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Broad RC, Bonneau JP, Hellens RP, Johnson AA. Manipulation of Ascorbate Biosynthetic, Recycling, and Regulatory Pathways for Improved Abiotic Stress Tolerance in Plants. Int J Mol Sci 2020; 21:E1790. [PMID: 32150968 PMCID: PMC7084844 DOI: 10.3390/ijms21051790] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 02/03/2023] Open
Abstract
Abiotic stresses, such as drought, salinity, and extreme temperatures, are major limiting factors in global crop productivity and are predicted to be exacerbated by climate change. The overproduction of reactive oxygen species (ROS) is a common consequence of many abiotic stresses. Ascorbate, also known as vitamin C, is the most abundant water-soluble antioxidant in plant cells and can combat oxidative stress directly as a ROS scavenger, or through the ascorbate-glutathione cycle-a major antioxidant system in plant cells. Engineering crops with enhanced ascorbate concentrations therefore has the potential to promote broad abiotic stress tolerance. Three distinct strategies have been utilized to increase ascorbate concentrations in plants: (i) increased biosynthesis, (ii) enhanced recycling, or (iii) modulating regulatory factors. Here, we review the genetic pathways underlying ascorbate biosynthesis, recycling, and regulation in plants, including a summary of all metabolic engineering strategies utilized to date to increase ascorbate concentrations in model and crop species. We then highlight transgene-free strategies utilizing genome editing tools to increase ascorbate concentrations in crops, such as editing the highly conserved upstream open reading frame that controls translation of the GDP-L-galactose phosphorylase gene.
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Affiliation(s)
- Ronan C. Broad
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Julien P. Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4001, Australia
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Broad RC, Bonneau JP, Beasley JT, Roden S, Sadowski P, Jewell N, Brien C, Berger B, Tako E, Glahn RP, Hellens RP, Johnson AAT. Effect of Rice GDP-L-Galactose Phosphorylase Constitutive Overexpression on Ascorbate Concentration, Stress Tolerance, and Iron Bioavailability in Rice. Front Plant Sci 2020; 11:595439. [PMID: 33343598 PMCID: PMC7744345 DOI: 10.3389/fpls.2020.595439] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 11/16/2020] [Indexed: 05/12/2023]
Abstract
Ascorbate (vitamin C) is an essential multifunctional molecule for both plants and mammals. In plants, ascorbate is the most abundant water-soluble antioxidant that supports stress tolerance. In humans, ascorbate is an essential micronutrient and promotes iron (Fe) absorption in the gut. Engineering crops with increased ascorbate levels have the potential to improve both crop stress tolerance and human health. Here, rice (Oryza sativa L.) plants were engineered to constitutively overexpress the rice GDP-L-galactose phosphorylase coding sequence (35S-OsGGP), which encodes the rate-limiting enzymatic step of the L-galactose pathway. Ascorbate concentrations were negligible in both null segregant (NS) and 35S-OsGGP brown rice (BR, unpolished grain), but significantly increased in 35S-OsGGP germinated brown rice (GBR) relative to NS. Foliar ascorbate concentrations were significantly increased in 35S-OsGGP plants in the vegetative growth phase relative to NS, but significantly reduced at the reproductive growth phase and were associated with reduced OsGGP transcript levels. The 35S-OsGGP plants did not display altered salt tolerance at the vegetative growth phase despite having elevated ascorbate concentrations. Ascorbate concentrations were positively correlated with ferritin concentrations in Caco-2 cells - an accurate predictor of Fe bioavailability in human digestion - exposed to in vitro digests of NS and 35S-OsGGP BR and GBR samples.
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Affiliation(s)
- Ronan C. Broad
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Ronan C. Broad,
| | - Julien P. Bonneau
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Jesse T. Beasley
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nathaniel Jewell
- Australian Plant Phenomics Facility and School for Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Chris Brien
- Australian Plant Phenomics Facility and School for Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Bettina Berger
- Australian Plant Phenomics Facility and School for Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Elad Tako
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Raymond P. Glahn
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY, United States
| | - Roger P. Hellens
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
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Broad RC, Bonneau JP, Beasley JT, Roden S, Philips JG, Baumann U, Hellens RP, Johnson AAT. Genome-wide identification and characterization of the GDP-L-galactose phosphorylase gene family in bread wheat. BMC Plant Biol 2019; 19:515. [PMID: 31771507 PMCID: PMC6878703 DOI: 10.1186/s12870-019-2123-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway-the dominant ascorbate biosynthetic pathway in plants-and is a promising gene candidate for increasing ascorbate in crops. In addition to transcriptional regulation, GGP production is regulated at the translational level through an upstream open reading frame (uORF) in the long 5'-untranslated region (5'UTR). The GGP genes have yet to be identified in bread wheat (Triticum aestivum L.), one of the most important food grain sources for humans. RESULTS Bread wheat chromosomal groups 4 and 5 were found to each contain three homoeologous TaGGP genes on the A, B, and D subgenomes (TaGGP2-A/B/D and TaGGP1-A/B/D, respectively) and a highly conserved uORF was present in the long 5'UTR of all six genes. Phylogenetic analyses demonstrated that the TaGGP genes separate into two distinct groups and identified a duplication event of the GGP gene in the ancestor of the Brachypodium/Triticeae lineage. A microsynteny analysis revealed that the TaGGP1 and TaGGP2 subchromosomal regions have no shared synteny suggesting that TaGGP2 may have been duplicated via a transposable element. The two groups of TaGGP genes have distinct expression patterns with the TaGGP1 homoeologs broadly expressed across different tissues and developmental stages and the TaGGP2 homoeologs highly expressed in anthers. Transient transformation of the TaGGP coding sequences in Nicotiana benthamiana leaf tissue increased ascorbate concentrations more than five-fold, confirming their functional role in ascorbate biosynthesis in planta. CONCLUSIONS We have identified six TaGGP genes in the bread wheat genome, each with a highly conserved uORF. Phylogenetic and microsynteny analyses highlight that a transposable element may have been responsible for the duplication and specialized expression of GGP2 in anthers in the Brachypodium/Triticeae lineage. Transient transformation of the TaGGP coding sequences in N. benthamiana demonstrated their activity in planta. The six TaGGP genes and uORFs identified in this study provide a valuable genetic resource for increasing ascorbate concentrations in bread wheat.
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Affiliation(s)
- Ronan C Broad
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Julien P Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Jesse T Beasley
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sally Roden
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Joshua G Philips
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Ute Baumann
- School of Agriculture, The University of Adelaide, Adelaide, South Australia, 5064, Australia
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Alexander A T Johnson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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Philips JG, Dudley KJ, Waterhouse PM, Hellens RP. The Rapid Methylation of T-DNAs Upon Agrobacterium Inoculation in Plant Leaves. Front Plant Sci 2019; 10:312. [PMID: 30930927 PMCID: PMC6428780 DOI: 10.3389/fpls.2019.00312] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/26/2019] [Indexed: 05/10/2023]
Abstract
Agrobacterium tumefaciens has been foundational in the development of transgenic plants for both agricultural biotechnology and plant molecular research. However, the transformation efficiency and level of transgene expression obtained for any given construct can be highly variable. These inefficiencies often require screening of many lines to find one with consistent and heritable transgene expression. Transcriptional gene silencing is known to affect transgene expression, and is associated with DNA methylation, especially of cytosines in symmetric CG and CHG contexts. While the specificity, heritability and silencing-associated effects of DNA methylation of transgene sequences have been analyzed in many stably transformed plants, the methylation status of transgene sequences in the T-DNA during the transformation process has not been well-studied. Here we used agro-infiltration of the eGFP reporter gene in Nicotiana benthamiana leaves driven by either an AtEF1α-A4 or a CaMV-35S promoter to study early T-DNA methylation patterns of these promoter sequences. The T-DNA was examined by amplicon sequencing following sodium bisulfite treatment using three different sequencing platforms: Sanger sequencing, Ion Torrent PGM, and the Illumina MiSeq. Rapid DNA methylation was detectable in each promoter region just 2-3 days post-infiltration and the levels continued to rapidly accumulate over the first week, then steadily up to 21 days later. Cytosines in an asymmetric context (CHH) were the most heavily and rapidly methylated. This suggests that early T-DNA methylation may be important in determining the epigenetic and transcriptional fate of integrated transgenes. The Illumina MiSeq platform was the most sensitive and robust way of detecting and following the methylation profiles of the T-DNA promoters. The utility of the methods was then used to show a subtle but significant difference in promoter methylation during intron-mediated enhancement. In addition, the method was able to detect an increase in promoter methylation when the eGFP reporter gene was targeted by siRNAs generated by co-infiltration of a hairpin RNAi construct.
