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Rothan C, Diouf I, Causse M. Trait discovery and editing in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:73-90. [PMID: 30417464 DOI: 10.1111/tpj.14152] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.
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Affiliation(s)
- Christophe Rothan
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Isidore Diouf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
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Zhang S, Yu H, Wang K, Zheng Z, Liu L, Xu M, Jiao Z, Li R, Liu X, Li J, Cui X. Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:312-323. [PMID: 29738097 DOI: 10.1111/tpj.13952] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F10 lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high-resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near-isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild-species alleles. These findings allowed us to construct a trait-locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties.
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Affiliation(s)
- Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zheng Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Huayuan Road 116, Zhengzhou, 450002, Henan, China
| | - Lei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhicheng Jiao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiyan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Pickersgill B. Parallel vs. Convergent Evolution in Domestication and Diversification of Crops in the Americas. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Laricchia KM, Johnson MG, Ragone D, Williams EW, Zerega NJC, Wickett NJ. A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). AMERICAN JOURNAL OF BOTANY 2018; 105:915-926. [PMID: 29882953 DOI: 10.1002/ajb2.1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3500 years ago. The goal of this research was to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future. METHODS A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and on carotenoid biosynthesis genes, which can impact the nutritional quality of the fruit. KEY RESULTS Over 1000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS-box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA-binding domains. A McDonald-Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8'-hydroxylase 3. CONCLUSIONS This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human-mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.
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Affiliation(s)
- Kristen M Laricchia
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Matthew G Johnson
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI, 96741, USA
| | - Evelyn W Williams
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Nyree J C Zerega
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
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Silva Ferreira D, Kevei Z, Kurowski T, de Noronha Fonseca ME, Mohareb F, Boiteux LS, Thompson AJ. BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2581-2593. [PMID: 29509915 PMCID: PMC5920302 DOI: 10.1093/jxb/ery076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
A mutant line, bifurcate flower truss (bif), was recovered from a tomato genetics programme. Plants from the control line produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The control line and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed, and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a mitogen-activated protein (MAP) kinase, contained a leucine to stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato.
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Affiliation(s)
| | - Zoltan Kevei
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Tomasz Kurowski
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | | | - Fady Mohareb
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Leonardo S Boiteux
- National Center for Vegetable Crops Research, CNPH—Embrapa Hortaliças, Brasília-DF, Brazil
| | - Andrew J Thompson
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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Wang Y, Zou W, Xiao Y, Cheng L, Liu Y, Gao S, Shi Z, Jiang Y, Qi M, Xu T, Li T. MicroRNA1917 targets CTR4 splice variants to regulate ethylene responses in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1011-1025. [PMID: 29365162 DOI: 10.1093/jxb/erx469] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/07/2017] [Indexed: 05/18/2023]
Abstract
Ethylene perception is regulated by receptors, and the downstream protein CONSTITUTIVE TRIPLE RESPONSE1 is a key suppressor of ethylene signalling. The non-conserved tomato (Solanum lycopersicum) microRNA1917 (Sly-miR1917) mediates degradation of SlCTR4 splice variants (SlCTR4sv) but the molecular details of this pathway remain unknown. Sly-miR1917 and the targeted SlCTR4sv are ubiquitously expressed in all tomato organs. Overexpression of Sly-miR1917 enhances ethylene responses, including the triple response in etiolated seedlings, in the absence of ethylene, as well as epinastic petiole growth, accelerated pedicel abscission, and fruit ripening. Enhanced ethylene signalling in Sly-miR1917-overexpressing plants (1917-OE) is accompanied by up-regulation of ethylene biosynthesis and signalling genes, and increased ethylene emission. These phenotypes were recovered by repressing the positive ethylene regulator EIN2. Moreover, the Sly-miR1917-targeted SlCTR4 splice variant SlCTR4sv3, expressed specifically in the abscission zone, exhibited the opposite expression pattern to Sly-miR1917. Complementation of the Arabidopsis thaliana ctr-1 mutant and yeast two-hybrid and bimolecular fluorescence complementation assays suggested that SlCTR4sv3 functions in ethylene signalling. Co-expression of Sly-miR1917 and SlCTR4sv3 in Nicotiana benthamiana further suggested that Sly-miR1917 cleaves SlCTR4sv3 in vivo. Database homology searching revealed a Solanum tuberosum CTR-like splice variant containing a Sly-miR1917 binding sequence, and a homologue of mature Sly-miR1917 in potato, indicating a conserved function for miR1917 and the regulatory miRNA-mediated ethylene network in solanaceous species.
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Affiliation(s)
- Yanling Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Wenxiong Zou
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yan Xiao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Lina Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yudong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Song Gao
- Liaoning Cash Crop Institute, Liaoyang, China
| | - Zihang Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yun Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
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A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening. Sci Rep 2018; 8:3413. [PMID: 29467500 PMCID: PMC5821886 DOI: 10.1038/s41598-018-21672-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT. The transcripts of ethylene biosynthesis genes (ACS2, ACS4, ACO1 and ACO3), ethylene-responsive genes (E4, E8 and ERF1) and fruit ripening-related genes (RIN, TAGL1, FUL1, FUL2, LoxC and PE) were inhibited in SlCMB1-RNAi fruits. The carotenoid accumulation was decreased and two carotenoid synthesis-related genes (PSY1 and PDS) were down-regulated while three lycopene cyclase genes (CYCB, LCYB and LCYE) were up-regulated in transgenic fruits. Furthermore, yeast two-hybrid assay showed that SlCMB1 could interact with SlMADS-RIN, SlMADS1, SlAP2a and TAGL1, respectively. Collectively, these results indicate that SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.
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Abstract
Abscission is a process in plants for shedding unwanted organs such as leaves, flowers, fruits, or floral organs. Shedding of leaves in the fall is the most visually obvious display of abscission in nature. The very shape plants take is forged by the processes of growth and abscission. Mankind manipulates abscission in modern agriculture to do things such as prevent pre-harvest fruit drop prior to mechanical harvesting in orchards. Abscission occurs specifically at abscission zones that are laid down as the organ that will one day abscise is developed. A sophisticated signaling network initiates abscission when it is time to shed the unwanted organ. In this article, we review recent advances in understanding the signaling mechanisms that activate abscission. Physiological advances and roles for hormones in abscission are also addressed. Finally, we discuss current avenues for basic abscission research and potentially lucrative future directions for its application to modern agriculture.
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Affiliation(s)
- O Rahul Patharkar
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - John C Walker
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
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Qi X, Hu S, Zhou H, Liu X, Wang L, Zhao B, Huang X, Zhang S. A MADS-box transcription factor of 'Kuerlexiangli'(Pyrus sinkiangensis Yu) PsJOINTLESS gene functions in floral organ abscission. Gene 2018; 642:163-171. [PMID: 29128637 DOI: 10.1016/j.gene.2017.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/25/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
MADS-box proteins have been implicated in many biological processes. However, plant MADS-box proteins functioning in floral organ abscission and the underlying physiological mechanisms remain poorly understood. Here, we report the identification and functional characterization of PsJOINTLESS isolated from 'Kuerlexiangli'. PsJOINTLESS had a complete open reading frame of 672bp, encoding a 224 amino acid peptide, and shared high sequence identities with MADS-box from other plants. PsJOINTLESS was subcellularly targeted to the nucleus, supporting its role as a transcription factor. Expression levels of PsJOINTLESS in the calyx tube were strongly induced by calyx abscission treatment at 6d after full bloom. Overexpression of PsJOINTLESS in tomato enhanced the rate of pedicel abscission rate. Of special note, the transgenic plants increased the abscission zone cell layer compared with wild type. Furthermore, the tomato transgenic lines showed thinner flower pedicels, more cell number and small pedicel cell size. The cellulase activity in pedicel abscission zone of transgenic plants was higher than that of wild type. In addition, steady-state mRNA levels of five cell wall hydrolase genes coding for either functional or regulatory proteins were induced to higher levels in the transgenic lines. These results clearly demonstrate that PsJOINTLESS may affect pedicel abscission zone development.
