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Leite JAS, Montoya CA, Maes E, Hefer C, Cruz RAPA, Roy NC, McNabb WC. Effect of Heat Treatment on Protein Self-Digestion in Ruminants' Milk. Foods 2023; 12:3511. [PMID: 37761220 PMCID: PMC10529618 DOI: 10.3390/foods12183511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
This study investigated whether heat treatments (raw, 63 °C for 30 min, and 85 °C for 5 min) affect protein hydrolysis by endogenous enzymes in the milk of ruminants (bovine, ovine, and caprine) using a self-digestion model. Self-digestion consisted of the incubation for six hours at 37 °C of the ruminants' milk. Free amino group concentration was measured by the o-phthaldialdehyde method, and peptide sequences were identified by chromatography-mass spectrometry. Results showed that heat treatments prior to self-digestion decreased the free NH2 by 59% in bovine milk heated at 85 °C/5 min, and by 44 and 53% in caprine milk heated at 63 °C/30 min and 85 °C/5 min, respectively. However, after self-digestion, only new free amino groups were observed for the raw and heated at 63 °C/30 min milk. β-Casein was the most cleaved protein in the raw and heated at 63 °C/30 min bovine milk. A similar trend was observed in raw ovine and caprine milk. Self-digestion increased 6.8-fold the potential antithrombin peptides in the bovine milk heated at 63 °C/30 min. Enhancing bioactive peptide abundance through self-digestion has potential applications in the industry for functional products. Overall, heat treatments affected the free amino groups according to the species and heat treatment applied, which was reflected in the varying degrees of cleaved peptide bonds and peptides released during self-digestion.
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Affiliation(s)
- Juliana A. S. Leite
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
| | - Carlos A. Montoya
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- Smart Foods & Bioproducts Innovation Centre of Excellence, AgResearch Limited, Palmerston North 4474, New Zealand
| | - Evelyne Maes
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- Proteins & Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Charles Hefer
- Data Science South Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand;
| | - Raul A. P. A. Cruz
- School of Food & Advanced Technology, Massey University, Palmerston North 4442, New Zealand;
| | - Nicole C. Roy
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
- Department of Nutrition, University of Otago, Dunedin 9016, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
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Schoof M, O'Callaghan M, Hefer C, Glare TR, Paulson AR, Hurst MRH. Lysis Cassette-Mediated Exoprotein Release in Yersinia entomophaga Is Controlled by a PhoB-Like Regulator. Microbiol Spectr 2023:e0036423. [PMID: 36951587 PMCID: PMC10101115 DOI: 10.1128/spectrum.00364-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Secretion of exoproteins is a key component of bacterial virulence, and is tightly regulated in response to environmental stimuli and host-dependent signals. The entomopathogenic bacterium Yersinia entomophaga MH96 produces a wide range of exoproteins including its main virulence factor, the 2.46 MDa insecticidal Yen-Tc toxin complex. Previously, a high-throughput transposon-based screening assay identified the region of exoprotein release (YeRER) as essential to exoprotein release in MH96. This study defines the role of the YeRER associated ambiguous holin/endolysin-based lysis cluster (ALC) and the novel RoeA regulator in the regulation and release of exoproteins in MH96. A mutation in the ambiguous lysis cassette (ALC) region abolished exoprotein release and caused cell elongation, a phenotype able to be restored through trans-complementation with an intact ALC region. Endogenous ALC did not impact cell growth of the wild type, while artificial expression of an optimized ALC caused cell lysis. Using HolA-sfGFP and Rz1-sfGFP reporters, Rz1 expression was observed in all cells while HolA expression was limited to a small proportion of cells, which increased over time. Transcriptomic assessments found expression of the genes encoding the prominent exoproteins, including the Yen-Tc, was reduced in the roeA mutant and identified a 220 ncRNA of the YeRER intergenic region that, when trans complemented in the wildtype, abolished exoprotein release. A model for Y. entomophaga mediated exoprotein regulation and release is proposed. IMPORTANCE While theoretical models exist, there is not yet any empirical data that links ALC phage-like lysis cassettes with the release of large macro-molecular toxin complexes, such as Yen-Tc in Gram-negative bacteria. In this study, we demonstrate that the novel Y. entomophaga RoeA activates the production of exoproteins (including Yen-Tc) and the ALC at the transcriptional level. The translation of the ALC holin is confined to a subpopulation of cells that then lyse over time, indicative of a complex hierarchical regulatory network. The presence of an orthologous RoeA and a HolA like holin 5' of an eCIS Afp element in Pseudomonas chlororaphis, combined with the presented data, suggests a shared mechanism is required for the release of some large macromolecular protein assemblies, such as the Yen-Tc, and further supports classification of phage-like lysis clusters as type 10 secretion systems.
