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Zhang D, Ai G, Ji K, Huang R, Chen C, Yang Z, Wang J, Cui L, Li G, Tahira M, Wang X, Wang T, Ye J, Hong Z, Ye Z, Zhang J. EARLY FLOWERING is a dominant gain-of-function allele of FANTASTIC FOUR 1/2c that promotes early flowering in tomato. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:698-711. [PMID: 37929693 PMCID: PMC10893951 DOI: 10.1111/pbi.14217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Flowering time, an important factor in plant adaptability and genetic improvement, is regulated by various genes in tomato (Solanum lycopersicum). In this study, we characterized a tomato mutant, EARLY FLOWERING (EF), that developed flowers much earlier than its parental control. EF is a dominant gain-of-function allele with a T-DNA inserted 139 bp downstream of the stop codon of FANTASTIC FOUR 1/2c (FAF1/2c). The transcript of SlFAF1/2c was at elevated levels in the EF mutant. Overexpressing SlFAF1/2c in tomato plants phenocopied the early flowering trait of the EF mutant. Knocking out SlFAF1/2c in the EF mutant reverted the early flowering phenotype of the mutant to the normal flowering time of the wild-type tomato plants. SlFAF1/2c promoted the floral transition by shortening the vegetative phase rather than by reducing the number of leaves produced before the emergence of the first inflorescence. The COP9 signalosome subunit 5B (CSN5B) was shown to interact with FAF1/2c, and knocking out CSN5B led to an early flowering phenotype in tomato. Interestingly, FAF1/2c was found to reduce the accumulation of the CSN5B protein by reducing its protein stability. These findings imply that FAF1/2c regulates flowering time in tomato by reducing the accumulation and stability of CSN5B, which influences the expression of SINGLE FLOWER TRUSS (SFT), JOINTLESS (J) and UNIFLORA (UF). Thus, a new allele of SlFAF1/2c was discovered and found to regulate flowering time in tomato.
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Affiliation(s)
- Dedi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Guo Ai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Kangna Ji
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Rong Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Chunrui Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Zixuan Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Jiafa Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Long Cui
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Guobin Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Maryam Tahira
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Jie Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Zonglie Hong
- Department of Plant SciencesUniversity of IdahoMoscowIdahoUSA
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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2
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Sun S, Liu Z, Wang X, Song J, Fang S, Kong J, Li R, Wang H, Cui X. Genetic control of thermomorphogenesis in tomato inflorescences. Nat Commun 2024; 15:1472. [PMID: 38368437 PMCID: PMC10874430 DOI: 10.1038/s41467-024-45722-0] [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: 10/30/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024] Open
Abstract
Understanding how plants alter their development and architecture in response to ambient temperature is crucial for breeding resilient crops. Here, we identify the quantitative trait locus qMULTIPLE INFLORESCENCE BRANCH 2 (qMIB2), which modulates inflorescence branching in response to high ambient temperature in tomato (Solanum lycopersicum). The non-functional mib2 allele may have been selected in large-fruited varieties to ensure larger and more uniform fruits under varying temperatures. MIB2 gene encodes a homolog of the Arabidopsis thaliana transcription factor SPATULA; its expression is induced in meristems at high temperature. MIB2 directly binds to the promoter of its downstream gene CONSTANS-Like1 (SlCOL1) by recognizing the conserved G-box motif to activate SlCOL1 expression in reproductive meristems. Overexpressing SlCOL1 rescue the reduced inflorescence branching of mib2, suggesting how the MIB2-SlCOL1 module helps tomato inflorescences adapt to high temperature. Our findings reveal the molecular mechanism underlying inflorescence thermomorphogenesis and provide a target for breeding climate-resilient crops.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - Siyu Fang
- 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
| | - Jisheng Kong
- 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
| | - Huanzhong Wang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
| | - Xia Cui
- 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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3
