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Gunaseelan K, Schröder R, Rebstock R, Ninan AS, Deng C, Khanal BP, Favre L, Tomes S, Dragulescu MA, O'Donoghue EM, Hallett IC, Schaffer RJ, Knoche M, Brummell DA, Atkinson RG. Constitutive expression of apple endo-POLYGALACTURONASE1 in fruit induces early maturation, alters skin structure and accelerates softening. Plant J 2024; 117:1413-1431. [PMID: 38038980 DOI: 10.1111/tpj.16571] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
During fruit ripening, polygalacturonases (PGs) are key contributors to the softening process in many species. Apple is a crisp fruit that normally exhibits only minor changes to cell walls and limited fruit softening. Here, we explore the effects of PG overexpression during fruit development using transgenic apple lines overexpressing the ripening-related endo-POLYGALACTURONASE1 gene. MdPG1-overexpressing (PGox) fruit displayed early maturation/ripening with black seeds, conversion of starch to sugars and ethylene production occurring by 80 days after pollination (DAP). PGox fruit exhibited a striking, white-skinned phenotype that was evident from 60 DAP and most likely resulted from increased air spaces and separation of cells in the hypodermis due to degradation of the middle lamellae. Irregularities in the integrity of the epidermis and cuticle were also observed. By 120 DAP, PGox fruit cracked and showed lenticel-associated russeting. Increased cuticular permeability was associated with microcracks in the cuticle around lenticels and was correlated with reduced cortical firmness at all time points and extensive post-harvest water loss from the fruit, resulting in premature shrivelling. Transcriptomic analysis suggested that early maturation was associated with upregulation of genes involved in stress responses, and overexpression of MdPG1 also altered the expression of genes involved in cell wall metabolism (e.g. β-galactosidase, MD15G1221000) and ethylene biosynthesis (e.g. ACC synthase, MD14G1111500). The results show that upregulation of PG not only has dramatic effects on the structure of the fruit outer cell layers, indirectly affecting water status and turgor, but also has unexpected consequences for fruit development.
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Affiliation(s)
- Kularajathevan Gunaseelan
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Roswitha Schröder
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Annu S Ninan
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Bishnu P Khanal
- Institute for Horticultural Production Systems, Leibniz-University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Laurie Favre
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sumathi Tomes
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Monica A Dragulescu
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Erin M O'Donoghue
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | | | - Moritz Knoche
- Institute for Horticultural Production Systems, Leibniz-University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - David A Brummell
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
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2
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Tomes S, Gunaseelan K, Dragulescu M, Wang YY, Guo L, Schaffer RJ, Varkonyi-Gasic E. A MADS-box gene-induced early flowering pear ( Pyrus communis L.) for accelerated pear breeding. Front Plant Sci 2023; 14:1235963. [PMID: 37818320 PMCID: PMC10560987 DOI: 10.3389/fpls.2023.1235963] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/28/2023] [Indexed: 10/12/2023]
Abstract
There have been a considerable number of studies that have successfully sped up the flowering cycle in woody perennial horticultural species. One particularly successful study in apple (Malus domestica) accelerated flowering using a silver birch (Betula pendula) APETALA1/FRUITFULL MADS-box gene BpMADS4, which yielded a good balance of vegetative growth to support subsequent flower and fruit development. In this study, BpMADS4 was constitutively expressed in European pear (Pyrus communis) to establish whether this could be used as a tool in a rapid pear breeding program. Transformed pear lines flowered within 6-18 months after grafting onto a quince (Cydonia oblonga) rootstock. Unlike the spindly habit of early flowering apples, the early flowering pear lines displayed a normal tree-like habit. Like apple, the flower appearance was normal, and the flowers were fertile, producing fruit and seed upon pollination. Seed from these transformed lines were germinated and 50% of the progeny flowered within 3 months of sowing, demonstrating a use for these in a fast breeding program.
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Affiliation(s)
- Sumathi Tomes
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Auckland, New Zealand
| | | | - Monica Dragulescu
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Auckland, New Zealand
| | - Yen-Yi Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Auckland, New Zealand
| | - Lindy Guo
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Auckland, New Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Motueka, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Auckland, New Zealand
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Thanomchit K, Imsabai W, Burns P, McAtee PA, Schaffer RJ, Allan AC, Ketsa S. Differential expression of ethylene biosynthetic and receptor genes in pollination-induced senescence of Dendrobium flowers. Plant Physiol Biochem 2022; 188:38-46. [PMID: 35981438 DOI: 10.1016/j.plaphy.2022.08.001] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Following successful pollination, Dendrobium orchid flowers rapidly undergo senescence. In Dendrobium cv. Khao Chaimongkol, compatible pollination resulted in faster ethylene production and more rapid development of senescence symptoms, such as drooping, epinasty, venation and yellowing, compared with non-pollinated controls or pollination with incompatible pollinia. The DenACS1 and DenACO1 genes in the perianth of florets that had been pollinated with compatible pollinia were expressed more highly than those in non-pollinated open florets. Incompatible pollinia reduced the expression of DenACS1 and DenACO1 genes in the perianth. Transcript levels of the ethylene receptor gene DenERS1 and signaling genes DenEIL1 and DenERF1 showed differential spatial regulation with greater expression in the perianth than in the column plus ovary following compatible pollination. Compatible pollinia increased ethylene production concomitant with premature senescence and the increased expression of the DenACS1 and DenACO1 genes, and suppressed the ethylene receptor gene DenERS1, whereas incompatible pollinia did not stimulate ethylene production nor induce premature senescence but induced higher expression of DenERS1 both in the perianth and in the column plus ovary. These results suggest that the increased ethylene production in open florets pollinated with compatible pollen was partially due to an increase in the expression of DenACS1 and DenACO1 genes. The compatible pollinia induced a negative regulation of DenERS1 which may play an important role in ethylene perception and in modulating ethylene signaling transduction during pollinia-induced flower senescence.
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Affiliation(s)
- Kanokwan Thanomchit
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Wachiraya Imsabai
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom, 73140, Thailand
| | - Parichart Burns
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, PathumThani, 12120, Thailand
| | - Peter A McAtee
- Plant and Food Research Institute, Mt Albert Research Center, Private Bag 92019, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- Plant and Food Research Institute, Mt Albert Research Center, Private Bag 92019, Auckland, 1142, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew C Allan
- Plant and Food Research Institute, Mt Albert Research Center, Private Bag 92019, Auckland, 1142, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Saichol Ketsa
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand; Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, 10300, Thailand.
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Tian Y, Thrimawithana A, Ding T, Guo J, Gleave A, Chagné D, Ampomah‐Dwamena C, Ireland HS, Schaffer RJ, Luo Z, Wang M, An X, Wang D, Gao Y, Wang K, Zhang H, Zhang R, Zhou Z, Yan Z, Zhang L, Zhang C, Cong P, Deng CH, Yao J. Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). Plant Biotechnol J 2022; 20:1285-1297. [PMID: 35258172 PMCID: PMC9241373 DOI: 10.1111/pbi.13806] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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Affiliation(s)
- Yi Tian
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Amali Thrimawithana
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Tiyu Ding
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Jian Guo
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Andrew Gleave
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - David Chagné
- PFRPalmerston North Research CentrePalmerston NorthNew Zealand
| | - Charles Ampomah‐Dwamena
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Hilary S. Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- School of Biological SciencesAuckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Meili Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xiuhong An
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Dajiang Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Yuan Gao
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Kun Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhe Zhou
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liyi Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Caixia Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Peihua Cong
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Jia‐Long Yao
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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5
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Ireland HS, Wu C, Deng CH, Hilario E, Saei A, Erasmuson S, Crowhurst RN, David KM, Schaffer RJ, Chagné D. The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae. Hortic Res 2021; 8:233. [PMID: 34719690 PMCID: PMC8558331 DOI: 10.1038/s41438-021-00662-4] [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] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/28/2021] [Accepted: 07/30/2021] [Indexed: 05/03/2023]
Abstract
The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a 'rosetta stone' for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.
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Affiliation(s)
- Hilary S Ireland
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ali Saei
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sylvia Erasmuson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 4704, Christchurch Mail Centre, Christchurch, 8140, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Karine M David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, 55 Old Mill Road, RD 3, Motueka, 7198, New Zealand
| | - David Chagné
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand.
