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Nishimura K, Kokaji H, Motoki K, Yamazaki A, Nagasaka K, Mori T, Takisawa R, Yasui Y, Kawai T, Ushijima K, Yamasaki M, Saito H, Nakano R, Nakazaki T. Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38459738 DOI: 10.1111/tpj.16708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Hiroyuki Kokaji
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Kyoka Nagasaka
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Mori
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu City, Shiga, 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2 no-cho, Nishi-ku, Niigata City, Niigata, 950-2181, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
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Ezura K, Nomura Y, Ariizumi T. Molecular, hormonal, and metabolic mechanisms of fruit set, the ovary-to-fruit transition, in horticultural crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6254-6268. [PMID: 37279328 DOI: 10.1093/jxb/erad214] [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: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Fruit set is the process by which the ovary develops into a fruit and is an important factor in determining fruit yield. Fruit set is induced by two hormones, auxin and gibberellin, and the activation of their signaling pathways, partly by suppressing various negative regulators. Many studies have investigated the structural changes and gene networks in the ovary during fruit set, revealing the cytological and molecular mechanisms. In tomato (Solanum lycopersicum), SlIAA9 and SlDELLA/PROCERA act as auxin and gibberellin signaling repressors, respectively, and are important regulators of the activity of transcription factors and downstream gene expression involved in fruit set. Upon pollination, SlIAA9 and SlDELLA are degraded, which subsequently activates downstream cascades and mainly contributes to active cell division and cell elongation, respectively, in ovaries during fruit setting. According to current knowledge, the gibberellin pathway functions as the most downstream signal in fruit set induction, and therefore its role in fruit set has been extensively explored. Furthermore, multi-omics analysis has revealed the detailed dynamics of gene expression and metabolites downstream of gibberellins, highlighting the rapid activation of central carbon metabolism. This review will outline the relevant mechanisms at the molecular and metabolic levels during fruit set, particularly focusing on tomato.
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Affiliation(s)
- Kentaro Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Research Fellow of Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo 102-0083, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yukako Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Tran LT, Sugimoto K, Kasozi M, Mitalo OW, Ezura H. Pollination, pollen tube growth, and fertilization independently contribute to fruit set and development in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1205816. [PMID: 37416886 PMCID: PMC10319911 DOI: 10.3389/fpls.2023.1205816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
In flowering plants, pollination, pollen tube growth, and fertilization are regarded as the first hierarchical processes of producing offspring. However, their independent contributions to fruit set and development remain unclear. In this study, we examined the effect of three different types of pollen, intact pollen (IP), soft X-ray-treated pollen (XP) and dead pollen (DP), on pollen tube growth, fruit development and gene expression in "Micro-Tom" tomato. Normal germination and pollen tube growth were observed in flowers pollinated with IP; pollen tubes started to penetrate the ovary at 9 h after pollination, and full penetration was achieved after 24 h (IP24h), resulting in ~94% fruit set. At earlier time points (3 and 6 h after pollination; IP3h and IP6h, respectively), pollen tubes were still in the style, and no fruit set was observed. Flowers pollinated with XP followed by style removal after 24 h (XP24h) also demonstrated regular pollen tubes and produced parthenocarpic fruits with ~78% fruit set. As expected, DP could not germinate and failed to activate fruit formation. Histological analysis of the ovary at 2 days after anthesis (DAA) revealed that IP and XP comparably increased cell layers and cell size; however, mature fruits derived from XP were significantly smaller than those derived from IP. Furthermore, there was a high correlation between seed number and fruit size in fruit derived from IP, illustrating the crucial role of fertilization in the latter stages of fruit development. RNA-Seq analysis was carried out in ovaries derived from IP6h, IP24h, XP24h and DP24h in comparison with emasculated and unpollinated ovaries (E) at 2 DAA. The results revealed that 65 genes were differentially expressed (DE) in IP6h ovaries; these genes were closely associated with cell cycle dormancy release pathways. Conversely, 5062 and 4383 DE genes were obtained in IP24h and XP24h ovaries, respectively; top enriched terms were mostly associated with cell division and expansion in addition to the 'plant hormone signal transduction' pathway. These findings indicate that full penetration of pollen tubes can initiate fruit set and development independently of fertilization, most likely by activating the expression of genes regulating cell division and expansion.
