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Rheological and structural properties of acid-induced milk gels as a function of β-casein phenotype. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Daniloski D, McCarthy NA, Huppertz T, Vasiljevic T. What is the impact of amino acid mutations in the primary structure of caseins on the composition and functionality of milk and dairy products? Curr Res Food Sci 2022; 5:1701-1712. [PMID: 36212081 PMCID: PMC9535159 DOI: 10.1016/j.crfs.2022.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
The impact of amino acid mutations within the peptide structure of bovine milk protein is important to understand as it can effect processability and subsequently effect its physiological properties. Genetic polymorphisms of bovine caseins can influence the chemical, structural, and technological properties, including casein micelle morphology, calcium distribution, network creation upon gelation, and surface activity. The A1 and A2 genetic variants of β-casein have recently acquired growing attention from both academia and industry, prompting new developments in the area. The difference between these two genetic variants is the inclusion of either proline in β-casein A2 or histidine in β-casein A1 at position 67 in the peptide chain. The aim of this review was to examine the extent to which milk and ingredient functionality is influenced by β-casein phenotype. One of the main findings of this review was although β-casein A1 was found to be the dominant variant in milks with superior acid gelation and rennet coagulation properties, milks comprised of β-casein A2 possessed greater emulsion and foam formation capabilities. The difference in the casein micelle assembly, hydrophobicity, and chaperone activity of caseins may explain the contrast in the functionality of milks containing β-casein from either A1 or A2 families. This review provides new insights into the subtle variations in the physicochemical properties of bovine milks, which could potentially support dairy producers in the development of new dairy products with different functional properties. Impact of β- and other caseins on the casein micelle structure and functionality. Proline and histidine in β-caseins play a key role in casein micelle conformation. Chaperone activity of β-casein A2 towards heat-induced aggregation of whey protein. Gels prepared of milks with β-casein A1 possess a denser and firmer structure. Ordered structure of β-casein A2 led to improved emulsion and foam formation.
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Affiliation(s)
- Davor Daniloski
- Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Victoria University, Melbourne, VIC, 8001, Australia
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Noel A. McCarthy
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Thom Huppertz
- Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Victoria University, Melbourne, VIC, 8001, Australia
- FrieslandCampina, Amersfoort, the Netherlands
- Wageningen University & Research, Wageningen, the Netherlands
| | - Todor Vasiljevic
- Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Victoria University, Melbourne, VIC, 8001, Australia
- Corresponding author.
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3
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Davis SR, Ward HE, Kelly V, Palmer D, Ankersmit-Udy AE, Lopdell TJ, Berry SD, Littlejohn MD, Tiplady K, Adams LF, Carnie K, Burrett A, Thomas N, Snell RG, Spelman RJ, Lehnert K. Screening for phenotypic outliers identifies an unusually low concentration of a β-lactoglobulin B protein isoform in bovine milk caused by a synonymous SNP. Genet Sel Evol 2022; 54:22. [PMID: 35296234 PMCID: PMC8925192 DOI: 10.1186/s12711-022-00711-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Background Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration. Results A cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide association study (GWAS) of BLG B protein isoform concentration in milk from AB heterozygous cows, detected a group of highly significant single nucleotide polymorphisms (SNPs) within or close to the BLG gene. Among these was a synonymous G/A variation at position + 78 bp in exon 1 of the BLG gene (chr11:103256256G > A). The effect of the A allele of this SNP (which we named B’) on BLG expression was evaluated in a luciferase reporter assay in transfected CHO-K1 and MCF-7 cells. In both cell types, the presence of the B’ allele in a plasmid containing the bovine BLG gene from -922 to + 898 bp (relative to the transcription initiation site) resulted in a 60% relative reduction in mRNA expression, compared to the plasmid containing the wild-type B sequence allele. Examination of a mammary RNAseq dataset (n = 391) identified 14 heterozygous carriers of the B’ allele which were homozygous for the BLG B protein isoform (BB’). The level of expression of the BLG B’ allele was 41.9 ± 1.0% of that of the wild-type BLG B allele. Milk samples from three cows, homozygous for the A allele at chr11:103,256,256 (B’B’), were analysed (HPLC) and showed BLG concentrations of 1.04, 1.26 and 1.83 g/L relative to a mean of 4.84 g/L in milk from 16 herd contemporaries of mixed (A and B) BLG genotypes. The mechanism by which B’ downregulates milk BLG concentration remains to be determined. Conclusions High-throughput screening and identification of outliers, enabled the discovery of a synonymous G > A mutation in exon 1 of the B allele of the BLG gene (B’), which reduced the milk concentration of β-lactoglobulin B protein isoform, by more than 50%. Milk from cows carrying the B’ allele is expected to have improved processing characteristics, particularly for cheese-making. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00711-z.