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6
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Nieuwenhuizen NJ, Chen X, Pellan M, Zhang L, Guo L, Laing WA, Schaffer RJ, Atkinson RG, Allan AC. Regulation of wound ethylene biosynthesis by NAC transcription factors in kiwifruit. BMC Plant Biol 2021; 21:411. [PMID: 34496770 PMCID: PMC8425125 DOI: 10.1186/s12870-021-03154-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 08/02/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The phytohormone ethylene controls many processes in plant development and acts as a key signaling molecule in response to biotic and abiotic stresses: it is rapidly induced by flooding, wounding, drought, and pathogen attack as well as during abscission and fruit ripening. In kiwifruit (Actinidia spp.), fruit ripening is characterized by two distinct phases: an early phase of system-1 ethylene biosynthesis characterized by absence of autocatalytic ethylene, followed by a late burst of autocatalytic (system-2) ethylene accompanied by aroma production and further ripening. Progress has been made in understanding the transcriptional regulation of kiwifruit fruit ripening but the regulation of system-1 ethylene biosynthesis remains largely unknown. The aim of this work is to better understand the transcriptional regulation of both systems of ethylene biosynthesis in contrasting kiwifruit organs: fruit and leaves. RESULTS A detailed molecular study in kiwifruit (A. chinensis) revealed that ethylene biosynthesis was regulated differently between leaf and fruit after mechanical wounding. In fruit, wound ethylene biosynthesis was accompanied by transcriptional increases in 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), ACC oxidase (ACO) and members of the NAC class of transcription factors (TFs). However, in kiwifruit leaves, wound-specific transcriptional increases were largely absent, despite a more rapid induction of ethylene production compared to fruit, suggesting that post-transcriptional control mechanisms in kiwifruit leaves are more important. One ACS member, AcACS1, appears to fulfil a dominant double role; controlling both fruit wound (system-1) and autocatalytic ripening (system-2) ethylene biosynthesis. In kiwifruit, transcriptional regulation of both system-1 and -2 ethylene in fruit appears to be controlled by temporal up-regulation of four NAC (NAM, ATAF1/2, CUC2) TFs (AcNAC1-4) that induce AcACS1 expression by directly binding to the AcACS1 promoter as shown using gel-shift (EMSA) and by activation of the AcACS1 promoter in planta as shown by gene activation assays combined with promoter deletion analysis. CONCLUSIONS Our results indicate that in kiwifruit the NAC TFs AcNAC2-4 regulate both system-1 and -2 ethylene biosynthesis in fruit during wounding and ripening through control of AcACS1 expression levels but not in leaves where post-transcriptional/translational regulatory mechanisms may prevail.
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Affiliation(s)
- Niels J. Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Xiuyin Chen
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - Mickaël Pellan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - Lei Zhang
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
| | - Lindy Guo
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | | | - Robert J. Schaffer
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
- PFR, 55 Old Mill Road, RD 3, Motueka, 7198 New Zealand
| | - Ross G. Atkinson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited (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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7
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Macnee N, Hilario E, Tahir J, Currie A, Warren B, Rebstock R, Hallett IC, Chagné D, Schaffer RJ, Bulley SM. Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation. BMC Plant Biol 2021; 21:334. [PMID: 34261431 PMCID: PMC8278711 DOI: 10.1186/s12870-021-03025-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.
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Affiliation(s)
- Nikolai Macnee
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Ben Warren
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
- PFR, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand
| | - Sean M Bulley
- PFR, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand.
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Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3 (Bethesda) 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
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Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
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9
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Brian L, Warren B, McAtee P, Rodrigues J, Nieuwenhuizen N, Pasha A, David KM, Richardson A, Provart NJ, Allan AC, Varkonyi-Gasic E, Schaffer RJ. A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors. BMC Plant Biol 2021; 21:121. [PMID: 33639842 PMCID: PMC7913447 DOI: 10.1186/s12870-021-02894-x] [Citation(s) in RCA: 3] [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: 10/13/2020] [Accepted: 02/18/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. RESULTS Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. CONCLUSIONS This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
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Affiliation(s)
- Lara Brian
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
| | - Ben Warren
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand
| | - Peter McAtee
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
| | - Jessica Rodrigues
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
| | - Niels Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
| | - Asher Pasha
- Department of Cell & Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
| | - Karine M David
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand
| | - Annette Richardson
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), 121 Keri Downs Road, Kerikeri, 0294, New Zealand
| | - Nicholas J Provart
- Department of Cell & Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand.
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), 55 Old Mill Road, Motueka, 7198, New Zealand.
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10
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Macnee NC, Rebstock R, Hallett IC, Schaffer RJ, Bulley SM. A review of current knowledge about the formation of native peridermal exocarp in fruit. Funct Plant Biol 2020; 47:1019-1031. [PMID: 32571472 DOI: 10.1071/fp19135] [Citation(s) in RCA: 2] [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: 05/21/2019] [Accepted: 05/29/2020] [Indexed: 05/09/2023]
Abstract
The outer skin layer in any plant is essential in offering a protective barrier against water loss and pathogen attack. Within fleshy fruit, the skin supports internal cell layers and can provide the initial cues in attracting seed-dispersing animals. The skin of a fruit, termed the exocarp, is a key element of consumer preference and a target for many breeding programs. Across fruiting species there is a huge diversity of exocarp types and these range from a simple single living cell layer (epidermis) often covered with a waxy layer, to complex multicellular suberised and dead cell layers (periderm), with various intermediate russet forms in between. Each exocarp can be interspersed with other structures such as hairs or spines. The epidermis has been well characterised and remains pluripotent with the help of the cells immediately under the epidermis. The periderm, in contrast, is the result of secondary meristematic activity, which replaces the epidermal layers, and is not well characterised in fruits. In this review we explore the structure, composition and mechanisms that control the development of a periderm type fruit exocarp. We draw upon literature from non-fleshy fruit species that form periderm tissue, from which a considerable amount of research has been undertaken.
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Affiliation(s)
- Nikolai C Macnee
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Mount Albert, Auckland 1025, New Zealand; and School of Biological Science, The University of Auckland, Auckland, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Mount Albert, Auckland 1025, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Mount Albert, Auckland 1025, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Auckland, New Zealand; and The New Zealand Institute for Plant and Food Research Limited, 55 Old Mill Road, RD3, Motueka 7198, New Zealand
| | - Sean M Bulley
- The New Zealand Institute for Plant and Food Research Limited, 412 No. 1 Road, RD2, Te Puke 3182, New Zealand; and Corresponding author.
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11
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Fullerton CG, Prakash R, Ninan AS, Atkinson RG, Schaffer RJ, Hallett IC, Schröder R. Fruit From Two Kiwifruit Genotypes With Contrasting Softening Rates Show Differences in the Xyloglucan and Pectin Domains of the Cell Wall. Front Plant Sci 2020; 11:964. [PMID: 32714354 PMCID: PMC7343912 DOI: 10.3389/fpls.2020.00964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Fruit softening is controlled by hormonal and developmental cues, causing an upregulation of cell wall-associated enzymes that break down the complex sugar matrices in the cell wall. The regulation of this process is complex, with different genotypes demonstrating quite different softening patterns, even when they are closely related. Currently, little is known about the relationship between cell wall structure and the rate of fruit softening. To address this question, the softening of two Actinidia chinensis var. chinensis (kiwifruit) genotypes (a fast 'AC-F' and a slow 'AC-S' softening genotype) was examined using a range of compositional, biochemical, structural, and molecular techniques. Throughout softening, the cell wall structure of the two genotypes was fundamentally different at identical firmness stages. In the hemicellulose domain, xyloglucanase enzyme activity was higher in 'AC-F' at the firm unripe stage, a finding supported by differential expression of xyloglucan transglycosylase/hydrolase genes during softening. In the pectin domain, differences in pectin solubilization and location of methyl-esterified homogalacturonan in the cell wall between 'AC-S' and 'AC-F' were shown. Side chain analyses and molecular weight elution profiles of polyuronides and xyloglucans of cell wall extracts revealed fundamental differences between the genotypes, pointing towards a weakening of the structural integrity of cell walls in the fast softening 'AC-F' genotype even at the firm, unripe stage. As a consequence, the polysaccharides in the cell walls of 'AC-F' may be easier to access and hence more susceptible to enzymatic degradation than in 'AC-S', resulting in faster softening. Together these results suggest that the different rates of softening between 'AC-F' and 'AC-S' are not due to changes in enzyme activities alone, but that fundamental differences in the cell wall structure are likely to influence the rates of softening through differential modification and accessibility of specific cell wall polysaccharides during ripening.
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Affiliation(s)
- Christina G. Fullerton
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
- Joint Graduate School of Plant and Food Science, University of Auckland, Auckland, New Zealand
| | - Roneel Prakash
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
| | - Annu Smitha Ninan
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
| | - Ross G. Atkinson
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
| | - Robert J. Schaffer
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
- Joint Graduate School of Plant and Food Science, University of Auckland, Auckland, New Zealand
| | - Ian C. Hallett
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
| | - Roswitha Schröder
- The New Zealand Institute For Plant & Food Research Limited (Plant & Food Research), Auckland, New Zealand
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12
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Richardson AT, Cho J, McGhie TK, Larsen DS, Schaffer RJ, Espley RV, Perry NB. Discovery of a stable vitamin C glycoside in crab apples (Malus sylvestris). Phytochemistry 2020; 173:112297. [PMID: 32070800 DOI: 10.1016/j.phytochem.2020.112297] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/10/2019] [Revised: 02/08/2020] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
Non-targeted LC-MS metabolomics on fruit of three wild and domesticated apple species (Malus sylvestris, M. sieversii and M. domestica) showed that two crab apple (M. sylvestris) accessions were distinguished by high concentrations of an ascorbic acid glycoside (AAG). This was partly purified, but key NMR signals were masked by inseparable sucrose. Reference samples of 2-O-β-D-glucopyranosyl L-ascorbic acid and 2-O-β-D-galactopyranosyl L-ascorbic acid were synthesised, but both coincided with the crab apple AAG on LC-MS. Peracetylation of the crab apple extract allowed both purification and characterisation, and the AAG was proven to be 2-O-β-D-glucopyranosyl L-ascorbic acid by comparison of 1H NMR, HRMS and HPLC data with synthesised peracetylated ascorbyl glycoside standards. The stability of the natural AA 2-β-glycoside was similar to synthetic 2-O-α-D-glucopyranosyl L-ascorbic acid, used widely in cosmetic and pharmaceutical products. This discovery in crab apples (Rosaceae) is only the fourth reported occurrence of any ascorbyl glycoside from plants, the others being from Cucurbitaceae, Solanaceae and Brassicaceae. It is hypothesised that AAGs may be more widespread in plants than currently realised.
