1
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Gaiani N, Bourgeois-Brunel L, Rocha D, Boulling A. Analysis of the impact of DGAT1 p.M435L and p.K232A variants on pre-mRNA splicing in a full-length gene assay. Sci Rep 2023; 13:8999. [PMID: 37268760 DOI: 10.1038/s41598-023-36142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
DGAT1 is playing a major role in fat metabolism and triacylglyceride synthesis. Only two DGAT1 loss-of-function variants altering milk production traits in cattle have been reported to date, namely p.M435L and p.K232A. The p.M435L variant is a rare alteration and has been associated with skipping of exon 16 which results in a non-functional truncated protein, and the p.K232A-containing haplotype has been associated with modifications of the splicing rate of several DGAT1 introns. In particular, the direct causality of the p.K232A variant in decreasing the splicing rate of the intron 7 junction was validated using a minigene assay in MAC-T cells. As both these DGAT1 variants were shown to be spliceogenic, we developed a full-length gene assay (FLGA) to re-analyse p.M435L and p.K232A variants in HEK293T and MAC-T cells. Qualitative RT-PCR analysis of cells transfected with the full-length DGAT1 expression construct carrying the p.M435L variant highlighted complete skipping of exon 16. The same analysis performed using the construct carrying the p.K232A variant showed moderate differences compared to the wild-type construct, suggesting a possible effect of this variant on the splicing of intron 7. Finally, quantitative RT-PCR analyses of cells transfected with the p.K232A-carrying construct did not show any significant modification on the splicing rate of introns 1, 2 and 7. In conclusion, the DGAT1 FLGA confirmed the p.M435L impact previously observed in vivo, but invalidated the hypothesis whereby the p.K232A variant strongly decreased the splicing rate of intron 7.
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Affiliation(s)
- Nicolas Gaiani
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Dominique Rocha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Arnaud Boulling
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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2
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Jiang A, Ankersmit-Udy A, Turner SA, Scholtens M, Littlejohn MD, Lopez-Villalobos N, Proser CG, Snell RG, Lehnert K. A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation. J Anim Sci Biotechnol 2022; 13:4. [PMID: 35144696 PMCID: PMC8832686 DOI: 10.1186/s40104-021-00667-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals. A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker rs268292132). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat, 1.9 kg protein and 73.6 kg milk yield. An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traits. Results The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 (SNP marker rs268292132) associated with an adverse change in UD, FUA and RUA. Conclusions Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00667-y.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alex Ankersmit-Udy
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Mathew D Littlejohn
- AL Rae Centre of Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Nicolas Lopez-Villalobos
- Dairy Cattle Breeding and Genetics, School of Agriculture & Environment, Massey University, Hamilton, New Zealand
| | | | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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3
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Khan MZ, Ma Y, Ma J, Xiao J, Liu Y, Liu S, Khan A, Khan IM, Cao Z. Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits. Front Vet Sci 2021; 8:712470. [PMID: 34485439 PMCID: PMC8415568 DOI: 10.3389/fvets.2021.712470] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiaying Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Adnan Khan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ibrar Muhammad Khan
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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4
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Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows. Genes (Basel) 2021; 12:genes12030456. [PMID: 33806889 PMCID: PMC8004844 DOI: 10.3390/genes12030456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 01/01/2023] Open
Abstract
The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.
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5
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Fink T, Lopdell TJ, Tiplady K, Handley R, Johnson TJJ, Spelman RJ, Davis SR, Snell RG, Littlejohn MD. A new mechanism for a familiar mutation - bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement. BMC Genomics 2020; 21:591. [PMID: 32847516 PMCID: PMC7449055 DOI: 10.1186/s12864-020-07004-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/19/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. RESULTS We used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA > GC variant that encodes the DGAT1 K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for DGAT1, where the K232A mutation appears as one of the top associated variants for this effect. By conducting in vitro expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. CONCLUSIONS The relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear; however, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at the DGAT1 locus.
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Affiliation(s)
- Tania Fink
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas J Lopdell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand. .,Livestock Improvement Corporation, Hamilton, New Zealand.
