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Gasparini K, Figueiredo YG, Araújo WL, Peres LE, Zsögön A. De novo domestication in the Solanaceae: advances and challenges. Curr Opin Biotechnol 2024; 89:103177. [PMID: 39106791 DOI: 10.1016/j.copbio.2024.103177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 08/09/2024]
Abstract
The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. De novo domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.
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Affiliation(s)
- Karla Gasparini
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Yuri G Figueiredo
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Lázaro Ep Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
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2
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Nan L, Li Y, Ma C, Meng X, Han Y, Li H, Huang M, Qin Y, Ren X. Identification and Expression Analysis of the WOX Transcription Factor Family in Foxtail Millet ( Setaria italica L.). Genes (Basel) 2024; 15:476. [PMID: 38674410 PMCID: PMC11050393 DOI: 10.3390/genes15040476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet WOX gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet WOX genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The SiWOX genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet WOX genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: SiWOX1 and SiWOX13, SiWOX4 and SiWOX5, and SiWOX11 and SiWOX12. Collinearity analysis demonstrated that WOX genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The SiWOX genes primarily harbor two categories of cis-acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of SiWOX expression patterns and hormone responses unveiled potential functional diversity among different SiWOX genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of SiWOX genes.
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Affiliation(s)
- Lizhang Nan
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Yajun Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Cui Ma
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Xiaowei Meng
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Hongying Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Mingjing Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (L.N.); (Y.L.); (C.M.); (X.M.); (Y.H.); (H.L.); (M.H.)
| | - Yingying Qin
- College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030800, China
| | - Xuemei Ren
- College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030800, China
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3
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Larriba E, Yaroshko O, Pérez-Pérez JM. Recent Advances in Tomato Gene Editing. Int J Mol Sci 2024; 25:2606. [PMID: 38473859 DOI: 10.3390/ijms25052606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.
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Affiliation(s)
- Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Olha Yaroshko
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
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4
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Baranov D, Dolgov S, Timerbaev V. New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:359. [PMID: 38337892 PMCID: PMC10856997 DOI: 10.3390/plants13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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5
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Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024:10.1038/s41587-023-02024-y. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
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Affiliation(s)
- Moritz Smolka
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | | | - Dominic W Horner
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sairam Behera
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Ester Kalef-Ezra
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Karl Hong
- Bionano Genomics, San Diego, CA, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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6
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Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, Xia R. TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining. MOLECULAR PLANT 2023; 16:1733-1742. [PMID: 37740491 DOI: 10.1016/j.molp.2023.09.010] [Citation(s) in RCA: 289] [Impact Index Per Article: 289.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/22/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles. Now, TBtools is a commonly used tool in biological laboratories. Over the past 3 years, thanks to invaluable feedback and suggestions from numerous users, we have optimized and expanded the functionality of the toolkit, leading to the development of an upgraded version-TBtools-II. In this upgrade, we have incorporated over 100 new features, such as those for comparative genomics analysis, phylogenetic analysis, and data visualization. Meanwhile, to better meet the increasing needs of personalized data analysis, we have launched the plugin mode, which enables users to develop their own plugins and manage their selection, installation, and removal according to individual needs. To date, the plugin store has amassed over 50 plugins, with more than half of them being independently developed and contributed by TBtools users. These plugins offer a range of data analysis options including co-expression network analysis, single-cell data analysis, and bulked segregant analysis sequencing data analysis. Overall, TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors. By promoting the theme "one for all, all for one", we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.
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Affiliation(s)
- Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China.
| | - Ya Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Junting Feng
- Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yehua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China.
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7
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Zemach I, Alseekh S, Tadmor-Levi R, Fisher J, Torgeman S, Trigerman S, Nauen J, Hayut SF, Mann V, Rochsar E, Finkers R, Wendenburg R, Osorio S, Bergmann S, Lunn JE, Semel Y, Hirschberg J, Fernie AR, Zamir D. Multi-year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1136-1151. [PMID: 37150955 DOI: 10.1111/tpj.16268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/09/2023]
Abstract
Tomato (Solanum lycopersicum) is a prominent fruit with rich genetic resources for crop improvement. By using a phenotype-guided screen of over 7900 tomato accessions from around the world, we identified new associations for complex traits such as fruit weight and total soluble solids (Brix). Here, we present the phenotypic data from several years of trials. To illustrate the power of this dataset we use two case studies. First, evaluation of color revealed allelic variation in phytoene synthase 1 that resulted in differently colored or even bicolored fruit. Secondly, in view of the negative relationship between fruit weight and Brix, we pre-selected a subset of the collection that includes high and low Brix values in each category of fruit size. Genome-wide association analysis allowed us to detect novel loci associated with total soluble solid content and fruit weight. In addition, we developed eight F2 biparental intraspecific populations. Furthermore, by taking a phenotype-guided approach we were able to isolate individuals with high Brix values that were not compromised in terms of yield. In addition, the demonstration of novel results despite the high number of previous genome-wide association studies of these traits in tomato suggests that adoption of a phenotype-guided pre-selection of germplasm may represent a useful strategy for finding target genes for breeding.