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Affiliation(s)
- Xiaoxiao Qi
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; College of Agriculture, Medicine and Health, Anhui Radio and Television University, China
| | - Shi Hu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongsheng Zhou
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Liu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifen Wang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Biying Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaosan Huang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shaoling Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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LaBonte NR, Zhao P, Woeste K. Signatures of Selection in the Genomes of Chinese Chestnut ( Castanea mollissima Blume): The Roots of Nut Tree Domestication. FRONTIERS IN PLANT SCIENCE 2018; 9:810. [PMID: 29988533 PMCID: PMC6026767 DOI: 10.3389/fpls.2018.00810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 05/18/2023]
Abstract
Chestnuts (Castanea) are major nut crops in East Asia and southern Europe, and are unique among temperate nut crops in that the harvested seeds are starchy rather than oily. Chestnut species have been cultivated for three millennia or more in China, so it is likely that artificial selection has affected the genome of orchard-grown chestnuts. The genetics of Chinese chestnut (Castanea mollissima Blume) domestication are also of interest to breeders of hybrid American chestnut, especially if the low-growing, branching habit of Chinese chestnut, an impediment to American chestnut restoration, is partly the result of artificial selection. We resequenced genomes of wild and orchard-derived Chinese chestnuts and identified selective sweeps based on pooled whole-genome SNP datasets. We present candidate gene loci for chestnut domestication and discuss the potential phenotypic effects of candidate loci, some of which may be useful genes for chestnut improvement in Asia and North America. Selective sweeps included predicted genes potentially related to flower phenology and development, fruit maturation, and secondary metabolism, and included some genes homologous to domestication candidates in other woody plants.
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Affiliation(s)
- Nicholas R. LaBonte
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Nicholas R. LaBonte
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Keith Woeste
- Hardwood Tree Improvement and Regeneration Center, Northern Research Station, USDA Forest Service, West Lafayette, IN, United States
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Yin W, Yu X, Chen G, Tang B, Wang Y, Liao C, Zhang Y, Hu Z. Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:938. [PMID: 30022990 PMCID: PMC6039764 DOI: 10.3389/fpls.2018.00938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/11/2018] [Indexed: 05/04/2023]
Abstract
MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2-4 days compared with that of the wild-type (WT). The accumulation of carotenoids and biosynthesis of ethylene in fruits were decreased in SlMBP15-silenced tomato. Genes related to carotenoid and ethylene biosynthesis were greatly repressed. SlMBP15 can interact with RIN, a MADS-box regulator affecting the carotenoid accumulation and ethylene biosynthesis in tomato. In addition, SlMBP15-silenced tomato produced dark green leaves, and its plant height was reduced. The gibberellin (GA) content of transgenic plants was lower than that of the WT and GA biosynthesis genes were repressed. These results demonstrated that SlMBP15 not only positively regulated tomato fruit ripening but also affected the morphogenesis of the vegetative organs.
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Affiliation(s)
- Wencheng Yin
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Boyan Tang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Yunshu Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Yanjie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
- *Correspondence: Zongli Hu,
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Zhou F, Zhang Y, Tang W, Wang M, Gao T. Transcriptomics analysis of the flowering regulatory genes involved in the herbicide resistance of Asia minor bluegrass (Polypogon fugax). BMC Genomics 2017; 18:953. [PMID: 29212446 PMCID: PMC5719899 DOI: 10.1186/s12864-017-4324-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/21/2017] [Indexed: 11/29/2022] Open
Abstract
Background Asia minor bluegrass (Polypogon fugax, P. fugax), a weed that is both distributed across China and associated with winter crops, has evolved resistance to acetyl-CoA carboxylase (ACCase) herbicides, but the resistance mechanism remains unclear. The goal of this study was to analyze the transcriptome between resistant and sensitive populations of P. fugax at the flowering stage. Results Populations resistant and susceptible to clodinafop-propargyl showed distinct transcriptome profiles. A total of 206,041 unigenes were identified; 165,901 unique sequences were annotated using BLASTX alignment databases. Among them, 5904 unigenes were classified into 58 transcription factor families. Nine families were related to the regulation of plant growth and development and to stress responses. Twelve unigenes were differentially expressed between the clodinafop-propargyl-sensitive and clodinafop-propargyl-resistant populations at the early flowering stage; among those unigenes, three belonged to the ABI3VP1, BHLH, and GRAS families, while the remaining nine belonged to the MADS family. Compared with the clodinafop-propargyl-sensitive plants, the resistant plants exhibited different expression pattern of these 12 unigenes. Conclusion This study identified differentially expressed unigenes related to ACCase-resistant P. fugax and thus provides a genomic resource for understanding the molecular basis of early flowering. Electronic supplementary material The online version of this article (10.1186/s12864-017-4324-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengyan Zhou
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230001, China.
| | - Yong Zhang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Mei Wang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
| | - Tongchun Gao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
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Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato. Sci Rep 2017; 7:4402. [PMID: 28667273 PMCID: PMC5493662 DOI: 10.1038/s41598-017-04556-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype. Targeted knockout of Solyc12g038510, using CRISPR/Cas9 system, validated our hypothesis. Solyc12g038510 encodes the MADS-box protein SlMBP21. Molecular analysis of j-2 natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a Rider retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of J and J-2 in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that J is epistatic to J-2 and that the branched inflorescences and the leafy sepals observed in accessions harboring j-2 alleles are likely the consequences of linkage drags.
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Soyk S, Lemmon ZH, Oved M, Fisher J, Liberatore KL, Park SJ, Goren A, Jiang K, Ramos A, van der Knaap E, Van Eck J, Zamir D, Eshed Y, Lippman ZB. Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell 2017; 169:1142-1155.e12. [PMID: 28528644 DOI: 10.1016/j.cell.2017.04.032] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 02/03/2023]
Abstract
Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing "jointless" fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms. VIDEO ABSTRACT.
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Affiliation(s)
- Sebastian Soyk
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Matan Oved
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Josef Fisher
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Katie L Liberatore
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Rep. of Korea
| | - Anna Goren
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ke Jiang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexis Ramos
- Institute of Plant Breeding, Genetic & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetic & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Guo X, Chen G, Naeem M, Yu X, Tang B, Li A, Hu Z. The MADS-box gene SlMBP11 regulates plant architecture and affects reproductive development in tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:90-101. [PMID: 28330566 DOI: 10.1016/j.plantsci.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/11/2017] [Accepted: 02/15/2017] [Indexed: 05/21/2023]
Abstract
MADS-domain proteins are important transcription factors that are involved in many biological processes of plants. In the present study, SlMBP11, a member of the AGL15 subfamily, was cloned in tomato plants (Solanum lycopersicon M.). SlMBP11 is ubiquitously expressed in all of the tissues we examined, whereas the SlMBP11 transcription levels were significantly higher in reproductive tissues than in vegetative tissues. Plants exhibiting increased SlMBP11 levels displayed reduced plant height, leaf size, and internode length as well as a loss of dominance in young seedlings, highly branched growth from each leaf axil, and increased number of nodes and leaves. Moreover, overexpression lines also exhibited reproductive phenotypes, such as those having a shorter style and split ovary, leading to polycarpous fruits, while the wild type showed normal floral organization. In addition, delayed perianth senescence was observed in transgenic tomatoes. These phenotypes were further confirmed by analyzing the morphological, anatomical and molecular features of lines exhibiting overexpression. These results suggest that SlMBP11 plays an important role in regulating plant architecture and reproductive development in tomato plants. These findings add a new class of transcription factors to the group of genes controlling axillary bud growth and illuminate a previously uncharacterized function of MADS-box genes in tomato plants.
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Affiliation(s)
- Xuhu Guo
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Muhammad Naeem
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Xiaohu Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Boyan Tang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Anzhou Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
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Zsögön A, Cermak T, Voytas D, Peres LEP. Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: Case study in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:120-130. [PMID: 28167025 DOI: 10.1016/j.plantsci.2016.12.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 05/02/2023]
Abstract
The ideotype is a theoretical model of an archetypal cultivated plant. Recent progress in genome editing is aiding the pursuit of this ideal in crop breeding. Breeding is relatively straightforward when the traits in question are monogenic in nature and show Mendelian inheritance. Conversely, traits with a diffuse, polygenic basis such as abiotic stress resistance are more difficult to harness. In recent years, many genes have been identified that are important for plant domestication and act by increasing yield, grain or fruit size or altering plant architecture. Here, we propose that (a) key monogenic traits whose physiology has been unveiled can be molecularly tailored to achieve the ideotype; and (b) wild relatives of crops harboring polygenic stress resistance genes or other traits of interest could be de novo domesticated by manipulating monogenic yield-related traits through state-of-the-art gene editing techniques. An overview of the genomic and physiological challenges in the world's main staple crops is provided. We focus on tomato and its wild Solanum (section Lycopersicon) relatives as a suitable model for molecular design in the pursuit of the ideotype for elite cultivars and to test de novo domestication of wild relatives.