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Affiliation(s)
- Long T. Tran
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Koichi Sugimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Centre, University of Tsukuba, Tsukuba, Japan
| | - Michael Kasozi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Oscar W. Mitalo
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Centre, University of Tsukuba, Tsukuba, Japan
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Maki T, Kusaka H, Matsumoto Y, Yamazaki A, Yamaoka S, Ohno S, Doi M, Tanaka Y. The mutation of CaCKI1 causes seedless fruits in chili pepper (Capsicum annuum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:85. [PMID: 36964815 DOI: 10.1007/s00122-023-04342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The seedless mutant tn-1 in chili pepper is caused by a mutation in CaCKI1 (CA12g21620), which encodes histidine kinase involving female gametophyte development. An amino acid insertion in the receiver domain of CaCKI1 may be the mutation responsible for tn-1. Seedlessness is a desirable trait in fruit crops because the removal of seeds is a troublesome step for consumers and processing industries. However, little knowledge is available to develop seedless chili peppers. In a previous study, a chili pepper mutant tn-1, which stably produces seedless fruits, was isolated. In this study, we report characterization of tn-1 and identification of the causative gene. Although pollen germination was normal, confocal laser microscopy observations revealed deficiency in embryo sac development in tn-1. By marker analysis, the tn-1 locus was narrowed down to a 313 kb region on chromosome 12. Further analysis combined with mapping-by-sequencing identified CA12g21620, which encodes histidine kinase as a candidate gene. Phylogenetic analysis revealed CA12g21620 was the homolog of Arabidopsis CKI1 (Cytokinin Independent 1), which plays an important role in female gametophyte development, and CA12g21620 was designated as CaCKI1. Sequence analysis revealed that tn-1 has a 3-bp insertion in the 6th exon resulting in one lysine (K) residue insertion in receiver domain of CaCKI1, and the sequence nearby the insertion is widely conserved among CKI1 orthologs in various plants. This suggested that one K residue insertion may reduce the phosphorylation relay downstream of CaCKI1 and impair normal development of female gametophyte, resulting in seedless fruits production in tn-1. Furthermore, we demonstrated that virus-induced gene silencing of CaCKI1 reduced normally developed female gametophyte in chili pepper. This study describes the significant role of CaCKI1 in seed development in chili pepper and the possibility of developing seedless cultivars using its mutation.
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Affiliation(s)
- Takahiro Maki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Hirokazu Kusaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuki Matsumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akira Yamazaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
- Faculty of Agriculture, Kindai University, Naka Machi, Nara, 631-8505, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
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Kaur H, Manchanda P, Kumar P, Dhall RK, Chhuneja P, Weng Y. Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.). Sci Rep 2023; 13:2403. [PMID: 36765113 PMCID: PMC9918540 DOI: 10.1038/s41598-023-29660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
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Cheng Z, Song W, Zhang X. Genic male and female sterility in vegetable crops. HORTICULTURE RESEARCH 2022; 10:uhac232. [PMID: 36643746 PMCID: PMC9832880 DOI: 10.1093/hr/uhac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato (Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.
