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Hu L, Tate JA, Gardiner SE, MacKay M. Ploidy variation in Rhododendron subsection Maddenia and its implications for conservation. AoB Plants 2023; 15:plad016. [PMID: 37197711 PMCID: PMC10184449 DOI: 10.1093/aobpla/plad016] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Polyploidy, which is common in plants, can confound taxon recognition and hence conservation assessments. In the taxonomically complex genus Rhododendron, 25 % of the over 1,300 taxa are considered under threat and 27 % Near Threatened or Data Deficient, with their taxonomy needing to be resolved urgently. Although ploidy levels of Rhododendron taxa range from diploid (2x) to dodecaploid (12x) according to previous reports, the extent of polyploidy across the genus has not been examined. We first summarized the taxonomic distribution of polyploids in the genus based on the literature. Then as a case study, we estimated ploidy levels of 47 taxa in subsection Maddenia (subgenus Rhododendron, section Rhododendron) using flow cytometry, together with verification of meiotic chromosome counts for representative taxa. The summary of reported ploidy in Rhododendron indicates that polyploidy is most common in subgenera Pentanthera and Rhododendron. In subsection Maddenia, all examined taxa are diploids except for the R. maddenii complex that shows a high ploidy variation (2-8x, 12x). We investigated ploidy level of 12 taxa in subsection Maddenia for the first time, and estimated genome sizes of two Rhododendron species. Knowledge of ploidy levels will inform phylogenetic analysis of unresolved species complexes. Overall, our study of subsection Maddenia provides a model for examining multiple issues including taxonomic complexity, ploidy variation and geographic distribution in relation to biodiversity conservation.
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Affiliation(s)
- Ling Hu
- Corresponding author’s e-mail address:
| | - Jennifer A Tate
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant and Food Research Limited, Fitzherbert Science Centre, Palmerston North 4472, New Zealand
| | - Marion MacKay
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
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Pasqualetto G, Palmieri L, Martens S, Bus VGM, Chagné D, Wiedow C, Malnoy MA, Gardiner SE. Molecular characterization of intergeneric hybrids between Malus and Pyrus. Hortic Res 2022; 10:uhac239. [PMID: 36643755 PMCID: PMC9832871 DOI: 10.1093/hr/uhac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Apple (Malus) and pear (Pyrus) are economically important fruit crops well known for their unique textures, flavours, and nutritional qualities. Both genera are characterised by a distinct pattern of secondary metabolites, which directly affect not only resistance to certain diseases, but also have significant impacts on the flavour and nutritional value of the fruit. The identical chromosome numbers, similar genome size, and their recent divergence date, together with DNA markers have shown that apple and pear genomes are highly co-linear. This study utilized comparative genomic approaches, including simple sequence repeats, high resolution single nucleotide polymorphism melting analysis, and single nucleotide polymorphism chip analysis to identify genetic differences among hybrids of Malus and Pyrus, and F2 offspring. This research has demonstrated and validated that these three marker types, along with metabolomics analysis are very powerful tools to detect and confirm hybridity of progeny derived from crosses between apple and pear in both cross directions. Furthermore, this work analysed the genus-specific metabolite patterns and the resistance to fire blight (Erwinia amylovora) in progeny. The findings of this work will enhance and accelerate the breeding of novel tree fruit crops that benefit producers and consumers, by enabling marker assisted selection of desired traits introgressed between pear and apple.
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Affiliation(s)
- Giulia Pasqualetto
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, UD 33100, Italy
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Luisa Palmieri
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Vincent G M Bus
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - David Chagné
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Claudia Wiedow
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Mickael A Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
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Tahir J, Crowhurst R, Deroles S, Hilario E, Deng C, Schaffer R, Le Lievre L, Brendolise C, Chagné D, Gardiner SE, Knaebel M, Catanach A, McCallum J, Datson P, Thomson S, Brownfield LR, Nardozza S, Pilkington SM. First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit. Front Genet 2022; 13:852161. [PMID: 35651931 PMCID: PMC9149279 DOI: 10.3389/fgene.2022.852161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Simon Deroles
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Robert Schaffer
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Liam Le Lievre
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Mareike Knaebel
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Andrew Catanach
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - John McCallum
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | | | - Simona Nardozza
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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Tahir J, Brendolise C, Hoyte S, Lucas M, Thomson S, Hoeata K, McKenzie C, Wotton A, Funnell K, Morgan E, Hedderley D, Chagné D, Bourke PM, McCallum J, Gardiner SE, Gea L. QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population. Pathogens 2020; 9:E967. [PMID: 33233616 PMCID: PMC7709049 DOI: 10.3390/pathogens9110967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/30/2022] Open
Abstract
Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields and resistance to the canker-causing dieback disease incited by Pseudomonas syringae pv. actinidiae (Psa) biovar 3. However, the genetic mechanism for resistance to Psa observed in polyploid kiwifruit is not yet known. In this study we performed detailed genetic analysis of a tetraploid Actinidia chinensis var. chinensis population derived from a cross between a female parent that exhibits weak tolerance to Psa and a highly Psa-resistant male parent. We used the capture-sequencing approach across the whole kiwifruit genome and generated the first ultra-dense maps in a tetraploid kiwifruit population. We located quantitative trait loci (QTLs) for Psa resistance on these maps. Our approach to QTL mapping is based on the use of identity-by-descent trait mapping, which allowed us to relate the contribution of specific alleles from their respective homologues in the male and female parent, to the control of Psa resistance in the progeny. We identified genes in the diploid reference genome whose function is suggested to be involved in plant defense, which underly the QTLs, including receptor-like kinases. Our study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.
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Affiliation(s)
- Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92-169, Auckland 1025, New Zealand; (J.T.); (C.B.)
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92-169, Auckland 1025, New Zealand; (J.T.); (C.B.)
| | - Stephen Hoyte
- The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand;
| | - Marielle Lucas
- Breeding Department, Enza Zaden, 1602 DB Enkhuizen, The Netherlands;
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln 7608, New Zealand;
| | - Kirsten Hoeata
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
| | - Catherine McKenzie
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
| | - Andrew Wotton
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Keith Funnell
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Ed Morgan
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Duncan Hedderley
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Peter M. Bourke
- Plant Sciences Group, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - John McCallum
- The New Zealand Institute for Plant and Food Research Limited, Lincoln 7608, New Zealand;
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Luis Gea
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
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Peil A, Hübert C, Wensing A, Horner M, Emeriewen OF, Richter K, Wöhner T, Chagné D, Orellana-Torrejon C, Saeed M, Troggio M, Stefani E, Gardiner SE, Hanke MV, Flachowsky H, Bus VG. Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation. BMC Plant Biol 2019; 19:532. [PMID: 31791233 PMCID: PMC6889339 DOI: 10.1186/s12870-019-2154-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 05/07/2019] [Accepted: 11/21/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the most common path of infection for fire blight, a severe bacterial disease on apple, is via host plant flowers, quantitative trait loci (QTLs) for fire blight resistance to date have exclusively been mapped following shoot inoculation. It is not known whether the same mechanism underlies flower and shoot resistance. RESULTS We report the detection of a fire blight resistance QTL following independent artificial inoculation of flowers and shoots on two F1 segregating populations derived from crossing resistant Malus ×robusta 5 (Mr5) with susceptible 'Idared' and 'Royal Gala' in experimental orchards in Germany and New Zealand, respectively. QTL mapping of phenotypic datasets from artificial flower inoculation of the 'Idared' × Mr5 population with Erwinia amylovora over several years, and of the 'Royal Gala' × Mr5 population in a single year, revealed a single major QTL controlling floral fire blight resistance on linkage group 3 (LG3) of Mr5. This QTL corresponds to the QTL on LG3 reported previously for the 'Idared' × Mr5 and an 'M9' × Mr5 population following shoot inoculation in the glasshouse. Interval mapping of phenotypic data from shoot inoculations of subsets from both flower resistance populations re-confirmed that the resistance QTL is in the same position on LG3 of Mr5 as that for flower inoculation. These results provide strong evidence that fire blight resistance in Mr5 is controlled by a major QTL on LG3, independently of the mode of infection, rootstock and environment. CONCLUSIONS This study demonstrates for the first time that resistance to fire blight caused by Erwinia amylovora is independent of the mode of inoculation at least in Malus ×robusta 5.
