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Liu T, Dong Y, Gao S, Zhou Y, Liu D, Wang J, Liu Z, Deng Y, Li F. Identification of CaPCR1, an OFP gene likely involved in pointed versus concave fruit tip regulation in pepper (Capsicum annuum L.) using recombinant inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:161. [PMID: 38874630 DOI: 10.1007/s00122-024-04675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
KEY MESSAGE CaPCR1 (Capana12g002165) was a candidate gene regulating fruit concave/pointed tip shape in pepper. The concave shape of the fruit tip in pepper plants is highly susceptible to drought and low temperature stresses, resulting in the appearance of a pointed tip fruit, which affects its commercial value. However, few studies on the process of fruit tip development and regulatory genes in pepper have been reported. Herein, the developmental process of the ovary before anthesis, especially changes in the shape of the ovary tip, was studied in detail. The results showed that the final fruit tip shape was consistent with the ovary tip shape before anthesis, and a concave tip shape gradually developed. F4 recombinant inbred lines (RILs) were constructed to map the genes regulating fruit tip shape through hybridization of the LRS and SBS pepper inbred lines. CaPCR1 (Capana12g002165), an OFP (OVATE Family Protein) family gene, was located in the candidate region on chr12. Three SNPs were found in the protein coding sequence of CaPCR1 between SBS and LRS, but only one SNP led to amino acid variation. Sequence variations, including base replacements, deletions and insertions, were also detected in the gene promoter region. The relative expression level of the CaPCR1 gene was significantly greater in the concave tip ovary than in the pointed tip ovary. qRT‒PCR analysis revealed that the CaPCR1 gene was expressed mainly in the gynoecium, placenta and green fruit pericarp, which was consistent with its function in ovary and fruit development. Taken together, these results suggested that CaPCR1 is a candidate gene involved in fruit tip shape determination in pepper.
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Affiliation(s)
- Tingting Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Traditional Chinese Medicine College, Bozhou University, Bozhou, 236800, Anhui, China
| | - Yiping Dong
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shenting Gao
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yingjia Zhou
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dan Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jubin Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenya Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
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Vega A, Brainard SH, Goldman IL. Linkage mapping of root shape traits in two carrot populations. G3 (BETHESDA, MD.) 2024; 14:jkae041. [PMID: 38412554 PMCID: PMC10989876 DOI: 10.1093/g3journal/jkae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.
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Affiliation(s)
- Andrey Vega
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Scott H Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irwin L Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Xia W, Chen C, Jin S, Chang H, Ding X, Fan Q, Zhang Z, Hua B, Miao M, Liu J. Multi-Omics Analysis Reveals the Distinct Features of Metabolism Pathways Supporting the Fruit Size and Color Variation of Giant Pumpkin. Int J Mol Sci 2024; 25:3864. [PMID: 38612673 PMCID: PMC11012166 DOI: 10.3390/ijms25073864] [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: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Pumpkin (Cucurbita maxima) is an important vegetable crop of the Cucurbitaceae plant family. The fruits of pumpkin are often used as directly edible food or raw material for a number of processed foods. In nature, mature pumpkin fruits differ in size, shape, and color. The Atlantic Giant (AG) cultivar has the world's largest fruits and is described as the giant pumpkin. AG is well-known for its large and bright-colored fruits with high ornamental and economic value. At present, there are insufficient studies that have focused on the formation factors of the AG cultivar. To address these knowledge gaps, we performed comparative transcriptome, proteome, and metabolome analysis of fruits from the AG cultivar and a pumpkin with relatively small fruit (Hubbard). The results indicate that up-regulation of gene-encoded expansins contributed to fruit cell expansion, and the increased presence of photoassimilates (stachyose and D-glucose) and jasmonic acid (JA) accumulation worked together in terms of the formation of large fruit in the AG cultivar. Notably, perhaps due to the rapid transport of photoassimilates, abundant stachyose that was not converted into glucose in time was detected in giant pumpkin fruits, implying that a unique mode of assimilate unloading is in existence in the AG cultivar. The potential molecular regulatory network of photoassimilate metabolism closely related to pumpkin fruit expansion was also investigated, finding that three MYB transcription factors, namely CmaCh02G015900, CmaCh01G018100, and CmaCh06G011110, may be involved in metabolic regulation. In addition, neoxanthin (a type of carotenoid) exhibited decreased accumulation that was attributed to the down-regulation of carotenoid biosynthesis genes in AG fruits, which may lead to pigmentation differences between the two pumpkin cultivars. Our current work will provide new insights into the potential formation factors of giant pumpkins for further systematic elucidation.