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Affiliation(s)
- Stephen R Davis
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand. .,ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand.
| | - Hamish E Ward
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Van Kelly
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - David Palmer
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Alexandra E Ankersmit-Udy
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Thomas J Lopdell
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Sarah D Berry
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Mathew D Littlejohn
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Kathryn Tiplady
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Linda F Adams
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Katie Carnie
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Alayna Burrett
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Natalie Thomas
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Russell G Snell
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Richard J Spelman
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Klaus Lehnert
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
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4
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Bisutti V, Pegolo S, Giannuzzi D, Mota L, Vanzin A, Toscano A, Trevisi E, Ajmone Marsan P, Brasca M, Cecchinato A. The β-casein (CSN2) A2 allelic variant alters milk protein profile and slightly worsens coagulation properties in Holstein cows. J Dairy Sci 2022; 105:3794-3809. [DOI: 10.3168/jds.2021-21537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
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5
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Maiorano AM, Cardoso DF, Carvalheiro R, Júnior GAF, de Albuquerque LG, de Oliveira HN. Signatures of selection in Nelore cattle revealed by whole-genome sequencing data. Genomics 2022; 114:110304. [DOI: 10.1016/j.ygeno.2022.110304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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6
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Cai W, Li C, Li J, Song J, Zhang S. Integrated Small RNA Sequencing, Transcriptome and GWAS Data Reveal microRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle. Front Genet 2021; 12:726706. [PMID: 34712266 PMCID: PMC8546187 DOI: 10.3389/fgene.2021.726706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Milk protein is one of the most important economic traits in the dairy industry. Yet, the regulatory network of miRNAs for the synthesis of milk protein in mammary is poorly understood. Samples from 12 Chinese Holstein cows with three high ( ≥ 3.5%) and three low ( ≤ 3.0%) phenotypic values for milk protein percentage in lactation and non-lactation were examined through deep small RNA sequencing. We characterized 388 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. We analyzed for enrichments of GWAS signals in miRNAs and their correlated targets. Our results demonstrated that genomic regions harboring DE miRNA genes in lactation were significantly enriched with GWAS signals for milk protein percentage traits and that enrichments within DE miRNA targets were significantly higher than in random gene sets for the majority of milk production traits. This integrated study on the transcriptome and posttranscriptional regulatory profiles between significantly differential phenotypes of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
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Affiliation(s)
- Wentao Cai
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species. BIOLOGY 2021; 10:biology10080790. [PMID: 34440019 PMCID: PMC8389679 DOI: 10.3390/biology10080790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.
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8
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Meta-analysis of genome-wide association studies and gene networks analysis for milk production traits in Holstein cows. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Hendriks SJ, Huzzey JM, Kuhn-Sherlock B, Turner SA, Mueller KR, Phyn CVC, Donaghy DJ, Roche JR. Associations between lying behavior and activity and hypocalcemia in grazing dairy cows during the transition period. J Dairy Sci 2020; 103:10530-10546. [PMID: 32861495 DOI: 10.3168/jds.2019-18111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/11/2020] [Indexed: 11/19/2022]
Abstract
Hypocalcemia is a common metabolic disorder of transition dairy cows that is considered a gateway disease, increasing the risk of other health disorders and reducing cow performance. Clinical milk fever is associated with long periods of recumbency, and it is plausible that cows experiencing non-paretic hypocalcemia may spend more time lying; hence, lying behavior and activity measures may be useful in identifying at-risk cows. The objective of this study was to describe associations among blood calcium (Ca) status at calving and lying behavior and activity measures during the transition period in grazing dairy cows. Blood was sampled on the day of calving (d 0), and d 1, 2, 3, and 4 postcalving, and analyzed for total plasma Ca concentration. Twenty-four multiparous Holstein-Friesian and Holstein-Friesian × Jersey grazing dairy cows were classified, retrospectively, as clinically hypocalcemic (CLIN; blood Ca ≤ 1.4 mmol/L at 1 or more consecutive samplings within 48 h postcalving, but without parturient paresis). These cows were pair-matched (using milk production potential from their estimated breeding value for milk protein, mean body weight at wk -5 and -6 precalving, and, where possible, parity) with 24 cows classified as subclinically hypocalcemic (SUB; blood Ca > 1.4 and < 2.0 mmol/L at 2 consecutive samplings within 48 h postcalving), and 24 cows classified as normocalcemic (NORM; blood Ca ≥ 2.0 mmol/L at 3 consecutive samplings within 72 h postcalving). Lying behavior and activity were monitored using triaxial accelerometers from -21 to +35 d relative to calving. Data were summarized to calculate daily lying time (h/d), daily number of lying bouts (LB; no./d), mean LB duration (min/bout), and the number of steps taken (steps/d). On d 0, the CLIN group were less active and spent approximately 2.6 h longer lying than the SUB and NORM groups, particularly between 0200 and 1400 h. On d 0, the NORM group had fewer LB (16.3/d) than the SUB and CLIN groups (18.2 and 19.2/d, respectively). These differences in behavior were no longer detected 2 d postcalving, and no further differences were observed. The day before calving, the CLIN group spent 1.4 h longer lying down than did the SUB and NORM groups. Further, the relative change in steps from a precalving baseline period (d -14 to -7) until d 0 was positively, linearly associated with blood Ca concentration within 24 h postcalving. Future work should consider daily and temporal changes in behavior in individual cows to determine the potential for these measures to allow early detection of hypocalcemia.