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Affiliation(s)
- Itay Zemach
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Roni Tadmor-Levi
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Josef Fisher
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Torgeman
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Shay Trigerman
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Nauen
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Shdema Filler Hayut
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Varda Mann
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Edan Rochsar
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Richard Finkers
- Plant Breeding, Wageningen Plant Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sonia Osorio
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora", University of Malaga-Consejo Superior de Investigaciones Cientıficas, Malaga, Spain
| | - Susan Bergmann
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - John E Lunn
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yaniv Semel
- Phenome Networks, 10 Plaut Street, Science Park, 76706, Rehovot, Israel
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Dani Zamir
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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8
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Koller F, Cieslak M. A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment. Front Bioeng Biotechnol 2023; 11:1276226. [PMID: 37965049 PMCID: PMC10641861 DOI: 10.3389/fbioe.2023.1276226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.
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Affiliation(s)
- Franziska Koller
- Fachstelle Gentechnik und Umwelt (FGU), Munich, Bavaria, Germany
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9
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Clifton BD, Hariyani I, Kimura A, Luo F, Nguyen A, Ranz JM. Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages. Commun Biol 2023; 6:1069. [PMID: 37864070 PMCID: PMC10589255 DOI: 10.1038/s42003-023-05427-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023] Open
Abstract
How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
| | - Imtiyaz Hariyani
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Fangning Luo
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Alvin Nguyen
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
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10
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Zahn IE, Roelofsen C, Angenent GC, Bemer M. TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2754. [PMID: 37570908 PMCID: PMC10420972 DOI: 10.3390/plants12152754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.
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Affiliation(s)
- Iris E. Zahn
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Chris Roelofsen
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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11
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. FRONTIERS IN PLANT SCIENCE 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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12
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Hummel NFC, Zhou A, Li B, Markel K, Ornelas IJ, Shih PM. The trans-regulatory landscape of gene networks in plants. Cell Syst 2023; 14:501-511.e4. [PMID: 37348464 DOI: 10.1016/j.cels.2023.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative transcriptional effector domains of over 400 Arabidopsis thaliana transcription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how our characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.
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Affiliation(s)
- Niklas F C Hummel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Department of Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Andy Zhou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Baohua Li
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Izaiah J Ornelas
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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13
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Wang X, Liu Z, Bai J, Sun S, Song J, Li R, Cui X. Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching. THE PLANT CELL 2023; 35:2062-2078. [PMID: 36881857 PMCID: PMC10226558 DOI: 10.1093/plcell/koad065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/30/2023]
Abstract
Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.
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Affiliation(s)
- Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
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14
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Sun S, Wang X, Liu Z, Bai J, Song J, Li R, Cui X. Tomato APETALA2 family member SlTOE1 regulates inflorescence branching by repressing SISTER OF TM3. PLANT PHYSIOLOGY 2023; 192:293-306. [PMID: 36747310 PMCID: PMC10152655 DOI: 10.1093/plphys/kiad075] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 05/03/2023]
Abstract
Inflorescence architecture directly impacts yield potential in most crops. As a model of sympodial plants, tomato (Solanum lycopersicum) inflorescence exhibits highly structural plasticity. However, the genetic regulatory network of inflorescence architecture in tomato remains unclear. Here, we investigated a modulator of inflorescence branching in tomato, TARGET OF EAT1 (SlTOE1), an APETALA2 (AP2) family member found to be predominantly expressed in the floral meristem (FM) of tomato. sltoe1 knockout mutants displayed highly branched inflorescences and defective floral organs. Transcriptome analysis revealed that SISTER OF TM3 (STM3) and certain floral development-related genes were upregulated in the flower meristem of sltoe1. SlTOE1 could directly bind the promoters of STM3 and Tomato MADS-box gene 3 (TM3) to repress their transcription. Simultaneous mutation of STM3 and TM3 partially restored the inflorescence branching of the sltoe1cr mutants, suggesting that SlTOE1 regulates inflorescence development, at least in part through an SlTOE1STM3/TM3 module. Genetic analysis showed that SlTOE1 and ENHANCER OF JOINTLESS 2 (EJ2) additively regulate tomato inflorescence branching; their double mutants showed more extensive inflorescence branching. Our findings uncover a pathway controlling tomato inflorescence branching and offer deeper insight into the functions of AP2 subfamily members.
