was located in the down-stream of 5-hydroxytryptamine receptor 1B (HTR1B) gene that has been shown to play an important role in the regulation of fatty acid oxidation. Hence, we considered it as a promising candidate gene for milk fatty acids in dairy cattle. In this study, we aimed to investigate whether the HTR1B gene had significant genetic effects on milk fatty acid traits.Results: We re-sequenced the entire coding region and 3,000 bp of 5' and 3' flanking regions of HTR1B gene. A total of 13 SNPs was identified, containing one in 5' flanking region, two in 5' untranslated region (UTR), two in exon 1, five in 3' UTR, and three in 3' flanking region. By performing genotype-phenotype association analysis with SAS9.2 software, we observed that 13 SNPs were significantly associated with medium-chain saturated fatty acids such as C6:0, C8:0 and C10:0 (P < 0.0001 ~ 0.042). With Haploview 4.1 software, linkage disequilibrium (LD) analysis was performed that two haplotype blocks formed by two and ten SNPs were observed. Haplotype-based association analysis indicated that both haplotype blocks were strongly associated with C6:0, C8:0 and C10:0 as well (P < 0.0001 ~ 0.0071). With regards to the missense mutation in exon 1 (g.17303383G>T) that reduced amino acid change from alanine to serine, we predicted that it altered the secondary structure of HTR1B protein with SOPMA. In addition, we predicted that three SNPs in promoter region, g.17307103A>T, g.17305206T>G and g.17303761C>T, altered the binding sites of transcription factors (TFs) HMX2, PAX2, FOXP1ES, MIZ1, CUX2, DREAM, and PPAR-RXR by Genomatix. Of them, luciferase assay experiment further confirmed that the allele T of g.17307103A>T significantly increased the transcriptional activity of HTR1B gene than allele A (P = 0.0007).Conclusions: In conclusion, our findings provided first evidence that the HTR1B gene had significant genetic effects on milk fatty acids in dairy cattle.

scholarly journals Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mingyue Cao ◽  
Lijun Shi ◽  
Peng Peng ◽  
Bo Han ◽  
Lin Liu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Dairy Cattle ◽  
Genetic Effects ◽  
Milk Fatty Acid ◽  
Milk Fatty Acids ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Exon 1 ◽  
Flanking Region

Abstract Background Our previous genome-wide association study (GWAS) on milk fatty acid traits in Chinese Holstein cows revealed, the SNP, BTB-01556197, was significantly associated with C10:0 at genome-wide level (P = 0.0239). It was located in the down-stream of 5-hydroxytryptamine receptor 1B (HTR1B) gene that has been shown to play an important role in the regulation of fatty acid oxidation. Hence, we considered it as a promising candidate gene for milk fatty acids in dairy cattle. In this study, we aimed to investigate whether the HTR1B gene had significant genetic effects on milk fatty acid traits. Results We re-sequenced the entire coding region and 3000 bp of 5′ and 3′ flanking regions of HTR1B gene. A total of 13 SNPs was identified, containing one in 5′ flanking region, two in 5′ untranslated region (UTR), two in exon 1, five in 3′ UTR, and three in 3′ flanking region. By performing genotype-phenotype association analysis with SAS9.2 software, we observed that 13 SNPs were significantly associated with medium-chain saturated fatty acids such as C6:0, C8:0 and C10:0 (P < 0.0001 ~ 0.042). With Haploview 4.1 software, linkage disequilibrium (LD) analysis was performed. Two haplotype blocks formed by two and ten SNPs were observed. Haplotype-based association analysis indicated that both haplotype blocks were strongly associated with C6:0, C8:0 and C10:0 as well (P < 0.0001 ~ 0.0071). With regards to the missense mutation in exon 1 (g.17303383G > T) that reduced amino acid change from alanine to serine, we predicted that it altered the secondary structure of HTR1B protein with SOPMA. In addition, we predicted that three SNPs in promoter region, g.17307103A > T, g.17305206 T > G and g.17303761C > T, altered the binding sites of transcription factors (TFs) HMX2, PAX2, FOXP1ES, MIZ1, CUX2, DREAM, and PPAR-RXR by Genomatix. Of them, luciferase assay experiment further confirmed that the allele T of g.17307103A > T significantly increased the transcriptional activity of HTR1B gene than allele A (P = 0.0007). Conclusions In conclusion, our findings provided first evidence that the HTR1B gene had significant genetic effects on milk fatty acids in dairy cattle.

scholarly journals Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 86 ◽  
Author(s):  
Lijun Shi ◽  
Bo Han ◽  
Lin Liu ◽  
Xiaoqing Lv ◽  
Zhu Ma ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Family Member ◽  
Genome Wide Association Study ◽  
Protein Secondary Structure ◽  
Genetic Effects ◽  
Nucleotide Polymorphisms ◽  
Milk Fatty Acids ◽  
Association Analyses ◽  
Genome Wide