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Affiliation(s)
- Joshua G. Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- *Correspondence: Joshua G. Philips,
| | - Kevin J. Dudley
- Institute for Future Environments, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
| | - Peter M. Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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5
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Moss SMA, Wang T, Voogd C, Brian LA, Wu R, Hellens RP, Allan AC, Putterill J, Varkonyi‐Gasic E. AcFT promotes kiwifruit in vitro flowering when overexpressed and Arabidopsis flowering when expressed in the vasculature under its own promoter. Plant Direct 2018; 2:e00068. [PMID: 31245732 PMCID: PMC6508797 DOI: 10.1002/pld3.68] [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: 05/02/2018] [Revised: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 05/24/2023]
Abstract
Kiwifruit (Actinidia chinensis) has three FLOWERING LOCUS T (FT) genes, AcFT, AcFT1, and AcFT2, with differential expression and potentially divergent roles. AcFT was previously shown to be expressed in source leaves and induced in dormant buds by winter chilling. Here, we show that AcFT promotes flowering in A. chinensis, despite a short sequence insertion not present in other FT-like genes. A 3.5-kb AcFT promoter region contained all the regulatory elements required to mediate vascular expression in transgenic Arabidopsis thaliana (Arabidopsis). The promoter activation was initially confined to the veins in the distal end of the leaf, before extending to the veins in the base of the leaf, and was detected in inductive and noninductive photoperiods. The 3-kb and 2.7-kb promoter regions of AcFT1 and AcFT2, respectively, demonstrated different activation patterns in Arabidopsis, corresponding to differential expression in kiwifruit. Expression of AcFT cDNA from the AcFT promoter was capable to induce early flowering in transgenic Arabidopsis in noninductive photoperiods. Further, expression of AcFT cDNA fused to the green fluorescent protein was detected in the vasculature and was also capable to advance flowering in noninductive photoperiods. Taken together, these studies implicate AcFT in regulation of kiwifruit flowering time and as a candidate for kiwifruit florigen.
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Affiliation(s)
- Sarah M. A. Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Present address:
The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston NorthPalmerston NorthNew Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Lara A. Brian
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- Present address:
Centre for Tropical Crops and BiocommoditiesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Joanna Putterill
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Erika Varkonyi‐Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
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6
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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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7
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Stewart C, Woods K, Macias G, Allan AC, Hellens RP, Noel JP. Molecular architectures of benzoic acid-specific type III polyketide synthases. Acta Crystallogr D Struct Biol 2017; 73:1007-1019. [PMID: 29199980 PMCID: PMC5713876 DOI: 10.1107/s2059798317016618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 07/11/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022] Open
Abstract
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica. Both biphenyl synthase and benzophenone synthase contain mutations that reshape their active-site cavities to prevent the binding of 4-coumaroyl-CoA and to favor the binding of small hydrophobic substrates. The active-site cavities of biphenyl synthase and benzophenone synthase also contain a novel pocket associated with their chain-elongation and cyclization reactions. Collectively, these results illuminate structural determinants of benzoic acid-specific type III PKSs and expand the understanding of the evolution of specialized metabolic pathways in plants.
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Affiliation(s)
- Charles Stewart
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, 0202 Molecular Biology Building, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Kate Woods
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Greg Macias
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Joseph P. Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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8
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Brendolise C, Espley RV, Lin-Wang K, Laing W, Peng Y, McGhie T, Dejnoprat S, Tomes S, Hellens RP, Allan AC. Multiple Copies of a Simple MYB-Binding Site Confers Trans-regulation by Specific Flavonoid-Related R2R3 MYBs in Diverse Species. Front Plant Sci 2017; 8:1864. [PMID: 29163590 PMCID: PMC5671642 DOI: 10.3389/fpls.2017.01864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
In apple, the MYB transcription factor MYB10 controls the accumulation of anthocyanins. MYB10 is able to auto-activate its expression by binding its own promoter at a specific motif, the R1 motif. In some apple accessions a natural mutation, termed R6, has more copies of this motif within the MYB10 promoter resulting in stronger auto-activation and elevated anthocyanins. Here we show that other anthocyanin-related MYBs selected from apple, pear, strawberry, petunia, kiwifruit and Arabidopsis are able to activate promoters containing the R6 motif. To examine the specificity of this motif, members of the R2R3 MYB family were screened against a promoter harboring the R6 mutation. Only MYBs from subgroups 5 and 6 activate expression by binding the R6 motif, with these MYBs sharing conserved residues in their R2R3 DNA binding domains. Insertion of the apple R6 motif into orthologous promoters of MYB10 in pear (PcMYB10) and Arabidopsis (AtMY75) elevated anthocyanin levels. Introduction of the R6 motif into the promoter region of an anthocyanin biosynthetic enzyme F3'5'H of kiwifruit imparts regulation by MYB10. This results in elevated levels of delphinidin in both tobacco and kiwifruit. Finally, an R6 motif inserted into the promoter the vitamin C biosynthesis gene GDP-L-Gal phosphorylase increases vitamin C content in a MYB10-dependent manner. This motif therefore provides a tool to re-engineer novel MYB-regulated responses in plants.
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Affiliation(s)
- Cyril Brendolise
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Richard V. Espley
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Kui Lin-Wang
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - William Laing
- Fitzherbert Science Centre, Plant and Food Research, Palmerston North, New Zealand
| | - Yongyan Peng
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Tony McGhie
- Fitzherbert Science Centre, Plant and Food Research, Palmerston North, New Zealand
| | - Supinya Dejnoprat
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Sumathi Tomes
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Andrew C. Allan
- Mt Albert Research Centre, Plant and Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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9
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Philips JG, Naim F, Lorenc MT, Dudley KJ, Hellens RP, Waterhouse PM. The widely used Nicotiana benthamiana 16c line has an unusual T-DNA integration pattern including a transposon sequence. PLoS One 2017; 12:e0171311. [PMID: 28231340 PMCID: PMC5322946 DOI: 10.1371/journal.pone.0171311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 11/17/2016] [Accepted: 01/19/2017] [Indexed: 11/29/2022] Open
Abstract
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site. Therefore, using next generation sequencing, genome mapping and local alignment, we identified the location and characteristics of the integrated T-DNA. As suggested from previous molecular hybridisation and inheritance data, the transgenic line contains a single GFP-expressing locus. However, the GFP coding sequence differs from that originally reported. Furthermore, a 3.2 kb portion of a transposon, appears to have co-integrated with the T-DNA. The location of the integration mapped to a region of the genome represented by Nbv0.5scaffold4905 in the www.benthgenome.com assembly, and with less integrity to Niben101Scf03641 in the www.solgenomics.net assembly. The transposon is not endogenous to laboratory strains of N. benthamiana or Agrobacterium tumefaciens strain GV3101 (MP90), which was reportedly used in the generation of line 16c. However, it is present in the popular LBA4404 strain. The integrated transposon sequence includes its 5' terminal repeat and a transposase gene, and is immediately adjacent to the GFP gene. This unexpected genetic arrangement may contribute to the characteristics that have made the 16c line such a popular research tool and alerts researchers, taking transgenic plants to commercial release, to be aware of this genomic hitchhiker.
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Affiliation(s)
- Joshua G. Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Michał T. Lorenc
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Kevin J. Dudley
- Institute for Future Environments, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
| | - Peter M. Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
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10
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Macknight RC, Laing WA, Bulley SM, Broad RC, Johnson AA, Hellens RP. Increasing ascorbate levels in crops to enhance human nutrition and plant abiotic stress tolerance. Curr Opin Biotechnol 2017; 44:153-160. [PMID: 28231513 DOI: 10.1016/j.copbio.2017.01.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/29/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022]
Abstract
Ascorbate (or vitamin C) is an essential human micronutrient predominantly obtained from plants. In addition to preventing scurvy, it is now known to have broader roles in human health, for example as a cofactor for enzymes involved in epigenetic programming and as regulator of cellular iron uptake. Furthermore, ascorbate is the major antioxidant in plants and underpins many environmentally induced abiotic stress responses. Biotechnological approaches to enhance the ascorbate content of crops therefore have potential to improve both human health and abiotic stress tolerance of crops. Identifying the genetic basis of ascorbate variation between plant varieties and discovering how some 'super fruits' accumulate extremely high levels of ascorbate should reveal new ways to more effectively manipulate the production of ascorbate in crops.
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Affiliation(s)
- Richard C Macknight
- University of Otago, Department of Biochemistry, PO Box 56, Dunedin 9054, New Zealand; Queensland University of Technology, Centre for Tropical Crops and Biocommodities, Institute for Future Environments, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - William A Laing
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Bachelor Road, Palmerston North 4474, New Zealand
| | - Sean M Bulley
- The New Zealand Institute for Plant & Food Research Limited, 412 No 1 Road, RD 2, Te Puke 3182, New Zealand
| | - Ronan C Broad
- The University of Melbourne, School of BioSciences, Parkville, Melbourne, 3010 VIC, Australia
| | - Alexander At Johnson
- The University of Melbourne, School of BioSciences, Parkville, Melbourne, 3010 VIC, Australia
| | - Roger P Hellens
- Queensland University of Technology, Centre for Tropical Crops and Biocommodities, Institute for Future Environments, GPO Box 2434, Brisbane, QLD 4001, Australia
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11
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Wu R, Tomes S, Karunairetnam S, Tustin SD, Hellens RP, Allan AC, Macknight RC, Varkonyi-Gasic E. SVP-like MADS Box Genes Control Dormancy and Budbreak in Apple. Front Plant Sci 2017; 8:477. [PMID: 28421103 PMCID: PMC5378812 DOI: 10.3389/fpls.2017.00477] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/20/2017] [Indexed: 05/18/2023]
Abstract
The annual growth cycle of trees is the result of seasonal cues. The onset of winter triggers an endodormant state preventing bud growth and, once a chilling requirement is satisfied, these buds enter an ecodormant state and resume growing. MADS-box genes with similarity to Arabidopsis SHORT VEGETATIVE PHASE (SVP) [the SVP-like and DORMANCY ASSOCIATED MADS-BOX (DAM) genes] have been implicated in regulating flowering and growth-dormancy cycles in perennials. Here, we identified and characterized three DAM-like (MdDAMs) and two SHORT VEGETATIVE PHASE-like (MdSVPs) genes from apple (Malus × domestica 'Royal Gala'). The expression of MdDAMa and MdDAMc indicated they may play a role in triggering autumn growth cessation. In contrast, the expression of MdDAMb, MdSVPa and MdSVPb suggested a role in maintaining bud dormancy. Consistent with this, ectopic expression of MdDAMb and MdSVPa in 'Royal Gala' apple plants resulted in delayed budbreak and architecture change due to constrained lateral shoot outgrowth, but normal flower and fruit development. The association of MdSVPa and MdSVPb expression with floral bud development in the low fruiting 'Off' trees of a biennial bearing cultivar 'Sciros' suggested the SVP genes might also play a role in floral meristem identity.