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Affiliation(s)
- Andreas Peil
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Christine Hübert
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Annette Wensing
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Mary Horner
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
| | - Ofere Francis Emeriewen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Klaus Richter
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Thomas Wöhner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - David Chagné
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | | | - Munazza Saeed
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Michela Troggio
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Susan E. Gardiner
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Magda-Viola Hanke
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Vincent G.M. Bus
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
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Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience 2019; 8:giz138. [PMID: 31816089 PMCID: PMC6901071 DOI: 10.1093/gigascience/giz138] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
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Affiliation(s)
- Gareth Linsmith
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stephane Rombauts
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Sara Montanari
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre,120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Jean-Marc Celton
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Philippe Guérif
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Chang Liu
- ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Rolf Lohaus
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Alessandro Cestaro
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Linda V Bakker
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Elio Schijlen
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Lespinasse
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Riccardo Velasco
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - David B Neale
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Roper street, Pretoria 0028, South Africa
| | - Michela Troggio
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
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7
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Cao K, Li Y, Deng CH, Gardiner SE, Zhu G, Fang W, Chen C, Wang X, Wang L. Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach. Plant Biotechnol J 2019; 17:1954-1970. [PMID: 30950186 PMCID: PMC6737019 DOI: 10.1111/pbi.13112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 08/29/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 05/21/2023]
Abstract
Crop evolution is a long-term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome-wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue-specific expression patterns indicated that the up-regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up-regulated selection genes were identified in leaves and seeds than in the other organs. Genome-wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large-scale characterization of key agronomic traits in this crop species.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR)Palmerston North Research CentrePalmerston NorthNew Zealand
| | - Gengrui Zhu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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8
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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. Hortic Res 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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9
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Chagné D, Vanderzande S, Kirk C, Profitt N, Weskett R, Gardiner SE, Peace CP, Volz RK, Bassil NV. Validation of SNP markers for fruit quality and disease resistance loci in apple ( Malus × domestica Borkh.) using the OpenArray® platform. Hortic Res 2019; 6:30. [PMID: 30854208 PMCID: PMC6395728 DOI: 10.1038/s41438-018-0114-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 05/22/2023]
Abstract
Genome mapping has promised much to tree fruit breeding during the last 10 years. Nevertheless, one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders, who must select genetically optimal parents and subsequently select genetically superior individuals among their progeny. To take this translational step, we designed the apple International RosBREED SNP Consortium OpenArray v1.0 (IRSCOA v1.0) assay using a set of 128 apple single nucleotide polymorphisms (SNPs) linked to fruit quality and pest and disease resistance trait loci. The Thermo Fisher Scientific OpenArray® technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman® assays. We validated the apple IRSCOA v1.0 multi-trait assay by screening 240 phenotyped individuals from the Plant & Food Research apple cultivar breeding programme. This set of individuals comprised commercial and heritage cultivars, elite selections, and families segregating for traits of importance to breeders. In total, 33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection (MAS) for the scab resistances Rvi2/Vh2, Rvi4/Vh4, Rvi6/Vf, fire blight resistance MR5/RLP1, powdery mildew resistance Pl2, fruit firmness, skin colour, flavour intensity, and acidity. The availability of this set of validated trait-associated SNP markers, which can be used individually on multiple genotyping platforms available to various apple breeding programmes or re-designed using the flanking sequences, represents a large translational genetics step from genomics to crop improvement of apple.
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Affiliation(s)
- David Chagné
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Chris Kirk
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Natalie Profitt
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Rosemary Weskett
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Richard K. Volz
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR USA
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10
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Tahir J, Hoyte S, Bassett H, Brendolise C, Chatterjee A, Templeton K, Deng C, Crowhurst R, Montefiori M, Morgan E, Wotton A, Funnell K, Wiedow C, Knaebel M, Hedderley D, Vanneste J, McCallum J, Hoeata K, Nath A, Chagné D, Gea L, Gardiner SE. Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit ( Actinidia chinensis). Hortic Res 2019; 6:101. [PMID: 31645956 PMCID: PMC6804790 DOI: 10.1038/s41438-019-0184-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 05/10/2023]
Abstract
Pseudomonas syringae pv. actinidiae (Psa) biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2×) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Psa resistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating resistance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible 'Hort16A' and a resistant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa resistance on Linkage Group (LG) 27 of 'Hort16A' revealing 16-19% phenotypic variance and candidate alleles for susceptibility and resistance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Resistance in the F1 population is improved by additive effects from 'Hort16A' and P1 QTLs providing evidence that divergent genetic pathways interact to combat the virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. The genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis populations. Transcriptome analysis of Psa-resistant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening for Psa resistance in greenhouse conditions.
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Affiliation(s)
- Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Stephen Hoyte
- The New Zealand Institute for Plant Food Research Limited, Hamilton, New Zealand
| | - Heather Bassett
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92–169, Auckland, 1025 New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92–169, Auckland, 1025 New Zealand
| | - Kerry Templeton
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92–169, Auckland, 1025 New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92–169, Auckland, 1025 New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92–169, Auckland, 1025 New Zealand
| | | | - Ed Morgan
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Andrew Wotton
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Keith Funnell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Claudia Wiedow
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Mareike Knaebel
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Duncan Hedderley
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Joel Vanneste
- The New Zealand Institute for Plant Food Research Limited, Hamilton, New Zealand
| | - John McCallum
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Kirsten Hoeata
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke, 3182 New Zealand
| | - Amardeep Nath
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke, 3182 New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
| | - Luis Gea
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke, 3182 New Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North, 4442 New Zealand
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11
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Pilkington SM, Crowhurst R, Hilario E, Nardozza S, Fraser L, Peng Y, Gunaseelan K, Simpson R, Tahir J, Deroles SC, Templeton K, Luo Z, Davy M, Cheng C, McNeilage M, Scaglione D, Liu Y, Zhang Q, Datson P, De Silva N, Gardiner SE, Bassett H, Chagné D, McCallum J, Dzierzon H, Deng C, Wang YY, Barron L, Manako K, Bowen J, Foster TM, Erridge ZA, Tiffin H, Waite CN, Davies KM, Grierson EP, Laing WA, Kirk R, Chen X, Wood M, Montefiori M, Brummell DA, Schwinn KE, Catanach A, Fullerton C, Li D, Meiyalaghan S, Nieuwenhuizen N, Read N, Prakash R, Hunter D, Zhang H, McKenzie M, Knäbel M, Harris A, Allan AC, Gleave A, Chen A, Janssen BJ, Plunkett B, Ampomah-Dwamena C, Voogd C, Leif D, Lafferty D, Souleyre EJF, Varkonyi-Gasic E, Gambi F, Hanley J, Yao JL, Cheung J, David KM, Warren B, Marsh K, Snowden KC, Lin-Wang K, Brian L, Martinez-Sanchez M, Wang M, Ileperuma N, Macnee N, Campin R, McAtee P, Drummond RSM, Espley RV, Ireland HS, Wu R, Atkinson RG, Karunairetnam S, Bulley S, Chunkath S, Hanley Z, Storey R, Thrimawithana AH, Thomson S, David C, Testolin R, Huang H, Hellens RP, Schaffer RJ. A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. BMC Genomics 2018; 19:257. [PMID: 29661190 PMCID: PMC5902842 DOI: 10.1186/s12864-018-4656-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Background Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Results A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models. Conclusions Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah M Pilkington
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Simona Nardozza
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lena Fraser
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Yongyan Peng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Robert Simpson
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Kerry Templeton
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marcus Davy
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Canhong Cheng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mark McNeilage
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Davide Scaglione
- IGA Technology Services, Parco Scientifico e Tecnologico, Udine, Italy
| | - Yifei Liu
- South China Botanic Gardens, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | - Paul Datson
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nihal De Silva
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | | | | | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - John McCallum
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Helge Dzierzon
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Yen-Yi Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lorna Barron
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kelvina Manako
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Judith Bowen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Toshi M Foster
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Zoe A Erridge
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Heather Tiffin
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Chethi N Waite
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Kevin M Davies
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | | | - Rebecca Kirk
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marion Wood
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mirco Montefiori
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | | | | | | | - Christina Fullerton
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | | | - Niels Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nicola Read
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Roneel Prakash
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Don Hunter
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Huaibi Zhang
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Mareike Knäbel
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Alastair Harris
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew Gleave
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Angela Chen
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Bart J Janssen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charles Ampomah-Dwamena
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Davin Leif
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Declan Lafferty
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Edwige J F Souleyre
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Francesco Gambi
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jenny Hanley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Joey Cheung
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Karine M David
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ken Marsh
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kimberley C Snowden
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lara Brian
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marcela Martinez-Sanchez
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mindy Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nadeesha Ileperuma
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nikolai Macnee
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Robert Campin
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Peter McAtee
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Revel S M Drummond
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Hilary S Ireland
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sean Bulley
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Shayhan Chunkath
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Zac Hanley
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Roy Storey
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Amali H Thrimawithana
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Susan Thomson
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Charles David
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Raffaele Testolin
- IGA Technology Services, Parco Scientifico e Tecnologico, Udine, Italy.,Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy
| | - Hongwen Huang
- South China Botanic Gardens, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | - Roger P Hellens
- Institute for Future Environments, Queensland University of Technology (QUT), Brisbane, 4001, Australia
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand. .,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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12
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Bastiaanse H, Bassett HCM, Kirk C, Gardiner SE, Deng C, Groenworld R, Chagné D, Bus VGM. Scab resistance in 'Geneva' apple is conditioned by a resistance gene cluster with complex genetic control. Mol Plant Pathol 2016; 17:159-72. [PMID: 25892110 PMCID: PMC6638522 DOI: 10.1111/mpp.12269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most severe diseases of apple worldwide. It is the most studied plant-pathogen interaction involving a woody species using modern genetic, genomic, proteomic and bioinformatic approaches in both species. Although 'Geneva' apple was recognized long ago as a potential source of resistance to scab, this resistance has not been characterized previously. Differential interactions between various monoconidial isolates of V. inaequalis and six segregating F1 and F2 populations indicate the presence of at least five loci governing the resistance in 'Geneva'. The 17 chromosomes of apple were screened using genotyping-by-sequencing, as well as single marker mapping, to position loci controlling the V. inaequalis resistance on linkage group 4. Next, we fine mapped a 5-cM region containing five loci conferring both dominant and recessive scab resistance to the distal end of the linkage group. This region corresponds to 2.2 Mbp (from 20.3 to 22.5 Mbp) on the physical map of 'Golden Delicious' containing nine candidate nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance genes. This study increases our understanding of the complex genetic basis of apple scab resistance conferred by 'Geneva', as well as the gene-for-gene (GfG) relationships between the effector genes in the pathogen and resistance genes in the host.