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Affiliation(s)
| | - Jung Cho
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Tony K McGhie
- Plant & Food Research, Private Bag 11600, Palmerston North, New Zealand
| | - David S Larsen
- Department of Chemistry, University of Otago, P. O. Box 56, Dunedin, New Zealand
| | - Robert J Schaffer
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Nigel B Perry
- Department of Chemistry, University of Otago, P. O. Box 56, Dunedin, New Zealand; Plant & Food Research, Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand.
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13
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Collins PP, O'donoghue EM, Rebstock R, Tiffin HR, Sutherland PW, Schröder R, McAtee PA, Prakash R, Ireland HS, Johnston JW, Atkinson RG, Schaffer RJ, Hallett IC, Brummell DA. Cell type-specific gene expression underpins remodelling of cell wall pectin in exocarp and cortex during apple fruit development. J Exp Bot 2019; 70:6085-6099. [PMID: 31408160 DOI: 10.1093/jxb/erz370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 06/14/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
In apple (Malus×domestica) fruit, the different layers of the exocarp (cuticle, epidermis, and hypodermis) protect and maintain fruit integrity, and resist the turgor-driven expansion of the underlying thin-walled cortical cells during growth. Using in situ immunolocalization and size exclusion epitope detection chromatography, distinct cell type differences in cell wall composition in the exocarp were revealed during apple fruit development. Epidermal cell walls lacked pectic (1→4)-β-d-galactan (associated with rigidity), whereas linear (1→5)-α-l-arabinan (associated with flexibility) was exclusively present in the epidermal cell walls in expanding fruit and then appeared in all cell types during ripening. Branched (1→5)-α-l-arabinan was uniformly distributed between cell types. Laser capture microdissection and RNA sequencing (RNA-seq) were used to explore transcriptomic differences controlling cell type-specific wall modification. The RNA-seq data indicate that the control of cell wall composition is achieved through cell-specific gene expression of hydrolases. In epidermal cells, this results in the degradation of galactan side chains by possibly five β-galactosidases (BGAL2, BGAL7, BGAL10, BGAL11, and BGAL103) and debranching of arabinans by α-arabinofuranosidases AF1 and AF2. Together, these results demonstrate that flexibility and rigidity of the different cell layers in apple fruit during development and ripening are determined, at least in part, by the control of cell wall pectin remodelling.
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Affiliation(s)
- Patrick P Collins
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Heather R Tiffin
- PFR, Food Industry Science Centre, Palmerston North, New Zealand
| | - Paul W Sutherland
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Roswitha Schröder
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Peter A McAtee
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Roneel Prakash
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Hilary S Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | | | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - Robert J Schaffer
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- PFR, Motueka, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand
- PFR, Food Industry Science Centre, Palmerston North, New Zealand
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14
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Gunaseelan K, McAtee PA, Nardozza S, Pidakala P, Wang R, David K, Burdon J, Schaffer RJ. Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes. PLoS One 2019; 14:e0216120. [PMID: 31083658 PMCID: PMC6513069 DOI: 10.1371/journal.pone.0216120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/14/2019] [Indexed: 12/31/2022] Open
Abstract
The ETYHLENE RESPONSE FACTOR/APETALA2 (ERF/AP2) transcription factors have been shown to control a wide range of developmental and environmental responses in plants. These include hormonal responses to ethylene and Abscisic Acid (ABA) as well as to cold and drought. In Actinidia chinensis (kiwifruit), ripening is unusual: although it is sometimes classed as a climacteric fruit (ethylene-associated ripening), much of fruit ripening occurs independently from autocatalytic ethylene production. Initiation of ripening appears to be strongly developmentally controlled and modulated by low temperature. In this study, fruit treated with different temperatures showed an increase in soluble sugar accumulation, and a corresponding increase in ß-AMYLASE (BAM) genes (predominantly BAM3.2 and BAM9) with lower temperatures. To investigate the potential role of the AP2/ERF gene family in the control of fruit ripening in kiwifruit this family was investigated further. Using the new genome annotation and further genome sequence analysis we identified 226 ERF-like genes, 10 AP2L/RAV-like genes and 32 AP2-like genes. An RNA-seq screen from kiwifruit of different maturities, and following treatment with ethylene and temperatures between 0 and 16°C, revealed 4%, 26% and 18% of the ERF-like genes were upregulated by maturation, ethylene and cold temperatures, respectively. Focusing on the C-REPEAT/DRE BINDING FACTOR (CBF) cold master regulators, nine potential genes were identified based on sequence similarity. Five of these CBF-like genes were found in a copy number variant (CNV) cluster of six genes on chromosome 14. Expression analysis showed that two homeologous genes (ERF41 and ERF180) increased in abundance with cold and ethylene, while the cluster of CNV CBF-like genes had lost the ability to respond to cold and increased only with ethylene, suggesting an evolutionary progression of function of these genes.
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Affiliation(s)
| | - Peter A. McAtee
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Simona Nardozza
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Paul Pidakala
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Ruiling Wang
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Karine David
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jeremy Burdon
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Robert J. Schaffer
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, New Zealand
- * E-mail:
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15
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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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16
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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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17
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Thongkum M, Imsabai W, Burns P, McAtee PA, Schaffer RJ, Allan AC, Ketsa S. The effect of 1-methylcyclopropene (1-MCP) on expression of ethylene receptor genes in durian pulp during ripening. Plant Physiol Biochem 2018; 125:232-238. [PMID: 29475089 DOI: 10.1016/j.plaphy.2018.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 01/04/2018] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 05/11/2023]
Abstract
Rapid fruit ripening is a significant problem that limits the shelf life of durian, with ethylene having a major impact on the regulation of this event. Durian treated with ethephon ripened 3 d after treatment with increased pulp total soluble solids, ethylene production of the whole fruit and decreased pulp firmness compared to the control fruit. 1-MCP treatment delayed ripening by up to 9 d with inhibited accumulation of total soluble solids, color change, softening and ethylene production. Genes related to ethylene perception (DzETR1 and DzETR2) and the signaling pathway (DzCTR1, DzEIL1 and DzEIL2) in the pulp were investigated during this process, using qPCR to quantify changes in gene transcription. All candidate genes were significantly up-regulated in ripening durian pulp. Ethephon treatment increased the expression of DzETR1 and DzETR2 genes, while expression of DzCTR1, DzEIL1 and DzEIL2 were slightly affected. 1-MCP treatment significantly inhibited the expression of the DzETR2 and DzEIL1 genes. The promoters of DzETR2 genes were isolated and their activation by fruit transcription factors studied using transient expression in tobacco leaves. It was found that members of the kiwifruit and apple EIL1, EIL2 and EIL3 genes strongly activated the DzETR2 promoter. These results suggest that ethylene-induced ripening of durian is via the regulation of DzETR2 by EIL transcription factors.
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Affiliation(s)
- Monthathip Thongkum
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Wachiraya Imsabai
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Parichart Burns
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, PathumThani 12120, Thailand
| | - Peter A McAtee
- Plant and Food Research Institute, Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Robert J Schaffer
- Plant and Food Research Institute, Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Andrew C Allan
- Plant and Food Research Institute, Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Saichol Ketsa
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand; Academy of Science, The Royal Society, Dusit, Bangkok 10300, Thailand.
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18
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Yao J, Xu J, Tomes S, Cui W, Luo Z, Deng C, Ireland HS, Schaffer RJ, Gleave AP. Ectopic expression of the PISTILLATA homologous MdPI inhibits fruit tissue growth and changes fruit shape in apple. Plant Direct 2018; 2:e00051. [PMID: 31245717 PMCID: PMC6508508 DOI: 10.1002/pld3.51] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
Abstract
Fruit shape represents a key trait that consumers use to identify and select preferred cultivars, and although the manipulation of this trait is an opportunity to create novel, differentiated products, the molecular mechanisms regulating fruit shape are poorly understood in tree fruits. In this study, we have shown that ectopic expression of Malus domestica PISTILLATA (MdPI), the apple ortholog of the floral organ identity gene PISTILLATA (PI), regulates apple fruit tissue growth and shape. MdPI is a single-copy gene, and its expression is high during flower development but barely detectable soon after pollination. Transgenic apple plants with ectopic expression of MdPI produced flowers with white sepals and a conversion of sepals to petals. Interestingly, these plants produced distinctly flattened fruit as a consequence of reduced cell growth at the basipetal position of the fruit. These altered sepal and fruit phenotypes have not been observed in studies using Arabidopsis. This study using apple has advanced our understanding of PI functions outside the control of petal and stamen identity and provided molecular genetic information useful for manipulating fruit tissue growth and fruit shape.