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Affiliation(s)
- S J Hendriks
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand.
| | - J M Huzzey
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, 93407
| | | | - S-A Turner
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | - K R Mueller
- School of Veterinary Sciences, Massey University, Palmerston North 4442, New Zealand
| | - C V C Phyn
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | - D J Donaghy
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - J R Roche
- DairyNZ Ltd., Hamilton 3240, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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10
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Srikanth K, Lee SH, Chung KY, Park JE, Jang GW, Park MR, Kim NY, Kim TH, Chai HH, Park WC, Lim D. A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:E316. [PMID: 32188084 PMCID: PMC7140899 DOI: 10.3390/genes11030316] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea;
| | - Ki-Yong Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Mi-Rim Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Na Yeon Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Won Cheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
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11
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Campos GS, Sollero BP, Reimann FA, Junqueira VS, Cardoso LL, Yokoo MJI, Boligon AA, Braccini J, Cardoso FF. Tag‐SNP selection using Bayesian genomewide association study for growth traits in Hereford and Braford cattle. J Anim Breed Genet 2019; 137:449-467. [DOI: 10.1111/jbg.12458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | - Leandro Lunardini Cardoso
- Departamento de Zootecnia Universidade Federal de Pelotas Pelotas Brazil
- Embrapa Pecuária Sul Bagé Brazil
| | | | | | - José Braccini
- Departamento de Zootecnia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Fernando Flores Cardoso
- Departamento de Zootecnia Universidade Federal de Pelotas Pelotas Brazil
- Embrapa Pecuária Sul Bagé Brazil
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12
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Sequence-based GWAS, network and pathway analyses reveal genes co-associated with milk cheese-making properties and milk composition in Montbéliarde cows. Genet Sel Evol 2019; 51:34. [PMID: 31262251 PMCID: PMC6604208 DOI: 10.1186/s12711-019-0473-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/07/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk's cheese-making properties (CMP) and composition. When this method of high-throughput phenotyping is combined with efficient imputations of whole-genome sequence data from cows' genotyping data, it provides a unique and powerful framework with which to carry out genomic analyses. The goal of this study was to use this approach to identify genes and gene networks associated with milk CMP and composition in the Montbéliarde breed. RESULTS Milk cheese yields, coagulation traits, milk pH and contents of proteins, fatty acids, minerals, citrate, and lactose were predicted from MIR spectra. Thirty-six phenotypes from primiparous Montbéliarde cows (1,442,371 test-day records from 189,817 cows) were adjusted for non-genetic effects and averaged per cow. 50 K genotypes, which were available for a subset of 19,586 cows, were imputed at the sequence level using Run6 of the 1000 Bull Genomes Project (comprising 2333 animals). The individual effects of 8.5 million variants were evaluated in a genome-wide association study (GWAS) which led to the detection of 59 QTL regions, most of which had highly significant effects on CMP and milk composition. The results of the GWAS were further subjected to an association weight matrix and the partial correlation and information theory approach and we identified a set of 736 co-associated genes. Among these, the well-known caseins, PAEP and DGAT1, together with dozens of other genes such as SLC37A1, ALPL, MGST1, SEL1L3, GPT, BRI3BP, SCD, GPAT4, FASN, and ANKH, explained from 12 to 30% of the phenotypic variance of CMP traits. We were further able to identify metabolic pathways (e.g., phosphate and phospholipid metabolism and inorganic anion transport) and key regulator genes, such as PPARA, ASXL3, and bta-mir-200c that are functionally linked to milk composition. CONCLUSIONS By using an approach that integrated GWAS with network and pathway analyses at the whole-genome sequence level, we propose candidate variants that explain a substantial proportion of the phenotypic variance of CMP traits and could thus be included in genomic evaluation models to improve milk CMP in Montbéliarde cows.
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13
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Pacheco HA, da Silva S, Sigdel A, Mak CK, Galvão KN, Texeira RA, Dias LT, Peñagaricano F. Gene Mapping and Gene-Set Analysis for Milk Fever Incidence in Holstein Dairy Cattle. Front Genet 2018; 9:465. [PMID: 30364193 PMCID: PMC6192420 DOI: 10.3389/fgene.2018.00465] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/24/2018] [Indexed: 01/02/2023] Open
Abstract
Milk fever is an important metabolic disorder that affects dairy cows around parturition. It is associated with a breakdown in the mechanisms of calcium homeostasis, resulting in very low blood calcium levels (hypocalcemia). The main objective of this study was to dissect the genetic basis underlying milk fever incidence in Holstein cattle. Data consisted of 31.6 k producer-recorded lactation incidence records from 15.3 k cows. The analysis included a whole-genome scan and a subsequent gene-set analysis in order to reveal individual genes, genetic mechanisms and biological pathways implicated in the incidence of periparturient hypocalcemia. The association analysis identified at least eight different genomic regions that explain considerable amounts of additive genetic variance for milk fever incidence. Notably, some of these regions harbor genes, such as CYP27A1, CYP2J2, GC, SNAI2, and PIM1, that are directly involved in vitamin D metabolic pathway. Moreover, the gene-set analysis revealed several functional terms, such as calcium ion binding, calcium ion transportation, T cell differentiation, B cell activation, protein phosphorylation, apoptosis, and protein kinase activity, among others, that could be implicated in the development of periparturient hypocalcemia. Overall, this comprehensive study contributes to a better understanding of the genetic control of this complex disease. In addition, these findings may contribute to the development of novel breeding strategies for reducing the incidence of milk fever in dairy cattle.