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Affiliation(s)
- Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
| | - Stuart D. Tustin
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchHawke’s Bay, New Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
- School of Biological Sciences, University of AucklandAuckland, New Zealand
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited – Plant & Food ResearchAuckland, New Zealand
- *Correspondence: Erika Varkonyi-Gasic,
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12
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Bond DM, Albert NW, Lee RH, Gillard GB, Brown CM, Hellens RP, Macknight RC. Infiltration-RNAseq: transcriptome profiling of Agrobacterium-mediated infiltration of transcription factors to discover gene function and expression networks in plants. Plant Methods 2016; 12:41. [PMID: 27777610 PMCID: PMC5069895 DOI: 10.1186/s13007-016-0141-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/04/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes. Therefore, fast, efficient, high-throughput methods for assaying TF function are needed. RESULTS Agroinfiltration is a simple plant biology method that allows transient gene expression. It is a rapid and powerful tool for the functional characterisation of TF genes in planta. High throughput RNA sequencing is now a widely used method for analysing gene expression profiles (transcriptomes). By coupling TF agroinfiltration with RNA sequencing (named here as Infiltration-RNAseq), gene expression networks and gene function can be identified within a few weeks rather than many months. As a proof of concept, we agroinfiltrated Medicago truncatula leaves with M. truncatula LEGUME ANTHOCYANIN PRODUCITION 1 (MtLAP1), a MYB transcription factor involved in the regulation of the anthocyanin pathway, and assessed the resulting transcriptome. Leaves infiltrated with MtLAP1 turned red indicating the production of anthocyanin pigment. Consistent with this, genes encoding enzymes in the anthocyanin biosynthetic pathway, and known transcriptional activators and repressors of the anthocyanin biosynthetic pathway, were upregulated. A novel observation was the induction of a R3-MYB transcriptional repressor that likely provides transcriptional feedback inhibition to prevent the deleterious effects of excess anthocyanins on photosynthesis. CONCLUSIONS Infiltration-RNAseq is a fast and convenient method for profiling TF-mediated gene expression changes. We utilised this method to identify TF-mediated transcriptional changes and TF target genes in M. truncatula and Nicotiana benthamiana. This included the identification of target genes of a TF not normally expressed in leaves, and targets of TFs from other plant species. Infiltration-RNAseq can be easily adapted to other plant species where agroinfiltration protocols have been optimised. The ability to identify downstream genes, including positive and negative transcriptional regulators, will result in a greater understanding of TF function.
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Affiliation(s)
- Donna M. Bond
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11-600, Palmerston North, New Zealand
| | - Robyn H. Lee
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
| | - Gareth B. Gillard
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Chris M. Brown
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001 Australia
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11-600, Palmerston North, New Zealand
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13
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Hellens RP, Brown CM, Chisnall MAW, Waterhouse PM, Macknight RC. The Emerging World of Small ORFs. Trends Plant Sci 2016; 21:317-328. [PMID: 26684391 DOI: 10.1016/j.tplants.2015.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 07/06/2015] [Revised: 10/23/2015] [Accepted: 11/05/2015] [Indexed: 05/10/2023]
Abstract
Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found in plant viral RNAs and considered an interesting curiosity, an increasing number of these sORFs have been shown to encode functional peptides or play a regulatory role. The recent discovery that many of these sORFs initiate with start codons other than AUG, together with the identification of functional small peptides encoded in supposedly noncoding primary miRNA transcripts (pri-miRs), has drastically increased the number of potentially functional sORFs within the genome. Here we review how advances in technology, notably ribosome profiling (RP) assays, are complementing bioinformatics and proteogenomic methods to provide powerful ways to identify these elusive features of plant genomes, and highlight the regulatory roles sORFs can play.
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Affiliation(s)
- Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Chris M Brown
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew A W Chisnall
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Richard C Macknight
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand; New Zealand Institute for Plant and Food Research Ltd.
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14
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Bally J, Nakasugi K, Jia F, Jung H, Ho SYW, Wong M, Paul CM, Naim F, Wood CC, Crowhurst RN, Hellens RP, Dale JL, Waterhouse PM. The extremophile Nicotiana benthamiana has traded viral defence for early vigour. Nat Plants 2015; 1:15165. [PMID: 27251536 DOI: 10.1038/nplants.2015.165] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/01/2015] [Indexed: 05/03/2023]
Abstract
A single lineage of Nicotiana benthamiana is widely used as a model plant(1) and has been instrumental in making revolutionary discoveries about RNA interference (RNAi), viral defence and vaccine production. It is peerless in its susceptibility to viruses and its amenability in transiently expressing transgenes(2,3). These unparalleled characteristics have been associated both positively and negatively with a disruptive insertion in the RNA-dependent RNA polymerase 1 gene, Rdr1(4-6). For a plant so routinely used in research, the origin, diversity and evolution of the species, and the basis of its unusual abilities, have been relatively unexplored. Here, by comparison with wild accessions from across the spectrum of the species' natural distribution, we show that the laboratory strain of N. benthamiana is an extremophile originating from a population that has retained a mutation in Rdr1 for ∼0.8 Myr and thereby traded its defence capacity for early vigour and survival in the extreme habitat of central Australia. Reconstituting Rdr1 activity in this isolate provided protection. Silencing the functional allele in a wild strain rendered it hypersusceptible and was associated with a doubling of seed size and enhanced early growth rate. These findings open the way to a deeper understanding of the delicate balance between protection and vigour.
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Affiliation(s)
- Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kenlee Nakasugi
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fangzhi Jia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Simon Y W Ho
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mei Wong
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chloe M Paul
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig C Wood
- Commonwealth Scientific and Industrial Research Organisation-Plant Industry, Canberra, Australia
| | - Ross N Crowhurst
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - James L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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15
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Boase MR, Brendolise C, Wang L, Ngo H, Espley RV, Hellens RP, Schwinn KE, Davies KM, Albert NW. Failure to launch: the self-regulating Md-MYB10 R6 gene from apple is active in flowers but not leaves of Petunia. Plant Cell Rep 2015; 34:1817-23. [PMID: 26113165 DOI: 10.1007/s00299-015-1827-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 04/14/2015] [Revised: 06/01/2015] [Accepted: 06/13/2015] [Indexed: 05/02/2023]
Abstract
The Md - MYB10 R6 gene from apple is capable of self-regulating in heterologous host species and enhancing anthocyanin pigmentation, but the activity of MYB10 is dependent on endogenous protein partners. Coloured foliage due to anthocyanin pigments (bronze/red/black) is an attractive trait that is often lacking in many bedding, ornamental and horticultural plants. Apples (Malus × domestica) containing an allelic variant of the anthocyanin regulator, Md-MYB10 R6 , are highly pigmented throughout the plant, due to autoregulation by MYB10 upon its own promoter. We investigated whether Md-MYB10 R6 from apple is capable of functioning within the heterologous host Petunia hybrida to generate plants with novel pigmentation patterns. The Md-MYB10 R6 transgene (MYB10-R6 pro :MYB10:MYB10 term ) activated anthocyanin synthesis when transiently expressed in Antirrhinum rosea (dorsea) petals and petunia leaf discs. Stable transgenic petunias containing Md-MYB10 R6 lacked foliar pigmentation but had coloured flowers, complementing the an2 phenotype of 'Mitchell' petunia. The absence of foliar pigmentation was due to the failure of the Md-MYB10 R6 gene to self-activate in vegetative tissues, suggesting that additional protein partners are required for Md-MYB10 to activate target genes in this heterologous system. In petunia flowers, where endogenous components including MYB-bHLH-WDR (MBW) proteins were present, expression of the Md-MYB10 R6 promoter was initiated, allowing auto-regulation to occur and activating anthocyanin production. Md-MYB10 is capable of operating within the petunia MBW gene regulation network that controls the expression of the anthocyanin biosynthesis genes, AN1 (bHLH) and MYBx (R3-MYB repressor) in petals.