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Affiliation(s)
- Jia‐Long Yao
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Wei Cui
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Hilary S. Ireland
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Andrew P. Gleave
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
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19
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Gapper NE, Hertog MLATM, Lee J, Buchanan DA, Leisso RS, Fei Z, Qu G, Giovannoni JJ, Johnston JW, Schaffer RJ, Nicolaï BM, Mattheis JP, Watkins CB, Rudell DR. Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. BMC Plant Biol 2017; 17:77. [PMID: 28431510 PMCID: PMC5399402 DOI: 10.1186/s12870-017-1030-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/12/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Superficial scald is a physiological disorder of apple fruit characterized by sunken, necrotic lesions appearing after prolonged cold storage, although initial injury occurs much earlier in the storage period. To determine the degree to which the transition to cell death is an active process and specific metabolism involved, untargeted metabolic and transcriptomic profiling was used to follow metabolism of peel tissue over 180 d of cold storage. RESULTS The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using antioxidant (diphenylamine; DPA) or rendered insensitive to ethylene using 1-methylcyclopropene (1-MCP) beginning between 30 and 60 days of storage. Overall metabolic and transcriptomic shifts, representing multiple pathways and processes, occurred alongside α-farnesene oxidation and, later, methanol production alongside symptom development. CONCLUSIONS Results indicate this form of peel necrosis is a product of an active metabolic transition involving multiple pathways triggered by chilling temperatures at cold storage inception rather than physical injury. Among multiple other pathways, enhanced methanol and methyl ester levels alongside upregulated pectin methylesterases are unique to peel that is developing scald symptoms similar to injury resulting from mechanical stress and herbivory in other plants.
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Affiliation(s)
- Nigel E. Gapper
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY 14853 USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
- Present addresses: AgroFresh, Wenatchee, WA 98801 USA
| | | | - Jinwook Lee
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
- Present addresses: Department of Horticultural Sciences, Mokpo National University, Muan, Korea
| | - David A. Buchanan
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | - Rachel S. Leisso
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Guiqin Qu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
- United States Department of Agriculture, Agricultural Research Service, Plant, Soil, and Nutrition Laboratory, Ithaca, NY 14853 USA
| | - Jason W. Johnston
- The New Zealand Institute for Plant and Food Research, Ltd, Havelock North, New Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research, Ltd, Auckland, New Zealand
| | | | - James P. Mattheis
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | | | - David R. Rudell
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
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20
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Leisso RS, Gapper NE, Mattheis JP, Sullivan NL, Watkins CB, Giovannoni JJ, Schaffer RJ, Johnston JW, Hanrahan I, Hertog MLATM, Nicolaï BM, Rudell DR. Gene expression and metabolism preceding soft scald, a chilling injury of 'Honeycrisp' apple fruit. BMC Genomics 2016; 17:798. [PMID: 27733113 PMCID: PMC5062943 DOI: 10.1186/s12864-016-3019-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/13/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND 'Honeycrisp' is an apple cultivar that is susceptible to soft scald, a chilling injury expressed as necrotic patches on the peel. Improved understanding of metabolism associated with the disorder would improve our understanding of soft scald and contribute to developing more effective management strategies for apple storage. It was expected that specific gene expression and specific metabolite levels in the peel would be linked with soft scald risk at harvest and/or specific time points during cold storage. RESULTS Fruit from nine 'Honeycrisp' apple orchards that would eventually develop different incidences of soft scald between 4 and 8 weeks of cold air storage were used to contrast and determine differential transcriptomic and metabolomic changes during storage. Untargeted metabolic profiling revealed changes in a number of distinct pathways preceding and concurrent with soft scald symptom development, including elevated γ-aminobutryic acid (GABA), 1-hexanol, acylated steryl glycosides, and free p-coumaryl acyl esters. At harvest, levels of sesquiterpenoid and triterpenoid acyl esters were relatively higher in peel of fruit that did not later develop the disorder. RNA-seq driven gene expression profiling highlighted possible involvement of genes and associated metabolic processes with soft scald development. These included elevated expression of genes involved in lipid peroxidation and phenolic metabolism in fruit with soft scald, and isoprenoid/brassinosteroid metabolism in fruit that did not develop soft scald. Expression of other stress-related genes in fruit that developed soft scald included chlorophyll catabolism, cell wall loosening, and lipid transport while superoxide dismutases were up-regulated in fruit that did not develop the disorder. CONCLUSIONS This study delineates the sequential transcriptomic and metabolomic changes preceding soft scald symptom development. Changes were differential depending on susceptibility of fruit to the disorder and could be attributed to key stress related and mediating pathways.
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Affiliation(s)
- Rachel S Leisso
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Nigel E Gapper
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY14853, USA
- AgroFresh Solutions Inc. 130 Technology Center Way Wenatchee, Wenatchee, WA 98801, WA, USA
| | - James P Mattheis
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Nathanael L Sullivan
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Christopher B Watkins
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY14853, USA
- United States Department of Agriculture, Agricultural Research Service, Plant, Soil, and Nutrition Laboratory, Ithaca, NY14853, USA
| | - Robert J Schaffer
- The New Zealand Institute for Plant and Food Research, Ltd, Auckland, New Zealand
| | - Jason W Johnston
- The New Zealand Institute for Plant and Food Research, Ltd, Havelock North, New Zealand
| | - Ines Hanrahan
- Washington Tree Fruit Research Commission, Wenatchee, WA, USA
| | | | | | - David R Rudell
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA.
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21
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McAtee PA, Richardson AC, Nieuwenhuizen NJ, Gunaseelan K, Hoong L, Chen X, Atkinson RG, Burdon JN, David KM, Schaffer RJ. The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of MADS-box transcription factors. BMC Plant Biol 2015; 15:304. [PMID: 26714876 PMCID: PMC4696264 DOI: 10.1186/s12870-015-0697-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ripening in tomato is predominantly controlled by ethylene, whilst in fruit such as grape, it is predominantly controlled by other hormones. The ripening response of many kiwifruit (Actinidia) species is atypical. The majority of ripening-associated fruit starch hydrolysis, colour change and softening occurs in the apparent absence of ethylene production (Phase 1 ripening) whilst Phase 2 ripening requires autocatalytic ethylene production and is associated with further softening and an increase in aroma volatiles. RESULTS To dissect the ripening response in the yellow-fleshed kiwifruit A. chinensis ('Hort16A'), a two dimensional developmental stage X ethylene response time study was undertaken. As fruit progressed through maturation and Phase 1 ripening, fruit were treated with different concentrations of propylene and ethylene. At the start of Phase 1 ripening, treated fruit responded to ethylene, and were capable of producing endogenous ethylene. As the fruit progressed through Phase 1 ripening, the fruit became less responsive to ethylene and endogeneous ethylene production was partially repressed. Towards the end of Phase 1 ripening the fruit were again able to produce high levels of ethylene. Progression through Phase 1 ripening coincided with a developmental increase in the expression of the ethylene-unresponsive MADS-box FRUITFUL-like gene (FUL1). The ability to respond to ethylene however coincided with a change in expression of another MADS-box gene SEPALLATA4/RIPENING INHIBITOR-like (SEP4/RIN). The promoter of SEP4/RIN was shown to be transactivated by EIN3-like transcription factors, but unlike tomato, not by SEP4/RIN itself. Transient over-expression of SEP4/RIN in kiwifruit caused an increase in ethylene production. CONCLUSIONS These results suggest that the non-ethylene/ethylene ripening response observed in kiwifruit is a hybrid of both the tomato and grape ripening progression, with Phase 1 being akin to the RIN/ethylene inhibitory response observed in grape and Phase 2 akin to the RIN-associated autocatalytic ethylene response observed in tomato.
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Affiliation(s)
- Peter A McAtee
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | | | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ling Hoong
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Jeremy N Burdon
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Karine M David
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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22
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Leisso RS, Buchanan DA, Lee J, Mattheis JP, Sater C, Hanrahan I, Watkins CB, Gapper N, Johnston JW, Schaffer RJ, Hertog MLATM, Nicolaï BM, Rudell DR. Chilling-related cell damage of apple (Malus × domestica Borkh.) fruit cortical tissue impacts antioxidant, lipid and phenolic metabolism. Physiol Plant 2015; 153:204-20. [PMID: 24944043 DOI: 10.1111/ppl.12244] [Citation(s) in RCA: 14] [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: 12/10/2013] [Revised: 04/07/2014] [Accepted: 05/14/2014] [Indexed: 05/09/2023]
Abstract
'Soggy breakdown' (SB) is an internal flesh disorder of 'Honeycrisp' apple (Malus × domestica Borkh.) fruit that occurs during low temperature storage. The disorder is a chilling injury (CI) in which visible symptoms typically appear after several weeks of storage, but information about the underlying metabolism associated with its induction and development is lacking. The metabolic profile of flesh tissue from wholly healthy fruit and brown and healthy tissues from fruit with SB was characterized using gas chromatography-mass spectrometry (GC-MS) and liquid chromatograph-mass spectrometry (LC-MS). Partial least squares discriminant analysis (PLS-DA) and correlation networks revealed correlation among ester volatile compounds by composition and differences in phytosterol, phenolic and putative triacylglycerides (TAGs) metabolism among the tissues. anova-simultaneous component analysis (ASCA) was used to test the significance of metabolic changes linked with tissue health status. ASCA-significant components included antioxidant compounds, TAGs, and phytosterol conjugates. Relative to entirely healthy tissues, elevated metabolite levels in symptomatic tissue included γ-amino butyric acid, glycerol, sitosteryl (6'-O-palmitoyl) β-d-glucoside and sitosteryl (6'-O-stearate) β-d-glucoside, and TAGs containing combinations of 16:0, 18:3, 18:2 and 18:1 fatty acids. Reduced metabolite levels in SB tissue included 5-caffeoyl quinate, β-carotene, catechin, epicatechin, α-tocopherol, violaxanthin and sitosteryl β-d glucoside. Pathway analysis indicated aspects of primary metabolism differed according to tissue condition, although differences in metabolites involved were more subtle than those of some secondary metabolites. The results implicate oxidative stress and membrane disruption processes in SB development and constitute a diagnostic metabolic profile for the disorder.