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Affiliation(s)
- Hendyel A Pacheco
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States.,Departamento de Zootecnia, Universidade Federal do Paranaì, Curitiba, Brazil
| | - Simone da Silva
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States.,Departamento de Zootecnia, Universidade Federal do Paranaì, Curitiba, Brazil
| | - Anil Sigdel
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Chun Kuen Mak
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Rodrigo A Texeira
- Departamento de Zootecnia, Universidade Federal do Paranaì, Curitiba, Brazil
| | - Laila T Dias
- Departamento de Zootecnia, Universidade Federal do Paranaì, Curitiba, Brazil
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, United States
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14
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Rezende FM, Dietsch GO, Peñagaricano F. Genetic dissection of bull fertility in US Jersey dairy cattle. Anim Genet 2018; 49:393-402. [PMID: 30109710 PMCID: PMC6175157 DOI: 10.1111/age.12710] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 02/06/2023]
Abstract
The service sire has been recognized as an important factor affecting herd fertility in dairy cattle. Recent studies suggest that genetic factors explain part of the difference in fertility among Holstein sires. The main objective of this study was to dissect the genetic architecture of sire fertility in US Jersey cattle. The dataset included 1.5 K Jersey bulls with sire conception rate (SCR) records and 96 K single nucleotide polymorphism (SNP) markers spanning the whole genome. The analysis included whole‐genome scans for both additive and non‐additive effects and subsequent functional enrichment analyses using KEGG Pathway, Gene Ontology (GO) and Medical Subject Headings (MeSH) databases. Ten genomic regions located on eight different chromosomes explained more than 0.5% of the additive genetic variance for SCR. These regions harbor genes, such as PKDREJ,EPB41L2,PDGFD,STX2,SLC25A20 and IP6K1, that are directly implicated in testis development and spermatogenesis, sperm motility and the acrosome reaction. In addition, the genomic scan for non‐additive effects identified two regions on BTA11 and BTA25 with marked recessive effects. These regions harbor three genes—FER1L5,CNNM4 and DNAH3—with known roles in sperm biology. Moreover, the gene‐set analysis revealed terms associated with calcium regulation and signaling, membrane fusion, sperm cell energy metabolism, GTPase activity and MAPK signaling. These gene sets are directly implicated in sperm physiology and male fertility. Overall, this integrative genomic study unravels genetic variants and pathways affecting Jersey bull fertility. These findings may contribute to the development of novel genomic strategies for improving sire fertility in Jersey cattle.
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Affiliation(s)
- F M Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.,Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil
| | - G O Dietsch
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - F Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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15
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Nakajima A, Kawaguchi F, Uemoto Y, Fukushima M, Yoshida E, Iwamoto E, Akiyama T, Kohama N, Kobayashi E, Honda T, Oyama K, Mannen H, Sasazaki S. A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle. Anim Sci J 2018; 89:743-751. [DOI: 10.1111/asj.12987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/30/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Ayaka Nakajima
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yoshinobu Uemoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Tohoku University; Sendai Japan
| | - Moriyuki Fukushima
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Emi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Takayuki Akiyama
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Namiko Kohama
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Eiji Kobayashi
- Division of Animal Breeding and Reproduction Research; Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Japan
| | - Takeshi Honda
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Kenji Oyama
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
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16
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Integration of GWAS, pathway and network analyses reveals novel mechanistic insights into the synthesis of milk proteins in dairy cows. Sci Rep 2018; 8:566. [PMID: 29330500 PMCID: PMC5766549 DOI: 10.1038/s41598-017-18916-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/18/2017] [Indexed: 01/30/2023] Open
Abstract
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11. Gene-set analysis and the network-based Associated Weight Matrix approach revealed that the milk proteins associated genes were involved in several biological functions, particularly ion and cation transmembrane transporter activity and neuronal and hormone signalling, according to the structure and function of casein micelles. Deeper analysis of the transcription factors and their predicted target genes within the network revealed that GFI1B, ZNF407 and NR5A1 might act as master regulators of milk protein synthesis and secretion. The information acquired provides novel insight into the regulatory mechanisms controlling milk protein synthesis and secretion in bovine mammary gland and may be useful in breeding programmes aimed at improving milk nutritional and/or technological properties.