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Affiliation(s)
- Agustin Zsögön
- Laboratory of Molecular Plant Physiology, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Tomas Cermak
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dan Voytas
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lázaro Eustáquio Pereira Peres
- Laboratory of Hormonal Control of Plant Development, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, CP 09 13418-900 Piracicaba, SP, Brazil.
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Poyatos-Pertíñez S, Quinet M, Ortíz-Atienza A, Bretones S, Yuste-Lisbona FJ, Lozano R. Genetic interactions of the unfinished flower development (ufd) mutant support a significant role of the tomato UFD gene in regulating floral organogenesis. PLANT REPRODUCTION 2016; 29:227-38. [PMID: 27295366 DOI: 10.1007/s00497-016-0286-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/31/2016] [Indexed: 05/08/2023]
Abstract
Genetic interactions of UFD gene support its specific function during reproductive development of tomato; in this process, UFD could play a pivotal role between inflorescence architecture and flower initiation genes. Tomato (Solanum lycopersicum L.) is a major vegetable crop that also constitutes a model species for the study of plant developmental processes. To gain insight into the control of flowering and floral development, a novel tomato mutant, unfinished flower development (ufd), whose inflorescence and flowers were unable to complete their normal development was characterized using double mutant and gene expression analyses. Genetic interactions of ufd with mutations affecting inflorescence fate (uniflora, jointless and single flower truss) were additive and resulted in double mutants displaying the inflorescence structure of the non-ufd parental mutant and the flower phenotype of the ufd mutant. In addition, ufd mutation promotes an earlier inflorescence meristem termination. Taken together, both results indicated that UFD is not involved in the maintenance of inflorescence meristem identity, although it could participate in the regulatory system that modulates the rate of meristem maturation. Regarding the floral meristem identity, the falsiflora mutation was epistatic to the ufd mutation even though FALSIFLORA was upregulated in ufd inflorescences. In terms of floral organ identity, the ufd mutation was epistatic to macrocalyx, and MACROCALYX expression was differently regulated depending on the inflorescence developmental stage. These results suggest that the UFD gene may play a pivotal role between the genes required for flowering initiation and inflorescence development (such as UNIFLORA, FALSIFLORA, JOINTLESS and SINGLE FLOWER TRUSS) and those required for further floral organ development such as the floral organ identity genes.
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Affiliation(s)
- Sandra Poyatos-Pertíñez
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain
| | - Muriel Quinet
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute, Université catholique de Louvain, Croix du Sud 4-5 bte L7.07.13, 1348, Louvain-la-Neuve, Belgium
| | - Ana Ortíz-Atienza
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain
| | - Sandra Bretones
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain
| | - Fernando J Yuste-Lisbona
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain
| | - Rafael Lozano
- Departamento de Biología y Geología (Genética), Edificio CITE II-B, Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Carretera de Sacramento s/n, 04120, Almería, Spain.
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Hodge JG, Kellogg EA. Abscission zone development in Setaria viridis and its domesticated relative, Setaria italica. AMERICAN JOURNAL OF BOTANY 2016; 103:998-1005. [PMID: 27257006 DOI: 10.3732/ajb.1500499] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/27/2016] [Indexed: 05/26/2023]
Abstract
PREMISE OF THE STUDY Development of an abscission zone (AZ) is needed for dispersal of seeds, and AZ loss was a critical early step in plant domestication. The AZ forms in different tissues in different species of plants, but whether the AZ is developmentally similar wherever it occurs is unknown. AZ development in Setaria viridis was studied as a representative of the previously uncharacterized subfamily Panicoideae. METHODS One accession of the wild species S. viridis and two of its domesticate, S. italica, were studied. Strength of the AZ was measured with a force gauge. Anatomy of the AZ was studied throughout development using bright field and confocal microscopy. KEY RESULTS The force required to remove a spikelet of S. viridis from the parent plant dropped steadily during development, whereas that required to remove spikelets of S. italica increased initially before stabilizing at a high level. Despite the clear difference in tensile strength of the AZ, anatomical differences between S. viridis and S. italica were subtle, and the position of the AZ was not easy to determine in cross sections of pedicel apices. Staining with DAPI showed that nuclei were present up to and presumably through abscission in S. viridis, and acridine orange staining showed much less lignification than in other cereals. CONCLUSIONS The AZ in Setaria is developmentally and anatomically different from that characterized in rice, barley, and many eudicots. In particular, no set of small, densely cytoplasmic cells is obvious. This difference in anatomy could point to differential genetic control of the structure.
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Affiliation(s)
- John G Hodge
- University of Missouri-St. Louis, One University Boulevard, St. Louis, Missouri, USA Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 USA
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70
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Pirone-Davies C, Prior N, von Aderkas P, Smith D, Hardie D, Friedman WE, Mathews S. Insights from the pollination drop proteome and the ovule transcriptome of Cephalotaxus at the time of pollination drop production. ANNALS OF BOTANY 2016; 117:973-84. [PMID: 27045089 PMCID: PMC4866313 DOI: 10.1093/aob/mcw026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/08/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Many gymnosperms produce an ovular secretion, the pollination drop, during reproduction. The drops serve as a landing site for pollen, but also contain a suite of ions and organic compounds, including proteins, that suggests diverse roles for the drop during pollination. Proteins in the drops of species of Chamaecyparis, Juniperus, Taxus, Pseudotsuga, Ephedra and Welwitschia are thought to function in the conversion of sugars, defence against pathogens, and pollen growth and development. To better understand gymnosperm pollination biology, the pollination drop proteomes of pollination drops from two species of Cephalotaxus have been characterized and an ovular transcriptome for C. sinensis has been assembled. METHODS Mass spectrometry was used to identify proteins in the pollination drops of Cephalotaxus sinensis and C. koreana RNA-sequencing (RNA-Seq) was employed to assemble a transcriptome and identify transcripts present in the ovules of C. sinensis at the time of pollination drop production. KEY RESULTS About 30 proteins were detected in the pollination drops of both species. Many of these have been detected in the drops of other gymnosperms and probably function in defence, polysaccharide metabolism and pollen tube growth. Other proteins appear to be unique to Cephalotaxus, and their putative functions include starch and callose degradation, among others. Together, the proteins appear either to have been secreted into the drop or to occur there due to breakdown of ovular cells during drop production. Ovular transcripts represent a wide range of gene ontology categories, and some may be involved in drop formation, ovule development and pollen-ovule interactions. CONCLUSIONS The proteome of Cephalotaxus pollination drops shares a number of components with those of other conifers and gnetophytes, including proteins for defence such as chitinases and for carbohydrate modification such as β-galactosidase. Proteins likely to be of intracellular origin, however, form a larger component of drops from Cephalotaxus than expected from studies of other conifers. This is consistent with the observation of nucellar breakdown during drop formation in Cephalotaxus The transcriptome data provide a framework for understanding multiple metabolic processes that occur within the ovule and the pollination drop just before fertilization. They reveal the deep conservation of WUSCHEL expression in ovules and raise questions about whether any of the S-locus transcripts in Cephalotaxus ovules might be involved in pollen-ovule recognition.
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Affiliation(s)
| | | | | | - Derek Smith
- UVic Genome BC Proteomics Centre, Victoria, BC, Canada
| | - Darryl Hardie
- UVic Genome BC Proteomics Centre, Victoria, BC, Canada
| | - William E Friedman
- The Arnold Arboretum of Harvard University, Boston, MA, USA, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sarah Mathews
- CSIRO, Centre for Australian National Biodiversity Research, Canberra, Australia and
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Li LF, Olsen KM. To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication. Curr Top Dev Biol 2016; 119:63-109. [PMID: 27282024 DOI: 10.1016/bs.ctdb.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.
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Affiliation(s)
- L-F Li
- Washington University in St. Louis, St. Louis, MO, United States; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, PR China.
| | - K M Olsen
- Washington University in St. Louis, St. Louis, MO, United States.