| | - Kathryn Tiplady
- Livestock Improvement Corporation, Hamilton, New Zealand.,Al Rae Centre, Massey University, Hamilton, New Zealand
| | - Renee Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mathew D Littlejohn
- Livestock Improvement Corporation, Hamilton, New Zealand.,Al Rae Centre, Massey University, Hamilton, New Zealand
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6
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Lopez-Villalobos N, Spelman RJ, Melis J, Davis SR, Berry SD, Lehnert K, Sneddon NW, Holroyd SE, MacGibbon AK, Snell RG. Genetic correlations of milk fatty acid contents predicted from milk mid-infrared spectra in New Zealand dairy cattle. J Dairy Sci 2020; 103:7238-7248. [PMID: 32534926 DOI: 10.3168/jds.2019-17971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/02/2020] [Indexed: 12/29/2022]
Abstract
The objective of this study was to estimate genetic correlations among milk fatty acid (FA) concentrations in New Zealand dairy cattle. Concentrations of each of the most common FA, expressed as a percentage of the total FA, were determined by gas chromatography on a specific cohort of animals. Using this data set, prediction equations were derived using mid-infrared (MIR) spectroscopy data collected from the same samples. These prediction equations were applied to a large data set of MIR measurements in 34,141 milk samples from 3,445 Holstein-Friesian, 2,935 Jersey, and 3,609 crossbred Holstein-Friesian × Jersey cows, sampled an average of 3.42 times during the 2007-2008 season. Data were analyzed using univariate and bivariate repeatability animal models. Heritability of predicted FA concentration in milk fat ranged from 0.21 to 0.42, indicating that genetic selection could be used to change the FA composition of milk. The de novo synthesized FA (C6:0, C8:0, C10:0, C12:0, and C14:0) showed strong positive genetic correlations with each other, ranging from 0.24 to 0.99. Saturated FA were negatively correlated with unsaturated (-0.93) and polyunsaturated (-0.84) FA. The saturated FA were positively correlated with milk fat yield and fat percentage, whereas the unsaturated FA were negatively associated with fat yield and fat percentage. Our results indicate that bovine milk FA composition can be changed through genetic selection using MIR as a phenotypic proxy.
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Affiliation(s)
- N Lopez-Villalobos
- School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
| | - R J Spelman
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - J Melis
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - S R Davis
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - S D Berry
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - K Lehnert
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - N W Sneddon
- School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - S E Holroyd
- Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - A K MacGibbon
- Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - R G Snell
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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7
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Wang T, Li J, Gao X, Song W, Chen C, Yao D, Ma J, Xu L, Ma Y. Genome-wide association study of milk components in Chinese Holstein cows using single nucleotide polymorphism. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Bhatt-Wessel B, Jordan TW, Miller JH, Peng L. Role of DGAT enzymes in triacylglycerol metabolism. Arch Biochem Biophys 2018; 655:1-11. [PMID: 30077544 DOI: 10.1016/j.abb.2018.08.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/25/2018] [Accepted: 08/02/2018] [Indexed: 01/22/2023]
Abstract
The esterification of a fatty acyl moiety to diacylglycerol to form triacylglycerol (TAG) is catalysed by two diacylglycerol O-acyltransferases (DGATs) encoded by genes belonging to two distinct gene families. The enzymes are referred to as DGAT1 and DGAT2 in order of their identification. Both proteins are transmembrane proteins localized in the endoplasmic reticulum. Their membrane topologies are however significantly different. This difference is hypothesized to give the two isozymes different abilities to interact with other proteins and organelles and access to different pools of fatty acids, thereby creating a distinction between the enzymes in terms of their role and contribution to lipid metabolism. DGAT1 is proposed to have dual topology contributing to TAG synthesis on both sides of the ER membrane and esterifying only the pre-formed fatty acids. There is evidence to suggest that DGAT2 translocates to the lipid droplet (LD), associates with other proteins, and synthesizes cytosolic and luminal apolipoprotein B associated LD-TAG from both endogenous and exogenous fatty acids. The aim of this review is to differentiate between the two DGAT enzymes by comparing the genes that encode them, their proposed topologies, the proteins they interact with, and their roles in lipid metabolism.
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Affiliation(s)
- Bhumika Bhatt-Wessel
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - T William Jordan
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - John H Miller
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Lifeng Peng
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, New Zealand.
