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

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.

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

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-020-00540-4 ◽

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.

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

10.21203/rs.3.rs-38950/v3 ◽

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.

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

10.21203/rs.3.rs-38950/v1 ◽

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.

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

10.21203/rs.3.rs-38950/v2 ◽

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.

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

Genes ◽

10.3390/genes10020086 ◽

2019 ◽

Vol 10 (2) ◽

pp. 86 ◽

Cited By ~ 1

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.

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Influence of canola oil on the fatty acid profile in goats’ milk

Canadian Journal of Animal Science ◽

10.4141/a03-003 ◽

2003 ◽

Vol 83 (2) ◽

pp. 323-325 ◽

Cited By ~ 2

Author(s):

E. K. Okine ◽

L. A. Goonewardene ◽

Z. Mir ◽

P. Mir ◽

Z. Wang ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Key Words ◽

Fatty Acid Profile ◽

Canola Oil ◽

Latin Square ◽

Goat Milk ◽

Milk Fatty Acid ◽

Milk Fatty Acids ◽

Four Levels

Four Alpine does were used in a 4 × 4 Latin square design to determine the effects of feeding canola oil at four levels: 0, 2, 4 and 6% on milk fatty acid profile. The sum of C12:0 + C14:0 + C16:0 (hypercholesterolemic fatty acids) decreased linearly and C18:0 + C18:1: C16:0 (indicator of cholesterolemic tendency of fat source) increased linearly (P < 0.01) with increased canola oil intake. Key words: Goat, milk, fatty acids, canola oil

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A novel polymorphism in the oxytocin receptor encoding gene (OXTR) affects milk fatty acid composition in Italian Mediterranean river buffalo

Journal of Dairy Research ◽

10.1017/s0022029917000127 ◽

2017 ◽

Vol 84 (2) ◽

pp. 170-180 ◽

Cited By ~ 4

Author(s):

Gianfranco Cosenza ◽

Nicolò P P Macciotta ◽

Anna Nudda ◽

Angelo Coletta ◽

Luigi Ramunno ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid Composition ◽

Fatty Acid ◽

Acid Composition ◽

Oxytocin Receptor ◽

Milk Fatty Acid ◽

River Buffalo ◽

Fatty Acids Composition ◽

Milk Fatty Acids ◽

Mediterranean River

The oxytocin receptor, also known as OXTR, is a protein which functions as receptor for the hormone and neurotransmitter oxytocin and the complex oxytocin–oxytocin receptor plays an important role in the uterus during calving. A characterisation of the river buffalo OXTR gene, amino acid sequences and phylogenetic analysis is presented. The DNA regions of the OXTR gene spanning exons 1, 2 and 3 of ten Mediterranean river buffalo DNA samples were analysed and 7 single nucleotide polymorphisms were found. We focused on the g.129C > T SNP detected in exon 3 and responsible for the amino acid replacement CGCArg > TGCCys in position 353. The relative frequency of T allele was of 0·257. An association study between this detected polymorphism and milk fatty acids composition in Italian Mediterranean river buffalo was carried out. The fatty acid composition traits, fatty acid classes and fat percentage of 306 individual milk samples were determined. Associations between OXTR g.129C > T genotype and milk fatty acids composition were tested using a mixed linear model. The OXTR CC genotype was found significantly associated with higher contents of odd branched-chain fatty acids (OBCFA) (P < 0·0006), polyunsaturated FA (PUFA n 3 and n 6) (P < 0·0032 and P < 0·0006, respectively), stearic acid (C18) (P < 0·02) and lower level of palmitic acid (C16) (P < 0·02). The results of this study suggest that the OXTR CC animals might be useful in selection toward the improvement of milk fatty acid composition.

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Fatty acid composition of milk fat from three breeds of dairy cattle

Canadian Journal of Animal Science ◽

10.4141/cjas95-040 ◽

1995 ◽

Vol 75 (2) ◽

pp. 267-269 ◽

Cited By ~ 34

Author(s):

E. J. DePeters ◽

J. F. Medrano ◽

B. A. Reed

Keyword(s):

Fatty Acids ◽

Fatty Acid Composition ◽

Fatty Acid ◽

Dairy Cattle ◽

Key Words ◽

Acid Composition ◽

Milk Fat ◽

Milk Fatty Acids ◽

Brown Swiss

The proportion of MCFA in milk fat was lowest for Holstein, highest for Jersey, and intermediate for Brown Swiss cows. Proportions of SCFA (C4:0 to C8:0) and LCFA (> 18 C) did not differ among breeds. Differences in fatty acid composition among breeds were small, but could contribute to differences in manufacturing properties of milk fat. Key words: Holstein, Jersey, Brown Swiss, milk fatty acids

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