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Affiliation(s)
- Zhihua Cheng
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiyuan Song
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
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Vignati E, Lipska M, Dunwell JM, Caccamo M, Simkin AJ. Options for the generation of seedless cherry, the ultimate snacking product. PLANTA 2022; 256:90. [PMID: 36171415 PMCID: PMC9519733 DOI: 10.1007/s00425-022-04005-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/21/2022] [Indexed: 05/09/2023]
Abstract
This manuscript identifies cherry orthologues of genes implicated in the development of pericarpic fruit and pinpoints potential options and restrictions in the use of these targets for commercial exploitation of parthenocarpic cherry fruit. Cherry fruit contain a large stone and seed, making processing of the fruit laborious and consumption by the consumer challenging, inconvenient to eat 'on the move' and potentially dangerous for children. Availability of fruit lacking the stone and seed would be potentially transformative for the cherry industry, since such fruit would be easier to process and would increase consumer demand because of the potential reduction in costs. This review will explore the background of seedless fruit, in the context of the ambition to produce the first seedless cherry, carry out an in-depth analysis of the current literature around parthenocarpy in fruit, and discuss the available technology and potential for producing seedless cherry fruit as an 'ultimate snacking product' for the twenty-first century.
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Affiliation(s)
- Edoardo Vignati
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EU, UK
| | - Marzena Lipska
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EU, UK
| | - Mario Caccamo
- NIAB, Cambridge Crop Research, Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Andrew J Simkin
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK.
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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Htwe YM, Shi P, Zhang D, Li Z, Xiao Y, Yang Y, Lei X, Wang Y. Programmed Cell Death May Be Involved in the Seedless Phenotype Formation of Oil Palm. FRONTIERS IN PLANT SCIENCE 2022; 13:832017. [PMID: 35401608 PMCID: PMC8984474 DOI: 10.3389/fpls.2022.832017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a well-known vegetable oil-yielding crop. Seedlessness is one of the most prominent traits in oil palm due to its low processing costs and high oil content. Nevertheless, an extensive study on molecular mechanisms regulating seedless phenotype formation in oil palm is very limited so far. In this study, stigma, style, and ovary from seedless and seeded (Tenera and Pisifera) oil palm trees were used to investigate the possible mechanism. Results showed that non-pollination resulted in no fruits, and self- and cross-pollinations resulted in seedless fruits, while boron treatment had no effect on seedless phenotype formation, implying that seedless trees have incomplete self and outcrossing incompatibility. Furthermore, the transcriptome data analysis highlighted eight programmed cell death (PCD) genes and three groups of PCD-related genes: 4-coumarate-CoA ligase (4CL), S-RNase, and MADS-box. The majority of these genes were significantly up-regulated in the stigma and style of Seedless palm trees compared to Tenera and Pisifera. In addition, the co-expression network analysis confirmed the significant correlation among these genes. Moreover, two simple sequence repeats (SSR) markers (S41 and S44) were developed to identify the seedless phenotype. The up-regulation of 4CL and MADS-box TFs activated the expression of PCD genes; on the other hand, S-RNase resulted in pollen tube RNA degradation and triggered PCD. While the link between PCD and seedless phenotype formation in oil palm has not been extensively studied to date, these findings suggest a role of PCD in pollen tube lethality, leading to double fertilization failure and the seedless phenotype.