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9
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Ning C, Wang D, Zheng X, Zhang Q, Zhang S, Mrode R, Liu JF. Eigen decomposition expedites longitudinal genome-wide association studies for milk production traits in Chinese Holstein. Genet Sel Evol 2018; 50:12. [PMID: 29576014 PMCID: PMC5868076 DOI: 10.1186/s12711-018-0383-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/01/2018] [Indexed: 11/16/2022] Open
Abstract
Background Pseudo-phenotypes, such as 305-day yields, estimated breeding values or deregressed proofs, are usually used as response variables for genome-wide association studies (GWAS) of milk production traits in dairy cattle. Computational inefficiency challenges the direct use of test-day records for longitudinal GWAS with large datasets. Results We propose a rapid longitudinal GWAS method that is based on a random regression model. Our method uses Eigen decomposition of the phenotypic covariance matrix to rotate the data, thereby transforming the complex mixed linear model into weighted least squares analysis. We performed a simulation study that showed that our method can control type I errors well and has higher power than a longitudinal GWAS method that does not include time-varied additive genetic effects. We also applied our method to the analysis of milk production traits in the first three parities of 6711 Chinese Holstein cows. The analysis for each trait was completed within 1 day with known variances. In total, we located 84 significant single nucleotide polymorphisms (SNPs) of which 65 were within previously reported quantitative trait loci (QTL) regions. Conclusions Our rapid method can control type I errors in the analysis of longitudinal data and can be applied to other longitudinal traits. We detected QTL that were for the most part similar to those reported in a previous study in Chinese Holstein. Moreover, six additional SNPs for fat percentage and 13 SNPs for protein percentage were identified by our method. These additional 19 SNPs could be new candidate quantitative trait nucleotides for milk production traits in Chinese Holstein. Electronic supplementary material The online version of this article (10.1186/s12711-018-0383-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dan Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, 00100, Kenya
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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10
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Frischknecht M, Pausch H, Bapst B, Signer-Hasler H, Flury C, Garrick D, Stricker C, Fries R, Gredler-Grandl B. Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle. BMC Genomics 2017; 18:999. [PMID: 29284405 PMCID: PMC5747239 DOI: 10.1186/s12864-017-4390-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 12/15/2017] [Indexed: 01/06/2023] Open
Abstract
Background Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. Results In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Conclusions Our study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection. Electronic supplementary material The online version of this article (10.1186/s12864-017-4390-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mirjam Frischknecht
- Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland. .,Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, 3052, Zollikofen, Switzerland.
| | - Hubert Pausch
- Chair of Animal Breeding, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,ETH Zurich, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Beat Bapst
- Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland
| | - Heidi Signer-Hasler
- Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, 3052, Zollikofen, Switzerland
| | - Christine Flury
- Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, 3052, Zollikofen, Switzerland
| | - Dorian Garrick
- Institute of Veterinary, Animal & Biomedical Sciences, Massey University, 4442, Palmerston North, New Zealand
| | | | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
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11
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Stephen J, Vilboux T, Haberman Y, Pri-Chen H, Pode-Shakked B, Mazaheri S, Marek-Yagel D, Barel O, Di Segni A, Eyal E, Hout-Siloni G, Lahad A, Shalem T, Rechavi G, Malicdan MCV, Weiss B, Gahl WA, Anikster Y. Congenital protein losing enteropathy: an inborn error of lipid metabolism due to DGAT1 mutations. Eur J Hum Genet 2016; 24:1268-73. [PMID: 26883093 PMCID: PMC4989215 DOI: 10.1038/ejhg.2016.5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 12/18/2022] Open
Abstract
Protein-losing enteropathy (PLE) is a clinical disorder of protein loss from the gastrointestinal system that results in hypoproteinemia and malnutrition. This condition is associated with a wide range of gastrointestinal disorders. Recently, a unique syndrome of congenital PLE associated with biallelic mutations in the DGAT1 gene has been reported in a single family. We hypothesize that mutations in this gene are responsible for undiagnosed cases of PLE in infancy. Here we investigated three children in two families presenting with severe diarrhea, hypoalbuminemia and PLE, using clinical studies, homozygosity mapping, and exome sequencing. In one family, homozygosity mapping using SNP arrays revealed the DGAT1 gene as the best candidate gene for the proband. Sequencing of all the exons including flanking regions and promoter regions of the gene identified a novel homozygous missense variant, p.(Leu295Pro), in the highly conserved membrane-bound O-acyl transferase (MBOAT) domain of the DGAT1 protein. Expression studies verified reduced amounts of DGAT1 in patient fibroblasts. In a second family, exome sequencing identified a previously reported splice site mutation in intron 8. These cases of DGAT1 deficiency extend the molecular and phenotypic spectrum of PLE, suggesting a re-evaluation of the use of DGAT1 inhibitors for metabolic disorders including obesity and diabetes.