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Affiliation(s)
- Héloïse Bastiaanse
- Plant Pathology Unit, Gembloux Agro-Bio Tech, University of Liège, avenue Maréchal Juin 13, Gembloux 5030, Belgium
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North 4442, New Zealand
- Plant & Food Research, Private Bag 1401, Havelock North 4157, New Zealand
| | - Heather C M Bassett
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North 4442, New Zealand
| | - Christopher Kirk
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North 4442, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North 4442, New Zealand
| | - Cecilia Deng
- Plant & Food Research, Private Bag 92169, Auckland 1142, New Zealand
| | - Remmelt Groenworld
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ Wageningen, the Netherlands
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North 4442, New Zealand
| | - Vincent G M Bus
- Plant & Food Research, Private Bag 1401, Havelock North 4157, New Zealand
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13
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Montanari S, Brewer L, Lamberts R, Velasco R, Malnoy M, Perchepied L, Guérif P, Durel CE, Bus VGM, Gardiner SE, Chagné D. Genome mapping of postzygotic hybrid necrosis in an interspecific pear population. Hortic Res 2016; 3:15064. [PMID: 26770810 PMCID: PMC4702180 DOI: 10.1038/hortres.2015.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 05/22/2023]
Abstract
Deleterious epistatic interactions in plant inter- and intraspecific hybrids can cause a phenomenon known as hybrid necrosis, characterized by a typical seedling phenotype whose main distinguishing features are dwarfism, tissue necrosis and in some cases lethality. Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes. Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes. Although hybrid necrosis has been reported in several plant taxa, including Rosaceae species, this phenomenon has not been described previously in pear. In the interspecific pear population resulting from a cross between PEAR3 (Pyrus bretschneideri × Pyrus communis) and 'Moonglow' (P. communis), we observed two types of hybrid necrosis, expressed at different stages of plant development. Using a combination of previously mapped and newly developed genetic markers, we identified three chromosome regions associated with these two types of lethality, which were genetically independent. One type resulted from a negative epistatic interaction between a locus on linkage group 5 (LG5) of PEAR3 and a locus on LG1 of 'Moonglow', while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from 'Moonglow'.
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Affiliation(s)
- Sara Montanari
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Lester Brewer
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Robert Lamberts
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Philippe Guérif
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
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14
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Yao JL, Xu J, Cornille A, Tomes S, Karunairetnam S, Luo Z, Bassett H, Whitworth C, Rees-George J, Ranatunga C, Snirc A, Crowhurst R, de Silva N, Warren B, Deng C, Kumar S, Chagné D, Bus VGM, Volz RK, Rikkerink EHA, Gardiner SE, Giraud T, MacDiarmid R, Gleave AP. A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. Plant J 2015; 84:417-27. [PMID: 26358530 DOI: 10.1111/tpj.13021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 06/02/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
The molecular genetic mechanisms underlying fruit size remain poorly understood in perennial crops, despite size being an important agronomic trait. Here we show that the expression level of a microRNA gene (miRNA172) influences fruit size in apple. A transposon insertional allele of miRNA172 showing reduced expression associates with large fruit in an apple breeding population, whereas over-expression of miRNA172 in transgenic apple significantly reduces fruit size. The transposon insertional allele was found to be co-located with a major fruit size quantitative trait locus, fixed in cultivated apples and their wild progenitor species with relatively large fruit. This finding supports the view that the selection for large size in apple fruit was initiated prior to apple domestication, likely by large mammals, before being subsequently strengthened by humans, and also helps to explain why signatures of genetic bottlenecks and selective sweeps are normally weaker in perennial crops than in annual crops.
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Affiliation(s)
- Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Juan Xu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Heather Bassett
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Claire Whitworth
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Jonathan Rees-George
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Chandra Ranatunga
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Alodie Snirc
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Ross Crowhurst
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Nihal de Silva
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Richard K Volz
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew P Gleave
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
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15
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Knäbel M, Friend AP, Palmer JW, Diack R, Wiedow C, Alspach P, Deng C, Gardiner SE, Tustin DS, Schaffer R, Foster T, Chagné D. Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci. BMC Plant Biol 2015; 15:230. [PMID: 26394845 PMCID: PMC4580296 DOI: 10.1186/s12870-015-0620-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND The vigour and precocity of trees highly influences their efficiency in commercial production. In apple, dwarfing rootstocks allow high-density plantings while their precocious flowering enables earlier fruit production. Currently, there is a lack of pear (Pyrus communis L.) rootstocks that are equivalent to the high yielding apple rootstock 'M9'. For the efficient breeding of new Pyrus rootstocks it is crucial to understand the genetic determinants of vigour control and precocity. In this study we used quantitative trait loci (QTLs) analysis to identify genetic loci associated with the desired traits, using a segregating population of 405 F1 P. communis seedlings from a cross between 'Old Home' and 'Louise Bonne de Jersey' (OHxLBJ). The seedlings were grafted as rootstocks with 'Doyenne du Comice' scions and comprehensively phenotyped over four growing seasons for traits related to tree architecture and flowering, in order to describe the growth of the scions. RESULTS A high density single nucleotide polymorphism (SNP)-based genetic map comprising 597 polymorphic pear and 113 apple markers enabled the detection of QTLs influencing expression of scion vigour and precocity located on linkage groups (LG)5 and LG6 of 'Old Home'. The LG5 QTL maps to a position that is syntenic to the apple 'Malling 9' ('M9') Dw1 locus at the upper end of LG5. An allele of a simple sequence repeat (SSR) associated with apple Dw1 segregated with dwarfing and precocity in pear and was identified in other pear germplasm accessions. The orthology of the vigour-controlling LG5 QTL between apple and pear raises the possibility that the dwarfing locus Dw1 arose before the divergence of apple and pear, and might therefore be present in other Rosaceae species. CONCLUSION We report the first QTLs associated with vigour control and flowering traits in pear rootstocks. Orthologous loci were found to control scion growth and precocity in apple and pear rootstocks. The application of our results may assist in the breeding process of a pear rootstock that confers both vigour control and precocity to the grafted scion cultivar.
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Affiliation(s)
- Mareike Knäbel
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Fitzherbert Science Centre, Batchelar Road, Palmerston North, 4474, New Zealand.
- School of Biological Sciences, University of Auckland, Thomas Building 110, 3a Symonds Street, Auckland Central, 1010, New Zealand.
| | - Adam P Friend
- Plant & Food Research, Motueka Research Centre, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand.
| | - John W Palmer
- Plant & Food Research, Motueka Research Centre, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand.
| | - Robert Diack
- Plant & Food Research, Motueka Research Centre, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand.
| | - Claudia Wiedow
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Fitzherbert Science Centre, Batchelar Road, Palmerston North, 4474, New Zealand.
| | - Peter Alspach
- Plant & Food Research, Motueka Research Centre, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand.
| | - Cecilia Deng
- Plant & Food Research, Mount Albert Research Centre, 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand.