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Kumar A, Singh N, Joshi R. Deciphering the metabolic signatures of Trigonella microgreens as a function of photoperiod and temperature using targeted compound analysis and non-targeted UHPLC-QTOF-IMS based approach. Food Res Int 2024; 176:113834. [PMID: 38163730 DOI: 10.1016/j.foodres.2023.113834] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Trigonella foenum-graecum L. (Fenugreek) is an annual herb that belongs to Fabaceae family. The compositional make-up of microgreens depends on prevailing environmental conditions. So, Trigonella microgreens were cultivated under different photoperiod and temperature conditions and evaluated for plant height, total chlorophyll content (TCC), targeted compound analysis and non-targeted UHPLC-QTOF-IMS based metabolomic profile. The plant height and TCC of Trigonella microgreens increased by approximately 22 % and 20 %, respectively under T1 conditions (longer photoperiod of 22 h with 22 °C in light and 17 °C in dark). The targeted phenolic profile analysis revealed the dominant presence of gallic acid, p-coumaric acid and apigenin in Trigonella microgreens. Also, the concentration of p-coumaric acid concentration raised from 3.51 mg/g to 5.83 mg/g as a response of T1 conditions. The sugar profile revealed augmented concentration of myo-inositol, glucose, fructose, xylose, maltose, and sucrose in longer photoperiod with T1 conditions. The microgreens were also rich in amino acids like aspartic acid, glutamic acid, leucine, isoleucine, and phenylalanine. Notably, the concentration of proline increased from 10.40 mg/g to 16.92 mg/g as a response to T1 growth conditions. The concentration of these metabolites varied significantly under different photoperiod and temperature conditions. The comprehensive non-targeted UHPLC-QTOF-IMS analysis of microgreens revealed different class of metabolites like organic compounds, alkaloids, coumarin-derivatives, phenolic and flavonoid derivatives, terpenoids, sugars, amino acids and few nucleic acid derivatives. The multivariate PLS-DA explained different expression level of metabolites under different growing conditions. The T1 growing condition resulted in the increased biosynthesis of phenolic compounds and various metabolites. The expression level of terpenoid derivatives specifically of Trigonelloside C and Trigoneoside XIIa/b increased under T1 conditions. The substantial alteration in the metabolites due to growing conditions may alter the microgreen's dietary benefits. So, additional research may be warranted.
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Affiliation(s)
- Arun Kumar
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun 248002, India
| | - Narpinder Singh
- Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun 248002, India.
| | - Robin Joshi
- Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, University of Pennsylvania (UPenn), Philadelphia, PA 19104, USA; Biotechnology Division, CSIR- Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.
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4
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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5
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KhokharVoytas A, Shahbaz M, Maqsood MF, Zulfiqar U, Naz N, Iqbal UZ, Sara M, Aqeel M, Khalid N, Noman A, Zulfiqar F, Al Syaad KM, AlShaqhaa MA. Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change. Funct Integr Genomics 2023; 23:283. [PMID: 37642792 DOI: 10.1007/s10142-023-01202-0] [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: 05/08/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Enhancing the resilience of plants to abiotic stresses, such as drought, salinity, heat, and cold, is crucial for ensuring global food security challenge in the context of climate change. The adverse effects of climate change, characterized by rising temperatures, shifting rainfall patterns, and increased frequency of extreme weather events, pose significant threats to agricultural systems worldwide. Genetic modification strategies offer promising approaches to develop crops with improved abiotic stress tolerance. This review article provides a comprehensive overview of various genetic modification techniques employed to enhance plant resilience. These strategies include the introduction of stress-responsive genes, transcription factors, and regulatory elements to enhance stress signaling pathways. Additionally, the manipulation of hormone signaling pathways, osmoprotectant accumulation, and antioxidant defense mechanisms is discussed. The use of genome editing tools, such as CRISPR-Cas9, for precise modification of target genes related to stress tolerance is also explored. Furthermore, the challenges and future prospects of genetic modification for abiotic stress tolerance are highlighted. Understanding and harnessing the potential of genetic modification strategies can contribute to the development of resilient crop varieties capable of withstanding adverse environmental conditions caused by climate change, thereby ensuring sustainable agricultural productivity and food security.
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Affiliation(s)
| | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, Pakistan.
| | | | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Usama Zafar Iqbal
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Maheen Sara
- Department of Nutritional Sciences, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Sialkot, Pakistan
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Khalid M Al Syaad
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
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6
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Steel L, Welling M, Ristevski N, Johnson K, Gendall A. Comparative genomics of flowering behavior in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1227898. [PMID: 37575928 PMCID: PMC10421669 DOI: 10.3389/fpls.2023.1227898] [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: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023]
Abstract
Cannabis sativa L. is a phenotypically diverse and multi-use plant used in the production of fiber, seed, oils, and a class of specialized metabolites known as phytocannabinoids. The last decade has seen a rapid increase in the licit cultivation and processing of C. sativa for medical end-use. Medical morphotypes produce highly branched compact inflorescences which support a high density of glandular trichomes, specialized epidermal hair-like structures that are the site of phytocannabinoid biosynthesis and accumulation. While there is a focus on the regulation of phytocannabinoid pathways, the genetic determinants that govern flowering time and inflorescence structure in C. sativa are less well-defined but equally important. Understanding the molecular mechanisms that underly flowering behavior is key to maximizing phytocannabinoid production. The genetic basis of flowering regulation in C. sativa has been examined using genome-wide association studies, quantitative trait loci mapping and selection analysis, although the lack of a consistent reference genome has confounded attempts to directly compare candidate loci. Here we review the existing knowledge of flowering time control in C. sativa, and, using a common reference genome, we generate an integrated map. The co-location of known and putative flowering time loci within this resource will be essential to improve the understanding of C. sativa phenology.
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Affiliation(s)
| | | | | | | | - Anthony Gendall
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
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7
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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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8
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Sun Y, Jia X, Yang Z, Fu Q, Yang H, Xu X. Genome-Wide Identification of PEBP Gene Family in Solanum lycopersicum. Int J Mol Sci 2023; 24:ijms24119185. [PMID: 37298136 DOI: 10.3390/ijms24119185] [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: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The PEBP gene family is crucial for the growth and development of plants, the transition between vegetative and reproductive growth, the response to light, the production of florigen, and the reaction to several abiotic stressors. The PEBP gene family has been found in numerous species, but the SLPEBP gene family has not yet received a thorough bioinformatics investigation, and the members of this gene family are currently unknown. In this study, bioinformatics was used to identify 12 members of the SLPEBP gene family in tomato and localize them on the chromosomes. The physicochemical characteristics of the proteins encoded by members of the SLPEBP gene family were also examined, along with their intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements. In parallel, a phylogenetic tree was built and the collinear relationships of the PEBP gene family among tomato, potato, pepper, and Arabidopsis were examined. The expression of 12 genes in different tissues and organs of tomato was analyzed using transcriptomic data. It was also hypothesized that SLPEBP3, SLPEBP5, SLPEBP6, SLPEBP8, SLPEBP9, and SLPEBP10 might be related to tomato flowering and that SLPEBP2, SLPEBP3, SLPEBP7, and SLPEBP11 might be related to ovary development based on the tissue-specific expression analysis of SLPEBP gene family members at five different stages during flower bud formation to fruit set. This article's goal is to offer suggestions and research directions for further study of tomato PEBP gene family members.
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Affiliation(s)
- Yimeng Sun
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xinyi Jia
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Zhenru Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Qingjun Fu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Huanhuan Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xiangyang Xu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
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9
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Moreira JDR, Quiñones A, Lira BS, Robledo JM, Curtin SJ, Vicente MH, Ribeiro DM, Ryngajllo M, Jiménez-Gómez JM, Peres LEP, Rossi M, Zsögön A. SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture, and drought responses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6226-6240. [PMID: 35710302 DOI: 10.1093/jxb/erac265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family controls agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine-binding proteins that have a central role in the timing of flowering as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering induction and repression. Here, we characterized the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines increases root length and reduces root side branching relative to the wild type. Higher SP3C expression in transgenic lines promotes the opposite effects in roots, represses seed germination, and also improves tolerance to water stress in seedlings. These discoveries provide new insights into the role of SP paralogs in agronomically relevant traits, and support future exploration of the involvement of CETS genes in abiotic stress responses.
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Affiliation(s)
| | - Alejandra Quiñones
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | - Jessenia M Robledo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
| | - Mateus H Vicente
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | - Lázaro Eustáquio Pereira Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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10
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Moreira JDR, Rosa BL, Lira BS, Lima JE, Correia LNF, Otoni WC, Figueira A, Freschi L, Sakamoto T, Peres LEP, Rossi M, Zsögön A. Auxin-driven ecophysiological diversification of leaves in domesticated tomato. PLANT PHYSIOLOGY 2022; 190:113-126. [PMID: 35639975 PMCID: PMC9434155 DOI: 10.1093/plphys/kiac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 05/29/2023]
Abstract
Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.