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17
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Abdollahi-Arpanahi R, Morota G, Peñagaricano F. Predicting bull fertility using genomic data and biological information. J Dairy Sci 2017; 100:9656-9666. [PMID: 28987577 DOI: 10.3168/jds.2017-13288] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/13/2017] [Indexed: 01/04/2023]
Abstract
The genomic prediction of unobserved genetic values or future phenotypes for complex traits has revolutionized agriculture and human medicine. Fertility traits are undoubtedly complex traits of great economic importance to the dairy industry. Although genomic prediction for improved cow fertility has received much attention, bull fertility largely has been ignored. The first aim of this study was to investigate the feasibility of genomic prediction of sire conception rate (SCR) in US Holstein dairy cattle. Standard genomic prediction often ignores any available information about functional features of the genome, although it is believed that such information can yield more accurate and more persistent predictions. Hence, the second objective was to incorporate prior biological information into predictive models and evaluate their performance. The analyses included the use of kernel-based models fitting either all single nucleotide polymorphisms (SNP; 55K) or only markers with presumed functional roles, such as SNP linked to Gene Ontology or Medical Subject Heading terms related to male fertility, or SNP significantly associated with SCR. Both single- and multikernel models were evaluated using linear and Gaussian kernels. Predictive ability was evaluated in 5-fold cross-validation. The entire set of SNP exhibited predictive correlations around 0.35. Neither Gene Ontology nor Medical Subject Heading gene sets achieved predictive abilities higher than their counterparts using random sets of SNP. Notably, kernel models fitting significant SNP achieved the best performance with increases in accuracy up to 5% compared with the standard whole-genome approach. Models fitting Gaussian kernels outperformed their counterparts fitting linear kernels irrespective of the set of SNP. Overall, our findings suggest that genomic prediction of bull fertility is feasible in dairy cattle. This provides potential for accurate genome-guided decisions, such as early culling of bull calves with low SCR predictions. In addition, exploiting nonlinear effects through the use of Gaussian kernels together with the incorporation of relevant markers seems to be a promising alternative to the standard approach. The inclusion of gene set results into prediction models deserves further research.
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Affiliation(s)
- Rostam Abdollahi-Arpanahi
- Department of Animal Sciences, University of Florida, Gainesville 32611; Department of Animal and Poultry Science, University of Tehran, Pakdasht, Iran 3391653755
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville 32611; University of Florida Genetics Institute, Gainesville 32611.
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18
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Dadousis C, Pegolo S, Rosa GJM, Bittante G, Cecchinato A. Genome-wide association and pathway-based analysis using latent variables related to milk protein composition and cheesemaking traits in dairy cattle. J Dairy Sci 2017; 100:9085-9102. [PMID: 28843680 DOI: 10.3168/jds.2017-13219] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/16/2017] [Indexed: 12/19/2022]
Abstract
The aim of this study was to perform genome-wide associations (GWAS) and gene-set enrichment analyses with protein composition and cheesemaking-related latent variables (factors; F) in a cohort of 1,011 Italian Brown Swiss cows. Factor analysis was applied to identify latent structures of 26 phenotypes related to bovine milk quantity and quality, protein fractions [αS1-, αS2-, β-, and κ-casein (CN), β-lactoglobulin, and α-lactalbumin (α-LA)], coagulation and curd firming at time t (CFt) measures, and cheese properties [cheese yield (%CY) and nutrients recovery in the curd] of individual cows. Ten orthogonal F were extracted, explaining 74% of the original variability. Factor 1%CY underlined the %CY characteristics, F2CFt was related to the CFt process parameters, F3Yield was considered as descriptor of milk and solids yield, whereas F4Cheese N underscored the presence of nitrogenous compounds (N) into the cheese. Four more F were related to the milk caseins (F5αS1-β-CN, F7β-κ-CN, F8αS2-CN, and F9αS1-CN-Ph) and 1 F was linked to the whey protein (F10α-LA); 1 F underlined the udder health status (F6Udder health). All cows were genotyped with the Illumina BovineSNP50 Bead Chip v.2 (Illumina Inc., San Diego, CA). Single marker regression GWAS were fitted. Gene-set enrichment analysis was run on GWAS results, using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases, to reveal ontologies or pathways associated with the F. All F but F3Yield showed significance in GWAS. Signals in 10 Bos taurus autosomes (BTA) were detected. High peaks on BTA6 (∼87 Mbp) were found for F6β-κ-CN, F5αS1-β-CN, and at the tail of BTA11 (∼104 Mbp) for F4Cheese N. Gene-set enrichment analyses showed significant results (false discovery rate at 5%) for F8αS2-CN, F1%CY, F4Cheese N, and F10α-LA. For F8αS2-CN, 33 Gene Ontology terms and 3 Kyoto Encyclopedia of Genes and Genomes categories were enriched, including terms related to ion transport and homeostasis, neuron function or part, and GnRH signaling pathway. Our results support the feasibility of factor analysis as a dimension reduction technique in genomic studies and evidenced a potential key role of αS2-CN in milk quality and composition.
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Affiliation(s)
- Christos Dadousis
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Guilherme J M Rosa
- Department of Animal Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison 53706
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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19
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Casas E, Kehrli ME. A Review of Selected Genes with Known Effects on Performance and Health of Cattle. Front Vet Sci 2016; 3:113. [PMID: 28018909 PMCID: PMC5156656 DOI: 10.3389/fvets.2016.00113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/28/2016] [Indexed: 11/21/2022] Open
Abstract
There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.