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Fitzherbert Science Centre, Batchelar Road, Palmerston North, 4474, New Zealand.
| | - D Stuart Tustin
- Plant & Food Research, Hawke's Bay Research Centre, Cnr Crosses and St George's Roads, Havelock North, 4130, New Zealand.
| | - Robert Schaffer
- School of Biological Sciences, University of Auckland, Thomas Building 110, 3a Symonds Street, Auckland Central, 1010, New Zealand.
- Plant & Food Research, Mount Albert Research Centre, 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand.
| | - Toshi Foster
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Fitzherbert Science Centre, Batchelar Road, Palmerston North, 4474, New Zealand.
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Fitzherbert Science Centre, Batchelar Road, Palmerston North, 4474, New Zealand.
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16
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Foster TM, Celton JM, Chagné D, Tustin DS, Gardiner SE. Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Hortic Res 2015; 2:15001. [PMID: 26504562 PMCID: PMC4595989 DOI: 10.1038/hortres.2015.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/05/2014] [Accepted: 01/07/2014] [Indexed: 05/04/2023]
Abstract
The apple dwarfing rootstock 'Malling9' ('M9') has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks. Progeny of 'M9' segregate for rootstock-induced dwarfing of the scion, indicating that this trait is controlled by one or more genetic factors. A quantitative trait locus (QTL) analysis of a rootstock population derived from the cross between 'M9' × 'Robusta5' (non-dwarfing) and grafted with 'Braeburn' scions identified a major QTL (Dw1) on linkage group (LG) 5, which exhibits a significant influence on dwarfing of the scion. A smaller-effect QTL affecting dwarfing (Dw2) was identified on LG11, and four minor-effect QTLs were found on LG6, LG9, LG10 and LG12. Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing, and that Dw1 has a stronger effect than Dw2. Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth. The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2. This suggests that most apple dwarfing rootstocks have been derived from the same genetic source.
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Affiliation(s)
- Toshi M Foster
- The New Zealand Institute for Plant & Food Research Ltd, Palmerston North Private Bag 11600, Palmerston North 4474, New Zealand
| | - Jean-Marc Celton
- INRA UMR 1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Ltd, Palmerston North Private Bag 11600, Palmerston North 4474, New Zealand
| | - D Stuart Tustin
- The New Zealand Institute for Plant & Food Research Ltd, Havelock North Private Bag 1401, Havelock North 4175, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Ltd, Palmerston North Private Bag 11600, Palmerston North 4474, New Zealand
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17
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Saeed M, Brewer L, Johnston J, McGhie TK, Gardiner SE, Heyes JA, Chagné D. Genetic, metabolite and developmental determinism of fruit friction discolouration in pear. BMC Plant Biol 2014; 14:241. [PMID: 25224302 PMCID: PMC4177423 DOI: 10.1186/s12870-014-0241-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 04/23/2014] [Accepted: 09/05/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The unattractive appearance of the surface of pear fruit caused by the postharvest disorder friction discolouration (FD) is responsible for significant consumer dissatisfaction in markets, leading to lower returns to growers. Developing an understanding of the genetic control of FD is essential to enable the full application of genomics-informed breeding for the development of new pear cultivars. Biochemical constituents [phenolic compounds and ascorbic acid (AsA)], polyphenol oxidase (PPO) activity, as well as skin anatomy, have been proposed to play important roles in FD susceptibility in studies on a limited number of cultivars. However, to date there has been no investigation on the biochemical and genetic control of FD, employing segregating populations. In this study, we used 250 seedlings from two segregating populations (POP369 and POP356) derived from interspecific crosses between Asian (Pyrus pyrifolia Nakai and P. bretschneideri Rehd.) and European (P. communis) pears to identify genetic factors associated with susceptibility to FD. RESULTS Single nucleotide polymorphism (SNP)-based linkage maps suitable for QTL analysis were developed for the parents of both populations. The maps for population POP369 comprised 174 and 265 SNP markers for the male and female parent, respectively, while POP356 maps comprised 353 and 398 SNP markers for the male and female parent, respectively. Phenotypic data for 22 variables were measured over two successive years (2011 and 2012) for POP369 and one year (2011) only for POP356. A total of 221 QTLs were identified that were linked to 22 phenotyped variables, including QTLs associated with FD for both populations that were stable over the successive years. In addition, clear evidence of the influence of developmental factors (fruit maturity) on FD and other variables was also recorded. CONCLUSIONS The QTLs associated with fruit firmness, PPO activity, AsA concentration and concentration of polyphenol compounds as well as FD are the first reported for pear. We conclude that the postharvest disorder FD is controlled by multiple small effect QTLs and that it will be very challenging to apply marker-assisted selection based on these QTLs. However, genomic selection could be employed to select elite genotypes with lower or no susceptibility to FD early in the breeding cycle.
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Affiliation(s)
- Munazza Saeed
- />Centre for Postharvest & Refrigeration Research, Massey University, Private Bag 11 222, Palmerston North, 4442 New Zealand
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Lester Brewer
- />Plant & Food Research, Motueka Research Centre, Old Mill Road, Motueka, 7198 New Zealand
| | - Jason Johnston
- />Plant & Food Research, Hawkes Bay Research Centre, Private Bag 1401, Havelock North, New Zealand
| | - Tony K McGhie
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Susan E Gardiner
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Julian A Heyes
- />Centre for Postharvest & Refrigeration Research, Massey University, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - David Chagné
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
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18
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Souleyre EJF, Chagné D, Chen X, Tomes S, Turner RM, Wang MY, Maddumage R, Hunt MB, Winz RA, Wiedow C, Hamiaux C, Gardiner SE, Rowan DD, Atkinson RG. The AAT1 locus is critical for the biosynthesis of esters contributing to 'ripe apple' flavour in 'Royal Gala' and 'Granny Smith' apples. Plant J 2014; 78:903-15. [PMID: 24661745 DOI: 10.1111/tpj.12518] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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: 10/07/2013] [Revised: 01/16/2014] [Accepted: 03/17/2014] [Indexed: 05/03/2023]
Abstract
The 'fruity' attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a 'Royal Gala' (RG; high ester production) × 'Granny Smith' (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co-located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1-RGa and AAT1-GSa) were functional. AAT1-RGa and AAT1-GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a 'ripe apple' flavour.
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Affiliation(s)
- Edwige J F Souleyre
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Victoria Street West, Auckland, 1025, New Zealand
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Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knäbel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VGM, Schaffer RJ, Gardiner SE, Velasco R. The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS One 2014; 9:e92644. [PMID: 24699266 PMCID: PMC3974708 DOI: 10.1371/journal.pone.0092644] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 02/25/2014] [Indexed: 01/03/2023] Open
Abstract
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.
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Affiliation(s)
- David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Massimo Pindo
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | | | - Cecilia Deng
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Hilary Ireland
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mark Fiers
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Helge Dzierzon
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Alessandro Cestaro
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Paolo Fontana
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Luca Bianco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Ashley Lu
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Roy Storey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Munazza Saeed
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Sara Montanari
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Yoon Kyeong Kim
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Daniela Nicolini
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Simone Larger
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Erika Stefani
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Andrew C. Allan
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Judith Bowen
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Isaac Harvey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Jason Johnston
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mickael Malnoy
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Greg Sawyer
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Claudia Wiedow
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Roberto Viola
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Roger P. Hellens
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Lester Brewer
- Motueka Research Centre, Plant & Food Research, Motueka, New Zealand
| | - Vincent G. M. Bus
- Hawke's Bay Research Centre, Plant & Food Research, Havelock North, New Zealand
| | - Robert J. Schaffer
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan E. Gardiner
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Riccardo Velasco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
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20
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Chagné D, Dayatilake D, Diack R, Oliver M, Ireland H, Watson A, Gardiner SE, Johnston JW, Schaffer RJ, Tustin S. Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus × domestica Borkh.). Hortic Res 2014; 1:14046. [PMID: 26504549 PMCID: PMC4596328 DOI: 10.1038/hortres.2014.46] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 07/22/2014] [Accepted: 07/30/2014] [Indexed: 05/19/2023]
Abstract
For any given genotype, the environment in which an apple is grown can influence the properties of the fruit considerably. While there has been extensive research on the mechanism of the genetic control of fruit quality traits, less effort has been made to investigate the way that these genetic mechanisms interact with the environment. To address this issue, we employed a large 'Royal Gala' × 'Braeburn' population of 572 seedlings replicated over sites in three climatically diverse apple-growing regions in New Zealand. Phenotyping for traits including fruit maturation timing, firmness and dry matter content was performed at each of these three sites for a single growing season (2011), and at two sites (Motueka and Hawke's Bay) for two seasons (2009 and 2010). The phenotype data collected over 2 years at two sites enabled the detection of 190 quantitative trait loci (QTL) that controlled these traits regardless of year or growing location, as well as some chromosomal loci that influenced the traits in a single given environment or year. For those loci that were environmentally stable over three sites, there was an interdependency of fruit maturation date, dry matter content and storage potential within this population, with two regions on Linkage Groups (LGs) 10 and 16 strongly contributing. If these loci were used in a marker-assisted selection programme to select for progeny bearing firmer fruit, this would have the unintentional consequence of selecting, high dry matter content, later maturing apples. In addition, a further 113 new QTLs with a smaller effect were identified, some of which were exhibited only in a single growing environment, demonstrating the underlying complexity of control of traits determining fruit quality, in addition to the need for being aware of environmental effects when developing new apple varieties.