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Affiliation(s)
- Juliene d R Moreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno L Rosa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno S Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Joni E Lima
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ludmila N F Correia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Wagner C Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, 13400-970 Piracicaba, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Tetsu Sakamoto
- Bioinformatics Multidisciplinary Environment, Instituto Metrópole Digital, Universidade Federal Do Rio Grande Do Norte, 59078-400 Natal, Rio Grande do Norte, Brazil
| | - Lázaro E P Peres
- Laboratory of Hormonal Control of Plant Development, Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, CP 09, 13418-900 Piracicaba, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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11
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Qu G, Gao Y, Wang X, Fu W, Sun Y, Gao X, Wang W, Hao C, Feng H, Wang Y. Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2233-2246. [PMID: 35532733 DOI: 10.1007/s00122-022-04108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F2 population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.
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Affiliation(s)
- Gaoyang Qu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xian Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Fu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yunxia Sun
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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12
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Rehman F, Gong H, Bao Y, Zeng S, Huang H, Wang Y. CRISPR gene editing of major domestication traits accelerating breeding for Solanaceae crops improvement. PLANT MOLECULAR BIOLOGY 2022; 108:157-173. [PMID: 35032250 DOI: 10.1007/s11103-021-01229-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Domestication traits particularly fruit size and plant architecture and flowering are critical in transforming a progenitor's wild stature into a super improved plant. The latest advancements in the CRISPR system, as well as its rapid adoption, are speeding up plant breeding. Solanaceae has a varied range of important crops, with a few model crops, such as tomato and, more recently, groundcherry, serving as a foundation for developing molecular techniques, genome editing tools, and establishing standards for other crops. Domestication traits in agricultural plants are quantified and widely adopted under modern plant breeding to improve small-fruited and bushy crop species like goji berry. The molecular mechanisms of the FW2.2, FW3.2, FW11.3, FAS/CLV3, LC/WUS, SP, SP5G, and CRISPR genome editing technology have been described in detail here. Furthermore, special focus has been placed on CRISPR gene editing achievements for revolutionizing Solanaceae breeding and changing the overall crop landscape. This review seeks to provide a thorough overview of the CRISPR technique's ongoing advancements, particularly in Solanaceae, in terms of domesticated features, future prospects, and regulatory risks. We believe that this vigorous discussion will lead to a broader understanding of CRISPR gene editing as a tool for achieving key breeding goals in other Solanaceae minor crops with significant industrial value.
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Affiliation(s)
- Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yufei Bao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Hongwen Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
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13
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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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14
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. BIOLOGY 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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15
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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
- Author for communication:
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16
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Bhat MA, Mir RA, Kumar V, Shah AA, Zargar SM, Rahman S, Jan AT. Mechanistic insights of CRISPR/Cas-mediated genome editing towards enhancing abiotic stress tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 172:1255-1268. [PMID: 33576013 DOI: 10.1111/ppl.13359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 05/28/2023]
Abstract
Abiotic stresses such as temperature (high/low), drought, salinity, and others make the environment hostile to plants. Abiotic stressors adversely affect plant growth and development; and thereby makes a direct impact on overall plant productivity. Plants confront stress by developing an internal defense system orchestrated by compatible solutes, reactive oxygen species scavengers and phytohormones. However, routine exposure to unpredictable environmental stressors makes it essential to equip plants with a system that contributes to sustainable agricultural productivity, besides imparting multi-stress tolerance. The sustainable approach against abiotic stress is accomplished through breeding of tolerant cultivars. Though eco-friendly, tedious screening and crossing protocol limits its usage to overcome stress and in attaining the goal of global food security. Advancement on the technological front has enabled adoption of genomic engineering approaches to perform site-specific modification in the plant genome for improving adaptability, increasing the yield and in attributing resilience against different stressors. Of the different genome editing approaches, CRISPR/Cas has revolutionized biological research with wider applicability to crop plants. CRISPR/Cas emerged as a versatile tool in editing genomes for desired traits in highly accurate and precise manner. The present study summarizes advancement of the CRISPR/Cas genome editing tool in its adoption to manipulate plant genomes for novel traits towards developing high-yielding and climate-resilient crop varieties.