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Affiliation(s)
- Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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15
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Li J, Zhu R, Zhang M, Cao B, Li X, Song B, Liu Z, Wu J. Natural variations in the PbCPK28 promoter regulate sugar content through interaction with PbTST4 and PbVHA-A1 in pear. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:124-141. [PMID: 36710644 DOI: 10.1111/tpj.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Soluble sugars play an important role in plant growth, development and fruit quality. Pear fruits have demonstrated a considerable improvement in sugar quality during their long history of selection. However, little is known about the underlying molecular mechanisms accompanying the changes in fruit sugar content as a result of selection by horticulturists. Here, we identified a calcium-dependent protein kinase (PbCPK28), which is located on LG15 and is present within a selective sweep region, thus linked to the quantitative trait loci for soluble solids. Association analysis indicates that a single nucleotide polymorphism-13 variation (SNP13T/C ) in the PbCPK28 regulatory region led to fructose content diversity in pear. Elevated expression of PbCPK28 resulted in significantly increased fructose levels in pear fruits. Furthermore, PbCPK28 interacts with and phosphorylates PbTST4, a proton antiporter, thereby coupling the sugar import into the vacuole with proton export. We demonstrated that residues S277 and S314 of PbTST4 are crucial for its function. Additionally, PbCPK28 interacts with and phosphorylates the vacuolar hydrogen proton pump PbVHA-A1, which could provide proton motive forces for PbTST4. We also found that the T11 and Y120 phosphorylation sites in PbVHA-A1 are essential for its function. Evolution analysis and yeast-two-hybrid results support that the CPK-TST/CPK-VHA-A regulatory network is highly conserved in plants, especially the corresponding phosphorylation sites. Together, our work identifies an agriculturally important natural variation and an important regulatory network, allowing genetic improvement of fruit sugar contents in pears through modulation of PbCPK28 expression and phosphorylation of PbTST4 and PbVHA-A1.
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Affiliation(s)
- Jiaming Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Rongxiang Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Beibei Cao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiaolong Li
- College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, 311200, China
| | - Bobo Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, 20742, USA
| | - Jun Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China
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16
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Tonutti P, Brizzolara S, Beckles DM. Reducing crop losses by gene-editing control of organ developmental physiology. Curr Opin Biotechnol 2023; 81:102925. [PMID: 37003167 DOI: 10.1016/j.copbio.2023.102925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 04/03/2023]
Abstract
Some physiological processes in reproductive organs, if not controlled, can lead to crop loss even in the absence of environmental stress. These processes may occur pre- or post- harvest, and in diverse species and include abscission processes in cereal grain, e.g., shattering and in immature fruit, e.g., preharvest drop, preharvest sprouting of cereals, and postharvest senescence in fruit. Some of the molecular mechanisms and genetic determinants underlying these processes are now better detailed, making it possible to refine them by gene editing. Here, we discuss using advanced genomics to identify genetic determinants underlying crop physiological traits. Examples of improved phenotypes developed for preharvest problems are provided, and suggestions for reducing postharvest fruit losses by gene and promoter editing were made.
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Affiliation(s)
- Pietro Tonutti
- Crop Science Research Center, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Stefano Brizzolara
- Crop Science Research Center, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA 95616, USA.
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17
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Lu L, Arif S, Yu JM, Lee JW, Park YH, Tucker ML, Kim J. Involvement of IDA-HAE Module in Natural Development of Tomato Flower Abscission. PLANTS (BASEL, SWITZERLAND) 2023; 12:185. [PMID: 36616314 PMCID: PMC9823658 DOI: 10.3390/plants12010185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The unwanted detachment of organs such as flowers, leaves, and fruits from the main body of a plant (abscission) has significant effects on agricultural practice. Both timely and precise regulation of organ abscission from a plant is crucial as it influences the agricultural yield. The tomato (Solanum lycopersicum) has become a model system for research on organ abscission. Here, we characterized four tomato natural abscission variants named jointless (j), functionally impaired jointless (fij), functionally impaired jointless like (fij like), and normal joint (NJ), based on their cellular features within the flower abscission zones (AZ). Using eight INFLORESCENCE DEFICIENT IN ABSCISSION (SlIDA) genes and eight HAESA genes (SlHAE) identified in the genome sequence of tomato, we analyzed the pattern of gene expression during flower abscission. The AZ-specific expression for three tomato abscission polygalacturonases (SlTAPGs) in the development of flower AZ, and the progression of abscission validated our natural abscission system. Compared to that of j, fij, and fij like variants, the AZ-specific expression for SlIDA, SlIDL2, SlIDL3, SlIDL4, and SlIDL5 in the NJ largely corelated and increased with the process of abscission. Of eight SlHAE genes examined, the expression for SlHSL6 and SlHSL7 were found to be AZ-specific and increased as abscission progressed in the NJ variant. Unlike the result of gene expression obtained from natural abscission system, an in silico analysis of transcriptional binding sites uncovered that SlIDA genes (SlIDA, SlIDL6, and SlIDL7) are predominantly under the control of environmental stress, while most of the SlHSL genes are affiliated with the broader context in developmental processes and stress responses. Our result presents the potential bimodal transcriptional regulation of the tomato IDA-HAE module associated with flower abscission in tomatoes.