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Affiliation(s)
- Rachel S Leisso
- United States Department of Agriculture - Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA; Department of Horticulture, Washington State University, Pullman, WA, USA
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23
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Mellidou I, Buts K, Hatoum D, Ho QT, Johnston JW, Watkins CB, Schaffer RJ, Gapper NE, Giovannoni JJ, Rudell DR, Hertog MLATM, Nicolai BM. Transcriptomic events associated with internal browning of apple during postharvest storage. BMC Plant Biol 2014; 14:328. [PMID: 25430515 PMCID: PMC4272543 DOI: 10.1186/s12870-014-0328-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 09/08/2014] [Accepted: 11/07/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Postharvest ripening of apple (Malus x domestica) can be slowed down by low temperatures, and a combination of low O2 and high CO2 levels. While this maintains the quality of most fruit, occasionally storage disorders such as flesh browning can occur. This study aimed to explore changes in the apple transcriptome associated with a flesh browning disorder related to controlled atmosphere storage using RNA-sequencing techniques. Samples from a browning-susceptible cultivar ('Braeburn') were stored for four months under controlled atmosphere. Based on a visual browning index, the inner and outer cortex of the stored apples was classified as healthy or affected tissue. RESULTS Over 600 million short single-end reads were mapped onto the Malus consensus coding sequence set, and differences in the expression profiles between healthy and affected tissues were assessed to identify candidate genes associated with internal browning in a tissue-specific manner. Genes involved in lipid metabolism, secondary metabolism, and cell wall modifications were highly modified in the affected inner cortex, while energy-related and stress-related genes were mostly altered in the outer cortex. The expression levels of several of them were confirmed using qRT-PCR. Additionally, a set of novel browning-specific differentially expressed genes, including pyruvate dehydrogenase and 1-aminocyclopropane-1-carboxylate oxidase, was validated in apples stored for various periods at different controlled atmosphere conditions, giving rise to potential biomarkers associated with high risk of browning development. CONCLUSIONS The gene expression data presented in this study will help elucidate the molecular mechanism of browning development in apples at controlled atmosphere storage. A conceptual model, including energy-related (linked to the tricarboxylic acid cycle and the electron transport chain) and lipid-related genes (related to membrane alterations, and fatty acid oxidation), for browning development in apple is proposed, which may be relevant for future studies towards improving the postharvest life of apple.
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Affiliation(s)
- Ifigeneia Mellidou
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
| | - Kim Buts
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
| | - Darwish Hatoum
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
| | - Quang Tri Ho
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
| | - Jason W Johnston
- />The New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Private Bag 92169, Auckland 1142 New Zealand
| | | | - Robert J Schaffer
- />The New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Private Bag 92169, Auckland 1142 New Zealand
- />The University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Nigel E Gapper
- />Department of Horticulture, Cornell University, Ithaca, NY 14853 USA
- />Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Jim J Giovannoni
- />Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
- />Plant, Soil, and Nutrition Laboratory, US Department of Agriculture/Agriculture Research Service, Ithaca, NY 14853 USA
| | - David R Rudell
- />Fruit Tree Research Laboratory, US Department of Agriculture/Agriculture Research Service, Wenatchee, WA 9880 USA
| | - Maarten LATM Hertog
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
| | - Bart M Nicolai
- />Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, Leuven, 3001 Belgium
- />Flanders Centre of Postharvest Technology, Willem de Croylaan 42, Leuven, 3001 Belgium
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24
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Ireland HS, Gunaseelan K, Muddumage R, Tacken EJ, Putterill J, Johnston JW, Schaffer RJ. Ethylene regulates Apple (Malus x domestica) fruit softening through a dose x time-dependent mechanism and through differential sensitivities and dependencies of cell wall-modifying genes. Plant Cell Physiol 2014; 55:1005-16. [PMID: 24553848 DOI: 10.1093/pcp/pcu034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 05/03/2023]
Abstract
In fleshy fruit species that have a strong requirement for ethylene to ripen, ethylene is synthesized autocatalytically, producing increasing concentrations as the fruits ripen. Apple fruit with the ACC OXIDASE 1 (ACO1) gene suppressed cannot produce ethylene autocatalytically at ripening. Using these apple lines, an ethylene sensitivity dependency model was previously proposed, with traits such as softening showing a high dependency for ethylene as well as low sensitivity. In this study, it is shown that the molecular control of fruit softening is a complex process, with different cell wall-related genes being independently regulated and exhibiting differential sensitivities to and dependencies on ethylene at the transcriptional level. This regulation is controlled through a dose × time mechanism, which results in a temporal transcriptional response that would allow for progressive cell wall disassembly and thus softening. This research builds on the sensitivity dependency model and shows that ethylene-dependent traits can progress over time to the same degree with lower levels of ethylene. This suggests that a developmental clock measuring cumulative ethylene controls the fruit ripening process.
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Affiliation(s)
- Hilary S Ireland
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92169, Auckland 1142, New Zealand
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25
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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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26
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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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27
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Ireland HS, Yao JL, Tomes S, Sutherland PW, Nieuwenhuizen N, Gunaseelan K, Winz RA, David KM, Schaffer RJ. Apple SEPALLATA1/2-like genes control fruit flesh development and ripening. Plant J 2013; 73:1044-56. [PMID: 23236986 DOI: 10.1111/tpj.12094] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/29/2012] [Accepted: 12/10/2012] [Indexed: 05/19/2023]
Abstract
Flowering plants utilize different floral structures to develop flesh tissue in fruits. Here we show that suppression of the homeologous SEPALLATA1/2-like genes MADS8 and MADS9 in the fleshy fruit apple (Malus x domestica) leads to sepaloid petals and greatly reduced fruit flesh. Immunolabelling of cell-wall epitopes and differential staining showed that the developing hypanthium (from which the apple flesh develops) of MADS8/9-suppressed apple flowers lacks a tissue layer, and the remaining flesh tissue of fully developed apples has considerably smaller cells. From these observations, it is proposed that MADS8 and MADS9 control the development of discrete zones within the hypanthium tissue, and therefore fruit flesh, and also act as foundations for development of different floral organs. At fruit maturity, the MADS8/9-suppressed apples do not ripen in terms of both developmentally controlled ripening characters, such as starch degradation, and ethylene-modulated ripening traits. Transient assays suggest that, like the RIN gene in tomato, the MADS9 gene acts as a transcriptional activator of the ethylene biosynthesis enzyme, 1-aminocyclopropane-1-carboxylate (ACC) synthase 1. The existence of a single class of genes that regulate both flesh formation and ripening provides an evolutionary tool for controlling two critical aspects of fleshy fruit development.
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Affiliation(s)
- Hilary S Ireland
- New Zealand Institute of Plant & Food Research Ltd, Private Bag 92169, Auckland, 1142, New Zealand
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28
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Schaffer RJ, Ireland HS, Ross JJ, Ling TJ, David KM. SEPALLATA1/2-suppressed mature apples have low ethylene, high auxin and reduced transcription of ripening-related genes. AoB Plants 2013; 5:pls047. [PMID: 23346344 PMCID: PMC3551604 DOI: 10.1093/aobpla/pls047] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 12/04/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Fruit ripening is an important developmental trait in fleshy fruits, making the fruit palatable for seed dispersers. In some fruit species, there is a strong association between auxin concentrations and fruit ripening. We investigated the relationship between auxin concentrations and the onset of ethylene-related ripening in Malus × domestica (apples) at both the hormone and transcriptome levels. METHODOLOGY Transgenic apples suppressed for the SEPALLATA1/2 (SEP1/2) class of gene (MADS8/9) that showed severely reduced ripening were compared with untransformed control apples. In each apple type, free indole-3-acetic acid (IAA) concentrations were measured during early ripening. The changes observed in auxin were assessed in light of global changes in gene expression. PRINCIPAL RESULTS It was found that mature MADS8/9-suppressed apples had a higher concentration of free IAA. This was associated with increased expression of the auxin biosynthetic genes in the indole-3-acetamide pathway. Additionally, in the MADS8/9-suppressed apples, there was less expression of the GH3 auxin-conjugating enzymes. A number of genes involved in the auxin-regulated transcription (AUX/IAA and ARF classes of genes) were also observed to change in expression, suggesting a mechanism for signal transduction at the start of ripening. CONCLUSIONS The delay in ripening observed in MADS8/9-suppressed apples may be partly due to high auxin concentrations. We propose that, to achieve low auxin associated with fruit maturation, the auxin homeostasis is controlled in a two-pronged manner: (i) by the reduction in biosynthesis and (ii) by an increase in auxin conjugation. This is associated with the change in expression of auxin-signalling genes and the up-regulation of ripening-related genes.