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Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, USDA, ARS, Ames, IA, USA
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20
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Dadousis C, Pegolo S, Rosa GJM, Gianola D, Bittante G, Cecchinato A. Pathway-based genome-wide association analysis of milk coagulation properties, curd firmness, cheese yield, and curd nutrient recovery in dairy cattle. J Dairy Sci 2016; 100:1223-1231. [PMID: 27988128 DOI: 10.3168/jds.2016-11587] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/20/2016] [Indexed: 01/02/2023]
Abstract
It is becoming common to complement genome-wide association studies (GWAS) with gene-set enrichment analysis to deepen the understanding of the biological pathways affecting quantitative traits. Our objective was to conduct a gene ontology and pathway-based analysis to identify possible biological mechanisms involved in the regulation of bovine milk technological traits: coagulation properties, curd firmness modeling, individual cheese yield (CY), and milk nutrient recovery into the curd (REC) or whey loss traits. Results from 2 previous GWAS studies using 1,011 cows genotyped for 50k single nucleotide polymorphisms were used. Overall, the phenotypes analyzed consisted of 3 traditional milk coagulation property measures [RCT: rennet coagulation time defined as the time (min) from addition of enzyme to the beginning of coagulation; k20: the interval (min) from RCT to the time at which a curd firmness of 20 mm is attained; a30: a measure of the extent of curd firmness (mm) 30 min after coagulant addition], 6 curd firmness modeling traits [RCTeq: RCT estimated through the CF equation (min); CFP: potential asymptotic curd firmness (mm); kCF: curd-firming rate constant (% × min-1); kSR: syneresis rate constant (% × min-1); CFmax: maximum curd firmness (mm); and tmax: time to CFmax (min)], 3 individual CY-related traits expressing the weight of fresh curd (%CYCURD), curd solids (%CYSOLIDS), and curd moisture (%CYWATER) as a percentage of weight of milk processed and 4 milk nutrient and energy recoveries in the curd (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk), milk pH, and protein percentage. Each trait was analyzed separately. In total, 13,269 annotated genes were used in the analysis. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases were queried for enrichment analyses. Overall, 21 Gene Ontology and 17 Kyoto Encyclopedia of Genes and Genomes categories were significantly associated (false discovery rate at 5%) with 7 traits (RCT, RCTeq, kCF, %CYSOLIDS, RECFAT, RECSOLIDS, and RECENERGY), with some being in common between traits. The significantly enriched categories included calcium signaling pathway, salivary secretion, metabolic pathways, carbohydrate digestion and absorption, the tight junction and the phosphatidylinositol pathways, as well as pathways related to the bovine mammary gland health status, and contained a total of 150 genes spanning all chromosomes but 9, 20, and 27. This study provided new insights into the regulation of bovine milk coagulation and cheese ability that were not captured by the GWAS.
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Affiliation(s)
- C Dadousis
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - S Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - G J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison 53706; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison 53706
| | - D Gianola
- Department of Animal Sciences, University of Wisconsin, Madison 53706; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison 53706
| | - G Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - A Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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21
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Han Y, Peñagaricano F. Unravelling the genomic architecture of bull fertility in Holstein cattle. BMC Genet 2016; 17:143. [PMID: 27842509 PMCID: PMC5109745 DOI: 10.1186/s12863-016-0454-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fertility is considered an important economic trait in dairy cattle. Most studies have investigated cow fertility while bull fertility has received much less consideration. The main objective of this study was to perform a comprehensive genomic analysis in order to unravel the genomic architecture underlying sire fertility in Holstein dairy cattle. The analysis included the application of alternative genome-wide association mapping approaches and the subsequent use of diverse gene set enrichment tools. RESULTS The association analyses identified at least eight genomic regions strongly associated with bull fertility. Most of these regions harbor genes, such as KAT8, CKB, TDRD9 and IGF1R, with functions related to sperm biology, including sperm development, motility and sperm-egg interaction. Moreover, the gene set analyses revealed many significant functional terms, including fertilization, sperm motility, calcium channel regulation, and SNARE proteins. Most of these terms are directly implicated in sperm physiology and male fertility. CONCLUSIONS This study contributes to the identification of genetic variants and biological processes underlying sire fertility. These findings can provide opportunities for improving bull fertility via marker-assisted selection.
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Affiliation(s)
- Yi Han
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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22
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MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken. G3-GENES GENOMES GENETICS 2016; 6:2447-53. [PMID: 27261003 PMCID: PMC4978898 DOI: 10.1534/g3.116.031096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO), and more recently by Medical Subject Headings (MeSH). Here, we report a suite of MeSH packages for chicken in Bioconductor, and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published datasets that were employed represent (i) differentially expressed genes, and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports the findings obtained from GO analysis, but also that MeSH is able to further enrich the representation of biological knowledge and often provide more interpretable results. Based on the hierarchical structures of MeSH and GO, we computed semantic similarities among vocabularies, as well as semantic similarities among selected genes. These yielded the similarity levels between significant functional terms, and the annotation of each gene yielded the measures of gene similarity. Our findings show the benefits of using MeSH as an alternative choice of annotation in order to draw biological inferences from a list of genes of interest. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the understanding of the genetic basis of complex traits.