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Qiao Z, Qi W, Wang Q, Feng Y, Yang Q, Zhang N, Wang S, Tang Y, Song R. ZmMADS47 Regulates Zein Gene Transcription through Interaction with Opaque2. PLoS Genet 2016; 12:e1005991. [PMID: 27077660 PMCID: PMC4831773 DOI: 10.1371/journal.pgen.1005991] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/24/2016] [Indexed: 11/19/2022] Open
Abstract
Zeins, the predominent storage proteins in maize endosperm, are encoded by multiple genes and gene families. However, only a few transcriptional factors for zein gene regulation have been functionally characterized. In this study, a MADS-box protein, namely ZmMADS47, was identified as an Opaque2 (O2) interacting protein via yeast two-hybrid screening. The N-terminal portion of ZmMADS47 contains a nuclear localization signal (NLS), and its C-terminal portion contains a transcriptional activation domain (AD). Interestingly, the transcriptional activation activity is blocked in its full length form, suggesting conformational regulation of the AD. Molecular and RNA-seq analyses of ZmMADS47 RNAi lines revealed down regulation of α-zein and 50-kD γ-zein genes. ZmMADS47 binds the CATGT motif in promoters of these zein genes, but ZmMADS47 alone is not able to transactivate the promoters. However, when both O2 and ZmMADS47 are present, the transactivation of these promoters was greatly enhanced. This enhancement was dependent on the AD function of ZmMADS47 and the interaction between ZmMADS47 and O2, but it was independent from the AD function of O2. Therefore, it appears interaction with O2 activates ZmMADS47 on zein gene promoters. A newly identified transcription factor of seed storage proteins can engage its transactivation ability after interacting with another seed storage protein transcription factor in maize.
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Affiliation(s)
- Zhenyi Qiao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
- Coordinated Crop Biology Research Center (CBRC), Beijing, China
| | - Qian Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Ya’nan Feng
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Qing Yang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Nan Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shanshan Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yuanping Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
- Coordinated Crop Biology Research Center (CBRC), Beijing, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
- * E-mail:
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Li M, Liang Z, Zeng Y, Jing Y, Wu K, Liang J, He S, Wang G, Mo Z, Tan F, Li S, Wang L. De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). BMC Genomics 2016; 17:195. [PMID: 26946183 PMCID: PMC4779555 DOI: 10.1186/s12864-016-2552-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/28/2016] [Indexed: 01/01/2023] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest. Results To determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants. Conclusion Our results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2552-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Jun Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Zhanghong Mo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
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Grimplet J, Martínez-Zapater JM, Carmona MJ. Structural and functional annotation of the MADS-box transcription factor family in grapevine. BMC Genomics 2016; 17:80. [PMID: 26818751 PMCID: PMC4729134 DOI: 10.1186/s12864-016-2398-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/14/2016] [Indexed: 02/02/2023] Open
Abstract
Background MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes. In plants, they are associated to numerous development processes most notably those related to reproductive development: flowering induction, specification of inflorescence and flower meristems, establishment of flower organ identity, as well as regulation of fruit, seed and embryo development. Genomic analyses of MADS-box genes in different plant species are providing new relevant information on the function and evolution of this transcriptional factor family. We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine (Vitis vinifera), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. This study was integrated to previous works on the family in grapevine. Results A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. We performed a thorough in-depth curation of all gene models and combined the results with gene expression information including RNAseq data to clarifying the expression of newly identified genes and improve their functional characterization. Curated data were uploaded to the ORCAE database for grapevine in the frame of the grapevine genome curation effort. This approach resulted in the identification of 30 additional MADS box genes. Among them, ten new MIKCC genes were identified, including a potential new group of short proteins similar to the SVP protein subfamily. The MIKC* subgroup contains six genes in grapevine that can be grouped in the S (4 genes) and P (2 genes) clades, showing less redundancy than that observed in Arabidopsis thaliana. Expression pattern of these genes in grapevine is compatible with a role in male gametophyte development. Most of the identified new genes belong to the type I MADS-box genes and were classified as members of the Mα and Mγ subclasses. Ours analyses indicate that only few members of type I genes in grapevine have homology in other species and that species-specific clades appeared both in the Mα and Mγ subclasses. On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants. Conclusions The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2398-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, 26007, Spain.
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, 26007, Spain.
| | - María José Carmona
- Departamento de Biotecnología, Escuela Técnica Superior Ingenieros Agrónomos, Universidad Politécnica de Madrid, Madrid, 28040, Spain.
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Patterson SE, Bolivar-Medina JL, Falbel TG, Hedtcke JL, Nevarez-McBride D, Maule AF, Zalapa JE. Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops? FRONTIERS IN PLANT SCIENCE 2016; 6:1268. [PMID: 26858730 PMCID: PMC4726918 DOI: 10.3389/fpls.2015.01268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/28/2015] [Indexed: 05/24/2023]
Abstract
As the world population grows and resources and climate conditions change, crop improvement continues to be one of the most important challenges for agriculturalists. The yield and quality of many crops is affected by abscission or shattering, and environmental stresses often hasten or alter the abscission process. Understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality and greater sustainability. As plant scientists, we have learned significant amounts about this process through the study of model plants such as Arabidopsis, tomato, rice, and maize. While these model systems have provided significant valuable information, we are sometimes challenged to use this knowledge effectively as variables including the economic value of the crop, the uniformity of the crop, ploidy levels, flowering and crossing mechanisms, ethylene responses, cultural requirements, responses to changes in environment, and cellular and tissue specific morphological differences can significantly influence outcomes. The value of genomic resources for lesser-studied crops such as cranberries and grapes and the orphan crop fonio will also be considered.
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Affiliation(s)
- Sara E. Patterson
- Department of Horticulture, University of Wisconsin–MadisonMadison, WI, USA
| | - Jenny L. Bolivar-Medina
- Department of Horticulture, University of Wisconsin–MadisonMadison, WI, USA
- Vegetable Crops Research Unit, United States Department of Agriculture – Agricultural Research ServiceMadison, WI, USA
| | - Tanya G. Falbel
- Department of Horticulture, University of Wisconsin–MadisonMadison, WI, USA
| | | | | | - Andrew F. Maule
- Department of Horticulture, University of Wisconsin–MadisonMadison, WI, USA
| | - Juan E. Zalapa
- Department of Horticulture, University of Wisconsin–MadisonMadison, WI, USA
- Vegetable Crops Research Unit, United States Department of Agriculture – Agricultural Research ServiceMadison, WI, USA
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Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, Wang L, Fellgett A, Sollars ESA, Janacek SH, Downie JA, Buggs RJA, Kjær ED, Bancroft I. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics. Sci Rep 2016; 6:19335. [PMID: 26757823 PMCID: PMC4725942 DOI: 10.1038/srep19335] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/07/2015] [Indexed: 11/24/2022] Open
Abstract
Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback.
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Affiliation(s)
| | - Lea Vig McKinney
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | - Lene Rostgaard Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | | | - Yi Li
- Department of Biology, University of York, York, UK
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, UK
| | - Fiona Fraser
- Department of Crop Genetics, John Innes Centre, Norwich, UK
| | - Lihong Wang
- Department of Biology, University of York, York, UK
| | | | | | | | - J. Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Richard. J. A. Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Erik Dahl Kjær
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
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Yuste-Lisbona FJ, Quinet M, Fernández-Lozano A, Pineda B, Moreno V, Angosto T, Lozano R. Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato. Sci Rep 2016; 6:18796. [PMID: 26727224 PMCID: PMC4698712 DOI: 10.1038/srep18796] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022] Open
Abstract
Inflorescence development is a key factor of plant productivity, as it determines flower number. Therefore, understanding the mechanisms that regulate inflorescence architecture is critical for reproductive success and crop yield. In this study, a new mutant, vegetative inflorescence (mc-vin), was isolated from the screening of a tomato (Solanum lycopersicum L.) T-DNA mutant collection. The mc-vin mutant developed inflorescences that reverted to vegetative growth after forming two to three flowers, indicating that the mutated gene is essential for the maintenance of inflorescence meristem identity. The T-DNA was inserted into the promoter region of the MACROCALYX (MC) gene; this result together with complementation test and expression analyses proved that mc-vin is a new knock-out allele of MC. Double combinations between mc-vin and jointless (j) and single flower truss (sft) inflorescence mutants showed that MC has pleiotropic effects on the reproductive phase, and that it interacts with SFT and J to control floral transition and inflorescence fate in tomato. In addition, MC expression was mis-regulated in j and sft mutants whereas J and SFT were significantly up-regulated in the mc-vin mutant. Together, these results provide new evidences about MC function as part of the genetic network regulating the development of tomato inflorescence meristem.