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Affiliation(s)
- Lu Lu
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Samiah Arif
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jun Myoung Yu
- Department of Applied Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - June Woo Lee
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
- Quality Assurance Team, Quality Assurance Department, Nongwoobio Co., Ltd., Yeoju 12655, Republic of Korea
| | - Young-Hoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Mark Leo Tucker
- Soybean Genomics and Improvement Lab, Agriculture Research Service, United States Department of Agriculture, Building 006, BARC-West, Beltsville, MD 20705, USA
| | - Joonyup Kim
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea
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18
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Monniaux M, Vandenbussche M. Flower Development in the Solanaceae. Methods Mol Biol 2023; 2686:39-58. [PMID: 37540353 DOI: 10.1007/978-1-0716-3299-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Flower development is the process leading from a reproductive meristem to a mature flower with fully developed floral organs. This multi-step process is complex and involves thousands of genes in intertwined regulatory pathways; navigating through the FLOR-ID website will give an impression of this complexity and of the astonishing amount of work that has been carried on the topic (Bouché et al., Nucleic Acids Res 44:D1167-D1171, 2016). Our understanding of flower development mostly comes from the model species Arabidopsis thaliana, but numerous other studies outside of Brassicaceae have helped apprehend the conservation of these mechanisms in a large evolutionary context (Moyroud and Glover, Curr Biol 27:R941-R951, 2017; Smyth, New Phytol 220:70-86, 2018; Soltis et al., Ann Bot 100:155-163, 2007). Integrating additional species and families to the research on this topic can only advance our understanding of flower development and its evolution.In this chapter, we review the contribution that the Solanaceae family has made to the comprehension of flower development. While many of the general features of flower development (i.e., the key molecular players involved in flower meristem identity, inflorescence architecture or floral organ development) are similar to Arabidopsis, our main objective in this chapter is to highlight the points of divergence and emphasize specificities of the Solanaceae. We will not discuss the large topics of flowering time regulation, inflorescence architecture and fruit development, and we will restrict ourselves to the mechanisms included in a time window after the floral transition and before the fertilization. Moreover, this review will not be exhaustive of the large amount of work carried on the topic, and the choices that we made to describe in large details some stories from the literature are based on the soundness of the functional work performed, and surely as well on our own preferences and expertise.First, we will give a brief overview of the Solanaceae family and some of its specificities. Then, our focus will be on the molecular mechanisms controlling floral organ identity, for which extended functional work in petunia led to substantial revisions to the famous ABC model. Finally, after reviewing some studies on floral organ initiation and growth, we will discuss floral organ maturation, using the examples of the inflated calyx of the Chinese lantern Physalis and petunia petal pigmentation.
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Affiliation(s)
- Marie Monniaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
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19
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Singh J, van der Knaap E. Unintended Consequences of Plant Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1573-1583. [PMID: 35715986 DOI: 10.1093/pcp/pcac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.
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Affiliation(s)
- Jugpreet Singh
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
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20
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Dreni L, Ferrándiz C. Tracing the Evolution of the SEPALLATA Subfamily across Angiosperms Associated with Neo- and Sub-Functionalization for Reproductive and Agronomically Relevant Traits. PLANTS (BASEL, SWITZERLAND) 2022; 11:2934. [PMID: 36365387 PMCID: PMC9656651 DOI: 10.3390/plants11212934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
SEPALLATA transcription factors (SEP TFs) have been extensively studied in angiosperms as pivotal components of virtually all the MADS-box tetrameric complex master regulators of floral organ identities. However, there are published reports that suggest that some SEP members also regulate earlier reproductive events, such as inflorescence meristem determinacy and inflorescence architecture, with potential for application in breeding programs in crops. The SEP subfamily underwent a quite complex pattern of duplications during the radiation of the angiosperms. Taking advantage of the many whole genomic sequences now available, we present a revised and expanded SEP phylogeny and link it to the known functions of previously characterized genes. This snapshot supports the evidence that the major SEP3 clade is highly specialized for the specification of the three innermost floral whorls, while its sister LOFSEP clade is functionally more versatile and has been recruited for diverse roles, such as the regulation of extra-floral bract formation and inflorescence determinacy and shape. This larger pool of angiosperm SEP genes confirms previous evidence that their evolution was driven by whole-genome duplications rather than small-scale duplication events. Our work may help to identify those SEP lineages that are the best candidates for the improvement of inflorescence traits, even in far distantly related crops.
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21
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Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species. Int J Mol Sci 2022; 23:ijms231911585. [PMID: 36232886 PMCID: PMC9569760 DOI: 10.3390/ijms231911585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cultivated tomato (Solanum lycopersicum) is bred for fruit production in optimized environments, in contrast to harsh environments where their ancestral relatives thrive. The process of domestication and breeding has profound impacts on the phenotypic plasticity of plant development and the stress response. Notably, the alternative splicing (AS) of precursor message RNA (pre-mRNA), which is one of the major factors contributing to transcriptome complexity, is responsive to developmental cues and environmental change. To determine a possible association between AS events and phenotypic plasticity, we investigated environment-responsive AS events in the inflorescences of cultivated tomato and its ancestral relatives S. pimpinellifolium. Despite that similar AS frequencies were detected in the cultivated tomato variety Moneymaker and two S. pimpinellifolium accessions under the same growth conditions, 528 genes including splicing factors showed differential splicing in the inflorescences of plants grown in open fields and plastic greenhouses in the Moneymaker variety. In contrast, the two S. pimpinellifolium accessions, LA1589 and LA1781, had 298 and 268 genes showing differential splicing, respectively. Moreover, seven heat responsive genes showed opposite expression patterns in response to changing growth conditions between Moneymaker and its ancestral relatives. Accordingly, there were eight differentially expressed splice variants from genes involved in heat response in Moneymaker. Our results reveal distinctive features of AS events in the inflorescences between cultivated tomato and its ancestral relatives, and show that AS regulation in response to environmental changes is genotype dependent.