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Affiliation(s)
- Joshi Stephen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Medical Genomics, Inova Translational Medicine Institute, Fairfax, VA, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hadass Pri-Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
- The Dr Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Sina Mazaheri
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dina Marek-Yagel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ayelet Di Segni
- Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Eran Eyal
- Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Goni Hout-Siloni
- Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Avishay Lahad
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Tzippora Shalem
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - May Christine V Malicdan
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Batia Weiss
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
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Tschapalda K, Zhang YQ, Liu L, Golovnina K, Schlemper T, Eichmann TO, Lal-Nag M, Sreenivasan U, McLenithan J, Ziegler S, Sztalryd C, Lass A, Auld D, Oliver B, Waldmann H, Li Z, Shen M, Boxer MB, Beller M. A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics. EBioMedicine 2016; 8:49-59. [PMID: 27428418 PMCID: PMC4919474 DOI: 10.1016/j.ebiom.2016.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/02/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022] Open
Abstract
Excess lipid storage is an epidemic problem in human populations. Thus, the identification of small molecules to treat or prevent lipid storage-related metabolic complications is of great interest. Here we screened > 320.000 compounds for their ability to prevent a cellular lipid accumulation phenotype. We used fly cells because the multifarious tools available for this organism should facilitate unraveling the mechanism-of-action of active small molecules. Of the several hundred lipid storage inhibitors identified in the primary screen we concentrated on three structurally diverse and potent compound classes active in cells of multiple species (including human) and negligible cytotoxicity. Together with Drosophila in vivo epistasis experiments, RNA-Seq expression profiles suggested that the target of one of the small molecules was diacylglycerol acyltransferase 1 (DGAT1), a key enzyme in the production of triacylglycerols and prominent human drug target. We confirmed this prediction by biochemical and enzymatic activity tests. We identified > 600 potent small molecule inhibitors of cellular lipid storage deposition. RNA-Seq expression profiling discriminated the activity of three lead scaffolds and guided subsequent functional studies. We discovered a class of DGAT1 inhibitors, which is active in fly and mammalian cell lines as well as whole flies.
Obesity and other lipid storage associated diseases are a growing health threat of human populations. In an undirected phenotypic screen, we identified pharmacologically active small molecules that reduce or enhance lipid storage. Our work focuses on three lead structures that prevent lipid storage in diverse cellular systems including cells from a diabetes patient. In order to elucidate the compound mechanisms-of-action and cellular targets, we used a combination of RNA-Seq transcriptional profiling and diverse functional assays. Our results strongly suggest that one of our lead structures represents a class of inhibitors targeting the key lipogenic enzyme diacylglycerol acyltransferase 1.
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Affiliation(s)
- Kirsten Tschapalda
- Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Germany; Institute for Mathematical Modeling of Biological Systems, Heinrich Heine University Düsseldorf, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany; Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ya-Qin Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Li Liu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Kseniya Golovnina
- National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA
| | - Thomas Schlemper
- Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Germany; Institute for Mathematical Modeling of Biological Systems, Heinrich Heine University Düsseldorf, Germany
| | | | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Urmila Sreenivasan
- Department of Medicine, Division of Endocrinology University of Maryland School of Medicine, USA
| | - John McLenithan
- Department of Medicine, Division of Endocrinology University of Maryland School of Medicine, USA
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Carole Sztalryd
- Department of Medicine, Division of Endocrinology University of Maryland School of Medicine, USA; Baltimore VA Medical Center, VA Research Service, Geriatric Research, Education and Clinical Center (GRECC) and VA Maryland Health Care System, Department of Medicine, Division of Endocrinology University of Maryland School of Medicine, USA
| | - Achim Lass
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Douglas Auld
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Brian Oliver
- National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Zhuyin Li
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, USA
| | - Mathias Beller
- Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Germany; Institute for Mathematical Modeling of Biological Systems, Heinrich Heine University Düsseldorf, Germany.
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APA-style human milk fat analogue from silkworm pupae oil: Enzymatic production and improving storage stability using alkyl caffeates. Sci Rep 2015; 5:17909. [PMID: 26643045 PMCID: PMC4672268 DOI: 10.1038/srep17909] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 11/09/2015] [Indexed: 01/16/2023] Open
Abstract
Silkworm pupae oil derived from reeling waste is a rich source of α-linolenic acid (ALA), which has multipal applications. ALAs were added in sn-1, 3 positions in a triacylglycerol (TAG) to produce an APA-human milk fat analogues (APA-HMFAs, A: α-linolenic acid, P: palmitic acid). The optimum condition is that tripalmitin to free fatty acids of 1:12 (mole ratio) at 65 °C for 48 h using lipase Lipozyme RM IM. Results show that, the major TAG species that comprised APA-HMFAs were rich in ALA and palmitic acid, which contained 64.52% total unsaturated fatty acids (UFAs) and 97.05% PA at the sn-2 position. The melting point of APA was −27.5 °C which is much lower than tripalmitin (40.5 °C) indicating more plastic character. In addition, the practical application of alkyl caffeates as liposoluble antioxidants in APA was developed. Alkyl caffeate showed a superior IC50 (1.25–1.66 μg/mL) compared to butyl hydroxy anisd (1.67 μg/mL) and L-ascorbic acid-6-palmitate (L-AP) (1.87 μg/mL) in DPPH analysis. The addition of ethyl caffeate to oil achieved a higher UFAs content (73.58%) at high temperatures. Overall, APA was obtained from silkworm pupae oil successfully, and the addition of caffeates extended storage ranges for APA-HMFAs.
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