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Affiliation(s)
- Murray R Boase
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169 Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Lei Wang
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Hahn Ngo
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169 Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169 Auckland Mail Centre, Auckland, 1142, New Zealand
- Biochemistry Department, University of Otago, Dunedin, New Zealand
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Brisbane, Australia
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand.
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Laing WA, Martínez-Sánchez M, Wright MA, Bulley SM, Brewster D, Dare AP, Rassam M, Wang D, Storey R, Macknight RC, Hellens RP. An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis. Plant Cell 2015; 27:772-86. [PMID: 25724639 PMCID: PMC4558653 DOI: 10.1105/tpc.114.133777] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/18/2015] [Accepted: 02/11/2015] [Indexed: 05/18/2023]
Abstract
Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms.
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Affiliation(s)
- William A Laing
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | | | - Michele A Wright
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Sean M Bulley
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Di Brewster
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Andrew P Dare
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Maysoon Rassam
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Daisy Wang
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Richard C Macknight
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
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Montefiori M, Brendolise C, Dare AP, Lin-Wang K, Davies KM, Hellens RP, Allan AC. In the Solanaceae, a hierarchy of bHLHs confer distinct target specificity to the anthocyanin regulatory complex. J Exp Bot 2015; 66:1427-36. [PMID: 25628328 PMCID: PMC4339601 DOI: 10.1093/jxb/eru494] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The anthocyanin biosynthetic pathway is regulated by a transcription factor complex consisting of an R2R3 MYB, a bHLH, and a WD40. Although R2R3 MYBs belonging to the anthocyanin-activating class have been identified in many plants, and their role well elucidated, the subgroups of bHLH implicated in anthocyanin regulation seem to be more complex. It is not clear whether these potential bHLH partners are biologically interchangeable with redundant functions, or even if heterodimers are involved. In this study, AcMYB110, an R2R3 MYB isolated from kiwifruit (Actinidia sp.) showing a strong activation of the anthocyanin pathway in tobacco (Nicotiana tabacum) was used to examine the function of interacting endogenous bHLH partners. Constitutive expression of AcMYB110 in tobacco leaves revealed different roles for two bHLHs, NtAN1 and NtJAF13. A hierarchical mechanism is shown to control the regulation of transcription factors and consequently of the anthocyanin biosynthetic pathway. Here, a model is proposed for the regulation of the anthocyanin pathway in Solanaceous plants in which AN1 is directly involved in the activation of the biosynthetic genes, whereas JAF13 is involved in the regulation of AN1 transcription.
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Affiliation(s)
- Mirco Montefiori
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand
| | - Andrew P Dare
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11 600, Palmerston North, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand Biochemistry Department, School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand Centre for Tropical Crops and Biocommodities Queensland University of Technology Brisbane, Queensland, Australia
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92 169, Auckland, New Zealand School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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Wu R, Wang T, McGie T, Voogd C, Allan AC, Hellens RP, Varkonyi-Gasic E. Overexpression of the kiwifruit SVP3 gene affects reproductive development and suppresses anthocyanin biosynthesis in petals, but has no effect on vegetative growth, dormancy, or flowering time. J Exp Bot 2014; 65:4985-95. [PMID: 24948678 PMCID: PMC4144777 DOI: 10.1093/jxb/eru264] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 05/23/2023]
Abstract
SVP-like MADS domain transcription factors have been shown to regulate flowering time and both inflorescence and flower development in annual plants, while having effects on growth cessation and terminal bud formation in perennial species. Previously, four SVP genes were described in woody perennial vine kiwifruit (Actinidia spp.), with possible distinct roles in bud dormancy and flowering. Kiwifruit SVP3 transcript was confined to vegetative tissues and acted as a repressor of flowering as it was able to rescue the Arabidopsis svp41 mutant. To characterize kiwifruit SVP3 further, ectopic expression in kiwifruit species was performed. Ectopic expression of SVP3 in A. deliciosa did not affect general plant growth or the duration of endodormancy. Ectopic expression of SVP3 in A. eriantha also resulted in plants with normal vegetative growth, bud break, and flowering time. However, significantly prolonged and abnormal flower, fruit, and seed development were observed, arising from SVP3 interactions with kiwifruit floral homeotic MADS-domain proteins. Petal pigmentation was reduced as a result of SVP3-mediated interference with transcription of the kiwifruit flower tissue-specific R2R3 MYB regulator, MYB110a, and the gene encoding the key anthocyanin biosynthetic step, F3GT1. Constitutive expression of SVP3 had a similar impact on reproductive development in transgenic tobacco. The flowering time was not affected in day-neutral and photoperiod-responsive Nicotiana tabacum cultivars, but anthesis and seed germination were significantly delayed. The accumulation of anthocyanin in petals was reduced and the same underlying mechanism of R2R3 MYB NtAN2 transcript reduction was demonstrated.
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Affiliation(s)
- Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Tony McGie
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston North, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
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Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knäbel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VGM, Schaffer RJ, Gardiner SE, Velasco R. The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS One 2014; 9:e92644. [PMID: 24699266 PMCID: PMC3974708 DOI: 10.1371/journal.pone.0092644] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 02/25/2014] [Indexed: 01/03/2023] Open
Abstract
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.
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Affiliation(s)
- David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Massimo Pindo
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | | | - Cecilia Deng
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Hilary Ireland
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mark Fiers
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Helge Dzierzon
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Alessandro Cestaro
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Paolo Fontana
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Luca Bianco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Ashley Lu
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Roy Storey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Munazza Saeed
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Sara Montanari
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Yoon Kyeong Kim
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Daniela Nicolini
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Simone Larger
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Erika Stefani
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Andrew C. Allan
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Judith Bowen
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Isaac Harvey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Jason Johnston
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mickael Malnoy
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Greg Sawyer
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Claudia Wiedow
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Roberto Viola
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Roger P. Hellens
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Lester Brewer
- Motueka Research Centre, Plant & Food Research, Motueka, New Zealand
| | - Vincent G. M. Bus
- Hawke's Bay Research Centre, Plant & Food Research, Havelock North, New Zealand
| | - Robert J. Schaffer
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan E. Gardiner
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Riccardo Velasco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
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Espley RV, Butts CA, Laing WA, Martell S, Smith H, McGhie TK, Zhang J, Paturi G, Hedderley D, Bovy A, Schouten HJ, Putterill J, Allan AC, Hellens RP. Dietary flavonoids from modified apple reduce inflammation markers and modulate gut microbiota in mice. J Nutr 2014; 144:146-54. [PMID: 24353343 DOI: 10.3945/jn.113.182659] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Apples are rich in polyphenols, which provide antioxidant properties, mediation of cellular processes such as inflammation, and modulation of gut microbiota. In this study we compared genetically engineered apples with increased flavonoids [myeloblastis transcription factor 10 (MYB10)] with nontransformed apples from the same genotype, "Royal Gala" (RG), and a control diet with no apple. Compared with the RG diet, the MYB10 diet contained elevated concentrations of the flavonoid subclasses anthocyanins, flavanol monomers (epicatechin) and oligomers (procyanidin B2), and flavonols (quercetin glycosides), but other plant secondary metabolites were largely unaltered. We used these apples to investigate the effects of dietary flavonoids on inflammation and gut microbiota in 2 mouse feeding trials. In trial 1, male mice were fed a control diet or diets supplemented with 20% MYB10 apple flesh and peel (MYB-FP) or RG apple flesh and peel (RG-FP) for 7 d. In trial 2, male mice were fed MYB-FP or RG-FP diets or diets supplemented with 20% MYB10 apple flesh or RG apple flesh for 7 or 21 d. In trial 1, the transcription levels of inflammation-linked genes in mice showed decreases of >2-fold for interleukin-2 receptor (Il2rb), chemokine receptor 2 (Ccr2), chemokine ligand 10 (Cxcl10), and chemokine receptor 10 (Ccr10) at 7 d for the MYB-FP diet compared with the RG-FP diet (P < 0.05). In trial 2, the inflammation marker prostaglandin E(2) (PGE(2)) in the plasma of mice fed the MYB-FP diet at 21 d was reduced by 10-fold (P < 0.01) compared with the RG-FP diet. In colonic microbiota, the number of total bacteria for mice fed the MYB-FP diet was 6% higher than for mice fed the control diet at 21 d (P = 0.01). In summary, high-flavonoid apple was associated with decreases in some inflammation markers and changes in gut microbiota when fed to healthy mice.
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Affiliation(s)
- Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
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Dare AP, Tomes S, Cooney JM, Greenwood DR, Hellens RP. The role of enoyl reductase genes in phloridzin biosynthesis in apple. Plant Physiol Biochem 2013; 72:54-61. [PMID: 23510577 DOI: 10.1016/j.plaphy.2013.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 11/30/2012] [Accepted: 02/22/2013] [Indexed: 05/14/2023]
Abstract
Phloridzin is the predominant polyphenol in apple (Malus × domestica Borkh.) where it accumulates to high concentrations in many tissues including the leaves, bark, roots and fruit. Despite its relative abundance in apple the biosynthesis of phloridzin and other related dihydrochalcones remains only partially understood. The key unidentified enzyme in phloridzin biosynthesis is a putative carbon double bond reductase which is thought to act on p-coumaroyl-CoA to produce the dihydro-p-coumaroyl-CoA precursor. A functional screen of six apple enoyl reductase-like (ENRL) genes was carried out using transient infiltration into tobacco and gene silencing by RNA interference (RNAi) in order to determine carbon double bond reductase activity and contribution to foliar phloridzin concentrations. The ENRL-3 gene caused a significant increase in phloridzin concentration when infiltrated into tobacco leaves whilst a second protein ENRL-5, with over 98% amino acid sequence similarity to ENRL-3, showed p-coumaroyl-CoA reductase activity in enzyme assays. Finally, an RNAi study showed that reducing the transcript levels of ENRL-3 in transgenic 'Royal Gala' led to a 66% decrease in the concentration of dihydrochalcones in the leaves in the one available silenced line. Overall these results suggest that ENRL-3, and its close homolog ENRL-5, may contribute to the biosynthesis of phloridzin in apple.