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Affiliation(s)
- Yin Min Htwe
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Peng Shi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Dapeng Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Zhiying Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xintao Lei
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yong Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
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Zhang S, Gu X, Shao J, Hu Z, Yang W, Wang L, Su H, Zhu L. Auxin Metabolism Is Involved in Fruit Set and Early Fruit Development in the Parthenocarpic Tomato "R35-P". FRONTIERS IN PLANT SCIENCE 2021; 12:671713. [PMID: 34408758 PMCID: PMC8365229 DOI: 10.3389/fpls.2021.671713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Parthenocarpic tomato can set fruit and develop without pollination and exogenous hormone treatments under unfavorable environmental conditions, which is beneficial to tomato production from late fall to early spring in greenhouses. In this study, the endogenous hormones in the ovaries of the parthenocarpic tomato line "R35-P" (stigma removed or self-pollination) and the non-parthenocarpic tomato line "R35-N" (self-pollination) at four stages between preanthesis and postanthesis investigated, using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). A nearly twofold IAA (indoleacetic acid) content was found in "R35-P" rather than in "R35-N" at -2 and 0 days after anthesis (DAA). Except at -2 DAA, a lower ABA (abscisic acid) content was observed in Pe (stigma removed in "R35-P") compared to that in Ps (self-pollination in "R35-P") or CK (self-pollination in "R35-N"). After pollination, although the content of GA1 (gibberellins acid 1) in CK increased, the levels of GAs (gibberellins acids) were notably low. At all four stages, a lower SA (salicylic acid) content was found in Ps and CK than in Pe, while the content and the change trend were similar in Ps and CK. The variation tendencies of JA (jasmonic acid) varied among Pe, Ps, and CK at the studied periods. Furthermore, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses of transcriptomic data identified 175 differentially expressed genes (DEGs) related to plant hormone signal transduction, including 63 auxin-related genes, 27 abscisic acid-related genes, 22 ethylene-related genes, 16 cytokinin-related genes, 16 salicylic acid-related genes, 14 brassinosteroid-related genes, 13 jasmonic acid-related genes, and 4 gibberellin-related genes at -2 DAA and 0 DAA. Our results suggest that the fate of a fruit set or degeneration occurred before anthesis in tomato. Auxins, whose levels were independent of pollination and fertilization, play prominent roles in controlling a fruit set in "R35-P," and other hormones are integrated in a synergistic or antagonistic way.
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Affiliation(s)
- Shaoli Zhang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Xin Gu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jingcheng Shao
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Zhifeng Hu
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Wencai Yang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Liping Wang
- Agricultural and Rural Bureau of Shouguang, Shouguang, China
| | - Hongyan Su
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
| | - Luying Zhu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
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10
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Gupta SK, Barg R, Arazi T. Tomato agamous-like6 parthenocarpy is facilitated by ovule integument reprogramming involving the growth regulator KLUH. PLANT PHYSIOLOGY 2021; 185:969-984. [PMID: 33793903 PMCID: PMC8133625 DOI: 10.1093/plphys/kiaa078] [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: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 05/07/2023]
Abstract
Fruit set is established during and soon after fertilization of the ovules inside the quiescent ovary, but the signaling pathways involved remain obscure. The tomato (Solanum lycopersicum) CRISPR loss-of-function mutant of the transcription factor gene AGAMOUS-like6 (SlAGL6; slagl6CR-sg1) is capable of fertilization-independent setting of normal, yet seedless (parthenocarpic), fruit. To gain insight into the mechanism of fleshy fruit set, in this study, we investigated how slagl6CR-sg1 uncouples fruit set from fertilization. We found that mutant ovules were enlarged due to integument over-proliferation and failed to differentiate an endothelium, the integument's innermost layer, upon maturation. A causal relationship between slagl6 loss-of-function and these abnormal phenotypes is inferred from the observation that SlAGL6 is predominantly expressed in the immature ovule integument, and upon ovule maturation, its expression shifts to the endothelium. The transcriptome of unfertilized mutant ovules profoundly differs from that of wild-type and exhibits substantial overlap with the transcriptomes of fertilized ovules sporophytic tissues. One prominent upregulated gene was the fertilization-induced cytochrome P450 cell proliferation regulator SlKLUH. Indeed, ectopic overexpression of SlKLUH stimulated both integument growth in unfertilized ovules and parthenocarpy, suggesting that its suppression by SlAGL6 is paramount for preventing fertilization-independent fruit set. Taken together, our study informs on the transcriptional programs that are regulated by SlAGL6 and demonstrates that it acts from within the ovule integument to inhibit ovary growth beyond anthesis. That by suppressing components of the fertilization-induced ovule reprogramming underlying fruit set.