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23
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Cardona SJC, Cadavid HC, Corrales JD, Munilla S, Cantet RJC, Rogberg-Muñoz A. Longitudinal data analysis of polymorphisms in the κ-casein and β-lactoglobulin genes shows differential effects along the trajectory of the lactation curve in tropical dairy goats. J Dairy Sci 2016; 99:7299-7307. [PMID: 27423955 DOI: 10.3168/jds.2016-10954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/07/2016] [Indexed: 01/19/2023]
Abstract
The κ-casein (CSN-3) and β-lactoglobulin (BLG) genes are extensively polymorphic in ruminants. Several association studies have estimated the effects of polymorphisms in these genes on milk yield, milk composition, and cheese-manufacturing properties. Usually, these results are based on production integrated over the lactation curve or on cross-sectional studies at specific days in milk (DIM). However, as differential expression of milk protein genes occurs over lactation, the effect of the polymorphisms may change over time. In this study, we fitted a mixed-effects regression model to test-day records of milk yield and milk quality traits (fat, protein, and total solids yields) from Colombian tropical dairy goats. We used the well-characterized A/B polymorphisms in the CSN-3 and BLG genes. We argued that this approach provided more efficient estimators than cross-sectional designs, given the same number and pattern of observations, and allowed exclusion of between-subject variation from model error. The BLG genotype AA showed a greater performance than the BB genotype for all traits along the whole lactation curve, whereas the heterozygote showed an intermediate performance. We observed no such constant pattern for the CSN-3 gene between the AA homozygote and the heterozygote (the BB genotype was absent from the sample). The differences among the genotypic effects of the BLG and the CSN-3 polymorphisms were statistically significant during peak and mid lactation (around 40-160 DIM) for the BLG gene and only for mid lactation (80-145 DIM) for the CSN-3 gene. We also estimated the additive and dominant effects of the BLG locus. The locus showed a statistically significant additive behavior along the whole lactation trajectory for all quality traits, whereas for milk yield the effect was not significant at later stages. In turn, we detected a statistically significant dominance effect only for fat yield in the early and peak stages of lactation (at about 1-45 DIM). The longitudinal analysis of test-day records allowed us to estimate the differential effects of polymorphisms along the lactation curve, pointing toward stages that could be affected by the gene.
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Affiliation(s)
- Samir Julián Calvo Cardona
- Grupo de Investigación en Genética, Mejoramiento y Modelación Animal (GaMMA), Facultad Ciencias Agrarias, Universidad de Antioquia, Calle 67, no 53-108, AA 1226, Medellín, Colombia 005043
| | - Henry Cardona Cadavid
- Grupo de Investigación en Genética, Mejoramiento y Modelación Animal (GaMMA), Facultad Ciencias Agrarias, Universidad de Antioquia, Calle 67, no 53-108, AA 1226, Medellín, Colombia 005043
| | - Juan David Corrales
- Facultad Ciencias Agropecuarias, Universidad de La Salle, Bogotá, Colombia 110231; Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Munilla
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
| | - Rodolfo J C Cantet
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina; Unidad Ejecutora de Investigaciones en Producción Animal (INPA), Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Cdad. Atma. Buenos Aires (1417), Argentina
| | - Andrés Rogberg-Muñoz
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina; IGEVET-Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP - CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, La Plata, Argentina 1900.
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24
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Abdalla EA, Peñagaricano F, Byrem TM, Weigel KA, Rosa GJM. Genome-wide association mapping and pathway analysis of leukosis incidence in a US Holstein cattle population. Anim Genet 2016; 47:395-407. [PMID: 27090879 DOI: 10.1111/age.12438] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 01/24/2023]
Abstract
Bovine leukosis virus is an oncogenic virus that infects B cells, causing bovine leukosis disease. This disease is known to have a negative impact on dairy cattle production and, because no treatment or vaccine is available, finding a possible genetic solution is important. Our objective was to perform a comprehensive genetic analysis of leukosis incidence in dairy cattle. Data on leukosis occurrence, pedigree and molecular information were combined into multitrait GBLUP models with milk yield (MY) and somatic cell score (SCS) to estimate genetic parameters and to perform whole-genome scans and pathway analysis. Leukosis data were available for 11 554 Holsteins daughters of 3002 sires from 112 herds in 16 US states. Genotypes from a 60K SNP panel were available for 961 of those bulls as well as for 2039 additional bulls. Heritability for leukosis incidence was estimated at about 8%, and the genetic correlations of leukosis disease incidence with MY and SCS were moderate at 0.18 and 0.20 respectively. The genome-wide scan indicated that leukosis is a complex trait, possibly modulated by many genes. The gene set analysis identified many functional terms that showed significant enrichment of genes associated with leukosis. Many of these terms, such as G-Protein Coupled Receptor Signaling Pathway, Regulation of Nucleotide Metabolic Process and different calcium-related processes, are known to be related to retrovirus infection. Overall, our findings contribute to a better understanding of the genetic architecture of this complex disease. The functional categories associated with leukosis may be useful in future studies on fine mapping of genes and development of dairy cattle breeding strategies.