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22
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Yang Y, Zhao T, Xu X, Jiang J, Li J. Transcriptome Analysis to Explore the Cause of the Formation of Different Inflorescences in Tomato. Int J Mol Sci 2022; 23:ijms23158216. [PMID: 35897806 PMCID: PMC9368726 DOI: 10.3390/ijms23158216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023] Open
Abstract
The number of inflorescence branches is an important agronomic character of tomato. The meristem differentiation and development pattern of tomato inflorescence is complex and its regulation mechanism is very different from those of other model plants. Therefore, in order to explore the cause of tomato inflorescence branching, transcriptome analysis was conducted on two kinds of tomato inflorescences (single racemes and compound inflorescences). According to the transcriptome data analysis, there were many DEGs of tomato inflorescences at early, middle, and late stages. Then, GO and KEGG enrichments of DEGs were performed. DEGs are mainly enriched in metabolic pathways, biohormone signaling, and cell cycle pathways. According to previous studies, DEGs were mainly enriched in metabolic pathways, and FALSIFLORA (FA) and ANANTHA (AN) genes were the most notable of 41 DEGs related to inflorescence branching. This study not only provides a theoretical basis for understanding inflorescence branching, but also provides a new idea for the follow-up study of inflorescence.
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23
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Blanca J, Pons C, Montero-Pau J, Sanchez-Matarredona D, Ziarsolo P, Fontanet L, Fisher J, Plazas M, Casals J, Rambla JL, Riccini A, Palombieri S, Ruggiero A, Sulli M, Grillo S, Kanellis A, Giuliano G, Finkers R, Cammareri M, Grandillo S, Mazzucato A, Causse M, Díez MJ, Prohens J, Zamir D, Cañizares J, Monforte AJ, Granell A. European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3431-3445. [PMID: 35358313 PMCID: PMC9162183 DOI: 10.1093/jxb/erac072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.
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Affiliation(s)
- Jose Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | | | - David Sanchez-Matarredona
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | | | - Josef Fisher
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, UPC-BarcelonaTech, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | | | - Alessandra Ruggiero
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Stephania Grillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Angelos Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, POB 386, 6700 AJ Wageningen, The Netherlands
| | - Maria Cammareri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Silvana Grandillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Domaine Saint Maurice, 67 Allée des Chênes, CS 60094, 84143 Montfavet, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Joaquin Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
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24
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Pons C, Casals J, Palombieri S, Fontanet L, Riccini A, Rambla JL, Ruggiero A, Figás MDR, Plazas M, Koukounaras A, Picarella ME, Sulli M, Fisher J, Ziarsolo P, Blanca J, Cañizares J, Cammareri M, Vitiello A, Batelli G, Kanellis A, Brouwer M, Finkers R, Nikoloudis K, Soler S, Giuliano G, Grillo S, Grandillo S, Zamir D, Mazzucato A, Causse M, Díez MJ, Prohens J, Monforte AJ, Granell A. Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato. HORTICULTURE RESEARCH 2022; 9:uhac112. [PMID: 35795386 PMCID: PMC9252105 DOI: 10.1093/hr/uhac112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.
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Affiliation(s)
- Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, Universitat Politècnica de Catalunya, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Samuela Palombieri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Lilian Fontanet
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- HM Clause, Portes-lès-Valence, France
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Alessandra Ruggiero
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Maria del Rosario Figás
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Athanasios Koukounaras
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Vegetable Crops, Thessaloniki, 54124 Greece
| | - Maurizio E Picarella
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Josef Fisher
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jose Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Joaquin Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Maria Cammareri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Antonella Vitiello
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Giorgia Batelli
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Angelos Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Matthijs Brouwer
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | - Richard Finkers
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | | | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Stephania Grillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Silvana Grandillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Dani Zamir
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Antonio Jose Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
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25
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Li S, Meng S, Weng J, Wu Q. Fine-tuning shoot meristem size to feed the world. TRENDS IN PLANT SCIENCE 2022; 27:355-363. [PMID: 34743928 DOI: 10.1016/j.tplants.2021.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
In order to maintain food security for the world's growing population, crop yields need to be significantly improved. Domestication and crop improvement involve modification of traits such as fruit size and seed number to optimize productivity. Although these traits are selected at the mature stage, they are determined during the development of shoot meristem, a tissue that forms successive meristems and reproductive organs that make edible fruits or seeds. Therefore, the architecture of reproductive organs and yield-related traits are determined during the maturation of shoot meristem. Here, we highlight recent progress in understanding how shoot meristem size affects yield-related traits and outline the strategies to fine-tune meristem regulatory genes to meet the demands of a growing population and promote sustainable agriculture.
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Affiliation(s)
- Shuping Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100091, China
| | - Shujun Meng
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Agriculture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jianfeng Weng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qingyu Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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26
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Jobson E, Roberts R. Genomic structural variation in tomato and its role in plant immunity. MOLECULAR HORTICULTURE 2022; 2:7. [PMID: 37789472 PMCID: PMC10515242 DOI: 10.1186/s43897-022-00029-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 10/05/2023]
Abstract
It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.