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Affiliation(s)
- Andrew P Dare
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169, Auckland 1141, New Zealand.
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23
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Abstract
Plants produce a vast array of phenolic compounds which are essential for their survival on land. One major class of polyphenols are the flavonoids and their formation is dependent on the enzyme chalcone synthase (CHS). In a recent study we silenced the CHS genes of apple (Malus × domestica Borkh.) and observed a loss of pigmentation in the fruit skin, flowers and stems. More surprisingly, highly silenced lines were significantly reduced in size, with small leaves and shortened internode lengths. Chemical analysis also revealed that the transgenic shoots contained greatly reduced concentrations of flavonoids which are known to modulate auxin flow. An auxin transport study verified this, with an increased auxin transport in the CHS-silenced lines. Overall, these findings suggest that auxin transport in apple has adapted to take place in the presence of high endogenous concentrations of flavonoids. Removal of these compounds therefore results in abnormal auxin movement and a highly disrupted growth pattern.
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Dare AP, Tomes S, Jones M, McGhie TK, Stevenson DE, Johnson RA, Greenwood DR, Hellens RP. Phenotypic changes associated with RNA interference silencing of chalcone synthase in apple (Malus × domestica). Plant J 2013; 74:398-410. [PMID: 23398045 DOI: 10.1111/tpj.12140] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 12/21/2012] [Accepted: 01/24/2013] [Indexed: 05/19/2023]
Abstract
We have identified in apple (Malus × domestica) three chalcone synthase (CHS) genes. In order to understand the functional redundancy of this gene family RNA interference knockout lines were generated where all three of these genes were down-regulated. These lines had no detectable anthocyanins and radically reduced concentrations of dihydrochalcones and flavonoids. Surprisingly, down-regulation of CHS also led to major changes in plant development, resulting in plants with shortened internode lengths, smaller leaves and a greatly reduced growth rate. Microscopic analysis revealed that these phenotypic changes extended down to the cellular level, with CHS-silenced lines showing aberrant cellular organisation in the leaves. Fruit collected from one CHS-silenced line was smaller than the 'Royal Gala' controls, lacked flavonoids in the skin and flesh and also had changes in cell morphology. Auxin transport experiments showed increased rates of auxin transport in a CHS-silenced line compared with the 'Royal Gala' control. As flavonoids are well known to be key modulators of auxin transport, we hypothesise that the removal of almost all flavonoids from the plant by CHS silencing creates a vastly altered environment for auxin transport to occur and results in the observed changes in growth and development.
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Affiliation(s)
- Andrew P Dare
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169, Auckland 1141, New Zealand.
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25
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Espley RV, Bovy A, Bava C, Jaeger SR, Tomes S, Norling C, Crawford J, Rowan D, McGhie TK, Brendolise C, Putterill J, Schouten HJ, Hellens RP, Allan AC. Analysis of genetically modified red-fleshed apples reveals effects on growth and consumer attributes. Plant Biotechnol J 2013; 11:408-19. [PMID: 23130849 DOI: 10.1111/pbi.12017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 09/12/2012] [Accepted: 09/25/2012] [Indexed: 05/03/2023]
Abstract
Consumers of whole foods, such as fruits, demand consistent high quality and seek varieties with enhanced health properties, convenience or novel taste. We have raised the polyphenolic content of apple by genetic engineering of the anthocyanin pathway using the apple transcription factor MYB10. These apples have very high concentrations of foliar, flower and fruit anthocyanins, especially in the fruit peel. Independent lines were examined for impacts on tree growth, photosynthesis and fruit characteristics. Fruit were analysed for changes in metabolite and transcript levels. Fruit were also used in taste trials to study the consumer perception of such a novel apple. No negative taste attributes were associated with the elevated anthocyanins. Modification with this one gene provides near isogenic material and allows us to examine the effects on an established cultivar, with a view to enhancing consumer appeal independently of other fruit qualities.
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Affiliation(s)
- Richard V Espley
- The New Zealand Institute for Plant & Food Research Limited-PFR, Auckland, New Zealand.
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26
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Varkonyi-Gasic E, Moss SMA, Voogd C, Wang T, Putterill J, Hellens RP. Homologs of FT, CEN and FD respond to developmental and environmental signals affecting growth and flowering in the perennial vine kiwifruit. New Phytol 2013; 198:732-746. [PMID: 23577598 DOI: 10.1111/nph.12162] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/01/2013] [Indexed: 05/08/2023]
Abstract
FLOWERING LOCUS T (FT) and CENTRORADIALIS (CEN) homologs have been implicated in regulation of growth, determinacy and flowering. The roles of kiwifruit FT and CEN were explored using a combination of expression analysis, protein interactions, response to temperature in high-chill and low-chill kiwifruit cultivars and ectopic expression in Arabidopsis and Actinidia. The expression and activity of FT was opposite from that of CEN and incorporated an interaction with a FLOWERING LOCUS D (FD)-like bZIP transcription factor. Accumulation of FT transcript was associated with plant maturity and particular stages of leaf, flower and fruit development, but could be detected irrespective of the flowering process and failed to induce precocious flowering in transgenic kiwifruit. Instead, transgenic plants demonstrated reduced growth and survival rate. Accumulation of FT transcript was detected in dormant buds and stem in response to winter chilling. In contrast, FD in buds was reduced by exposure to cold. CEN transcript accumulated in developing latent buds, but declined before the onset of dormancy and delayed flowering when ectopically expressed in kiwifruit. Our results suggest roles for FT, CEN and FD in integration of developmental and environmental cues that affect dormancy, budbreak and flowering in kiwifruit.
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Affiliation(s)
- Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sarah M A Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 92169, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 92169, Auckland, 1142, New Zealand
| | - Joanna Putterill
- Flowering Laboratory, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 92169, Auckland, 1142, New Zealand
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Ravaglia D, Espley RV, Henry-Kirk RA, Andreotti C, Ziosi V, Hellens RP, Costa G, Allan AC. Transcriptional regulation of flavonoid biosynthesis in nectarine (Prunus persica) by a set of R2R3 MYB transcription factors. BMC Plant Biol 2013; 13:68. [PMID: 23617716 PMCID: PMC3648406 DOI: 10.1186/1471-2229-13-68] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/12/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Flavonoids such as anthocyanins, flavonols and proanthocyanidins, play a central role in fruit colour, flavour and health attributes. In peach and nectarine (Prunus persica) these compounds vary during fruit growth and ripening. Flavonoids are produced by a well studied pathway which is transcriptionally regulated by members of the MYB and bHLH transcription factor families. We have isolated nectarine flavonoid regulating genes and examined their expression patterns, which suggests a critical role in the regulation of flavonoid biosynthesis. RESULTS In nectarine, expression of the genes encoding enzymes of the flavonoid pathway correlated with the concentration of proanthocyanidins, which strongly increases at mid-development. In contrast, the only gene which showed a similar pattern to anthocyanin concentration was UDP-glucose-flavonoid-3-O-glucosyltransferase (UFGT), which was high at the beginning and end of fruit growth, remaining low during the other developmental stages. Expression of flavonol synthase (FLS1) correlated with flavonol levels, both temporally and in a tissue specific manner. The pattern of UFGT gene expression may be explained by the involvement of different transcription factors, which up-regulate flavonoid biosynthesis (MYB10, MYB123, and bHLH3), or repress (MYB111 and MYB16) the transcription of the biosynthetic genes. The expression of a potential proanthocyanidin-regulating transcription factor, MYBPA1, corresponded with proanthocyanidin levels. Functional assays of these transcription factors were used to test the specificity for flavonoid regulation. CONCLUSIONS MYB10 positively regulates the promoters of UFGT and dihydroflavonol 4-reductase (DFR) but not leucoanthocyanidin reductase (LAR). In contrast, MYBPA1 trans-activates the promoters of DFR and LAR, but not UFGT. This suggests exclusive roles of anthocyanin regulation by MYB10 and proanthocyanidin regulation by MYBPA1. Further, these transcription factors appeared to be responsive to both developmental and environmental stimuli.