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Affiliation(s)
- Robert J. Schaffer
- The New Zealand Institute of Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Corresponding author's e-mail address:
| | - Hilary S. Ireland
- The New Zealand Institute of Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand
| | - John J. Ross
- School of Plant Science, University of Tasmania, GPO Box 252-55, Hobart, Tasmania 7001, Australia
| | - Toby J. Ling
- School of Plant Science, University of Tasmania, GPO Box 252-55, Hobart, Tasmania 7001, Australia
| | - Karine M. David
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Tacken EJ, Ireland HS, Wang YY, Putterill J, Schaffer RJ. Apple EIN3 BINDING F-box 1 inhibits the activity of three apple EIN3-like transcription factors. AoB Plants 2012; 2012:pls034. [PMID: 23585922 PMCID: PMC3624930 DOI: 10.1093/aobpla/pls034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 09/25/2012] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Fruit ripening in Malus× domestica (apple) is controlled by ethylene. Work in model species has shown that following the detection of ethylene, the ETHYLENE INSENSITIVE 3 (EIN3) transcription factor is stabilized, leading to an increase in transcript accumulation of ethylene-responsive genes, such as POLYGALACTURONASE1 (PG1). In the absence of ethylene, the EIN3 BINDING F-box (EBF) proteins rapidly degrade EIN3 via the ubiquitination/SCF (Skp, Cullin, F-Box) proteasome pathway. In this study, we aim to identify and characterize the apple EBF genes, and test their activity against apple EIN3-like proteins (EILs). METHODOLOGY The apple genome sequence was mined for EBF-like genes. The expression of EBF-like genes was measured during fruit development. Using a transient assay in Nicotiana benthamiana leaves, the activity of three apple EILs was tested against the PG1 promoter, with and without ethylene and EBF1. PRINCIPAL RESULTS Four EBF-like genes in apple were identified and grouped into two sub-clades. Sub-clade I genes had constant expression over fruit development while sub-clade II genes increased in expression at ripening. EBF1 was shown to reduce the transactivation of the apple PG1 promoter by the EIL1, EIL2 and EIL3 transcription factors in the presence of ethylene. CONCLUSIONS The apple EBF1 gene identified here is likely to be a functionally conserved EBF orthologue, modulating EIL activity in apples. The activity of EBF1 suggests that it is not specific to a single EIL, instead acting as a global regulator of apple EIL transcription factors.
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Affiliation(s)
- Emma J. Tacken
- The New Zealand Institute of Plant and Food
Research, Private Bag 92169, Auckland 1142,
New Zealand
- School of Biological Sciences, University of
Auckland, Private Bag 92019, Auckland 1142,
New Zealand
| | - Hilary S. Ireland
- The New Zealand Institute of Plant and Food
Research, Private Bag 92169, Auckland 1142,
New Zealand
| | - Yen-Yi Wang
- The New Zealand Institute of Plant and Food
Research, Private Bag 92169, Auckland 1142,
New Zealand
| | - Jo Putterill
- School of Biological Sciences, University of
Auckland, Private Bag 92019, Auckland 1142,
New Zealand
| | - Robert J. Schaffer
- The New Zealand Institute of Plant and Food
Research, 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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30
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Atkinson RG, Sutherland PW, Johnston SL, Gunaseelan K, Hallett IC, Mitra D, Brummell DA, Schröder R, Johnston JW, Schaffer RJ. Down-regulation of POLYGALACTURONASE1 alters firmness, tensile strength and water loss in apple (Malus x domestica) fruit. BMC Plant Biol 2012; 12:129. [PMID: 22856470 PMCID: PMC3509026 DOI: 10.1186/1471-2229-12-129] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/25/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND While there is now a significant body of research correlating apple (Malus x domestica) fruit softening with the cell wall hydrolase ENDO-POLYGALACTURONASE1 (PG1), there is currently little knowledge of its physiological effects in planta. This study examined the effect of down regulation of PG1 expression in 'Royal Gala' apples, a cultivar that typically has high levels of PG1, and softens during fruit ripening. RESULTS PG1-suppressed 'Royal Gala' apples harvested from multiple seasons were firmer than controls after ripening, and intercellular adhesion was higher. Cell wall analyses indicated changes in yield and composition of pectin, and a higher molecular weight distribution of CDTA-soluble pectin. Structural analyses revealed more ruptured cells and free juice in pulled apart sections, suggesting improved integrity of intercellular connections and consequent cell rupture due to failure of the primary cell walls under stress. PG1-suppressed lines also had reduced expansion of cells in the hypodermis of ripe apples, resulting in more densely packed cells in this layer. This change in morphology appears to be linked with reduced transpirational water loss in the fruit. CONCLUSIONS These findings confirm PG1's role in apple fruit softening and suggests that this is achieved in part by reducing cellular adhesion. This is consistent with previous studies carried out in strawberry but not with those performed in tomato. In apple PG1 also appears to influence other fruit texture characters such as juiciness and water loss.
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Affiliation(s)
- Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Paul W Sutherland
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Sarah L Johnston
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Deepali Mitra
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - David A Brummell
- PFR, Food Industry Science Centre, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Roswitha Schröder
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Jason W Johnston
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand
- The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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31
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Richardson AC, Boldingh HL, McAtee PA, Gunaseelan K, Luo Z, Atkinson RG, David KM, Burdon JN, Schaffer RJ. Fruit development of the diploid kiwifruit, Actinidia chinensis 'Hort16A'. BMC Plant Biol 2011; 11:182. [PMID: 22204446 PMCID: PMC3261216 DOI: 10.1186/1471-2229-11-182] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 12/28/2011] [Indexed: 05/05/2023]
Abstract
BACKGROUND With the advent of high throughput genomic tools, it is now possible to undertake detailed molecular studies of individual species outside traditional model organisms. Combined with a good understanding of physiological processes, these tools allow researchers to explore natural diversity, giving a better understanding of biological mechanisms. Here a detailed study of fruit development from anthesis through to fruit senescence is presented for a non-model organism, kiwifruit, Actinidia chinensis ('Hort16A'). RESULTS Consistent with previous studies, it was found that many aspects of fruit morphology, growth and development are similar to those of the model fruit tomato, except for a striking difference in fruit ripening progression. The early stages of fruit ripening occur as the fruit is still growing, and many ripening events are not associated with autocatalytic ethylene production (historically associated with respiratory climacteric). Autocatalytic ethylene is produced late in the ripening process as the fruit begins to senesce. CONCLUSION By aligning A. chinensis fruit development to a phenological scale, this study provides a reference framework for subsequent physiological and genomic studies, and will allow cross comparison across fruit species, leading to a greater understanding of the diversity of fruits found across the plant kingdom.
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Affiliation(s)
- Annette C Richardson
- The New Zealand Institute for Plant & Food Research Limited (PFR), PO Box 23, Kerikeri, 0245, New Zealand
| | | | - Peter A McAtee
- PFR Mount Albert Private Bag 92169, Auckland, 1142, New Zealand
- The University of Auckland, School of Biological Sciences, Private Bag 92019 Auckland, 1142, New Zealand
| | | | - Zhiwei Luo
- PFR Mount Albert Private Bag 92169, Auckland, 1142, New Zealand
| | - Ross G Atkinson
- PFR Mount Albert Private Bag 92169, Auckland, 1142, New Zealand
| | - Karine M David
- The University of Auckland, School of Biological Sciences, Private Bag 92019 Auckland, 1142, New Zealand
| | - Jeremy N Burdon
- PFR Mount Albert Private Bag 92169, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- PFR Mount Albert Private Bag 92169, Auckland, 1142, New Zealand
- The University of Auckland, School of Biological Sciences, Private Bag 92019 Auckland, 1142, New Zealand
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32
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Atkinson RG, Gunaseelan K, Wang MY, Luo L, Wang T, Norling CL, Johnston SL, Maddumage R, Schröder R, Schaffer RJ. Dissecting the role of climacteric ethylene in kiwifruit (Actinidia chinensis) ripening using a 1-aminocyclopropane-1-carboxylic acid oxidase knockdown line. J Exp Bot 2011; 62:3821-35. [PMID: 21511911 DOI: 10.1093/jxb/err063] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
During climacteric fruit ripening, autocatalytic (Type II) ethylene production initiates a transcriptional cascade that controls the production of many important fruit quality traits including flavour production and softening. The last step in ethylene biosynthesis is the conversion of 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene by the enzyme ACC oxidase (ACO). Ten independent kiwifruit (Actinidia chinensis) lines were generated targeting suppression of fruit ripening-related ACO genes and the fruit from one of these lines (TK2) did not produce detectable levels of climacteric ethylene. Ripening behaviour in a population of kiwifruit at harvest is asynchronous, so a short burst of exogenous ethylene was used to synchronize ripening in TK2 and control fruit. Following such a treatment, TK2 and control fruit softened to an 'eating-ripe' firmness. Control fruit produced climacteric ethylene and softened beyond eating-ripe by 5 d. In contrast, TK2 fruit maintained an eating-ripe firmness for >25 d and total volatile production was dramatically reduced. Application of continuous exogenous ethylene to the ripening-arrested TK2 fruit re-initiated fruit softening and typical ripe fruit volatiles were detected. A 17 500 gene microarray identified 401 genes that changed after ethylene treatment, including a polygalacturonase and a pectate lyase involved in cell wall breakdown, and a quinone oxidoreductase potentially involved in volatile production. Many of the gene changes were consistent with the softening and flavour changes observed after ethylene treatment. However, a surprisingly large number of genes of unknown function were also observed, which could account for the unique flavour and textural properties of ripe kiwifruit.
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Affiliation(s)
- Ross G Atkinson
- New Zealand Institute for Plant and Food Research Ltd , Auckland, New Zealand.