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Affiliation(s)
- Fernando J Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Muriel Quinet
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Antonia Fernández-Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia. Avenida de los Naranjos s/n. 46022 Valencia, Spain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia. Avenida de los Naranjos s/n. 46022 Valencia, Spain
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
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Couzigou JM, Magne K, Mondy S, Cosson V, Clements J, Ratet P. The legume NOOT-BOP-COCH-LIKE genes are conserved regulators of abscission, a major agronomical trait in cultivated crops. THE NEW PHYTOLOGIST 2016; 209:228-40. [PMID: 26390061 DOI: 10.1111/nph.13634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/04/2015] [Indexed: 05/05/2023]
Abstract
Plants are able to lose organs selectively through a process called abscission. This process relies on the differentiation of specialized territories at the junction between organs and the plant body that are called abscission zones (AZ). Several genes control the formation or functioning of these AZ. We have characterized BLADE-ON-PETIOLE (BOP) orthologues from several legume plants and studied their roles in the abscission process using a mutant approach. Here, we show that the Medicago truncatula NODULE ROOT (NOOT), the Pisum sativum COCHLEATA (COCH) and their orthologue in Lotus japonicus are strictly necessary for the abscission of not only petals, but also leaflets, leaves and fruits. We also showed that the expression pattern of the M. truncatula pNOOT::GUS fusion is associated with functional and vestigial AZs when expressed in Arabidopsis. In addition, we show that the stip mutant from Lupinus angustifolius, defective in stipule formation and leaf abscission, is mutated in a BOP orthologue. In conclusion, this study shows that this clade of proteins plays an important conserved role in promoting abscission of all aerial organs studied so far.
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Affiliation(s)
- Jean-Malo Couzigou
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, CNRS, 31326, Castanet Tolosan, France
| | - Kevin Magne
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
| | - Samuel Mondy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
| | - Viviane Cosson
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
| | | | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
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80
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Kim J, Yang J, Yang R, Sicher RC, Chang C, Tucker ML. Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate. FRONTIERS IN PLANT SCIENCE 2016; 7:125. [PMID: 26925069 PMCID: PMC4756167 DOI: 10.3389/fpls.2016.00125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/22/2016] [Indexed: 05/19/2023]
Abstract
Abscission, organ separation, is a developmental process that is modulated by endogenous and environmental factors. To better understand the molecular events underlying the progression of abscission in soybean, an agriculturally important legume, we performed RNA sequencing (RNA-seq) of RNA isolated from the leaf abscission zones (LAZ) and petioles (Non-AZ, NAZ) after treating stem/petiole explants with ethylene for 0, 12, 24, 48, and 72 h. As expected, expression of several families of cell wall modifying enzymes and many pathogenesis-related (PR) genes specifically increased in the LAZ as abscission progressed. Here, we focus on the 5,206 soybean genes we identified as encoding transcription factors (TFs). Of the 5,206 TFs, 1,088 were differentially up- or down-regulated more than eight-fold in the LAZ over time, and, within this group, 188 of the TFs were differentially regulated more than eight-fold in the LAZ relative to the NAZ. These 188 abscission-specific TFs include several TFs containing domains for homeobox, MYB, Zinc finger, bHLH, AP2, NAC, WRKY, YABBY, and auxin-related motifs. To discover the connectivity among the TFs and highlight developmental processes that support organ separation, the 188 abscission-specific TFs were then clustered based on a >four-fold up- or down-regulation in two consecutive time points (i.e., 0 and 12 h, 12 and 24 h, 24 and 48 h, or 48 and 72 h). By requiring a sustained change in expression over two consecutive time intervals and not just one or several time intervals, we could better tie changes in TFs to a particular process or phase of abscission. The greatest number of TFs clustered into the 0 and 12 h group. Transcriptional network analysis for these abscission-specific TFs indicated that most of these TFs are known as key determinants in the maintenance of organ polarity, lateral organ growth, and cell fate. The abscission-specific expression of these TFs prior to the onset of abscission and their functional properties as defined by studies in Arabidopsis indicate that these TFs are involved in defining the separation cells and initiation of separation within the AZ by balancing organ polarity, roles of plant hormones, and cell differentiation.
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Affiliation(s)
- Joonyup Kim
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MD, USA
- *Correspondence: Joonyup Kim
| | - Jinyoung Yang
- Crop Systems and Global Change Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Richard C. Sicher
- Crop Systems and Global Change Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Caren Chang
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MD, USA
| | - Mark L. Tucker
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
- Mark L. Tucker
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Roongsattham P, Morcillo F, Fooyontphanich K, Jantasuriyarat C, Tragoonrung S, Amblard P, Collin M, Mouille G, Verdeil JL, Tranbarger TJ. Cellular and Pectin Dynamics during Abscission Zone Development and Ripe Fruit Abscission of the Monocot Oil Palm. FRONTIERS IN PLANT SCIENCE 2016; 7:540. [PMID: 27200017 PMCID: PMC4844998 DOI: 10.3389/fpls.2016.00540] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/05/2016] [Indexed: 05/09/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) fruit primary abscission zone (AZ) is a multi-cell layered boundary region between the pedicel (P) and mesocarp (M) tissues. To examine the cellular processes that occur during the development and function of the AZ cell layers, we employed multiple histological and immunohistochemical methods combined with confocal, electron and Fourier-transform infrared (FT-IR) microspectroscopy approaches. During early fruit development and differentiation of the AZ, the orientation of cell divisions in the AZ was periclinal compared with anticlinal divisions in the P and M. AZ cell wall width increased earlier during development suggesting cell wall assembly occurred more rapidly in the AZ than the adjacent P and M tissues. The developing fruit AZ contain numerous intra-AZ cell layer plasmodesmata (PD), but very few inter-AZ cell layer PD. In the AZ of ripening fruit, PD were less frequent, wider, and mainly intra-AZ cell layer localized. Furthermore, DAPI staining revealed nuclei are located adjacent to PD and are remarkably aligned within AZ layer cells, and remain aligned and intact after cell separation. The polarized accumulation of ribosomes, rough endoplasmic reticulum, mitochondria, and vesicles suggested active secretion at the tip of AZ cells occurred during development which may contribute to the striated cell wall patterns in the AZ cell layers. AZ cells accumulated intracellular pectin during development, which appear to be released and/or degraded during cell separation. The signal for the JIM5 epitope, that recognizes low methylesterified and un-methylesterified homogalacturonan (HG), increased in the AZ layer cell walls prior to separation and dramatically increased on the separated AZ cell surfaces. Finally, FT-IR microspectroscopy analysis indicated a decrease in methylesterified HG occurred in AZ cell walls during separation, which may partially explain an increase in the JIM5 epitope signal. The results obtained through a multi-imaging approach allow an integrated view of the dynamic developmental processes that occur in a multi-layered boundary AZ and provide evidence for distinct regulatory mechanisms that underlie oil palm fruit AZ development and function.
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Affiliation(s)
| | | | - Kim Fooyontphanich
- UMR DIADE, Institut de Recherche pour le DéveloppementMontpellier, France
| | | | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, Genome InstitutePathum Thani, Thailand
| | | | - Myriam Collin
- UMR DIADE, Institut de Recherche pour le DéveloppementMontpellier, France
| | - Gregory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 Institut National de la Recherche Agronomique -AgroParisTechERL3559 Centre National de la Recherche Scientifique, France
| | | | - Timothy J. Tranbarger
- UMR DIADE, Institut de Recherche pour le DéveloppementMontpellier, France
- *Correspondence: Timothy J. Tranbarger
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Wang D, Chen X, Zhang Z, Liu D, Song G, Kong X, Geng S, Yang J, Wang B, Wu L, Li A, Mao L. A MADS-box gene NtSVP regulates pedicel elongation by directly suppressing a KNAT1-like KNOX gene NtBPL in tobacco (Nicotiana tabacum L.). JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6233-44. [PMID: 26175352 PMCID: PMC4588881 DOI: 10.1093/jxb/erv332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Optimal inflorescence architecture is important for plant reproductive success by affecting the ultimate number of flowers that set fruits and for plant competitiveness when interacting with biotic or abiotic conditions. The pedicel is one of the key contributors to inflorescence architecture diversity. To date, knowledge about the molecular mechanisms of pedicel development is derived from Arabidopsis. Not much is known regarding other plants. Here, an SVP family MADS-box gene, NtSVP, in tobacco (Nicotiana tabacum) that is required for pedicel elongation was identified. It is shown that knockdown of NtSVP by RNA interference (RNAi) caused elongated pedicels, while overexpression resulted in compact inflorescences with much shortened pedicels. Moreover, an Arabidopsis BREVIPEDECELLUS/KNAT1 homologue NtBP-Like (NtBPL) was significantly up-regulated in NtSVP-RNAi plants. Disruption of NtBPL decreased pedicel lengths and shortened cortex cells. Consistent with the presence of a CArG-box at the NtBPL promoter, the direct binding of NtSVP to the NtBPL promoter was demonstrated by yeast one-hybrid assay, electrophoretic mobility shift assay, and dual-luciferase assay, in which NtSVP may act as a repressor of NtBPL. Microarray analysis showed that down-regulation of NtBPL resulted in differential expression of genes associated with a number of hormone biogenesis and signalling genes such as those for auxin and gibberellin. These findings together suggest the function of a MADS-box transcription factor in plant pedicel development, probably via negative regulation of a BP-like class I KNOX gene. The present work thus postulates the conservation and divergence of the molecular regulatory pathways underlying the development of plant inflorescence architecture.