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Affiliation(s)
- Daniela Ravaglia
- Department of Fruit Tree and Woody Plant Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research (PFR), Private Bag 92 169, Auckland, New Zealand
| | - Rebecca A Henry-Kirk
- The New Zealand Institute for Plant and Food Research (PFR), Private Bag 92 169, Auckland, New Zealand
| | - Carlo Andreotti
- Faculty of Science and Technology, Free University of Bozen, Piazza Università 5, Bozen, 39100, Italy
| | - Vanina Ziosi
- Department of Fruit Tree and Woody Plant Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research (PFR), Private Bag 92 169, Auckland, New Zealand
| | - Guglielmo Costa
- Department of Fruit Tree and Woody Plant Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research (PFR), Private Bag 92 169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92 019, Auckland, New Zealand
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Nakasugi K, Crowhurst RN, Bally J, Wood CC, Hellens RP, Waterhouse PM. De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PLoS One 2013; 8:e59534. [PMID: 23555698 PMCID: PMC3610648 DOI: 10.1371/journal.pone.0059534] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [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: 12/19/2012] [Accepted: 02/15/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. METHODOLOGY/RESULTS RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of 16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. CONCLUSIONS The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant.
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Affiliation(s)
- Kenlee Nakasugi
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Ross N. Crowhurst
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Julia Bally
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Craig C. Wood
- Commonwealth Scientific and Industrial Research Organisation–Plant Industry, Canberra, Australia
| | - Roger P. Hellens
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
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Wood M, Rae GM, Wu RM, Walton EF, Xue B, Hellens RP, Uversky VN. Actinidia DRM1--an intrinsically disordered protein whose mRNA expression is inversely correlated with spring budbreak in kiwifruit. PLoS One 2013; 8:e57354. [PMID: 23516402 PMCID: PMC3596386 DOI: 10.1371/journal.pone.0057354] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 01/21/2013] [Indexed: 11/27/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein levels. It is predicted to be an intrinsically disordered protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia.
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Affiliation(s)
- Marion Wood
- Genomics Research, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand.
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30
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Fraser LG, Seal AG, Montefiori M, McGhie TK, Tsang GK, Datson PM, Hilario E, Marsh HE, Dunn JK, Hellens RP, Davies KM, McNeilage MA, De Silva HN, Allan AC. An R2R3 MYB transcription factor determines red petal colour in an Actinidia (kiwifruit) hybrid population. BMC Genomics 2013; 14:28. [PMID: 23324587 PMCID: PMC3618344 DOI: 10.1186/1471-2164-14-28] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 01/07/2013] [Indexed: 11/21/2022] Open
Abstract
Background Red colour in kiwifruit results from the presence of anthocyanin pigments. Their expression, however, is complex, and varies among genotypes, species, tissues and environments. An understanding of the biosynthesis, physiology and genetics of the anthocyanins involved, and the control of their expression in different tissues, is required. A complex, the MBW complex, consisting of R2R3-MYB and bHLH transcription factors together with a WD-repeat protein, activates anthocyanin 3-O-galactosyltransferase (F3GT1) to produce anthocyanins. We examined the expression and genetic control of anthocyanins in flowers of Actinidia hybrid families segregating for red and white petal colour. Results Four inter-related backcross families between Actinidia chinensis Planch. var. chinensis and Actinidia eriantha Benth. were identified that segregated 1:1 for red or white petal colour. Flower pigments consisted of five known anthocyanins (two delphinidin-based and three cyanidin-based) and three unknowns. Intensity and hue differed in red petals from pale pink to deep magenta, and while intensity of colour increased with total concentration of anthocyanin, no association was found between any particular anthocyanin data and hue. Real time qPCR demonstrated that an R2R3 MYB, MYB110a, was expressed at significant levels in red-petalled progeny, but not in individuals with white petals. A microsatellite marker was developed that identified alleles that segregated with red petal colour, but not with ovary, stamen filament, or fruit flesh colour in these families. The marker mapped to chromosome 10 in Actinidia. The white petal phenotype was complemented by syringing Agrobacterium tumefaciens carrying Actinidia 35S::MYB110a into the petal tissue. Red pigments developed in white petals both with, and without, co-transformation with Actinidia bHLH partners. MYB110a was shown to directly activate Actinidia F3GT1 in transient assays. Conclusions The transcription factor, MYB110a, regulates anthocyanin production in petals in this hybrid population, but not in other flower tissues or mature fruit. The identification of delphinidin-based anthocyanins in these flowers provides candidates for colour enhancement in novel fruits.
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Affiliation(s)
- Lena G Fraser
- The New Zealand Institute for Plant & Food Research Limited, 120 Mt. Albert Road, Auckland 1142, New Zealand.
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31
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Chagné D, Lin-Wang K, Espley RV, Volz RK, How NM, Rouse S, Brendolise C, Carlisle CM, Kumar S, De Silva N, Micheletti D, McGhie T, Crowhurst RN, Storey RD, Velasco R, Hellens RP, Gardiner SE, Allan AC. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol 2013; 161:225-39. [PMID: 23096157 PMCID: PMC3532254 DOI: 10.1104/pp.112.206771] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/23/2012] [Indexed: 05/18/2023]
Abstract
Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.
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Affiliation(s)
- David Chagné
- New Zealand Institute for Plant and Food Research Limited , Palmerston North Research Centre, Palmerston North 4442, New Zealand.
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32
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Naim F, Nakasugi K, Crowhurst RN, Hilario E, Zwart AB, Hellens RP, Taylor JM, Waterhouse PM, Wood CC. Advanced engineering of lipid metabolism in Nicotiana benthamiana using a draft genome and the V2 viral silencing-suppressor protein. PLoS One 2012; 7:e52717. [PMID: 23300750 PMCID: PMC3530501 DOI: 10.1371/journal.pone.0052717] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/20/2012] [Indexed: 01/05/2023] Open
Abstract
The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18∶1 to elongation reactions beginning with 18∶1 as substrate. These V2-based leaf assays produced ∼50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays.
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Affiliation(s)
- Fatima Naim
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Kenlee Nakasugi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ross N. Crowhurst
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Elena Hilario
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Alexander B. Zwart
- Mathematics, Informatics and Statistics, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Roger P. Hellens
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Jennifer M. Taylor
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Peter M. Waterhouse
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Molecular Bioscience, School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Craig C. Wood
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
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Abstract
Proanthocyanidins (PAs) are products of the flavonoid pathway, which also leads to the production of anthocyanins and flavonols. Many flavonoids have antioxidant properties and may have beneficial effects for human health. PAs are found in the seeds and fruits of many plants. In apple fruit (Malus × domestica Borkh.), the flavonoid biosynthetic pathway is most active in the skin, with the flavan-3-ols, catechin, and epicatechin acting as the initiating units for the synthesis of PA polymers. This study examined the genes involved in the production of PAs in three apple cultivars: two heritage apple cultivars, Hetlina and Devonshire Quarrenden, and a commercial cultivar, Royal Gala. HPLC analysis shows that tree-ripe fruit from Hetlina and Devonshire Quarrenden had a higher phenolic content than Royal Gala. Epicatechin and catechin biosynthesis is under the control of the biosynthetic enzymes anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR1), respectively. Counter-intuitively, real-time quantitative PCR analysis showed that the expression levels of Royal Gala LAR1 and ANR were significantly higher than those of both Devonshire Quarrenden and Hetlina. This suggests that a compensatory feedback mechanism may be active, whereby low concentrations of PAs may induce higher expression of gene transcripts. Further investigation is required into the regulation of these key enzymes in apple.
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Affiliation(s)
- Rebecca A Henry-Kirk
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92 169 Auckland, New Zealand.
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Varkonyi-Gasic E, Lough RH, Moss SMA, Wu R, Hellens RP. Kiwifruit floral gene APETALA2 is alternatively spliced and accumulates in aberrant indeterminate flowers in the absence of miR172. Plant Mol Biol 2012; 78:417-29. [PMID: 22290408 DOI: 10.1007/s11103-012-9877-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/23/2011] [Indexed: 05/22/2023]
Abstract
In Arabidopsis, the identity of perianth and reproductive organs are specified by antagonistic action of two floral homeotic genes, APETALA2 (AP2) and AGAMOUS (AG). AP2 is also negatively regulated by an evolutionary conserved interaction with a microRNA, miR172, and has additional roles in general plant development. A kiwifruit gene with high levels of homology to AP2 and AP2-like genes from other plant species was identified. The transcript was abundant in the kiwifruit flower, particularly petal, suggesting a role in floral organ identity. Splice variants were identified, all containing both AP2 domains, including a variant that potentially produces a shorter transcript without the miRNA172 targeting site. Increased AP2 transcript accumulation was detected in the aberrant flowers of the mutant ‘Pukekohe dwarf’ with multiple perianth whorls and extended petaloid features. In contrast to normal kiwifruit flowers, the aberrant flowers failed to accumulate miR172 in the developing whorls, although accumulation was detected at the base of the flower. An additional role during dormancy in kiwifruit was proposed based on AP2 transcript accumulation in axillary buds before and after budbreak.
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Affiliation(s)
- Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland 1142, New Zealand.