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33
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Tacken E, Ireland H, Gunaseelan K, Karunairetnam S, Wang D, Schultz K, Bowen J, Atkinson RG, Johnston JW, Putterill J, Hellens RP, Schaffer RJ. The role of ethylene and cold temperature in the regulation of the apple POLYGALACTURONASE1 gene and fruit softening. Plant Physiol 2010; 153:294-305. [PMID: 20237022 PMCID: PMC2862417 DOI: 10.1104/pp.109.151092] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/12/2010] [Indexed: 05/18/2023]
Abstract
Fruit softening in apple (Malus x domestica) is associated with an increase in the ripening hormone ethylene. Here, we show that in cv Royal Gala apples that have the ethylene biosynthetic gene ACC OXIDASE1 suppressed, a cold treatment preconditions the apples to soften independently of added ethylene. When a cold treatment is followed by an ethylene treatment, a more rapid softening occurs than in apples that have not had a cold treatment. Apple fruit softening has been associated with the increase in the expression of cell wall hydrolase genes. One such gene, POLYGALACTURONASE1 (PG1), increases in expression both with ethylene and following a cold treatment. Transcriptional regulation of PG1 through the ethylene pathway is likely to be through an ETHYLENE-INSENSITIVE3-like transcription factor, which increases in expression during apple fruit development and transactivates the PG1 promoter in transient assays in the presence of ethylene. A cold-related gene that resembles a COLD BINDING FACTOR (CBF) class of gene also transactivates the PG1 promoter. The transactivation by the CBF-like gene is greatly enhanced by the addition of exogenous ethylene. These observations give a possible molecular mechanism for the cold- and ethylene-regulated control of fruit softening and suggest that either these two pathways act independently and synergistically with each other or cold enhances the ethylene response such that background levels of ethylene in the ethylene-suppressed apples is sufficient to induce fruit softening in apples.
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Dardick CD, Callahan AM, Chiozzotto R, Schaffer RJ, Piagnani MC, Scorza R. Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. BMC Biol 2010; 8:13. [PMID: 20144217 PMCID: PMC2830173 DOI: 10.1186/1741-7007-8-13] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [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: 10/29/2009] [Accepted: 02/09/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Lignification of the fruit endocarp layer occurs in many angiosperms and plays a critical role in seed protection and dispersal. This process has been extensively studied with relationship to pod shatter or dehiscence in Arabidopsis. Dehiscence is controlled by a set of transcription factors that define the fruit tissue layers and whether or not they lignify. In contrast, relatively little is known about similar processes in other plants such as stone fruits which contain an extremely hard lignified endocarp or stone surrounding a single seed. RESULTS Here we show that lignin deposition in peach initiates near the blossom end within the endocarp layer and proceeds in a distinct spatial-temporal pattern. Microarray studies using a developmental series from young fruits identified a sharp and transient induction of phenylpropanoid, lignin and flavonoid pathway genes concurrent with lignification and subsequent stone hardening. Quantitative polymerase chain reaction studies revealed that specific phenylpropanoid (phenylalanine ammonia-lyase and cinnamate 4-hydroxylase) and lignin (caffeoyl-CoA O-methyltransferase, peroxidase and laccase) pathway genes were induced in the endocarp layer over a 10 day time period, while two lignin genes (p-coumarate 3-hydroxylase and cinnamoyl CoA reductase) were co-regulated with flavonoid pathway genes (chalcone synthase, dihydroflavanol 4-reductase, leucoanthocyanidin dioxygen-ase and flavanone-3-hydrosylase) which were mesocarp and exocarp specific. Analysis of other fruit development expression studies revealed that flavonoid pathway induction is conserved in the related Rosaceae species apple while lignin pathway induction is not. The transcription factor expression of peach genes homologous to known endocarp determinant genes in Arabidopsis including SHATTERPROOF, SEEDSTCK and NAC SECONDARY WALL THICENING PROMOTING FACTOR 1 were found to be specifically expressed in the endocarp while the negative regulator FRUITFUL predominated in exocarp and mesocarp. CONCLUSIONS Collectively, the data suggests, first, that the process of endocarp determination and differentiation in peach and Arabidopsis share common regulators and, secondly, reveals a previously unknown coordination of competing lignin and flavonoid biosynthetic pathways during early fruit development.
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Affiliation(s)
- Christopher D Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture, Agricultural Research Service, Kearneysville, WV, 25430, USA
| | - Ann M Callahan
- Appalachian Fruit Research Station, United States Department of Agriculture, Agricultural Research Service, Kearneysville, WV, 25430, USA
| | - Remo Chiozzotto
- Department of Crop Production, Fruit Tree Unit, University of Milan, Milan 20133, Italy
| | - Robert J Schaffer
- The New Zealand Institute of Plant and Food Research, Mt Albert, Auckland 1142, New Zealand
| | - M Claudia Piagnani
- Department of Crop Production, Fruit Tree Unit, University of Milan, Milan 20133, Italy
| | - Ralph Scorza
- Appalachian Fruit Research Station, United States Department of Agriculture, Agricultural Research Service, Kearneysville, WV, 25430, USA
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35
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Johnston JW, Gunaseelan K, Pidakala P, Wang M, Schaffer RJ. Co-ordination of early and late ripening events in apples is regulated through differential sensitivities to ethylene. J Exp Bot 2009; 60:2689-99. [PMID: 19429839 PMCID: PMC2692014 DOI: 10.1093/jxb/erp122] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [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: 01/18/2009] [Revised: 03/22/2009] [Accepted: 03/24/2009] [Indexed: 05/19/2023]
Abstract
In this study, it is shown that anti-sense suppression of Malus domestica 1-AMINO-CYCLOPROPANE-CARBOXYLASE OXIDASE (MdACO1) resulted in fruit with an ethylene production sufficiently low to be able to assess ripening in the absence of ethylene. Exposure of these fruit to different concentrations of exogenous ethylene showed that flesh softening, volatile biosynthesis, and starch degradation, had differing ethylene sensitivity and dependency. Early ripening events such as the conversion of starch to sugars showed a low dependency for ethylene, but a high sensitivity to low concentrations of ethylene (0.01 microl l(-1)). By contrast, later ripening events such as flesh softening and ester volatile production showed a high dependency for ethylene but were less sensitive to low concentrations (needing 0.1 microl l(-1) for a response). A sustained exposure to ethylene was required to maintain ripening, indicating that the role of ethylene may go beyond that of ripening initiation. These results suggest a conceptual model for the control of individual ripening characters in apple, based on both ethylene dependency and sensitivity.
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Affiliation(s)
| | | | | | | | - Robert J. Schaffer
- The New Zealand Institute For Plant & Food Research Limited, Private Bag 92169, Auckland, New Zealand
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36
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McAtee PA, Hallett IC, Johnston JW, Schaffer RJ. A rapid method of fruit cell isolation for cell size and shape measurements. Plant Methods 2009; 5:5. [PMID: 19402911 PMCID: PMC2685799 DOI: 10.1186/1746-4811-5-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 04/29/2009] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cell size is a structural component of fleshy fruit, contributing to important traits such as fruit size and texture. There are currently a number of methods for measuring cell size; most rely either on tissue sectioning or digestion of the tissue with cell wall degrading enzymes or chemicals to release single cells. Neither of these approaches is ideal for assaying large fruit numbers as both require a considerable time to prepare the tissue, with current methods of cell wall digestions taking 24 to 48 hours. Additionally, sectioning can lead to a measurement of a plane that does not represent the widest point of the cell. RESULTS To develop a more rapid way of measuring fruit cell size we have developed a protocol that solubilises pectin in the middle lamella of the plant cell wall releasing single cells into a buffered solution. Gently boiling small fruit samples in a 0.05 M Na2CO3 solution, osmotically balanced with 0.3 M mannitol, produced good cell separation with little cellular damage in less than 30 minutes. The advantage of combining a chemical treatment with boiling is that the cells are rapidly killed. This stopped cell shape changes that could potentially occur during separation. With this method both the rounded and angular cells of the apple cultivars SciRos 'Pacific Rose' and SciFresh 'Jazz' were observed in the separated cells. Using this technique, an in-depth analysis was performed measuring cell size from 5 different apple cultivars. Cell size was measured using the public domain ImageJ software. For each cultivar a minimum of 1000 cells were measured and it was found that each cultivar displayed a different distribution of cell size. Cell size within cultivars was similar and there was no correlation between flesh firmness and cell size. This protocol was tested on tissue from other fleshy fruit including tomato, rock melon and kiwifruit. It was found that good cell separation was achieved with flesh tissue from all these fruit types, showing a broad utility to this protocol. CONCLUSION We have developed a method for isolating single cells from fleshy fruit that reduces the time needed for fruit cell separation. This method was used to demonstrate differences in cell size and shape for 5 different apple cultivars. While firmness between the different cultivars is independent of cell size, apples with more angular cells appear to be firmer.