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Affiliation(s)
- Emma Jobson
- Montana State University Extension, Montana State University, Bozeman, MT, 59717, United States
| | - Robyn Roberts
- Agricultural Biology Department, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
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27
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Jiang X, Lubini G, Hernandes-Lopes J, Rijnsburger K, Veltkamp V, de Maagd RA, Angenent GC, Bemer M. FRUITFULL-like genes regulate flowering time and inflorescence architecture in tomato. THE PLANT CELL 2022; 34:1002-1019. [PMID: 34893888 PMCID: PMC8894982 DOI: 10.1093/plcell/koab298] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/30/2021] [Indexed: 05/23/2023]
Abstract
The timing of flowering and the inflorescence architecture are critical for the reproductive success of tomato (Solanum lycopersicum), but the gene regulatory networks underlying these traits have not been fully explored. Here, we show that the tomato FRUITFULL-like (FUL-like) genes FUL2 and MADS-BOX PROTEIN 20 (MBP20) promote the vegetative-to-reproductive transition and repress inflorescence branching by inducing floral meristem (FM) maturation. FUL1 fulfils a less prominent role and appears to depend on FUL2 and MBP20 for its upregulation in the inflorescence- and floral meristems. MBP10, the fourth tomato FUL-like gene, has probably lost its function. The tomato FUL-like proteins cannot homodimerize in in vitro assays, but heterodimerize with various other MADS-domain proteins, potentially forming distinct complexes in the transition meristem and FM. Transcriptome analysis of the primary shoot meristems revealed various interesting downstream targets, including four repressors of cytokinin signaling that are upregulated during the floral transition in ful1 ful2 mbp10 mbp20 mutants. FUL2 and MBP20 can also bind in vitro to the upstream regions of these genes, thereby probably directly stimulating cell division in the meristem upon the transition to flowering. The control of inflorescence branching does not occur via the cytokinin oxidase/dehydrogenases (CKXs) but may be regulated by repression of transcription factors such as TOMATO MADS-box gene 3 (TM3) and APETALA 2b (AP2b).
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Affiliation(s)
- Xiaobing Jiang
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Greice Lubini
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - José Hernandes-Lopes
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090 São Paulo, Brazil
| | - Kim Rijnsburger
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Vera Veltkamp
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ruud A de Maagd
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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28
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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29
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Joo KA, Muszynski MG, Kantar MB, Wang ML, He X, Del Valle Echevarria AR. Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species. Front Genet 2021; 12:786140. [PMID: 34868276 PMCID: PMC8633396 DOI: 10.3389/fgene.2021.786140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.
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Affiliation(s)
- Kathleen A Joo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael G Muszynski
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Xiaoling He
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Angel R Del Valle Echevarria
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.,Hawaii Agriculture Research Center, Waipahu, HI, United States
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30
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Wang X, Liu Z, Sun S, Wu J, Li R, Wang H, Cui X. SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato. HORTICULTURE RESEARCH 2021; 8:251. [PMID: 34848688 PMCID: PMC8633288 DOI: 10.1038/s41438-021-00677-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 05/19/2023]
Abstract
Selection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.
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Affiliation(s)
- Xiaotian 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
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiqiang 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
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuai Sun
- 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
| | - Jianxin Wu
- 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
| | - Haijing 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
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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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31
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Nakayama H, Rowland SD, Cheng Z, Zumstein K, Kang J, Kondo Y, Sinha NR. Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes. Curr Biol 2021; 31:4788-4799.e5. [PMID: 34473947 DOI: 10.1101/2020.09.08.287011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/17/2021] [Accepted: 08/05/2021] [Indexed: 05/22/2023]
Abstract
Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo and is unique to SiFT and not introgressed from other tomato genomes. These results provide new insights into the natural variation in phenotypic traits introduced into crops during improvement processes after domestication and establish homeobox genes as evolutionary hotspots.
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Affiliation(s)
- Hokuto Nakayama
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven D Rowland
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Zizhang Cheng
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Julie Kang
- Biology Department, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Yohei Kondo
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji, Higashiyama 5-1, Okazaki, Aichi 444-8787, Japan
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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32
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Nakayama H, Rowland SD, Cheng Z, Zumstein K, Kang J, Kondo Y, Sinha NR. Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes. Curr Biol 2021; 31:4788-4799.e5. [PMID: 34473947 DOI: 10.1016/j.cub.2021.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/17/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022]
Abstract
Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo and is unique to SiFT and not introgressed from other tomato genomes. These results provide new insights into the natural variation in phenotypic traits introduced into crops during improvement processes after domestication and establish homeobox genes as evolutionary hotspots.