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35
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Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 2012; 7:e31745. [PMID: 22363718 PMCID: PMC3283661 DOI: 10.1371/journal.pone.0031745] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023] Open
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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Affiliation(s)
- David Chagné
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Barbara Gilmore
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cindy Lawley
- Illumina Inc., Hayward, California, United States of America
| | - Stijn Vanderzande
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Roger P. Hellens
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Satish Kumar
- Plant and Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Alessandro Cestaro
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Jasper D. Rees
- Agricultural Research Council, Onderstepoort, South Africa
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Todd Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Susan E. Gardiner
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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36
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Kasai M, Koseki M, Goto K, Masuta C, Ishii S, Hellens RP, Taneda A, Kanazawa A. Coincident sequence-specific RNA degradation of linked transgenes in the plant genome. Plant Mol Biol 2012; 78:259-73. [PMID: 22146813 DOI: 10.1007/s11103-011-9863-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/18/2011] [Indexed: 05/23/2023]
Abstract
The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.
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Affiliation(s)
- Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Wu RM, Walton EF, Richardson AC, Wood M, Hellens RP, Varkonyi-Gasic E. Conservation and divergence of four kiwifruit SVP-like MADS-box genes suggest distinct roles in kiwifruit bud dormancy and flowering. J Exp Bot 2012; 63:797-807. [PMID: 22071267 PMCID: PMC3254681 DOI: 10.1093/jxb/err304] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [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: 07/05/2011] [Revised: 08/16/2011] [Accepted: 08/30/2011] [Indexed: 05/18/2023]
Abstract
MADS-box genes similar to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been implicated in the regulation of flowering in annual species and bud dormancy in perennial species. Kiwifruit (Actinidia spp.) are woody perennial vines where bud dormancy and out-growth affect flower development. To determine the role of SVP-like genes in dormancy and flowering of kiwifruit, four MADS-box genes with homology to Arabidopsis SVP, designated SVP1, SVP2, SVP3, and SVP4, have been identified and analysed in kiwifruit and functionally characterized in Arabidopsis. Phylogenetic analysis indicate that these genes fall into different sub-clades within the SVP-like gene group, suggesting distinct functions. Expression was generally confined to vegetative tissues, and increased transcript accumulation in shoot buds over the winter period suggests a role for these genes in bud dormancy. Down-regulation before flower differentiation indicate possible roles as floral repressors. Over-expression and complementation studies in Arabidopsis resulted in a range of floral reversion phenotypes arising from interactions with Arabidopsis MADS-box proteins, but only SVP1 and SVP3 were able to complement the svp mutant. These results suggest that the kiwifruit SVP-like genes may have distinct roles during bud dormancy and flowering.
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Affiliation(s)
- Rong-Mei Wu
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Eric F. Walton
- University of Otago, PO Box 5543, Auckland 1141, New Zealand
| | - Annette C. Richardson
- The New Zealand Institute for Plant and Food Research Limited, Kerikeri, PO Box 23, Kerikeri 0245, New Zealand
| | - Marion Wood
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
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Ellis THN, Hofer JMI, Timmerman-Vaughan GM, Coyne CJ, Hellens RP. Mendel, 150 years on. Trends Plant Sci 2011; 16:590-6. [PMID: 21775188 DOI: 10.1016/j.tplants.2011.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/07/2011] [Accepted: 06/21/2011] [Indexed: 05/10/2023]
Abstract
Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.
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Affiliation(s)
- T H Noel Ellis
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Gogerddan Campus, Aberystwyth, Ceredigion SY233EB, UK
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Johnson RA, Hellens RP, Love DR. A transient assay for recombination demonstrates that Arabidopsis SNM1 and XRCC3 enhance non-homologous recombination. Genet Mol Res 2011; 10:2104-32. [PMID: 21968679 DOI: 10.4238/vol10-3gmr1347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Replacement of endogenous genes by homologous recombination is rare in plants; the majority of genetic modifications are the result of transforming DNA molecules undergoing random genomic insertion by way of non-homologous recombination. Factors that affect chromatin remodeling and DNA repair are thought to have the potential to enhance the frequency of homologous recombination in plants. Conventional tools to study the frequencies of genetic recombination often rely on stable transformation-based approaches, with these systems being rarely capable of high-throughput or combinatorial analysis. We developed a series of vectors that use chemiluminescent (LUC and REN) reporter genes to assay the relative frequency of homologous and non-homologous recombination in plants. These transient assay vectors were used to screen 14 candidate genes for their effects on recombination frequencies in Nicotiana benthamiana plants. Over-expression of Arabidopsis genes with sequence similarity to SNM1 from yeast and XRCC3 from humans enhanced the frequency of non-homologous recombination when assayed using two different donor vectors. Transient N. benthamiana leaf systems were also used in an alternative assay for preliminary measurements of homologous recombination frequencies, which were found to be enhanced by over-expression of RAD52, MIM and RAD51 from yeast, as well as CHR24 from Arabidopsis. The findings for the assays described here are in line with previous studies that analyzed recombination frequencies using stable transformation. The assays we report have revealed functions in non-homologous recombination for the Arabidopsis SNM1 and XRCC3 genes, so the suppression of these genes' expression offers a potential means to enhance the gene targeting frequency in plants. Furthermore, our findings also indicate that plant gene targeting frequencies could be enhanced by over-expression of RAD52, MIM, CHR24, and RAD51 genes.
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Affiliation(s)
- R A Johnson
- The New Zealand Institute for Plant & Food Research Limited, Sandringham, Auckland, New Zealand.
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Lin-Wang K, Micheletti D, Palmer J, Volz R, Lozano L, Espley R, Hellens RP, Chagnè D, Rowan DD, Troggio M, Iglesias I, Allan AC. High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex. Plant Cell Environ 2011; 34:1176-90. [PMID: 21410713 DOI: 10.1111/j.1365-3040.2011.02316.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The biosynthesis of anthocyanin in many plants is affected by environmental conditions. In apple (Malus × domestica Borkh.), concentrations of fruit anthocyanins are lower under hot climatic conditions. We examined the anthocyanin accumulation in the peel of maturing 'Mondial Gala' and 'Royal Gala' apples, grown in both temperate and hot climates, and using artificial heating of on-tree fruit. Heat caused a dramatic reduction of both peel anthocyanin concentration and transcripts of the genes of the anthocyanin biosynthetic pathway. Heating fruit rapidly reduced expression of the R2R3 MYB transcription factor (MYB10) responsible for coordinative regulation for red skin colour, as well as expression of other genes in the transcriptional activation complex. A single night of low temperatures is sufficient to elicit a large increase in transcription of MYB10 and consequently the biosynthetic pathway. Candidate genes that can repress anthocyanin biosynthesis did not appear to be responsible for reductions in anthocyanin content. We propose that temperature-induced regulation of anthocyanin biosynthesis is primarily caused by altered transcript levels of the activating anthocyanin regulatory complex.
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Affiliation(s)
- Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Private Bag, Auckland
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Telias A, Lin-Wang K, Stevenson DE, Cooney JM, Hellens RP, Allan AC, Hoover EE, Bradeen JM. Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 2011; 11:93. [PMID: 21599973 PMCID: PMC3127826 DOI: 10.1186/1471-2229-11-93] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 05/20/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Some apple (Malus × domestica Borkh.) varieties have attractive striping patterns, a quality attribute that is important for determining apple fruit market acceptance. Most apple cultivars (e.g. 'Royal Gala') produce fruit with a defined fruit pigment pattern, but in the case of 'Honeycrisp' apple, trees can produce fruits of two different kinds: striped and blushed. The causes of this phenomenon are unknown. RESULTS Here we show that striped areas of 'Honeycrisp' and 'Royal Gala' are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, nucleotide changes in the promoter and coding sequence of MYB10 do not correlate with skin pattern in 'Honeycrisp' and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MYB10 and a 2.5 Kb region 5' of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Cytosine methylation was present in all three contexts, with higher methylation levels observed for CHH and CHG (where H is A, C or T) than for CG. Comparisons of methylation levels of the MYB10 promoter in 'Honeycrisp' red and green stripes indicated that they correlate with peel phenotypes, with an enrichment of methylation observed in green stripes. CONCLUSIONS Differences in anthocyanin levels between red and green stripes can be explained by differential transcript accumulation of MYB10. Different levels of MYB10 transcript in red versus green stripes are inversely associated with methylation levels in the promoter region. Although observed methylation differences are modest, trends are consistent across years and differences are statistically significant. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in 'Honeycrisp'. We suggest that methylation in the MYB10 promoter is more variable in 'Honeycrisp' than in 'Royal Gala', leading to more variable color patterns in the peel of this cultivar.