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Affiliation(s)
- Peter A McAtee
- The New Zealand Institute for Plant & Food Research, Private Bag 92169, Auckland 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant & Food Research, Private Bag 92169, Auckland 1142, New Zealand
| | - Jason W Johnston
- The New Zealand Institute for Plant & Food Research, Private Bag 92169, Auckland 1142, New Zealand
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research, Private Bag 92169, Auckland 1142, New Zealand
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37
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Rowan DD, Cao M, Lin-Wang K, Cooney JM, Jensen DJ, Austin PT, Hunt MB, Norling C, Hellens RP, Schaffer RJ, Allan AC. Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis thaliana. New Phytol 2009; 182:102-115. [PMID: 19192188 DOI: 10.1111/j.1469-8137.2008.02737.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
* High-temperature, low-light (HTLL) treatment of 35S:PAP1 Arabidopsis thaliana over-expressing the PAP1 (Production of Anthocyanin Pigment 1) gene results in reversible reduction of red colouration, suggesting the action of additional anthocyanin regulators. High-performance liquid chromatography (HPLC), liquid chromatography mass spectrometry (LCMS) and Affimetrix-based microarrays were used to measure changes in anthocyanin, flavonoids, and gene expression in response to HTLL. * HTLL treatment of control and 35S:PAP1 A. thaliana resulted in a reversible reduction in the concentrations of major anthocyanins despite ongoing over-expression of the PAP1 MYB transcription factor. Twenty-one anthocyanins including eight cis-coumaryl esters were identified by LCMS. The concentrations of nine anthocyanins were reduced and those of three were increased, consistent with a sequential process of anthocyanin degradation. Analysis of gene expression showed down-regulation of flavonol and anthocyanin biosynthesis and of transport-related genes within 24 h of HTLL treatment. No catabolic genes up-regulated by HTLL were found. * Reductions in the concentrations of anthocyanins and down-regulation of the genes of anthocyanin biosynthesis were achieved by environmental manipulation, despite ongoing over-expression of PAP1. Quantitative PCR showed reduced expression of three genes (TT8, TTG1 and EGL3) of the PAP1 transcriptional complex, and increased expression of the potential transcriptional repressors AtMYB3, AtMYB6 and AtMYBL2 coincided with HTLL-induced down-regulation of anthocyanin biosynthesis. * HTLL treatment offers a model system with which to explore anthocyanin catabolism and to discover novel genes involved in the environmental control of anthocyanins.
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Affiliation(s)
- Daryl D Rowan
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11 030, Palmerston North, New Zealand
| | - Mingshu Cao
- AgResearch Grasslands, AgResearch Limited, Private Bag 11008, Palmerston North, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92 169, Auckland, New Zealand
| | - Janine M Cooney
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3123, Hamilton, New Zealand
| | - Dwayne J Jensen
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3123, Hamilton, New Zealand
| | - Paul T Austin
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11 030, Palmerston North, New Zealand
| | - Martin B Hunt
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11 030, Palmerston North, New Zealand
| | - Cara Norling
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11 030, Palmerston North, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92 169, Auckland, New Zealand
| | - Robert J Schaffer
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92 169, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92 169, Auckland, New Zealand
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38
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Walton EF, Wu RM, Richardson AC, Davy M, Hellens RP, Thodey K, Janssen BJ, Gleave AP, Rae GM, Wood M, Schaffer RJ. A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds. J Exp Bot 2009; 60:3835-48. [PMID: 19651683 PMCID: PMC2736901 DOI: 10.1093/jxb/erp231] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [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: 04/30/2009] [Revised: 06/19/2009] [Accepted: 06/22/2009] [Indexed: 05/19/2023]
Abstract
Budbreak in kiwifruit (Actinidia deliciosa) can be poor in locations that have warm winters with insufficient winter chilling. Kiwifruit vines are often treated with the dormancy-breaking chemical hydrogen cyanamide (HC) to increase and synchronize budbreak. This treatment also offers a tool to understand the processes involved in budbreak. A genomics approach is presented here to increase our understanding of budbreak in kiwifruit. Most genes identified following HC application appear to be associated with responses to stress, but a number of genes appear to be associated with the reactivation of growth. Three patterns of gene expression were identified: Profile 1, an HC-induced transient activation; Profile 2, an HC-induced transient activation followed by a growth-related activation; and Profile 3, HC- and growth-repressed. One group of genes that was rapidly up-regulated in response to HC was the glutathione S-transferase (GST) class of genes, which have been associated with stress and signalling. Previous budbreak studies, in three other species, also report up-regulated GST expression. Phylogenetic analysis of these GSTs showed that they clustered into two sub-clades, suggesting a strong correlation between their expression and budbreak across species.
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Affiliation(s)
- Eric F Walton
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand.
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Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, Bulley SM, Chagne D, Marsh KB, Matich AJ, Montefiori M, Newcomb RD, Schaffer RJ, Usadel B, Allan AC, Boldingh HL, Bowen JH, Davy MW, Eckloff R, Ferguson AR, Fraser LG, Gera E, Hellens RP, Janssen BJ, Klages K, Lo KR, MacDiarmid RM, Nain B, McNeilage MA, Rassam M, Richardson AC, Rikkerink EH, Ross GS, Schröder R, Snowden KC, Souleyre EJF, Templeton MD, Walton EF, Wang D, Wang MY, Wang YY, Wood M, Wu R, Yauk YK, Laing WA. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 2008; 9:351. [PMID: 18655731 PMCID: PMC2515324 DOI: 10.1186/1471-2164-9-351] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [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: 03/25/2008] [Accepted: 07/27/2008] [Indexed: 11/13/2022] Open
Abstract
Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.
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Affiliation(s)
- Ross N Crowhurst
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, New Zealand.
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Dare AP, Schaffer RJ, Lin-Wang K, Allan AC, Hellens RP. Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes. Plant Methods 2008; 4:17. [PMID: 18601751 PMCID: PMC2491621 DOI: 10.1186/1746-4811-4-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2008] [Accepted: 07/07/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND Transcription factors (TFs) co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs.In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1) leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. RESULTS Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. CONCLUSION Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA, it does provide a tool to characterise cis-regulatory sequences that are necessary for transcription activation in a complex list of co-ordinately regulated genes.
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Affiliation(s)
- Andrew P Dare
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, 1142, New Zealand
| | - Kui Lin-Wang
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, 1142, New Zealand
| | - Andrew C Allan
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, 1142, New Zealand
| | - Roger P Hellens
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, 1142, New Zealand
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Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Bowen JH, Crowhurst RN, Gleave AP, Ledger S, McArtney S, Pichler FB, Snowden KC, Ward S. Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 2008; 8:16. [PMID: 18990244 PMCID: PMC2287172 DOI: 10.1186/1471-2229-8-16] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 02/17/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45-55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple. RESULTS Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes. CONCLUSION Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.
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Affiliation(s)
- Bart J Janssen
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Kate Thodey
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Robert J Schaffer
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Rob Alba
- Boyce Thompson Institute for Plant Research, Tower Road, Cornell University Campus, Ithaca, NY 14853, USA
- Monsanto Company – O3D, Product Safety Center, 800 North Lindbergh Blvd., St. Louis, MO 63167, USA
| | | | - Rebecca Bishop
- 4 La Trobe Track, RD2 New Lynn, Karekare, Auckland, New Zealand
| | - Judith H Bowen
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Ross N Crowhurst
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Andrew P Gleave
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Susan Ledger
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Steve McArtney
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Centre, 455 Research Drive, Fletcher, NC 28732-9244, USA
| | - Franz B Pichler
- Microbial Ecology & Genomics Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kimberley C Snowden
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Shayna Ward
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
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Schaffer RJ, Friel EN, Souleyre EJF, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma JH, Nain B, Cohen D, Gleave AP, Crowhurst RN, Janssen BJ, Yao JL, Newcomb RD. A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway. Plant Physiol 2007; 144:1899-912. [PMID: 17556515 PMCID: PMC1949883 DOI: 10.1104/pp.106.093765] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ethylene is the major effector of ripening in many fleshy fruits. In apples (Malus x domestica) the addition of ethylene causes a climacteric burst of respiration, an increase in aroma, and softening of the flesh. We have generated a transgenic line of 'Royal Gala' apple that produces no detectable levels of ethylene using antisense ACC OXIDASE, resulting in apples with no ethylene-induced ripening attributes. In response to external ethylene these antisense fruits undergo a normal climacteric burst and produced increasing concentrations of ester, polypropanoid, and terpene volatile compounds over an 8-d period. A total of 186 candidate genes that might be involved in the production of these compounds were mined from expressed sequence tags databases and full sequence obtained. Expression patterns of 179 of these were assessed using a 15,720 oligonucleotide apple microarray. Based on sequence similarity and gene expression patterns we identified 17 candidate genes that are likely to be ethylene control points for aroma production in apple. While many of the biosynthetic steps in these pathways were represented by gene families containing two or more genes, expression patterns revealed that only a single member is typically regulated by ethylene. Only certain points within the aroma biosynthesis pathways were regulated by ethylene. Often the first step, and in all pathways the last steps, contained enzymes that were ethylene regulated. This analysis suggests that the initial and final enzymatic steps with the biosynthetic pathways are important transcriptional regulation points for aroma production in apple.
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Affiliation(s)
- Robert J Schaffer
- Horticulture and Food Research Institute of New Zealand, Mt. Albert, Auckland, New Zealand
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Fuller RW, Schaffer RJ, Roush BW, Molloy BB. Drug disposition as a factor in the lowering of brain serotonin by chloroamphetamines in the rat. Biochem Pharmacol 1972; 21:1413-7. [PMID: 5029422 DOI: 10.1016/0006-2952(72)90365-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Stark P, Fuller RW, Hartlery LW, Schaffer RJ, Turk JA. Dissociation of the effects of p-chlorophenylalanine on self-stimulation and on brain serotonin. Life Sci 1970; 9:41-8. [PMID: 5435853 DOI: 10.1016/0024-3205(70)90008-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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