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Affiliation(s)
- David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Daya Dayatilake
- Plant & Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Robert Diack
- Plant & Food Research, Motueka Research Centre, Motueka, New Zealand
| | - Murray Oliver
- Plant & Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Hilary Ireland
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Amy Watson
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Jason W Johnston
- Plant & Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Robert J Schaffer
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Stuart Tustin
- Plant & Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
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van Nocker S, Gardiner SE. Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops. Hortic Res 2014; 1:14022. [PMID: 26504538 PMCID: PMC4596317 DOI: 10.1038/hortres.2014.22] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 03/16/2014] [Indexed: 05/18/2023]
Abstract
Woody perennial plants, including trees that produce fruits and nuts of horticultural value, typically have long breeding cycles, and development and introduction of improved cultivars by plant breeders may require many breeding cycles and dozens of years. However, recent advances in biotechnologies and genomics have the potential to accelerate cultivar development greatly in all crops. This mini-review summarizes approaches to reduce the number and the duration of breeding cycles for horticultural tree crops, and outlines the challenges that remain to implement these into efficient breeding pipelines.
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Affiliation(s)
- Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited Plant and Food Research Palmerston North Private Bag 11030 Manawatu Mail Centre, Palmerston North, 4442, New Zealand
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22
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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23
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Bushakra JM, Krieger C, Deng D, Stephens MJ, Allan AC, Storey R, Symonds VV, Stevenson D, McGhie T, Chagné D, Buck EJ, Gardiner SE. QTL involved in the modification of cyanidin compounds in black and red raspberry fruit. Theor Appl Genet 2013; 126:847-65. [PMID: 23224381 DOI: 10.1007/s00122-012-2022-4] [Citation(s) in RCA: 5] [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: 08/08/2012] [Accepted: 11/15/2012] [Indexed: 05/24/2023]
Abstract
Fruit from Rubus species are highly valued for their flavor and nutritive qualities. Anthocyanin content contributes to these qualities, and although many studies have been conducted to identify and quantify the major anthocyanin compounds from various Rubus species, the genetic control of the accumulation of these complex traits in Rubus is not yet well understood. The identification of the regions of the genome involved in the production of anthocyanins is an important first step in identifying the genes underlying their expression. In this study, ultra and high-performance liquid chromatography (UHPLC and HPLC) and two newly developed Rubus linkage maps were used to conduct QTL analyses to explore the presence of associations between concentrations of five anthocyanins in fruit and genotype. In total, 27 QTL were identified on the Rubus linkage maps, four of which are associated with molecular markers designed from transcription factors and three of which are associated with molecular markers designed from anthocyanin biosynthetic pathway candidate genes. The results of this study suggest that, while QTL for anthocyanin accumulation have been identified on six of seven Rubus linkage groups (RLG), the QTL on RLG2 and RLG7 may be very important for genetic control of cyanidin modification in Rubus.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited (PFR), Batchelar Road, Private Bag 11600, Palmerston North, 4442, New Zealand.
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24
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Chagné D, Lin-Wang K, Espley RV, Volz RK, How NM, Rouse S, Brendolise C, Carlisle CM, Kumar S, De Silva N, Micheletti D, McGhie T, Crowhurst RN, Storey RD, Velasco R, Hellens RP, Gardiner SE, Allan AC. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol 2013; 161:225-39. [PMID: 23096157 PMCID: PMC3532254 DOI: 10.1104/pp.112.206771] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/23/2012] [Indexed: 05/18/2023]
Abstract
Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.
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Affiliation(s)
- David Chagné
- New Zealand Institute for Plant and Food Research Limited , Palmerston North Research Centre, Palmerston North 4442, New Zealand.
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25
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Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 2012; 125:311-27. [PMID: 22398438 DOI: 10.1007/s00122-012-1835-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/17/2012] [Indexed: 05/23/2023]
Abstract
The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited, Batchelar Road, Private Bag 11600, Palmerston North 4442, New Zealand.
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26
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Gardiner SE, Norelli JL, Silva ND, Fazio G, Peil A, Malnoy M, Horner M, Bowatte D, Carlisle C, Wiedow C, Wan Y, Bassett CL, Baldo AM, Celton JM, Richter K, Aldwinckle HS, Bus VGM. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions. BMC Genet 2012; 13:25. [PMID: 22471693 PMCID: PMC3443455 DOI: 10.1186/1471-2156-13-25] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 03/19/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus 'Robusta 5'. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. RESULTS When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with 'Robusta 5' as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand 'Malling 9' X 'Robusta 5' population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein (MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German 'Idared' X 'Robusta 5' population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene (HSP90). In the US 'Otawa3' X 'Robusta5' population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance. However, this QTL was not observed in the New Zealand or German populations. CONCLUSIONS The results suggest that the upper region of 'Robusta 5' linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative fire blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of fire blight resistance.
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Affiliation(s)
- Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR) Palmerston North, Private Bag 11600, Manawatu Mail Centre, 4442, Palmerston North, New Zealand
| | - John L Norelli
- USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
| | - Nihal de Silva
- PFR Mt Albert, Private Bag 92169, Auckland Mail Centre, 1142, Auckland, New Zealand
| | - Gennaro Fazio
- USDA-ARS, Plant Genetic Resources Unit, 630W. North St., Geneva, NY, 14456, USA
| | - Andreas Peil
- Julius Kühn-Institut (JKI), Institute for Breeding Research on Horticultural and Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
| | - Mickael Malnoy
- Foundation E. Mach - Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Mary Horner
- PFR Hawke’s Bay, Private Bag 1401, 4157, Havelock North, New Zealand
| | - Deepa Bowatte
- The New Zealand Institute for Plant & Food Research Limited (PFR) Palmerston North, Private Bag 11600, Manawatu Mail Centre, 4442, Palmerston North, New Zealand
| | - Charmaine Carlisle
- The New Zealand Institute for Plant & Food Research Limited (PFR) Palmerston North, Private Bag 11600, Manawatu Mail Centre, 4442, Palmerston North, New Zealand
| | - Claudia Wiedow
- The New Zealand Institute for Plant & Food Research Limited (PFR) Palmerston North, Private Bag 11600, Manawatu Mail Centre, 4442, Palmerston North, New Zealand
| | - Yizhen Wan
- Apple Research Center, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Carole L Bassett
- USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
| | - Angela M Baldo
- USDA-ARS, Plant Genetic Resources Unit, 630W. North St., Geneva, NY, 14456, USA
| | - Jean-Marc Celton
- UMR Génétique et Horticulture (GenHort), INRA ⁄ Agrocampus-ouest ⁄ Université d’Angers, Centre Angers-Nantes, 42 rue Georges Morel – BP 60057, 49071, Beaucouze´ Cedex, France
| | - Klaus Richter
- JKI, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany
| | - Herb S Aldwinckle
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 630W. North St., Geneva, NY, 14456, USA
| | - Vincent GM Bus
- PFR Hawke’s Bay, Private Bag 1401, 4157, Havelock North, New Zealand
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27
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Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 2012; 7:e31745. [PMID: 22363718 PMCID: PMC3283661 DOI: 10.1371/journal.pone.0031745] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023] Open
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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Affiliation(s)
- David Chagné
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Barbara Gilmore
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cindy Lawley
- Illumina Inc., Hayward, California, United States of America
| | - Stijn Vanderzande
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Roger P. Hellens
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Satish Kumar
- Plant and Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Alessandro Cestaro
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Jasper D. Rees
- Agricultural Research Council, Onderstepoort, South Africa
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Todd Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Susan E. Gardiner
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Chagné D, Krieger C, Rassam M, Sullivan M, Fraser J, André C, Pindo M, Troggio M, Gardiner SE, Henry RA, Allan AC, McGhie TK, Laing WA. QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biol 2012; 12:12. [PMID: 22269060 PMCID: PMC3285079 DOI: 10.1186/1471-2229-12-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [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: 07/18/2011] [Accepted: 01/23/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin. RESULTS Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL) for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1) co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG) 16, while hydroxy cinnamate/quinate transferase (HCT/HQT) co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17. CONCLUSION We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.