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Affiliation(s)
- Marion Schoof
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Maureen O'Callaghan
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Charles Hefer
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Travis R Glare
- Wine and Molecular Biosciences Dept, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Amber R Paulson
- British Columbia Ministry of Environment and Climate Change Strategy, Victoria, British Columbia, Canada
| | - Mark R H Hurst
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
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Maes E, Bell F, Hefer C, Thomas A, Harland D, Noble A, Plowman J, Clerens S, Grosvenor A. Insights in Human Hair Curvature by Proteome Analysis of Two Distinct Hair Shapes. J Cosmet Sci 2021; 72:249-267. [PMID: 35361314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Scalp hair is a universal human characteristic, and a wide range of hair shape and color variations exists. Although differences in human scalp hair shape are visually apparent, the underpinning molecular insights are yet to be fully explored. This work reports the determination of differences at the protein level between two distinct groups of hair shape: very straight samples versus very curly hair samples. An in-depth highresolution liquid-chromatography mass spectrometry proteome analysis study was performed on hair samples from 50 individuals (pooled in 10 × 5 samples) with very curly hair and 50 subjects with very straight hair (pooled in 10 × 5 samples) to decipher differences between the two experimental groups at the protein level. Our results demonstrate that a distinction between the two experimental groups (very straight vs. very curly) can be made based on their overall protein profiles in a multivariate analysis approach. Further investigation of the protein expression levels between these two groups pinpointed 13 unique proteins which were found to be significantly different between the two groups, with an adjusted p-value < 0.05 and a fold change of more than two. Although differences between the very curly and the very straight hair sample groups could be identified, linkage between population differences and curl phenotype is currently unknown and requires further investigation.
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Affiliation(s)
- Evelyne Maes
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Fraser Bell
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Charles Hefer
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Ancy Thomas
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Duane Harland
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Alasdair Noble
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Jeffrey Plowman
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Stefan Clerens
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Anita Grosvenor
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
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Plowman JE, Harland DP, Campos AM, Rocha e Silva S, Thomas A, Vernon JA, van Koten C, Hefer C, Clerens S, de Almeida AM. The wool proteome and fibre characteristics of three distinct genetic ovine breeds from Portugal. J Proteomics 2020; 225:103853. [DOI: 10.1016/j.jprot.2020.103853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
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Unda F, Kim H, Hefer C, Ralph J, Mansfield SD. Altering carbon allocation in hybrid poplar (Populus alba × grandidentata) impacts cell wall growth and development. Plant Biotechnol J 2017; 15:865-878. [PMID: 27998032 PMCID: PMC5466441 DOI: 10.1111/pbi.12682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 05/20/2023]
Abstract
Galactinol synthase is a pivotal enzyme involved in the synthesis of the raffinose family of oligosaccharides (RFOs) that function as transport carbohydrates in the phloem, as storage compounds in sink tissues and as soluble metabolites that combat both abiotic and biotic stress in several plant species. Hybrid poplar (Populus alba × grandidentata) overexpressing the Arabidopsis thaliana GolS3 (AtGolS3) gene showed clear effects on development; the extreme overexpressing lines were stunted and had cell wall traits characteristic of tension wood, whereas lines with only moderate up-regulation grew normally and had moderately altered secondary cell wall composition and ultrastructure. Stem cross-sections of the developing xylem revealed a significant increase in the number of vessels, as well as the clear presence of a G-layer in the fibres. Furthermore, AtGolS3-OE lines possessed higher cellulose and lower lignin contents, an increase in cellulose crystallinity, and significantly altered hemicellulose-derived carbohydrates, notably manifested by their mannose and xylose contents. In addition, the transgenic plants displayed elevated xylem starch content. Transcriptome interrogation of the transgenic plants showed a significant up-regulation of genes involved in the synthesis of myo-inositol, along with genes involved in sucrose degradation. The results suggest that the overexpression of GolS and its product galactinol may serve as a molecular signal that initiates metabolic changes, culminating in a change in cell wall development and potentially the formation of tension wood.