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Affiliation(s)
- Hokuto Nakayama
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven D Rowland
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Zizhang Cheng
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Julie Kang
- Biology Department, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Yohei Kondo
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji, Higashiyama 5-1, Okazaki, Aichi 444-8787, Japan
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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33
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Gaarslev N, Swinnen G, Soyk S. Meristem transitions and plant architecture-learning from domestication for crop breeding. PLANT PHYSIOLOGY 2021; 187:1045-1056. [PMID: 34734278 PMCID: PMC8566237 DOI: 10.1093/plphys/kiab388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/19/2021] [Indexed: 05/20/2023]
Abstract
Genetic networks that regulate meristem transitions were recurrent targets of selection during crop domestication and allow fine-tuning of plant architecture for improved crop productivity.
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Affiliation(s)
- Natalia Gaarslev
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Gwen Swinnen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sebastian Soyk
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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34
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Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA. Domestication shapes recombination patterns in tomato. Mol Biol Evol 2021; 39:6379725. [PMID: 34597400 PMCID: PMC8763028 DOI: 10.1093/molbev/msab287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Sander A Peters
- Applied Bioinformatics, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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35
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Gupta PK. GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers. Bioessays 2021; 43:e2100109. [PMID: 34486143 DOI: 10.1002/bies.202100109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.
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Affiliation(s)
- Pushpendra K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University Meerut, Meerut, Uttar Pradesh, India
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36
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Liang Y, Liu HJ, Yan J, Tian F. Natural Variation in Crops: Realized Understanding, Continuing Promise. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:357-385. [PMID: 33481630 DOI: 10.1146/annurev-arplant-080720-090632] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.
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Affiliation(s)
- Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
| | - Hai-Jun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria;
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
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37
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Bastiaanse H, Henry IM, Tsai H, Lieberman M, Canning C, Comai L, Groover A. A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus. THE PLANT CELL 2021; 33:940-960. [PMID: 33793772 PMCID: PMC8226299 DOI: 10.1093/plcell/koaa016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.
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Affiliation(s)
- Héloïse Bastiaanse
- Present address: VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - Isabelle M Henry
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Helen Tsai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Meric Lieberman
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Courtney Canning
- Pacific Southwest Research Station, US Forest Service, Davis, California 95618
| | - Luca Comai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
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38
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Chen Z, Li W, Gaines C, Buck A, Galli M, Gallavotti A. Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences. Nat Commun 2021; 12:2378. [PMID: 33888716 PMCID: PMC8062686 DOI: 10.1038/s41467-021-22699-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/23/2021] [Indexed: 01/28/2023] Open
Abstract
Structural variation in plant genomes is a significant driver of phenotypic variability in traits important for the domestication and productivity of crop species. Among these are traits that depend on functional meristems, populations of stem cells maintained by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop that controls the expression of the WUS homeobox transcription factor. WUS function and impact on maize development and yield remain largely unexplored. Here we show that the maize dominant Barren inflorescence3 (Bif3) mutant harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. Overexpression of ZmWUS1-B is due to multimerized binding sites for type-B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. Hypersensitivity to cytokinin causes stem cell overproliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears and severely affecting productivity. These findings establish ZmWUS1 as an essential meristem size regulator in maize and highlight the striking effect of cis-regulatory variation on a key developmental program. The WUSCHEL transcription factor promotes plant stem cell proliferation. Here the authors show that the maize Bif3 mutant contains a duplication of the ZmWUS1 locus leading to cytokinin hypersensitivity and overproliferation at the shoot meristem demonstrating the role of WUSCHEL in maize and how structural variation can impact plant morphology.
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Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Wei Li
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Craig Gaines
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Amy Buck
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA.,Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA. .,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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39
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Göktay M, Fulgione A, Hancock AM. A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes. Mol Biol Evol 2021; 38:1498-1511. [PMID: 33247723 PMCID: PMC8042739 DOI: 10.1093/molbev/msaa309] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a "core" genome underlying basic cellular processes and a "flexible" genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.
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Affiliation(s)
- Mehmet Göktay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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40
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Israeli A, Ben-Herzel O, Burko Y, Shwartz I, Ben-Gera H, Harpaz-Saad S, Bar M, Efroni I, Ori N. Coordination of differentiation rate and local patterning in compound-leaf development. THE NEW PHYTOLOGIST 2021; 229:3558-3572. [PMID: 33259078 DOI: 10.1111/nph.17124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The variability in leaf form in nature is immense. Leaf patterning occurs by differential growth, taking place during a limited window of morphogenetic activity at the leaf marginal meristem. While many regulators have been implicated in the designation of the morphogenetic window and in leaf patterning, how these effectors interact to generate a particular form is still not well understood. We investigated the interaction among different effectors of tomato (Solanum lycopersicum) compound-leaf development, using genetic and molecular analyses. Mutations in the tomato auxin response factor SlARF5/SlMP, which normally promotes leaflet formation, suppressed the increased leaf complexity of mutants with extended morphogenetic window. Impaired activity of the NAC/CUC transcription factor GOBLET (GOB), which specifies leaflet boundaries, also reduced leaf complexity in these backgrounds. Analysis of genetic interactions showed that the patterning factors SlMP, GOB and the MYB transcription factor LYRATE (LYR) coordinately regulate leaf patterning by modulating in parallel different aspects of leaflet formation and shaping. This work places an array of developmental regulators in a morphogenetic context. It reveals how organ-level differentiation rate and local growth are coordinated to sculpture an organ. These concepts are applicable to the coordination of pattering and differentiation in other species and developmental processes.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Ori Ben-Herzel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Yogev Burko
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ido Shwartz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Hadas Ben-Gera
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, PO Box 102, Ramat Yishay, 30095, Israel
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, 7505101, Israel
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
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41
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Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
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Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
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42
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Wang X, Gao L, Jiao C, Stravoravdis S, Hosmani PS, Saha S, Zhang J, Mainiero S, Strickler SR, Catala C, Martin GB, Mueller LA, Vrebalov J, Giovannoni JJ, Wu S, Fei Z. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat Commun 2020; 11:5817. [PMID: 33199703 PMCID: PMC7670462 DOI: 10.1038/s41467-020-19682-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding. Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.