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Affiliation(s)
- David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - Célia Krieger
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
- UMR 1121 Nancy Université-Institut National de la Recherche Agronomique Agronomie Environnement Nancy-Colmar, 2 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Maysoon Rassam
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Mike Sullivan
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Jenny Fraser
- Plant & Food Research, Central Otago Research Centre, Clyde, New Zealand
| | - Christelle André
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Massimo Pindo
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - Rebecca A Henry
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Andrew C Allan
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Tony K McGhie
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - William A Laing
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
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Abstract
Although flowering in mature fruit trees is recurrent, floral induction can be strongly inhibited by concurrent fruiting, leading to a pattern of irregular fruiting across consecutive years referred to as biennial bearing. The genetic determinants of biennial bearing in apple were investigated using the 114 flowering individuals from an F(1) population of 122 genotypes, from a 'Starkrimson' (strong biennial bearer)×'Granny Smith' (regular bearer) cross. The number of inflorescences, and the number and the mass of harvested fruit were recorded over 6 years and used to calculate 26 variables and indices quantifying yield, precocity of production, and biennial bearing. Inflorescence traits exhibited the highest genotypic effect, and three quantitative trait loci (QTLs) on linkage group (LG) 4, LG8, and LG10 explained 50% of the phenotypic variability for biennial bearing. Apple orthologues of flowering and hormone-related genes were retrieved from the whole-genome assembly of 'Golden Delicious' and their position was compared with QTLs. Four main genomic regions that contain floral integrator genes, meristem identity genes, and gibberellin oxidase genes co-located with QTLs. The results indicated that flowering genes are less likely to be responsible for biennial bearing than hormone-related genes. New hypotheses for the control of biennial bearing emerged from QTL and candidate gene co-locations and suggest the involvement of different physiological processes such as the regulation of flowering genes by hormones. The correlation between tree architecture and biennial bearing is also discussed.
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Affiliation(s)
- Baptiste Guitton
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue Agropolis-TA-A-108/03, 34398 Montpellier Cedex 01, France
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Jean-Jacques Kelner
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue Agropolis-TA-A-108/03, 34398 Montpellier Cedex 01, France
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Evelyne Costes
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue Agropolis-TA-A-108/03, 34398 Montpellier Cedex 01, France
- To whom correspondence should be addressed. E-mail:
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Sarkhosh A, Zamani Z, Fatahi R, Hassani ME, Wiedow C, Buck E, Gardiner SE. Genetic diversity of Iranian soft-seed pomegranate genotypes as revealed by fluorescent-AFLP markers. Physiol Mol Biol Plants 2011; 17:305-311. [PMID: 23573023 PMCID: PMC3550573 DOI: 10.1007/s12298-011-0070-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The amplified fragment length polymorphism (AFLP) technique was used to examine the genetic relationships among 21 Iranian soft-seeded pomegranate (Punica granatum L.) genotypes. Out of 72 fluorescent-AFLP primer combinations screened, 31 were selected to produce the 503 polymorphic markers used in this study. Genetic similarity estimates between genotypes, calculated by the Jaccard's similarity coefficient, ranged from 0.17 to 1.00, while the cophenetic correlation coefficient between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) dendrogram was 0.98. The AFLP-based UPGMA dendrogram revealed two groups within the genotypes at 0.33 similarity coefficient, which reflect fruit traits such as peel and aril color, and seed firmness, as well as region of origin. Our study shows that the use of molecular markers is essential during all steps of germplasm management to avoid genotype redundancy and mislabeling. The present study will be used as a reliable reference to discriminate among these genotypes, to aid management of germplasm collections used to breed new varieties for the Iranian pomegranate industry.
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Affiliation(s)
- Ali Sarkhosh
- />Department of Horticultural Sciences, Faculty of Agriculture, University of Tehran, Karaj, 31587 Iran
| | - Zabihollah Zamani
- />Department of Horticultural Sciences, Faculty of Agriculture, University of Tehran, Karaj, 31587 Iran
| | - Reza Fatahi
- />Department of Horticultural Sciences, Faculty of Agriculture, University of Tehran, Karaj, 31587 Iran
| | - Mohammad E. Hassani
- />Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2015 Australia
| | - Claudia Wiedow
- />The New Zealand Institute for Plant & Food Research Ltd., Private Bag 11030, Palmerston North, 4442 New Zealand
| | - Emily Buck
- />The New Zealand Institute for Plant & Food Research Ltd., Private Bag 11030, Palmerston North, 4442 New Zealand
| | - Susan E. Gardiner
- />The New Zealand Institute for Plant & Food Research Ltd., Private Bag 11030, Palmerston North, 4442 New Zealand
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Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 2010; 42:833-9. [DOI: 10.1038/ng.654] [Citation(s) in RCA: 1538] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
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Celton JM, Chagné D, Tustin SD, Terakami S, Nishitani C, Yamamoto T, Gardiner SE. Update on comparative genome mapping between Malus and Pyrus. BMC Res Notes 2009; 2:182. [PMID: 19747407 PMCID: PMC2749866 DOI: 10.1186/1756-0500-2-182] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 09/14/2009] [Indexed: 11/13/2022] Open
Abstract
Background Comparative genome mapping determines the linkage between homologous genes of related taxa. It has already been used in plants to characterize agronomically important genes in lesser studied species, using information from better studied species. In the Maloideae sub-family, which includes fruit species such as apple, pear, loquat and quince, genome co-linearity has been suggested between the genera Malus and Pyrus; however map comparisons are incomplete to date. Findings Genetic maps for the apple rootstocks 'Malling 9' ('M.9') (Malus × domestica) and 'Robusta 5' ('R5') (Malus × robusta), and pear cultivars 'Bartlett' and 'La France' (Pyrus communis) were constructed using Simple Sequence Repeat (SSR) markers developed from both species, including a new set of 73 pear Expressed Sequence Tag (EST) SSR markers. Integrated genetic maps for apple and pear were then constructed using 87 and 131 SSR markers in common, respectively. The genetic maps were aligned using 102 markers in common, including 64 pear SSR markers and 38 apple SSR markers. Of these 102 markers, 90 anchor markers showed complete co-linearity between the two genomes. Conclusion Our alignment of the genetic maps of two Malus cultivars of differing species origin with two Pyrus communis cultivars confirms the ready transferability of SSR markers from one genus to the other and supports a high level of co-linearity within the sub-family Maloideae between the genomes of Malus and Pyrus.
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Affiliation(s)
- Jean-Marc Celton
- University of Western Cape, Biotechnology Department, Modderdam Road, Bellville, Cape Town, 7535, South Africa.
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Rowan DD, Hunt MB, Dimouro A, Alspach PA, Weskett R, Volz RK, Gardiner SE, Chagné D. Profiling fruit volatiles in the progeny of a 'Royal Gala' x 'Granny Smith' apple (Malus x domestica) cross. J Agric Food Chem 2009; 57:7953-7961. [PMID: 19691320 DOI: 10.1021/jf901678v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Volatile flavor compounds from the fruit of the progeny of two apple (Malus x domestica) cultivars with distinctive flavor and volatile profiles, 'Royal Gala' and 'Granny Smith', were measured by headspace gas chromatography-mass spectrometry over two fruiting seasons. Principal component analysis separated the volatile profiles into two groups according to the amounts produced of butyl, 2-methybutyl, pentyl, and hexyl acetates and of ethyl butanoate, butanol, 2-methylbutanol, and hexanol. Fruit containing the four acetate esters clustered with the 'Royal Gala' parent and were scored more similar to 'Royal Gala' than to "Granny Smith' in flavor. Fruit clustering with the 'Granny Smith' parent contained higher levels of ethyl butanoate and alcohols. Levels of acetate esters correlated to levels of their alcohol precursors, and control of this trait segregated in Mendelian fashion. The locus was mapped to the top of 'Royal Gala' linkage group 2 close to the Rvi4 (Vh4) locus for resistance to Venturia inaequalis , the causal agent of apple scab.