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Affiliation(s)
- Faride Unda
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCCanada
| | - Hoon Kim
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
- Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Charles Hefer
- Biotechnology PlatformAgricultural Research CouncilPretoriaSouth Africa
| | - John Ralph
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
- Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCCanada
- Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
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Wang MD, Dzama K, Rees J, Hefer C, Muchadeyi FC. P3019 Screening and characterization of copy number cariation in South African nguni cattle using next-generation sequencing data. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement461x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
BACKGROUND Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and intra- specific variation of terpenes is common in eucalypts. RESULTS The genome sequences of Eucalyptus grandis and E. globulus were mined for terpene synthase genes (TPS) and compared to other plant species. We investigated the relative expression of TPS in seven plant tissues and functionally characterized five TPS genes from E. grandis. Compared to other sequenced plant genomes, Eucalyptus grandis has the largest number of putative functional TPS genes of any sequenced plant. We discovered 113 and 106 putative functional TPS genes in E. grandis and E. globulus, respectively. All but one TPS from E. grandis were expressed in at least one of seven plant tissues examined. Genomic clusters of up to 20 genes were identified. Many TPS are expressed in tissues other than leaves which invites a re-evaluation of the function of terpenes in Eucalyptus. CONCLUSIONS Our data indicate that terpenes in Eucalyptus may play a wider role in biotic and abiotic interactions than previously thought. Tissue specific expression is common and the possibility of stress induction needs further investigation. Phylogenetic comparison of the two investigated Eucalyptus species gives insight about recent evolution of different clades within the TPS gene family. While the majority of TPS genes occur in orthologous pairs some clades show evidence of recent gene duplication, as well as loss of function.
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Affiliation(s)
- Carsten Külheim
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
| | - Amanda Padovan
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
| | - Charles Hefer
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Sandra T Krause
- Institut für Pharmazie, Martin-Luther Universität Halle-Wittenberg, 06120, Halle, (Saale), Germany.
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Private Bag X20, Pretoria, 0028, South Africa.
| | - Jörg Degenhardt
- Institut für Pharmazie, Martin-Luther Universität Halle-Wittenberg, 06120, Halle, (Saale), Germany.
| | - William J Foley
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
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Carocha V, Soler M, Hefer C, Cassan-Wang H, Fevereiro P, Myburg AA, Paiva JAP, Grima-Pettenati J. Genome-wide analysis of the lignin toolbox of Eucalyptus grandis. New Phytol 2015; 206:1297-313. [PMID: 25684249 DOI: 10.1111/nph.13313] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/19/2014] [Indexed: 05/18/2023]
Abstract
Lignin, a major component of secondary cell walls, hinders the optimal processing of wood for industrial uses. The recent availability of the Eucalyptus grandis genome sequence allows comprehensive analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway and identification of those mainly involved in xylem developmental lignification. We performed genome-wide identification of putative members of the lignin gene families, followed by comparative phylogenetic studies focusing on bona fide clades inferred from genes functionally characterized in other species. RNA-seq and microfluid real-time quantitative PCR (RT-qPCR) expression data were used to investigate the developmental and environmental responsive expression patterns of the genes. The phylogenetic analysis revealed that 38 E. grandis genes are located in bona fide lignification clades. Four multigene families (shikimate O-hydroxycinnamoyltransferase (HCT), p-coumarate 3-hydroxylase (C3H), caffeate/5-hydroxyferulate O-methyltransferase (COMT) and phenylalanine ammonia-lyase (PAL)) are expanded by tandem gene duplication compared with other plant species. Seventeen of the 38 genes exhibited strong, preferential expression in highly lignified tissues, probably representing the E. grandis core lignification toolbox. The identification of major genes involved in lignin biosynthesis in E. grandis, the most widely planted hardwood crop world-wide, provides the foundation for the development of biotechnology approaches to develop tree varieties with enhanced processing qualities.