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Affiliation(s)
- Adriana Telias
- Plant Science and Landscape Architecture Department, University of Maryland 2102 Plant Sciences Building, College Park, MD 21201, USA
| | - Kui Lin-Wang
- Plant and Food Research, Mt Albert Research Centre Private Bag 92169, Auckland, New Zealand
| | - David E Stevenson
- Plant and Food Research, Ruakura Research Centre Private Bag 3123, Hamilton, New Zealand
| | - Janine M Cooney
- Plant and Food Research, Ruakura Research Centre Private Bag 3123, Hamilton, New Zealand
| | - Roger P Hellens
- Plant and Food Research, Mt Albert Research Centre Private Bag 92169, Auckland, New Zealand
| | - Andrew C Allan
- Plant and Food Research, Mt Albert Research Centre Private Bag 92169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Emily E Hoover
- Department of Horticultural Science, University of Minnesota 305 Alderman Hall, 1970 Folwell Ave., St. Paul, MN 55108, USA
| | - James M Bradeen
- Department of Plant Pathology, University of Minnesota 495 Borlaug, 1991 Upper Buford Cir., St. Paul, MN 55108, USA
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Varkonyi-Gasic E, Moss SM, Voogd C, Wu R, Lough RH, Wang YY, Hellens RP. Identification and characterization of flowering genes in kiwifruit: sequence conservation and role in kiwifruit flower development. BMC Plant Biol 2011; 11:72. [PMID: 21521532 PMCID: PMC3103426 DOI: 10.1186/1471-2229-11-72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 04/27/2011] [Indexed: 05/06/2023]
Abstract
BACKGROUND Flower development in kiwifruit (Actinidia spp.) is initiated in the first growing season, when undifferentiated primordia are established in latent shoot buds. These primordia can differentiate into flowers in the second growing season, after the winter dormancy period and upon accumulation of adequate winter chilling. Kiwifruit is an important horticultural crop, yet little is known about the molecular regulation of flower development. RESULTS To study kiwifruit flower development, nine MADS-box genes were identified and functionally characterized. Protein sequence alignment, phenotypes obtained upon overexpression in Arabidopsis and expression patterns suggest that the identified genes are required for floral meristem and floral organ specification. Their role during budbreak and flower development was studied. A spontaneous kiwifruit mutant was utilized to correlate the extended expression domains of these flowering genes with abnormal floral development. CONCLUSIONS This study provides a description of flower development in kiwifruit at the molecular level. It has identified markers for flower development, and candidates for manipulation of kiwifruit growth, phase change and time of flowering. The expression in normal and aberrant flowers provided a model for kiwifruit flower development.
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Affiliation(s)
- Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Sarah M Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Robyn H Lough
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Yen-Yi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
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Abstract
Plant microRNAs (miRNAs) are a class of endogenous small RNAs that are essential for plant development and survival. They arise from larger precursor RNAs with a characteristic hairpin structure and regulate gene activity by targeting mRNA transcripts for cleavage or translational repression. Efficient and reliable detection and quantification of miRNA expression has become an essential step in understanding their specific roles. The expression levels of miRNAs can vary dramatically between samples and they often escape detection by conventional technologies such as cloning, northern hybridization and microarray analysis. The stem-loop RT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate and reliable manner. First, a miRNA-specific stem-loop RT primer is hybridized to the miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and the universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA and is suitable for high-throughput miRNA expression analysis.
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Affiliation(s)
- Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research, Mt. Albert Research Centre, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
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Montefiori M, Espley RV, Stevenson D, Cooney J, Datson PM, Saiz A, Atkinson RG, Hellens RP, Allan AC. Identification and characterisation of F3GT1 and F3GGT1, two glycosyltransferases responsible for anthocyanin biosynthesis in red-fleshed kiwifruit (Actinidia chinensis). Plant J 2011; 65:106-118. [PMID: 21175894 DOI: 10.1111/j.1365-313x.2010.04409.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Much of the diversity of anthocyanins is due to the action of glycosyltransferases, which add sugar moieties to anthocyanidins. We identified two glycosyltransferases, F3GT1 and F3GGT1, from red-fleshed kiwifruit (Actinidia chinensis) that perform sequential glycosylation steps. Red-fleshed genotypes of kiwifruit accumulate anthocyanins mainly in the form of cyanidin 3-O-xylo-galactoside. Genes in the anthocyanin and flavonoid biosynthetic pathway were identified and shown to be expressed in fruit tissue. However, only the expression of the glycosyltransferase F3GT1 was correlated with anthocyanin accumulation in red tissues. Recombinant enzyme assays in vitro and in vivo RNA interference (RNAi) demonstrated the role of F3GT1 in the production of cyanidin 3-O-galactoside. F3GGT1 was shown to further glycosylate the sugar moiety of the anthocyanins. This second glycosylation can affect the solubility and stability of the pigments and modify their colour. We show that recombinant F3GGT1 can catalyse the addition of UDP-xylose to cyanidin 3-galactoside. While F3GGT1 is responsible for the end-product of the pathway, F3GT1 is likely to be the key enzyme regulating the accumulation of anthocyanin in red-fleshed kiwifruit varieties.
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Affiliation(s)
- Mirco Montefiori
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - David Stevenson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Paul M Datson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Anna Saiz
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92 169, Auckland, New ZealandSchool of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandThe New Zealand Institute for Plant and Food Research Ltd, East Street 3214, Hamilton, New Zealand
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Hellens RP, Moreau C, Lin-Wang K, Schwinn KE, Thomson SJ, Fiers MWEJ, Frew TJ, Murray SR, Hofer JMI, Jacobs JME, Davies KM, Allan AC, Bendahmane A, Coyne CJ, Timmerman-Vaughan GM, Ellis THN. Identification of Mendel's white flower character. PLoS One 2010; 5:e13230. [PMID: 20949001 PMCID: PMC2952588 DOI: 10.1371/journal.pone.0013230] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [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: 06/24/2010] [Accepted: 09/01/2010] [Indexed: 11/18/2022] Open
Abstract
Background The genetic regulation of flower color has been widely studied, notably as a character used by Mendel and his predecessors in the study of inheritance in pea. Methodology/Principal Findings We used the genome sequence of model legumes, together with their known synteny to the pea genome to identify candidate genes for the A and A2 loci in pea. We then used a combination of genetic mapping, fast neutron mutant analysis, allelic diversity, transcript quantification and transient expression complementation studies to confirm the identity of the candidates. Conclusions/Significance We have identified the pea genes A and A2. A is the factor determining anthocyanin pigmentation in pea that was used by Gregor Mendel 150 years ago in his study of inheritance. The A gene encodes a bHLH transcription factor. The white flowered mutant allele most likely used by Mendel is a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon, and we have identified a second rare mutant allele. The A2 gene encodes a WD40 protein that is part of an evolutionarily conserved regulatory complex.
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Affiliation(s)
- Roger P. Hellens
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Carol Moreau
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Kathy E. Schwinn
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, New Zealand
| | - Susan J. Thomson
- The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - Mark W. E. J. Fiers
- The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - Tonya J. Frew
- The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - Sarah R. Murray
- The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - Julie M. I. Hofer
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Jeanne M. E. Jacobs
- The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | | | - Clarice J. Coyne
- United States Department of Agriculture-Agricultural Research Service Western Regional Plant Introduction Station, Pullman, Washington, United States of America
| | | | - T. H. Noel Ellis
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
- * E-mail:
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Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 2010; 42:833-9. [DOI: 10.1038/ng.654] [Citation(s) in RCA: 1538] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
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Abstract
Plant small RNAs are a class of 19- to 25-nucleotide (nt) RNA molecules that are essential for genome stability, development and differentiation, disease, cellular communication, signaling, and adaptive responses to biotic and abiotic stress. Small RNAs comprise two major RNA classes, short interfering RNAs (siRNAs) and microRNAs (miRNAs). Efficient and reliable detection and quantification of small RNA expression has become an essential step in understanding their roles in specific cells and tissues. Here we provide protocols for the detection of miRNAs by stem-loop RT-PCR. This method enables fast and reliable miRNA expression profiling from as little as 20 pg of total RNA extracted from plant tissue and is suitable for high-throughput miRNA expression analysis. In addition, this method can be used to detect other classes of small RNAs, provided the sequence is known and their GC contents are similar to those specific for miRNAs.
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48
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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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49
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Lin-Wang K, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie TK, Espley RV, Hellens RP, Allan AC. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol 2010; 10:50. [PMID: 20302676 PMCID: PMC2923524 DOI: 10.1186/1471-2229-10-50] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 03/21/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The control of plant anthocyanin accumulation is via transcriptional regulation of the genes encoding the biosynthetic enzymes. A key activator appears to be an R2R3 MYB transcription factor. In apple fruit, skin anthocyanin levels are controlled by a gene called MYBA or MYB1, while the gene determining fruit flesh and foliage anthocyanin has been termed MYB10. In order to further understand tissue-specific anthocyanin regulation we have isolated orthologous MYB genes from all the commercially important rosaceous species. RESULTS We use gene specific primers to show that the three MYB activators of apple anthocyanin (MYB10/MYB1/MYBA) are likely alleles of each other. MYB transcription factors, with high sequence identity to the apple gene were isolated from across the rosaceous family (e.g. apples, pears, plums, cherries, peaches, raspberries, rose, strawberry). Key identifying amino acid residues were found in both the DNA-binding and C-terminal domains of these MYBs. The expression of these MYB10 genes correlates with fruit and flower anthocyanin levels. Their function was tested in tobacco and strawberry. In tobacco, these MYBs were shown to induce the anthocyanin pathway when co-expressed with bHLHs, while over-expression of strawberry and apple genes in the crop of origin elevates anthocyanins. CONCLUSIONS This family-wide study of rosaceous R2R3 MYBs provides insight into the evolution of this plant trait. It has implications for the development of new coloured fruit and flowers, as well as aiding the understanding of temporal-spatial colour change.
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Affiliation(s)
- Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Karen Bolitho
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Karryn Grafton
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Anne Kortstee
- Wageningen UR Plant Breeding, Postbus 386, 6700 AJ, Wageningen, The Netherlands
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Tony K McGhie
- Plant and Food Research, Palmerston North 4442, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Ltd, (Plant and Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
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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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