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Affiliation(s)
- Daryl D Rowan
- The New Zealand Institute for Plant and Food Research, Private Bag 11600, Palmerston North 4442, New Zealand.
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Espley RV, Brendolise C, Chagné D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten HJ, Gardiner SE, Hellens RP, Allan AC. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell 2009; 21:168-83. [PMID: 19151225 PMCID: PMC2648084 DOI: 10.1105/tpc.108.059329] [Citation(s) in RCA: 305] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 12/19/2008] [Accepted: 01/06/2009] [Indexed: 05/18/2023]
Abstract
Mutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an apple (Malus x domestica) anthocyanin-regulating transcription factor, MYB10. We show that this modification is responsible for increasing the level of anthocyanin throughout the plant to produce a striking phenotype that includes red foliage and red fruit flesh. This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. This MYB10 rearrangement is present in all the red foliage apple varieties and species tested but in none of the white fleshed varieties. Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. Taken together, these results indicate that an allelic rearrangement in the promoter of MYB10 has generated an autoregulatory locus, and this autoregulation is sufficient to account for the increase in MYB10 transcript levels and subsequent ectopic accumulation of anthocyanins throughout the plant.
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Affiliation(s)
- Richard V Espley
- New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Auckland 1025, New Zealand
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Han Y, Chagné D, Gasic K, Rikkerink EHA, Beever JE, Gardiner SE, Korban SS. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple. Genomics 2008; 93:282-8. [PMID: 19059473 DOI: 10.1016/j.ygeno.2008.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/05/2008] [Accepted: 11/06/2008] [Indexed: 11/26/2022]
Abstract
A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.
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Affiliation(s)
- Yuepeng Han
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
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36
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Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS. Development of a set of SNP markers present in expressed genes of the apple. Genomics 2008; 92:353-8. [PMID: 18721872 DOI: 10.1016/j.ygeno.2008.07.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/25/2022]
Abstract
Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.
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Affiliation(s)
- David Chagné
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, Palmerston North 4442, New Zealand
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Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arús P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE. Multiple models for Rosaceae genomics. Plant Physiol 2008; 147:985-1003. [PMID: 18487361 PMCID: PMC2442536 DOI: 10.1104/pp.107.115618] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 05/13/2008] [Indexed: 05/19/2023]
Abstract
The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.
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Cooter RD, Rudkin GE, Gardiner SE. Day case breast augmentation under paravertebral blockade: a prospective study of 100 consecutive patients. Aesthetic Plast Surg 2007; 31:666-73. [PMID: 17486400 DOI: 10.1007/s00266-006-0230-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND An increasing trend toward day surgery management requires plastic surgeons not only to be cognizant of block techniques, but also to assess their safety and efficacy objectively. Paravertebral block offers benefits by enhancing surgical anesthesia and postoperative analgesia. This study aimed to assess the safety and efficacy of paravertebral block for day patients undergoing submuscular breast augmentation. The primary outcome measure was the rate of block failure. The secondary outcome measures included recovery room stay, pain management, and block complications. On the basis of a literature review and audit results, the study objective also aimed to propose safe guidelines for ambulatory paravertebral block patients undergoing breast surgery. METHODS A total of 100 patients undergoing 172 single-level paravertebral blocks (72 bilateral blocks) and sedation for submuscular breast augmentation were studied prospectively. A single-injection paravertebral block was performed at the T4 level using a loss of resistance technique. Surgical, anesthetic, and recovery room details were recorded. Analyses were performed to determine the association between recovery room times, body mass index, pain scores, and requirements for opioids, antiemetics, and vasopressors. RESULTS The findings showed that 87% of the blocks were successful for surgical anesthesia and 94% of the blocks were successful for postoperative analgesia. The pain score for 74% of the subjects was 3 or less. Antiemetics were given for 10% of the patients with significantly longer recovery room times. Vasopressors were required for 6% of the patients. A surgically caused pneumothorax resulted in the only unplanned admission. CONCLUSION The study findings suggest that paravertebral block is a safe and effective technique for day case submuscular breast augmentation.
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Affiliation(s)
- Rodney Dean Cooter
- Waverley House Plastic Surgery Centre, Level 1, Waverley House, 360 South Terrace, Adelaide, SA 5000, Australia.
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Chagné D, Carlisle CM, Blond C, Volz RK, Whitworth CJ, Oraguzie NC, Crowhurst RN, Allan AC, Espley RV, Hellens RP, Gardiner SE. Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 2007; 8:212. [PMID: 17608951 PMCID: PMC1939713 DOI: 10.1186/1471-2164-8-212] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 07/03/2007] [Indexed: 12/02/2022] Open
Abstract
Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species.
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Affiliation(s)
- David Chagné
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Charmaine M Carlisle
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Céline Blond
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Richard K Volz
- HortResearch Hawke's Bay, PB 1401, Havelock North 4157, New Zealand
| | | | | | | | - Andrew C Allan
- HortResearch Mount Albert, PB 92169, Auckland 1142, New Zealand
| | | | - Roger P Hellens
- HortResearch Mount Albert, PB 92169, Auckland 1142, New Zealand
| | - Susan E Gardiner
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
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Bus VGM, Laurens FND, van de Weg WE, Rusholme RL, Rikkerink EHA, Gardiner SE, Bassett HCM, Kodde LP, Plummer KM. The Vh8 locus of a new gene-for-gene interaction between Venturia inaequalis and the wild apple Malus sieversii is closely linked to the Vh2 locus in Malus pumila R12740-7A. New Phytol 2005; 166:1035-49. [PMID: 15869661 DOI: 10.1111/j.1469-8137.2005.01395.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The wild apple (Malus sieversii) is a large-fruited species from Central Asia, which is used as a source of scab resistance in cultivar breeding. Phytopathological tests with races of Venturia inaequalis were performed to differentiate scab-resistance genes in Malus as well as an avirulence gene in the pathogen. A novel gene-for-gene interaction between V. inaequalis and Malus was identified. The locus of the scab-resistance gene Vh8 is linked with, or possibly allelic to, that of the Vh2 gene in Malus pumila Russian apple R12740-7A, at the lower end of linkage group 2 of Malus. Race 8 isolate NZ188B.2 is compatible with Vh8, suggesting the loss or modification of the complementary AvrVh8 gene, while isolate 1639 overcomes both Vh2 and Vh8, but is incompatible with at least one other gene not detected by any of the other race isolates tested. Our research is the first to differentiate scab-resistance genes in a putative gene cluster in apple with the aid of races of V. inaequalis.
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Affiliation(s)
- Vincent G M Bus
- The Horticulture and Food Research Institute of New Zealand Ltd, Hawkes Bay Research Centre, Havelock North, Private Bag 1401, New Zealand.
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Cheng FS, Weeden NF, Brown SK, Aldwinckle HS, Gardiner SE, Bus VG. Development of a DNA marker for Vm, a gene conferring resistance to apple scab. Genome 1998. [DOI: 10.1139/g98-020] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Primers of arbitrary sequence were screened by bulked segregant analysis to identify DNA fragments linked to Vm, a gene conferring resistance to apple scab (Venturia inaequalis). A 687-bp fragment generated by 10-base primer OPB12 gave tight linkage (no recombinants) in a population of 59 individuals from the cross 'Empire' x NY74828-12. The DNA fragment was sequenced, and two specific primers were generated to produce a STS marker for Vm. These primers were used in New Zealand to screen a second population of 180 individuals from a different cross. In this population, the marker displayed 8% recombination with Vm. A survey of Malus germplasm indicated that the marker was present in relatively few accessions, but was present in all known sources of Vm, including the cultivar Murray. However, none of the other sources of scab resistance, nor any other commercial cultivar, displayed the OPB12 fragment. These results suggest that this marker should be useful for the pyramiding of scab resistance genes in cultivated apple and, perhaps, for identifying other accessions in the Malus germplasm collection that possess Vm.Key words: sequence tagged site, gene pyramiding, Malus, Vm.