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Affiliation(s)
- Victor Carocha
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France
- Instituto de Tecnologia de Química Biológica (ITQB), Biotecnologia de Células Vegetais, Av. da República, 2781-157, Oeiras, Portugal
- Instituto de Investigação Científica e Tropical (IICT/MNE), Palácio Burnay, Rua da Junqueira, 30, 1349-007, Lisboa, Portugal
| | - Marçal Soler
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Charles Hefer
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, South Africa
| | - Hua Cassan-Wang
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Pedro Fevereiro
- Instituto de Tecnologia de Química Biológica (ITQB), Biotecnologia de Células Vegetais, Av. da República, 2781-157, Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Campo Grande, 1749-016, Lisboa, Portugal
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Jorge A P Paiva
- Instituto de Investigação Científica e Tropical (IICT/MNE), Palácio Burnay, Rua da Junqueira, 30, 1349-007, Lisboa, Portugal
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France
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Van Schalkwyk A, Wenzl P, Smit S, Lopez-Cobollo R, Kilian A, Bishop G, Hefer C, Berger DK. Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines. Theor Appl Genet 2012; 124:947-56. [PMID: 22159755 PMCID: PMC3284683 DOI: 10.1007/s00122-011-1759-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 11/24/2011] [Indexed: 05/11/2023]
Abstract
Marker-trait association studies in tomato have progressed rapidly due to the availability of several populations developed between wild species and domesticated tomato. However, in the absence of whole genome sequences for each wild species, molecular marker methods for whole genome comparisons and fine mapping are required. We describe the development and validation of a diversity arrays technology (DArT) platform for tomato using an introgression line (IL) population consisting of wild Solanum pennellii introgressed into Solanum lycopersicum (cv. M82). A tomato diversity array consisting of 6,912 clones from domesticated tomato and twelve wild tomato/Solanaceous species was constructed. We successfully bin-mapped 990 polymorphic DArT markers together with 108 RFLP markers across the IL population, increasing the number of markers available for each S. pennellii introgression by tenfold on average. A subset of DArT markers from ILs previously associated with increased levels of lycopene and carotene were sequenced, and 44% matched protein coding genes. The bin-map position and order of sequenced DArT markers correlated well with their physical position on scaffolds of the draft tomato genome sequence (SL2.40). The utility of sequenced DArT markers was illustrated by converting several markers in both the S. pennellii and S. lycopersicum phases to cleaved amplified polymorphic sequence (CAPS) markers. Genotype scores from the CAPS markers confirmed the genotype scores from the DArT hybridizations used to construct the bin map. The tomato diversity array provides additional "sequence-characterized" markers for fine mapping of QTLs in S. pennellii ILs and wild tomato species.
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Affiliation(s)
- Antoinette Van Schalkwyk
- Present Address: Inqaba Biotechnical Industries (Pty) Ltd, P.O. Box 14356, Hatfield, 0028 South Africa
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | - Peter Wenzl
- Diversity Arrays Technology P/L, GPO Box 7141, Yarralumla, ACT 2600 Australia
- Present Address: Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, DF Mexico
| | - Sandra Smit
- Applied Bioinformatics, Plant Research International and Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Andrzej Kilian
- Diversity Arrays Technology P/L, GPO Box 7141, Yarralumla, ACT 2600 Australia
| | | | - Charles Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | - Dave K. Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
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Hefer C, Mizrachi E, Joubert F, Myburg A. The Eucalyptus genome integrative explorer (EucGenIE): a resource for Eucalyptusgenomics and transcriptomics. BMC Proc 2011. [PMCID: PMC3239921 DOI: 10.1186/1753-6561-5-s7-o49] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Myburg A, Grattapaglia D, Tuskan G, Jenkins J, Schmutz J, Mizrachi E, Hefer C, Pappas G, Sterck L, Van De Peer Y, Hayes R, Rokhsar D. The Eucalyptus grandisGenome Project: Genome and transcriptome resources for comparative analysis of woody plant biology. BMC Proc 2011. [PMCID: PMC3239864 DOI: 10.1186/1753-6561-5-s7-i20] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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