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Affiliation(s)
- Di Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xiaobo Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zenglin Zhang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Danmei Liu
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Gaoyuan Song
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xingchen Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jiayue Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Bingnan Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Liang Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Crop Germplasm and Biotechnology, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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Nakano T, Kato H, Shima Y, Ito Y. Apple SVP Family MADS-Box Proteins and the Tomato Pedicel Abscission Zone Regulator JOINTLESS have Similar Molecular Activities. PLANT & CELL PHYSIOLOGY 2015; 56:1097-106. [PMID: 25746985 DOI: 10.1093/pcp/pcv034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/22/2015] [Indexed: 05/22/2023]
Abstract
Pedicel abscission occurs widely in fruit-bearing plants to detach ripe, senescent or diseased organs, and regulation of abscission plays a substantial role in regulating yield and quality in fruit crops. In tomato, development of pedicel abscission zones (AZs) requires the MADS-box genes JOINTLESS (J), MACROCALYX (MC) and SlMBP21. In other plants, however, the involvement of MADS-box genes in pedicel abscission remains unclear. Here, we used genetic and biochemical methods to characterize apple J homologs in the context of the regulation of abscission in tomato. We identified three genes encoding two J homologs, MdJa and MdJb. Similarly to J, MdJa and MdJb interacted with MC and SlMBP21, but their interactions differed slightly: like J, MdJb formed a multimer (probably a tetramer) with SlMBP21; however, MdJa formed multimers to a lesser extent. Ectopic expression of MdJb in a J-deficient tomato mutant restored development of functional pedicel AZs, but ectopic expression of MdJa did not complement j mutants. Introduction of MdJb also restored expression of J-dependent genes in the mutant, such as genes for polygalacturonase, cellulase and AZ-specific transcription factors. These results suggest a potentially conserved mechanism of pedicel AZ development in apple and other plants, regulated by MADS-box transcription factors.
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Affiliation(s)
- Toshitsugu Nakano
- National Food Research Institute, NARO, Ibaraki, 305-8642 Japan Present address: Institute of Crops Research and Development, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Hiroki Kato
- National Food Research Institute, NARO, Ibaraki, 305-8642 Japan Department of Applied Biological Science, Tokyo University of Science, Chiba, 278-8510 Japan
| | - Yoko Shima
- National Food Research Institute, NARO, Ibaraki, 305-8642 Japan
| | - Yasuhiro Ito
- National Food Research Institute, NARO, Ibaraki, 305-8642 Japan
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84
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Saha G, Park JI, Jung HJ, Ahmed NU, Kayum MA, Chung MY, Hur Y, Cho YG, Watanabe M, Nou IS. Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa. BMC Genomics 2015; 16:178. [PMID: 25881193 PMCID: PMC4422603 DOI: 10.1186/s12864-015-1349-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 02/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa. RESULTS Whole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (MIKC(c) and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKC(c) and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively. CONCLUSION The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.
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Affiliation(s)
- Gopal Saha
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Nasar Uddin Ahmed
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
| | - Yoonkang Hur
- Department of Biology, Chungnam National University, 96 Daehangno, Gung-dong, Yuseong-gu, Daejeon, 305-764, Republic of Korea.
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, 410 Seongbongro, Heungdokgu, Cheongju, 361-763, Republic of Korea.
| | - Masao Watanabe
- Laboratory of Plant Reproductive Genetics, Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea.
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85
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Ma C, Meir S, Xiao L, Tong J, Liu Q, Reid MS, Jiang CZ. A KNOTTED1-LIKE HOMEOBOX protein regulates abscission in tomato by modulating the auxin pathway. PLANT PHYSIOLOGY 2015; 167:844-53. [PMID: 25560879 PMCID: PMC4348773 DOI: 10.1104/pp.114.253815] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/30/2014] [Indexed: 05/20/2023]
Abstract
A gene encoding a KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) is highly expressed in both leaf and flower abscission zones. Reducing the abundance of transcripts of this gene in tomato (Solanum lycopersicum) by both virus-induced gene silencing and stable transformation with a silencing construct driven by an abscission-specific promoter resulted in a striking retardation of pedicel and petiole abscission. In contrast, Petroselinum, a semidominant KD1 mutant, showed accelerated pedicel and petiole abscission. Complementary DNA microarray and quantitative reverse transcription-polymerase chain reaction analysis indicated that regulation of abscission by KD1 was associated with changed abundance of genes related to auxin transporters and signaling components. Measurement of auxin content and activity of a DR5::β-glucuronidase auxin reporter assay showed that changes in KD1 expression modulated the auxin concentration and response gradient in the abscission zone.
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Affiliation(s)
- Chao Ma
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Shimon Meir
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Langtao Xiao
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Jianhua Tong
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Qing Liu
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Michael S Reid
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, California 95616 (C.M., M.S.R.);Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250, Israel (S.M.);Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China (L.X., J.T., Q.L.); andCrops Pathology and Genetic Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, California 95616 (C.-Z.J.)
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86
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Li XF, Wu WT, Zhang XP, Qiu Y, Zhang W, Li R, Xu J, Sun Y, Wang Y, Xu L. Narcissus tazetta SVP-like gene NSVP1 affects flower development in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2015; 173:89-96. [PMID: 25462082 DOI: 10.1016/j.jplph.2014.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/24/2014] [Accepted: 08/07/2014] [Indexed: 06/04/2023]
Abstract
SHORT VEGETATIVE PHASE (SVP) related genes have important functions in regulating floral transition and inflorescence structure in many plant species. Some SVP related genes have been shown associated with dormancy transition. Narcissus tazetta var. chinensis exhibits summer dormancy release and floral transition promoted by extended high temperature exposure. However, the molecular mechanism underlying such development remains unknown. In this study, we isolated and characterized one SVP-like gene, NSVP1 from N. tazetta var. chinensis. The results of RT-PCR and in situ hybridization assay showed that NSVP1 was expressed in both vegetative and floral tissues. The highest level of NSVP1 in the bulb apices was detected when the above-ground just senesced and its transcripts declined gradually during endo-dormany. The lowest level was found at the beginning of flower differentiation and the release of endo-dormancy. These data suggest that NSVP1 is differentially regulated coordinately with endo-dormancy induction and release. Ectopic expression of NSVP1 neither complemented the early flowering phenotype of svp mutant nor altered the rosette leaf number in Col background. However, NSVP1 in svp mutant and Ler plants increased the number of lateral inflorescence and caused abnormal floral morphologies. In addition, strong expression of NSVP1 in Ler background affected plastochron. These results suggest that NSVP1 might play a role in the regulation of flower development.
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Affiliation(s)
- Xiao-Fang Li
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
| | - Wen-Ting Wu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Xue-Ping Zhang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yan Qiu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Wei Zhang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Rui Li
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jing Xu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yue Sun
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yang Wang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Ling Xu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
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Sundaresan S, Philosoph-Hadas S, Riov J, Mugasimangalam R, Kuravadi NA, Kochanek B, Salim S, Tucker ML, Meir S. De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission. FRONTIERS IN PLANT SCIENCE 2015; 6:1258. [PMID: 26834766 PMCID: PMC4712312 DOI: 10.3389/fpls.2015.01258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/24/2015] [Indexed: 05/19/2023]
Abstract
Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.
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Affiliation(s)
- Srivignesh Sundaresan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Sonia Philosoph-Hadas
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Joseph Riov
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Raja Mugasimangalam
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Nagesh A. Kuravadi
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Bettina Kochanek
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Mark L. Tucker
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Shimon Meir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- *Correspondence: Shimon Meir
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88
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Ito Y, Nakano T. Development and regulation of pedicel abscission in tomato. FRONTIERS IN PLANT SCIENCE 2015; 6:442. [PMID: 26124769 PMCID: PMC4462994 DOI: 10.3389/fpls.2015.00442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/29/2015] [Indexed: 05/05/2023]
Abstract
To shed unfertilized flowers or ripe fruits, many plant species develop a pedicel abscission zone (AZ), a specialized tissue that develops between the organ and the main body of the plant. Regulation of pedicel abscission is an important agricultural concern because pre-harvest abscission can reduce yields of fruit or grain crops, such as apples, rice, wheat, etc. Tomato has been studied as a model system for abscission, as tomato plants develop a distinct AZ at the midpoint of the pedicel and several tomato mutants, such as jointless, have pedicels that lack an AZ. This mini-review focuses on recent advances in research on the mechanisms regulating tomato pedicel abscission. Molecular genetic studies revealed that three MADS-box transcription factors interactively play a central role in pedicel AZ development. Transcriptome analyses identified activities involved in abscission and also found novel transcription factors that may regulate AZ activities. Another study identified transcription factors mediating abscission pathways from induction signals to activation of cell wall hydrolysis. These recent findings in tomato will enable significant advances in understanding the regulation of abscission in other key agronomic species.