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Affiliation(s)
- Mujtaba Aamir Bhat
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Vijay Kumar
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajad Majeed Zargar
- Proteomics Lab., Division of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir, India
| | - Safikur Rahman
- Department of Botany, MS College, BR Ambedkar Bihar University, Muzaffarpur, India
| | - Arif Tasleem Jan
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation. ABIOTECH 2021; 2:156-169. [PMID: 36304754 PMCID: PMC9590489 DOI: 10.1007/s42994-021-00039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information. Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment. The domestication of plants into crops, and later crop expansion and improvement, has often involved selection for early flowering. In this review, we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species. The ancestors of rice (Oryza sativa), maize (Zea mays), soybean (Glycine max), and tomato (Solanum lycopersicum) are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas. Wheat (Triticum aestivum) and barley (Hordeum vulgare) are long-day crops whose photosensitivity is influenced by both latitude and vernalization type. Here, we summarize recent studies about where these crops were domesticated, how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions, and how allelic variants of photoperiodic flowering genes were selected during this process. A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00039-0.
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Lebedeva MA, Dodueva IE, Gancheva MS, Tvorogova VE, Kuznetsova KA, Lutova LA. The Evolutionary Aspects of Flowering Control: Florigens and Anti-Florigens. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542011006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Li R, Sun S, Wang H, Wang K, Yu H, Zhou Z, Xin P, Chu J, Zhao T, Wang H, Li J, Cui X. FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato. Nat Commun 2020; 11:5844. [PMID: 33203832 PMCID: PMC7673020 DOI: 10.1038/s41467-020-19705-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Fruit firmness is a target trait in tomato breeding because it facilitates transportation and storage. However, it is also a complex trait and uncovering the molecular genetic mechanisms controlling fruit firmness has proven challenging. Here, we report the map-based cloning and functional characterization of qFIRM SKIN 1 (qFIS1), a major quantitative trait locus that partially determines the difference in compression resistance between cultivated and wild tomato accessions. FIS1 encodes a GA2-oxidase, and its mutation leads to increased bioactive gibberellin content, enhanced cutin and wax biosynthesis, and increased fruit firmness and shelf life. Importantly, FIS1 has no unfavorable effect on fruit weight or taste, making it an ideal target for breeders. Our study demonstrates that FIS1 mediates gibberellin catabolism and regulates fruit firmness, and it offers a potential strategy for tomato breeders to produce firmer fruit.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Ketao Wang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhen Zhou
- 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
| | - Peiyong Xin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tongmin Zhao
- Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Huanzhong Wang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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20
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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: 17] [Impact Index Per Article: 4.3] [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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21
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Song J, Zhang S, Wang X, Sun S, Liu Z, Wang K, Wan H, Zhou G, Li R, Yu H, Cui X. Variations in Both FTL1 and SP5G, Two Tomato FT Paralogs, Control Day-Neutral Flowering. MOLECULAR PLANT 2020; 13:939-942. [PMID: 32417308 DOI: 10.1016/j.molp.2020.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Jia Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiqiang Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ketao Wang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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22
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Basso MF, Arraes FBM, Grossi-de-Sa M, Moreira VJV, Alves-Ferreira M, Grossi-de-Sa MF. Insights Into Genetic and Molecular Elements for Transgenic Crop Development. FRONTIERS IN PLANT SCIENCE 2020; 11:509. [PMID: 32499796 PMCID: PMC7243915 DOI: 10.3389/fpls.2020.00509] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/03/2020] [Indexed: 05/21/2023]
Abstract
Climate change and the exploration of new areas of cultivation have impacted the yields of several economically important crops worldwide. Both conventional plant breeding based on planned crosses between parents with specific traits and genetic engineering to develop new biotechnological tools (NBTs) have allowed the development of elite cultivars with new features of agronomic interest. The use of these NBTs in the search for agricultural solutions has gained prominence in recent years due to their rapid generation of elite cultivars that meet the needs of crop producers, and the efficiency of these NBTs is closely related to the optimization or best use of their elements. Currently, several genetic engineering techniques are used in synthetic biotechnology to successfully improve desirable traits or remove undesirable traits in crops. However, the features, drawbacks, and advantages of each technique are still not well understood, and thus, these methods have not been fully exploited. Here, we provide a brief overview of the plant genetic engineering platforms that have been used for proof of concept and agronomic trait improvement, review the major elements and processes of synthetic biotechnology, and, finally, present the major NBTs used to improve agronomic traits in socioeconomically important crops.