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Affiliation(s)
- Xin Wang
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Lei Gao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chen Jiao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jing Zhang
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | | | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA. .,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%. Sci Rep 2020; 10:17219. [PMID: 33057137 PMCID: PMC7560729 DOI: 10.1038/s41598-020-73709-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.
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44
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Alonge M, Shumate A, Puiu D, Zimin AV, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics 2020; 216:599-608. [PMID: 32796007 PMCID: PMC7536849 DOI: 10.1534/genetics.120.303501] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC CS v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all three wheat subgenomes at chromosome-scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 Gbp of genomic sequence. We earlier published an independent wheat assembly (Triticum_aestivum_3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC CS v1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum_aestivum_4.0, contains 15.07 Gbp of nongap sequence anchored to chromosomes, which is 1.2 Gbps more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered >5700 additional gene copies, facilitating the accurate annotation of functional gene duplications including at the Ppd-B1 photoperiod response locus.
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Affiliation(s)
- Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
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45
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Israeli A, Reed JW, Ori N. Genetic dissection of the auxin response network. NATURE PLANTS 2020; 6:1082-1090. [PMID: 32807951 DOI: 10.1038/s41477-020-0739-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/06/2020] [Indexed: 05/24/2023]
Abstract
The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel
| | - Jason W Reed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel.
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46
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Soyk S, Benoit M, Lippman ZB. New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. Annu Rev Genet 2020; 54:287-307. [PMID: 32870731 DOI: 10.1146/annurev-genet-050720-122916] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.
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Affiliation(s)
- Sebastian Soyk
- Center for Integrative Genomics, University of Lausanne, CH-1005 Lausanne, Switzerland;
| | - Matthias Benoit
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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47
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Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Commun Biol 2020; 3:432. [PMID: 32792560 PMCID: PMC7426833 DOI: 10.1038/s42003-020-01172-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/24/2020] [Indexed: 11/08/2022] Open
Abstract
Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.
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48
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Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J, Robitaille G, Kramer M, Goodwin S, McCombie WR, Hutton S, Van Eck J, Gillis J, Eshed Y, Sedlazeck FJ, van der Knaap E, Schatz MC, Lippman ZB. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell 2020; 182:145-161.e23. [PMID: 32553272 PMCID: PMC7354227 DOI: 10.1016/j.cell.2020.05.021] [Citation(s) in RCA: 377] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022]
Abstract
Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.
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Affiliation(s)
- Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xingang Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Matthias Benoit
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sebastian Soyk
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lara Pereira
- Center for Applied Genetic Technologies, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Lei Zhang
- Center for Applied Genetic Technologies, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Hamsini Suresh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Danielle Ciren
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yuval Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tom Hai Harel
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gili Shalev-Schlosser
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ziva Amsellem
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hamid Razifard
- Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ana L Caicedo
- Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Denise M Tieman
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL 32611, USA
| | - Harry Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL 32611, USA
| | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jennifer Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - W Richard McCombie
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Samuel Hutton
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA; Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA; Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice. BMC Biol 2020; 18:73. [PMID: 32591023 PMCID: PMC7318451 DOI: 10.1186/s12915-020-00798-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022] Open
Abstract
Background Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools. Results Here, we generated genomic and transcriptomic data of 93 rice (Oryza sativa L.) accessions and developed a comprehensive pipeline to call CNVs in this large-scale dataset. We analyzed the correlation between CNVs and gene expression levels and found that approximately 13% of the identified genes showed a significant correlation between their expression levels and copy numbers. Further analysis showed that about 36% of duplicate pairs were involved in pseudogenetic events while only 5% of them showed functional differentiation. Moreover, the offspring copy mainly contributed to the expression levels and seemed more likely to become a pseudogene, whereas the parent copy tended to maintain the function of ancestral gene. Conclusion We provide a high-accuracy CNV dataset that will contribute to functional genomics studies and molecular breeding in rice. We also showed that gene dosage effect of CNVs in rice is not exponential or linear. Our work demonstrates that the evolution of duplicated genes is asymmetric in both expression levels and gene fates, shedding a new insight into the evolution of duplicated genes.
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50
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Sun S, Wang X, Wang K, Cui X. Dissection of complex traits of tomato in the post-genome era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1763-1776. [PMID: 31745578 DOI: 10.1007/s00122-019-03478-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.
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Affiliation(s)
- Shuai Sun
- 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
| | - Xiaotian 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
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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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