In our previous genome-wide association study (GWAS) on milk fatty acids (FAs) in Chinese Holstein, we discovered 83 genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk FAs. Two of them were close to lipase family member K (LIPK) and lipase family member J (LIPJ), respectively. Hence, this study is a follow-up to verify whether the LIPK and LIPJ have significant genetic effects on milk FAs in dairy cattle. By re-sequencing the entire exons, and 3 kb of 5′ and 3′ flanking regions, two and seven SNPs were identified in LIPK and LIPJ, respectively, including a novel SNP, ss158213049726. With the Haploview 4.1 software, we found that five of the SNPs in LIPJ formed a haplotype block (D′ = 0.96 ~ 1.00). Single-locus association analyses revealed that each SNP in LIPK and LIPJ was significantly associated with at least one milk FA (p = < 1.00×10-4 ~ 4.88×10-2), and the haplotype-based association analyses showed significant genetic effects on nine milk FAs (p = < 1.00×10-4 ~ 3.98×10-2). Out of these SNPs, the missense mutation in LIPK gene, rs42774527, could change the protein secondary structure and function predicted by SOPMA, SIFT, and PROVEAN softwares. With the Genomatix software, we predicted that two SNPs, rs110322221 in LIPK and rs211373799 in LIPJ, altered the transcription factors binding sites (TFBSs), indicating their potential regulation on promoter activity of the genes. Furthermore, we found that both LIPK and LIPJ had relatively high expressions in the mammary gland. In conclusion, our research is the first to demonstrate that LIPK and LIPJ genes have significant associations with milk FAs, and the identified SNPs might be served as genetic markers to optimize breeding programs for milk FAs in dairy cattle. This research deserves in-depth verification.

scholarly journals Genome-wide association of milk fatty acids in Dutch dairy cattle

BMC Genetics ◽  
2011 ◽  
Vol 12 (1) ◽  
pp. 43 ◽  
Author(s):  
Aniek C Bouwman ◽  
Henk Bovenhuis ◽  
Marleen HPW Visker ◽  
Johan AM van Arendonk
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Genome Wide Association ◽  
Milk Fatty Acids ◽  
Genome Wide

GENOME-WIDE ASSOCIATION STUDY FOR COWS’ MILK FATTY ACIDS DERIVED BY INFRARED SPECTRA

2021 ◽  
Vol 1 (19) ◽  
pp. 352-354
Author(s):  
E.A. Gladyr ◽  
L.P. Ignatieva ◽  
I.A. Lashneva ◽  
A.A. Kositsin ◽  
O.A. Artemieva ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Milk Fat ◽  
Genome Wide Association Study ◽  
Cow Milk ◽  
Fat Percentage ◽  
Milk Fatty Acids ◽  
Linear Type ◽  
Black And White ◽  
Genome Wide ◽  
First Results

The first results of the genome-wide associations analysis for fatty acids composition in cow milk by Russian Holsteinized Black-and-White and Holstein breeds were obtained. Genomic regions (QTL) associated with milk fat percentage, fatty acids synthesis, functional parameters of linear type for udder and leg traits, fertility features have been detected.

scholarly journals In vitro antimicrobial effect of palm oils rich in medium-chain fatty acids against mastitis-causing Gram-positive bacteria

2019 ◽  
Vol 64 (No. 8) ◽  
pp. 325-331
Author(s):  
Klára Laloučková ◽  
Lucie Malá ◽  
Paula Slaničková ◽  
Eva Skřivanová
Keyword(s):  
Fatty Acids ◽  
Dairy Cattle ◽  
Antibacterial Effect ◽  
Bovine Mastitis ◽  
Medium Chain ◽  
Medium Chain Fatty Acids ◽  
Streptococcus Uberis ◽  
Broth Microdilution Method ◽  
Chain Fatty Acids

Various pathogens causing mastitis in dairy cattle are of serious concern due to their increasing antibacterial resistance and potential transmission to other cows, calves, and the environment, especially through the milking process. Therefore, alternative approaches to antimicrobial usage in the treatment or control of mastitis in dairy cattle are severely needed. The antibacterial effect of medium-chain fatty acids (MCFAs) is known to be significant for various pathogens, but there is only limited information about the activity of MCFAs on mastitis-causing pathogens. Moreover, no evidence about the antimicrobial effects of palm oils rich in MCFAs, such as coconut, palm kernel, and tucuma oil, can be found in the current literature. The aim of this study was to evaluate the in vitro antibacterial effect of palm oils rich in MCFAs, after cleavage by an exogenous lipase from Mucor javanicus, on bovine mastitis-causing strains (Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis) by the broth microdilution method. All tested palm oils exerted antibacterial activity against eight tested bacterial strains in the range of 64–8192 µl/ml with Str. agalactiae being the most sensitive and S. aureus being the most resistant species. The results of the present study demonstrate that palm oils rich in MCFAs can serve as an alternative to the predominantly used predip and postdip procedures in bovine mastitis control, but further in vivo studies are needed to confirm the findings for their possible applications.

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