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Affiliation(s)
| | - Fabrício Barbosa Monteiro Arraes
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Maíra Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Valdeir Junio Vaz Moreira
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
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23
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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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24
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Gaudinier A, Blackman BK. Evolutionary processes from the perspective of flowering time diversity. THE NEW PHYTOLOGIST 2020; 225:1883-1898. [PMID: 31536639 DOI: 10.1111/nph.16205] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/30/2019] [Indexed: 05/18/2023]
Abstract
Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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25
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Wang S, Li H, Li Y, Li Z, Qi J, Lin T, Yang X, Zhang Z, Huang S. FLOWERING LOCUS T Improves Cucumber Adaptation to Higher Latitudes. PLANT PHYSIOLOGY 2020; 182:908-918. [PMID: 31843803 PMCID: PMC6997709 DOI: 10.1104/pp.19.01215] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/22/2019] [Indexed: 05/10/2023]
Abstract
Flowering time plays a crucial role in the geographical adaptation of most crops during domestication. Cucumber (Cucumis sativus) is a major vegetable crop worldwide. From its tropical origin on the southern Asian continent, cucumber has spread over a wide latitudinal cline, but the molecular mechanisms underlying this latitudinal adaptation and the expansion of domesticated cucumber are largely unclear. Here, we report the cloning of two flowering time loci from two distinct cucumber populations and show that two large deletions upstream from FLOWERING LOCUS T (FT) are associated with higher expression of FT and earlier flowering. We determined that the two large deletions are pervasive and occurred independently in Eurasian and East-Asian populations. Nucleotide diversity analysis further revealed that the FT locus region of the cucumber genome contains a signature for a selective sweep during domestication. Our results suggest that large genetic structural variations upstream from FT were selected for and have been important in the geographic spread of cucumber from its tropical origin to higher latitudes.
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Affiliation(s)
- Shenhao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hongbo Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangyang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zheng Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jianjian Qi
- Inner Mongolia Potato Engineering and Technology Research Centre, Inner Mongolia University, Hohhot 010021, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing 100094, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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26
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Rosado D, Trench B, Bianchetti R, Zuccarelli R, Rodrigues Alves FR, Purgatto E, Segal Floh EI, Silveira Nogueira FT, Freschi L, Rossi M. Downregulation of PHYTOCHROME-INTERACTING FACTOR 4 Influences Plant Development and Fruit Production. PLANT PHYSIOLOGY 2019; 181:1360-1370. [PMID: 31519788 PMCID: PMC6836831 DOI: 10.1104/pp.19.00833] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/04/2019] [Indexed: 05/27/2023]
Abstract
Plant development is highly dependent on the ability to perceive and cope with environmental changes. In this context, PIF proteins are key players in the cellular hub controlling responses to fluctuating light and temperature conditions. Reports in various plant species show that manipulation of the PIF4 level affects important agronomical traits. In tomato (Solanum lycopersicum), SlPIF1a and SlPIF3 regulate fruit nutraceutical composition. However, the wider role of this protein family, and the potential of their manipulation for the improvement of other traits, has not been explored. Here we report the effects of constitutive silencing of tomato SlPIF4 on whole-plant physiology and development. Ripening anticipation and higher carotenoid levels observed in SlPIF4-silenced fruits revealed a redundant role of SlPIF4 in the accumulation of nutraceutical compounds. Furthermore, silencing triggered a significant reduction in plant size, flowering, fruit yield, and fruit size. This phenotype was most likely caused by reduced auxin levels and altered carbon partitioning. Impaired thermomorphogenesis and delayed leaf senescence were also observed in silenced plants, highlighting the functional conservation of PIF4 homologs in angiosperms. Overall, this work improves our understanding of the role of PIF proteins-and light signaling-in metabolic and developmental processes that affect yield and composition of fleshy fruits.
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Affiliation(s)
- Daniele Rosado
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bruna Trench
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Ricardo Bianchetti
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Rafael Zuccarelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | | | - Eduardo Purgatto
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Eny Iochevet Segal Floh
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | | | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
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27
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Yang T, Deng L, Zhao W, Zhang R, Jiang H, Ye Z, Li CB, Li C. Rapid breeding of pink-fruited tomato hybrids using the CRISPR/Cas9 system. J Genet Genomics 2019; 46:505-508. [PMID: 31734133 DOI: 10.1016/j.jgg.2019.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/19/2022]
Affiliation(s)
- Tianxia Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zhao
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruoxi Zhang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongling Jiang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chang-Bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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