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Affiliation(s)
- Yasuhiro Ito
- *Correspondence: Yasuhiro Ito, Food Biotechnology Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan,
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89
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Arisha MH, Shah SNM, Gong ZH, Jing H, Li C, Zhang HX. Ethyl methane sulfonate induced mutations in M2 generation and physiological variations in M1 generation of peppers (Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2015; 6:399. [PMID: 26089827 PMCID: PMC4454883 DOI: 10.3389/fpls.2015.00399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/18/2015] [Indexed: 05/10/2023]
Abstract
This study was conducted to enhance genetic variability in peppers (Capsicum annuum, cv B12) using ethyl methanesulphonate (EMS). Exposure to an EMS concentration of 0.6%, v/v for 12 h was used to mutagenize 2000 seeds for the first generation (M1). It was observed that the growth behaviors including plant height, flowering date, and number of seeds per first fruit were different in the M1 generation than in wild type (WT) plants. In addition one phenotypic mutation (leaf shape and plant architecture) was observed during the M1 generation. During the seedling stage in the M2 generation, the observed changes were in the form of slow growth or chlorophyll defect (e.g., albino, pale green, and yellow seedlings). At maturity, there were three kinds of phenotypic mutations observed in three different families of the mutant population. The first observed change was a plant with yellow leaf color, and the leaves of this mutant plant contained 62.19% less chlorophyll a and 64.06% less chlorophyll b as compared to the wild-type. The second mutation resulted in one dwarf plant with a very short stature (6 cm), compact internodes and the leaves and stem were rough and thick. The third type of mutation occurred in four plants and resulted in the leaves of these plants being very thick and longer than those of WT plants. Furthermore, anatomical observations of the leaf blade section of this mutant plant type contained more xylem and collenchyma tissue in the leaf midrib of the mutant plant than WT. In addition, its leaf blade contained thicker palisade and spongy tissue than the WT.
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Affiliation(s)
- Mohamed H. Arisha
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Zagazig University, ZagazigEgypt
| | - Syed N. M. Shah
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail KhanPakistan
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- *Correspondence: Zhen-Hui Gong, College of Horticulture, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi Province 712100, China
| | - Hua Jing
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Chao Li
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, YanglingChina
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90
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Dong Y, Wang YZ. Seed shattering: from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:476. [PMID: 26157453 PMCID: PMC4478375 DOI: 10.3389/fpls.2015.00476] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/15/2015] [Indexed: 05/19/2023]
Abstract
Seed shattering (or pod dehiscence, or fruit shedding) is essential for the propagation of their offspring in wild plants but is a major cause of yield loss in crops. In the dicot model species, Arabidopsis thaliana, pod dehiscence necessitates a development of the abscission zones along the pod valve margins. In monocots, such as cereals, an abscission layer in the pedicle is required for the seed shattering process. In the past decade, great advances have been made in characterizing the genetic contributors that are involved in the complex regulatory network in the establishment of abscission cell identity. We summarize the recent burgeoning progress in the field of genetic regulation of pod dehiscence and fruit shedding, focusing mainly on the model species A. thaliana with its close relatives and the fleshy fruit species tomato, as well as the genetic basis responsible for the parallel loss of seed shattering in domesticated crops. This review shows how these individual genes are co-opted in the developmental process of the tissues that guarantee seed shattering. Research into the genetic mechanism underlying seed shattering provides a premier prerequisite for the future breeding program for harvest in crops.
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Affiliation(s)
| | - Yin-Zheng Wang
- *Correspondence: Yin-Zheng Wang, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China,
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91
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Jin X, Zimmermann J, Polle A, Fischer U. Auxin is a long-range signal that acts independently of ethylene signaling on leaf abscission in Populus. FRONTIERS IN PLANT SCIENCE 2015; 6:634. [PMID: 26322071 PMCID: PMC4532917 DOI: 10.3389/fpls.2015.00634] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/31/2015] [Indexed: 05/04/2023]
Abstract
Timing of leaf abscission is an important trait for biomass production and seasonal acclimation in deciduous trees. The signaling leading to organ separation, from the external cue (decreasing photoperiod) to ethylene-regulated hydrolysis of the middle lamellae in the abscission zone, is only poorly understood. Data from annual species indicate that the formation of an auxin gradient spanning the abscission zone regulates the timing of abscission. We established an experimental system in Populus to induce leaf shedding synchronously under controlled greenhouse conditions in order to test the function of auxin in leaf abscission. Here, we show that exogenous auxin delayed abscission of dark-induced leaves over short and long distances and that a new auxin response maximum preceded the formation of an abscission zone. Several auxin transporters were down-regulated during abscission and inhibition of polar auxin transport delayed leaf shedding. Ethylene signaling was not involved in the regulation of these auxin transporters and in the formation of an abscission zone, but was required for the expression of hydrolytic enzymes associated with cell separation. Since exogenous auxin delayed abscission in absence of ethylene signaling auxin likely acts independently of ethylene signaling on cell separation.
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Affiliation(s)
- Xu Jin
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural SciencesUmeå, Sweden
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Jorma Zimmermann
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural SciencesUmeå, Sweden
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
- *Correspondence: Urs Fischer, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden,
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92
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Tsuchiya M, Satoh S, Iwai H. Distribution of XTH, expansin, and secondary-wall-related CesA in floral and fruit abscission zones during fruit development in tomato (Solanum lycopersicum). FRONTIERS IN PLANT SCIENCE 2015; 6:323. [PMID: 26029225 PMCID: PMC4432578 DOI: 10.3389/fpls.2015.00323] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/24/2015] [Indexed: 05/11/2023]
Abstract
After fruit development is triggered by pollination, the abscission zone (AZ) in the fruit pedicel strengthens its adhesion to keep the fruit attached. We previously reported that xyloglucan and arabinan accumulation in the AZ accompanies the shedding of unpollinated flowers. After the fruit has developed and is fully ripened, shedding occurs easily in the AZ due to lignin accumulation. Regulation of cell wall metabolism may play an important role in these processes, but it is not well understood. In the present report, we used immunohistochemistry to visualize changes in the distributions of xyloglucan and arabinan metabolism-related enzymes in the AZs of pollinated and unpollinated flowers, and in ripened fruits. During floral abscission, we observed a gradual increase in polyclonal antibody labeling of expansin in the AZ. The intensities of LM6 and LM15 labeling of arabinan and xyloglucan, respectively, also increased. However, during floral abscission, we observed a large 1 day post anthesis (DPA) peak in the polyclonal antibody labeling of XTH in the AZ, which then decreased. These results suggest that expansin and XTH play important, but different roles in the floral abscission process. During fruit abscission, unlike during floral abscission, no AZ-specific expansin and XTH were observed. Although lignification was seen in the AZ of over-ripe fruit pedicels, secondary cell wall-specific cellulose synthase signals were not observed. This suggests that cellulose metabolism-related enzymes do not play important roles in the AZ prior to fruit abscission.
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Affiliation(s)
- Mutsumi Tsuchiya
- Faculty of Life and Environmental Sciences, University of Tsukuba , Tsukuba, Japan
| | - Shinobu Satoh
- Faculty of Life and Environmental Sciences, University of Tsukuba , Tsukuba, Japan
| | - Hiroaki Iwai
- Faculty of Life and Environmental Sciences, University of Tsukuba , Tsukuba, Japan
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93
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Hu G, Fan J, Xian Z, Huang W, Lin D, Li Z. Overexpression of SlREV alters the development of the flower pedicel abscission zone and fruit formation in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:86-95. [PMID: 25443836 DOI: 10.1016/j.plantsci.2014.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/29/2014] [Accepted: 08/20/2014] [Indexed: 05/22/2023]
Abstract
Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been depicted mainly in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Overexpression of a microRNA166-resistant version of SlREV (35S::REV(Ris)) not only resulted in vegetative abnormalities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at the pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged from the exodermises of the pedicel AZs and that ectopic carpels formed between the first and second whorl of floral buds in 35S::REV(Ris) plants. Transcriptional data suggest that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of the flower pedicel abscission zone, and modulate genes in homeodomain and MADS-box families and hormone pathways during fruit formation. Altogether, these results reveal novel roles of SlREV in tomato flower development and fruit formation.