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Affiliation(s)
- E A Abdalla
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Animal Science, University of Benghazi, Benghazi, 21861, Libya
| | - F Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - T M Byrem
- Antel BioSystems, Inc., Lansing, MI, 48910, USA
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - G J M Rosa
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Bertelsen HP, Gregersen VR, Poulsen N, Nielsen RO, Das A, Madsen LB, Buitenhuis AJ, Holm LE, Panitz F, Larsen LB, Bendixen C. Detection of genetic variation affecting milk coagulation properties in Danish Holstein dairy cattle by analyses of pooled whole-genome sequences from phenotypically extreme samples (pool-seq)1. J Anim Sci 2016; 94:1365-76. [DOI: 10.2527/jas.2015-9884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- H. P. Bertelsen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - V. R. Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - N. Poulsen
- Department of Food Science, Aarhus University, Tjele, Denmark
| | - R. O. Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - A. Das
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - L. B. Madsen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - A. J. Buitenhuis
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - L.-E. Holm
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - F. Panitz
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - L. B. Larsen
- Department of Food Science, Aarhus University, Tjele, Denmark
| | - C. Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
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26
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Gregersen V, Gustavsson F, Glantz M, Christensen O, Stålhammar H, Andrén A, Lindmark-Månsson H, Poulsen N, Larsen L, Paulsson M, Bendixen C. Bovine chromosomal regions affecting rheological traits in rennet-induced skim milk gels. J Dairy Sci 2015; 98:1261-72. [DOI: 10.3168/jds.2014-8136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 11/04/2014] [Indexed: 11/19/2022]
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27
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Glantz M, Gustavsson F, Bertelsen HP, Stålhammar H, Lindmark-Månsson H, Paulsson M, Bendixen C, Gregersen VR. Bovine chromosomal regions affecting rheological traits in acid-induced skim milk gels. J Dairy Sci 2014; 98:1273-85. [PMID: 25529417 DOI: 10.3168/jds.2014-8137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 11/15/2014] [Indexed: 11/19/2022]
Abstract
The production of fermented milk products has increased worldwide during the last decade and is expected to continue to increase during the coming decade. The quality of these products may be optimized through breeding practices; however, the relations between cow genetics and technological properties of acid milk gels are not fully known. Therefore, the aim of this study was to identify chromosomal regions affecting acid-induced coagulation properties and possible candidate genes. Skim milk samples from 377 Swedish Red cows were rheologically analyzed for acid-induced coagulation properties using low-amplitude oscillation measurements. The resulting traits, including gel strength, coagulation time, and yield stress, were used to conduct a genome-wide association study. Single nucleotide polymorphisms (SNP) were identified using the BovineHD SNPChip (Illumina Inc., San Diego, CA), resulting in almost 621,000 segregating markers. The genome was scanned for putative quantitative trait loci (QTL) regions, haplotypes based on highly associated SNP were inferred, and the additive genetic effects of haplotypes within each QTL region were analyzed using mixed models. A total of 8 genomic regions were identified, with large effects of the significant haplotype explaining between 4.8 and 9.8% of the phenotypic variance of the studied traits. One major QTL was identified to overlap between gel strength and yield stress, the QTL identified with the most significant SNP closest to the gene coding for κ-casein (CSN3). In addition, a chromosome-wide significant region affecting yield stress on BTA 11 was identified to be colocated with PAEP, coding for β-lactoglobulin. Furthermore, the coagulation properties of the genetic variants within the 2 genes were compared with the coagulation properties identified by the patterns of the haplotypes within the regions, and it was discovered that the haplotypes were more diverse and in one case slightly better at explaining the phenotypic variance. Besides these significant QTL comprising the 2 milk proteins, 3 additional genes are proposed as possible candidates, namely RAB22A, CDH13, and STAT1, and all have previously been found to be expressed in the mammary gland. To our knowledge, this is the first attempt to map QTL regions for acid-induced coagulation properties.
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Affiliation(s)
- M Glantz
- Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - F Gustavsson
- Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - H P Bertelsen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Blichers Allé 20, PO Box 50, DK-8830 Tjele, Denmark
| | - H Stålhammar
- VikingGenetics, PO Box 64, SE-532 21 Skara, Sweden
| | - H Lindmark-Månsson
- Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-221 00 Lund, Sweden; Lantbrukarnas Riksförbund Dairy Sweden, Ideon Science Park, SE-223 70 Lund, Sweden
| | - M Paulsson
- Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - C Bendixen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Blichers Allé 20, PO Box 50, DK-8830 Tjele, Denmark
| | - V R Gregersen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Blichers Allé 20, PO Box 50, DK-8830 Tjele, Denmark.
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