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Affiliation(s)
- Suresh Kumar Gupta
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Rivka Barg
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Tzahi Arazi
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
- Author for communication:
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11
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How Hormones and MADS-Box Transcription Factors Are Involved in Controlling Fruit Set and Parthenocarpy in Tomato. Genes (Basel) 2020; 11:genes11121441. [PMID: 33265980 PMCID: PMC7760363 DOI: 10.3390/genes11121441] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 02/03/2023] Open
Abstract
Fruit set is the earliest phase of fruit growth and represents the onset of ovary growth after successful fertilization. In parthenocarpy, fruit formation is less affected by environmental factors because it occurs in the absence of pollination and fertilization, making parthenocarpy a highly desired agronomic trait. Elucidating the genetic program controlling parthenocarpy, and more generally fruit set, may have important implications in agriculture, considering the need for crops to be adaptable to climate changes. Several phytohormones play an important role in the transition from flower to fruit. Further complexity emerges from functional analysis of floral homeotic genes. Some homeotic MADS-box genes are implicated in fruit growth and development, displaying an expression pattern commonly observed for ovary growth repressors. Here, we provide an overview of recent discoveries on the molecular regulatory gene network underlying fruit set in tomato, the model organism for fleshy fruit development due to the many genetic and genomic resources available. We describe how the genetic modification of components of this network can cause parthenocarpy, discussing the contribution of hormonal signals and MADS-box transcription factors.
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12
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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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13
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Takei H, Shinozaki Y, Yano R, Kashojiya S, Hernould M, Chevalier C, Ezura H, Ariizumi T. Loss-of-Function of a Tomato Receptor-Like Kinase Impairs Male Fertility and Induces Parthenocarpic Fruit Set. FRONTIERS IN PLANT SCIENCE 2019; 10:403. [PMID: 31040856 PMCID: PMC6477066 DOI: 10.3389/fpls.2019.00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/18/2019] [Indexed: 05/12/2023]
Abstract
Parthenocarpy arises when an ovary develops into fruit without pollination/fertilization. The mechanisms involved in genetic parthenocarpy have attracted attention because of their potential application in plant breeding and also for their elucidation of the mechanisms involved in early fruit development. We have isolated and characterized a novel small parthenocarpic fruit and flower (spff) mutant in the tomato (Solanum lycopersicum) cultivar Micro-Tom. This plant showed both vegetative and reproductive phenotypes including dwarfism of floral organs, male sterility, delayed flowering, altered axillary shoot development, and parthenocarpic production of small fruits. Genome-wide single nucleotide polymorphism array analysis coupled with mapping-by-sequencing using next generation sequencing-based high-throughput approaches resulted in the identification of a candidate locus responsible for the spff mutant phenotype. Subsequent linkage analysis and RNA interference-based silencing indicated that these phenotypes were caused by a loss-of-function mutation of a single gene (Solyc04g077010), which encodes a receptor-like protein kinase that was expressed in vascular bundles in young buds. Cytological and transcriptomic analyses suggested that parthenocarpy in the spff mutant was associated with enlarged ovarian cells and with elevated expression of the gibberellin metabolism gene, GA20ox1. Taken together, our results suggest a role for Solyc04g077010 in male organ development and indicate that loss of this receptor-like protein kinase activity could result in parthenocarpy.
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Affiliation(s)
- Hitomi Takei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Japan Society for the Promotion of Science (JSPS), Kôjimachi, Japan
| | - Yoshihito Shinozaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Japan Society for the Promotion of Science (JSPS), Kôjimachi, Japan
| | - Ryoichi Yano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sachiko Kashojiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Michel Hernould
- UMR1332 BFP, Institut National de la Recherche Agronomique (INRA), Villenave-d’Ornon, France
- UMR1332 BFP, University of Bordeaux, Bordeaux, France
| | - Christian Chevalier
- UMR1332 BFP, Institut National de la Recherche Agronomique (INRA), Villenave-d’Ornon, France
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Tohru Ariizumi,
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