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Affiliation(s)
- Guojian Hu
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Jing Fan
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China; Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhiqiang Xian
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Wei Huang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Dongbo Lin
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China.
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94
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Daminato M, Masiero S, Resentini F, Lovisetto A, Casadoro G. Characterization of TM8, a MADS-box gene expressed in tomato flowers. BMC PLANT BIOLOGY 2014; 14:319. [PMID: 25433802 PMCID: PMC4258831 DOI: 10.1186/s12870-014-0319-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/06/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND The identity of flower organs is specified by various MIKC MADS-box transcription factors which act in a combinatorial manner. TM8 is a MADS-box gene that was isolated from the floral meristem of a tomato mutant more than twenty years ago, but is still poorly known from a functional point of view in spite of being present in both Angiosperms and Gymnosperms, with some species harbouring more than one copy of the gene. This study reports a characterization of TM8 that was carried out in transgenic tomato plants with altered expression of the gene. RESULTS Tomato plants over-expressing either TM8 or a chimeric repressor form of the gene (TM8:SRDX) were prepared. In the TM8 up-regulated plants it was possible to observe anomalous stamens with poorly viable pollen and altered expression of several floral identity genes, among them B-, C- and E-function ones, while no apparent morphological modifications were visible in the other whorls. Oblong ovaries and fruits, that were also parthenocarpic, were obtained in the plants expressing the TM8:SRDX repressor gene. Such ovaries showed modified expression of various carpel-related genes. No apparent modifications could be seen in the other flower whorls. The latter plants had also epinastic leaves and malformed flower abscission zones. By using yeast two hybrid assays it was possible to show that TM8 was able to interact in yeast with MACROCALIX. CONCLUSIONS The impact of the ectopically altered TM8 expression on the reproductive structures suggests that this gene plays some role in the development of the tomato flower. MACROCALYX, a putative A-function MADS-box gene, was expressed in all the four whorls of fully developed flowers, and showed quantitative variations that were opposite to those of TM8 in the anomalous stamens and ovaries. Since the TM8 protein interacted in vitro only with the A-function MADS-box protein MACROCALYX, it seems that for the correct differentiation of the tomato reproductive structures possible interactions between TM8 and MACROCALYX proteins might be important.
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Affiliation(s)
- Margherita Daminato
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
| | - Simona Masiero
- />Department of Bioscience, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Francesca Resentini
- />Department of Bioscience, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Alessandro Lovisetto
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
| | - Giorgio Casadoro
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
- />Botanical Garden, University of Padua, Via Orto Botanico, 15, 35123 Padua, Italy
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95
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Zhang JZ, Zhao K, Ai XY, Hu CG. Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis). BMC Genomics 2014; 15:892. [PMID: 25308090 PMCID: PMC4209071 DOI: 10.1186/1471-2164-15-892] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022] Open
Abstract
Background Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looked into the morphological aspects of self-pruning process, the underlying molecular mechanisms remain unknown. Results In this study, the hallmarks of programmed cell death (PCD) were identified by TUNEL experiments, transmission electron microscopy (TEM) and histochemical staining for reactive oxygen species (ROS) during self-pruning of the spring shoots in sweet orange. Our results indicated that PCD occurred systematically and progressively and may play an important role in the control of self-pruning of citrus. Microarray analysis was used to examine transcriptome changes at three stages of self-pruning, and 1,378 differentially expressed genes were identified. Some genes were related to PCD, while others were associated with cell wall biosynthesis or metabolism. These results strongly suggest that abscission layers activate both catabolic and anabolic wall modification pathways during the self-pruning process. In addition, a strong correlation was observed between self-pruning and the expression of hormone-related genes. Self-pruning plays an important role in citrus floral bud initiation. Therefore, several key flowering homologs of Arabidopsis and tomato shoot apical meristem (SAM) activity genes were investigated in sweet orange by real-time PCR and in situ hybridization, and the results indicated that these genes were preferentially expressed in SAM as well as axillary meristem. Conclusion Based on these findings, a model for sweet orange spring shoot self-pruning is proposed, which will enable us to better understand the mechanism of self-pruning and abscission. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-892) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
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96
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Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S. Genomic analyses provide insights into the history of tomato breeding. Nat Genet 2014; 46:1220-6. [PMID: 25305757 DOI: 10.1038/ng.3117] [Citation(s) in RCA: 527] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.
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Affiliation(s)
- Tao Lin
- 1] Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. [2] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guangtao Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Xiangyang Xu
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Qinghui Yu
- Institute of Horticulture, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Zheng Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaoyao Lun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuai Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoxuan Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zejun Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junming Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunzhi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Aoxue Wang
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Yancong Zhang
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Kui Lin
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China
| | - Guosheng Xiong
- 1] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. [2] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China
| | - Yongbiao Xue
- 1] State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China. [2] Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Andrea Mazzucato
- Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - Mathilde Causse
- Institut National de la Recherche Agronomique (INRA), Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, Montfavet, France
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA
| | - Roger T Chetelat
- C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, Davis, California, USA
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Jingfu Li
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Yongchen Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sanwen Huang
- 1] Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. [2] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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97
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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. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4985-95. [PMID: 24948678 PMCID: PMC4144777 DOI: 10.1093/jxb/eru264] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [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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98
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Nakano T, Fujisawa M, Shima Y, Ito Y. The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3111-9. [PMID: 24744429 PMCID: PMC4071829 DOI: 10.1093/jxb/eru154] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In plants, abscission removes senescent, injured, infected, or dispensable organs. Induced by auxin depletion and an ethylene burst, abscission requires pronounced changes in gene expression, including genes for cell separation enzymes and regulators of signal transduction and transcription. However, the understanding of the molecular basis of this regulation remains incomplete. To examine gene regulation in abscission, this study examined an ERF family transcription factor, tomato (Solanum lycopersicum) ETHYLENE-RESPONSIVE FACTOR 52 (SlERF52). SlERF52 is specifically expressed in pedicel abscission zones (AZs) and SlERF52 expression is suppressed in plants with impaired function of MACROCALYX and JOINTLESS, which regulate pedicel AZ development. RNA interference was used to knock down SlERF52 expression to show that SlERF52 functions in flower pedicel abscission. When treated with an abscission-inducing stimulus, the SlERF52-suppressed plants showed a significant delay in flower abscission compared with wild type. They also showed reduced upregulation of the genes for the abscission-associated enzymes cellulase and polygalacturonase. SlERF52 suppression also affected gene expression before the abscission stimulus, inhibiting the expression of pedicel AZ-specific transcription factor genes, such as the tomato WUSCHEL homologue, GOBLET, and Lateral suppressor, which may regulate meristematic activities in pedicel AZs. These results suggest that SlERF52 plays a pivotal role in transcriptional regulation in pedicel AZs at both pre-abscission and abscission stages.
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Affiliation(s)
- Toshitsugu Nakano
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Masaki Fujisawa
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yoko Shima
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yasuhiro Ito
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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99
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Parapunova V, Busscher M, Busscher-Lange J, Lammers M, Karlova R, Bovy AG, Angenent GC, de Maagd RA. Identification, cloning and characterization of the tomato TCP transcription factor family. BMC PLANT BIOLOGY 2014; 14:157. [PMID: 24903607 PMCID: PMC4070083 DOI: 10.1186/1471-2229-14-157] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/22/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. RESULTS We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato. CONCLUSIONS The comprehensive analysis we performed, like phylogenetic analysis, expression studies, identification of the upstream regulators and the dimerization specificity of the tomato TCP transcription factor family provides the basis for functional studies to reveal the role of this family in tomato development.
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Affiliation(s)
- Violeta Parapunova
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Marco Busscher
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | | | - Michiel Lammers
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Rumyana Karlova
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arnaud G Bovy
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Ruud A de Maagd
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
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100
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Astola L, Stigter H, van Dijk ADJ, van Daelen R, Molenaar J. Inferring the gene network underlying the branching of tomato inflorescence. PLoS One 2014; 9:e89689. [PMID: 24699171 PMCID: PMC3974656 DOI: 10.1371/journal.pone.0089689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/24/2014] [Indexed: 12/21/2022] Open
Abstract
The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.
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Affiliation(s)
- Laura Astola
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
- * E-mail:
| | - Hans Stigter
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
| | - Raymond van Daelen
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
- Keygene N.V., Wageningen, The Netherlands
| | - Jaap Molenaar
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
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