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Cheng FS, Weeden NF, Brown SK, Aldwinckle HS, Gardiner SE, Bus VG. Development of a DNA marker for Vm, a gene conferring resistance to apple scab. Genome 1998. [DOI: 10.1139/gen-41-2-208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gardiner SE, Bassett HC, Noiton DA, Bus VG, Hofstee ME, White AG, Ball RD, Forster RL, Rikkerink EH. A detailed linkage map around an apple scab resistance gene demonstrates that two disease resistance classes both carry the V f gene. Theor Appl Genet 1996; 93:485-493. [PMID: 24162339 DOI: 10.1007/bf00417939] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/1995] [Accepted: 03/01/1996] [Indexed: 06/02/2023]
Abstract
A detailed genetic map has been constructed in apple (Malus x domestica Borkh.) in the region of the v f gene. This gene confers resistance to the apple scab fungus Venturia inaequalis (Cooke) Wint. Linkage data on four RAPD (random amplified polymorphic DNA) markers and the isoenzyme marker PGM-1, previously reported to be linked to the v f gene, are integrated using two populations segregating for resistance to apple scab. Two new RAPD markers linked to v f (identified by bulked segregant analysis) and a third marker previously reported as being present in several cultivars containing v f are also placed on the map. The map around v f now contains eight genetic markers spread over approximately 28 cM, with markers on both sides of the resistance gene. The study indicates that RAPD markers in the region of crab apple DNA introgressed with resistance are often transportable between apple clones carrying resistance from the same source. Analysis of co-segregation of the resistance classes 3A (weakly resistant) and 3B (weakly susceptible) with the linked set of genetic markers demonstrates that progeny of both classes carry the resistance gene.
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Affiliation(s)
- S E Gardiner
- Batchelar Research Centre, Private Bag 11 030, Palmerston North, New Zealand
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Zhu J, Gardiner SE. Chromosomal localization of ribosomal DNA sequences in an apple rootstock using a digoxygenin detection system. Cell Res 1995. [DOI: 10.1038/cr.1995.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Aiken SG, Gardiner SE, Forde MB. Taxonomic implications of SDS-PAGE analyses of seed proteins in North American taxa of Festuca subgenus Festuca (Poaceae). BIOCHEM SYST ECOL 1992. [DOI: 10.1016/0305-1978(92)90019-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Thompson GA, Roughan PG, Browse JA, Slack CR, Gardiner SE. Spinach Leaves Desaturate Exogenous [C]Palmitate to Hexadecatrienoate : Evidence that de Novo Glycerolipid Synthesis in Chloroplasts Can Utilize Free Fatty Acids Imported from Other Cellular Compartments. Plant Physiol 1986; 82:357-62. [PMID: 16665035 PMCID: PMC1056122 DOI: 10.1104/pp.82.2.357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Long-chain (14)C-fatty acids applied to the surface of expanding spinach leaves were incorporated into all major lipid classes. When applied in diethyleneglycol monomethyl ether solution, as done by previous workers, [(14)C]palmitic acid uptake was much lower than that of [(14)C] oleic acid. However, when applied in a thin film of liquid paraffin the rate of [(14)C] palmitic acid metabolism was rapid and virtually complete. Considerable radioactivity from [(14)C]palmitate incorporated into lipids following either application method gradually appeared in polyunsaturated C(16) fatty acids esterified to those molecular species of galactolipids previously thought to be made using only fatty acids synthesized and retained within the chloroplast. Evidence for the incorporation of radioactivity from exogenous [(14)C]oleate into those same molecular species of galactolipids was less compelling. The unexpected availability of fatty acids bound to extrachloroplastidal lipids for incorporation into galactolipids characteristically assembled entirely within the chloroplast emphasizes the need to reassess interrelations between the "prokaryotic" and "eukaryotic" pathways of galactolipid formation.
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Affiliation(s)
- G A Thompson
- Division of Horticulture and Processing, Department of Scientific and Industrial Research, Auckland, New Zealand
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Abstract
Glycerolipid synthesis was studied in intact chloroplasts isolated from three different plant species. The sequential acylation of sn-glycerol 3-phosphate and lysophosphatidate (1-acyl-sn-glycerol 3-phosphate) was confirmed by monitoring the incorporation of oleate synthesized in situ into lysophosphatidate, phosphatidate and diacylglycerol. Lysophosphatidate was not only readily detected in these experiments, but was also present in the chloroplasts at the beginning of the time courses. The rate of glycerolipid synthesis depended primarily on sn-glycerol 3-phosphate supply, and given adequate sn-glycerol 3-phosphate, the proportion of newly synthesized fatty acids diverted into glycerolipids appeared to be determined by differing acyltransferase activities in the chloroplasts isolated from different plant species.
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Gardiner SE, Heinz E, Roughan PG. Rates and products of long-chain Fatty Acid synthesis from [1-C]acetate in chloroplasts isolated from leaves of 16:3 and 18:3 plants. Plant Physiol 1984; 74:890-6. [PMID: 16663528 PMCID: PMC1066787 DOI: 10.1104/pp.74.4.890] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chloroplasts highly active in the synthesis of long-chain fatty acids from [1-(14)C]acetate were prepared from leaves of Solanum nodiflorum, Chenopodium quinoa, Carthamus tinctorius, and Pisum sativum. These preparations were used to test whether the various additions to incubation media found to stimulate the synthesis of particular lipid classes in vitro by Spinacia oleracea chloroplasts were applicable generally. Chloroplasts from 18:3 plants incorporated a greater proportion of radioactivity into unesterified fatty acids under control conditions than did those from 16:3 plants. Supplying exogenous sn-glycerol 3-phosphate or Triton X-100 to chloroplasts increased the synthesis of glycerolipids in all cases and accentuated the capacity of chloroplasts from 18:3 plants to accumulate phosphatidic acid rather than the diacylglycerol accumulated by chloroplasts from 16:3 plants. The UDP-galactose-dependent synthesis of labeled diacylgalactosylglycerol was much less active in incubations of chloroplasts from 18:3 plants also containing sn-glycerol 3-phosphate and Triton X-100 compared with similar incubations from 16:3 plants. Exogenous CoA stimulated total fatty acid synthesis in all chloroplast preparations and the further addition of ATP diverted radioactivity from the unesterified fatty acid to acyl-CoA. The results have been discussed in terms of the two pathway hypothesis for lipid synthesis in leaves.
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Affiliation(s)
- S E Gardiner
- Plant Physiology Division, Department of Scientific and Industrial Research, Private Bag, Palmerston North, New Zealand
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Gardiner SE, Roughan PG. Relationship between fatty-acyl composition of diacylgalactosylglycerol and turnover of chloroplast phosphatidate. Biochem J 1983; 210:949-52. [PMID: 6870812 PMCID: PMC1154312 DOI: 10.1042/bj2100949] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Chloroplasts from plants that contain different proportions of the 2-hexadecatrienoyl-1-linolenoyl molecular species in total diacylgalactosylglycerol were examined for their ability to dephosphorylate phosphatidate that had been labelled in situ with [1-14C]acetate. The turnover rate of chloroplast phosphatidate may be related to the accumulation of a prokaryotic diacylgalactosylglycerol, suggesting that chloroplast phosphatidate phosphatase controls the fatty acyl composition of the diacylgalactosylglycerol synthesized in the intact plant.
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Gardiner SE, Roughan PG, Slack CR. Manipulating the incorporation of [1-C]acetate into different leaf glycerolipids in several plant species. Plant Physiol 1982; 70:1316-20. [PMID: 16662673 PMCID: PMC1065881 DOI: 10.1104/pp.70.5.1316] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
During short term labeling of expanding leaves of seven plant species with [1-(14)C]acetate, 35 to 64% of the label incorporated into lipids was found in phosphatidylcholine and 5 to 24% in phosphatidylglycerol. In pumpkin, sunflower, broad bean, and maize, only 4 to 12% of the label was found in diacylgalactosylglycerol, but in tomato, parsley, and spinach, the proportion was 17 to 31%. The latter group was further distinguished by having diacylgalactosylglycerol containing C16:3.The proportions of total incorporated [1-(14)C]acetate entering the lipids could be manipulated in a predictable manner. Phosphatidylcholine labeling was depressed by treating intact leaves with glycerol or ethylene glycol monomethyl ether or by incubating leaf discs in vitro. An associated increase in phosphatidylglycerol labeling occurred within the first group of plants, whereas an increase in labeling of either diacylgalactosylglycerol, phosphatidylglycerol, or sulfolipid occurred within the second group. Treating intact leaves with glycerol or incubating leaf discs in vitro was shown to elevate cellular concentrations of sn-glycerol 3-phosphate.These results have been interpreted in terms of the two-pathway hypothesis for glycerolipid biosynthesis, in which it is proposed that phosphatidylcholine is synthesized via a different pathway (eukaryotic) to that for synthesis of phosphatidylglycerol (prokaryotic). Both pathways may contribute toward the synthesis of diacylgalactosylglycerol, with the contribution of each being assessed from the proportion of hexadecatrienoic acid found in the particular plant.
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Affiliation(s)
- S E Gardiner
- Plant Physiology Division, Department of Scientific and Industrial Research, Private Bag, Palmerston North, New Zealand
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