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Affiliation(s)
- Wenhao Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Chen Chen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Siying Jin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Huimin Chang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Xianjun Ding
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Qinyi Fan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Bing Hua
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jiexia Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
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Eun CH, Ko JG, Kim IJ. Characterization of a New Citrus Mutant Induced by Gamma Irradiation with a Unique Fruit Shape, Gwonje-Early, and Determination of Specific Selection Markers Using Allele-Specific PCR. PLANTS (BASEL, SWITZERLAND) 2024; 13:911. [PMID: 38592930 PMCID: PMC10974580 DOI: 10.3390/plants13060911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Gamma-ray irradiation is one of the most widely used mutagens worldwide. We previously conducted mutation breeding using gamma irradiation to develop new Citrus unshiu varieties. Among these mutants, Gwonje-early had an ovate shape, a protrusion of the upper part of the fruit, and a large fruit size compared with wild-type (WT) fruits. We investigated the external/internal morphological characteristics and fruit sugar/acid content of Gwonje-early. Additionally, we investigated genome-wide single-nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variants in Gwonje-early using whole-genome re-sequencing. Functional annotation by Gene Ontology analysis confirmed that InDels were more commonly annotated than SNPs. To identify specific molecular markers for Gwonje-early, allele-specific PCR was performed using homozygous SNPs detected via Gwonje-early genome re-sequencing. The GJ-SNP1 and GJ-SNP4 primer sets were effectively able to distinguish Gwonje-early from the WT and other commercial citrus varieties, demonstrating their use as specific molecular markers for Gwonje-early. These findings also have important implications in terms of intellectual property rights and the variety protection of Gwonje-early. Our results may provide insights into the understanding of morphological traits and the molecular breeding mechanisms of citrus species.
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Affiliation(s)
- Chang-Ho Eun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju-Si 63243, Republic of Korea
| | - Jung-Gwon Ko
- Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-Si 63243, Republic of Korea
| | - In-Jung Kim
- Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-Si 63243, Republic of Korea
- Research Institute for Subtropical Agriculture and Biotechnology, SARI, Jeju National University, Jeju-Si 63243, Republic of Korea
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Li Q, Luo S, Zhang L, Feng Q, Song L, Sapkota M, Xuan S, Wang Y, Zhao J, van der Knaap E, Chen X, Shen S. Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice. HORTICULTURE RESEARCH 2023; 10:uhad108. [PMID: 37577396 PMCID: PMC10419822 DOI: 10.1093/hr/uhad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/12/2023] [Indexed: 08/15/2023]
Abstract
Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference. Thus, modification of fruit shape has become one of the major objectives for crop improvement. However, the underlying mechanisms of fruit shape regulation are poorly understood. In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato, cucumber, and peach as examples. Comparative analyses suggest that the OFP-TRM (OVATE Family Protein - TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species. Interestingly, cucumber homologs of FRUITFULL (FUL1), CRABS CLAW (CRC) and 1-aminocyclopropane-1-carboxylate synthase 2 (ACS2) were found to regulate fruit elongation. We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice, and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones, including brassinosteroids, gibberellic acids, and auxin, and microtubule organization. In addition, functional redundancy and divergence of the members of each of the OFP, TRM, and IQD families are also shown. This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.
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Affiliation(s)
- Qiang Li
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Shuangxia Luo
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Liying Zhang
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Qian Feng
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, Department of Horticulture, University of Georgia, Athens, GA, USA
| | - Lijun Song
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Manoj Sapkota
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, Department of Horticulture, University of Georgia, Athens, GA, USA
| | - Shuxin Xuan
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Yanhua Wang
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Jianjun Zhao
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, Department of Horticulture, University of Georgia, Athens, GA, USA
| | - Xueping Chen
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Shuxing Shen
- College of Horticulture, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Hebei Agricultural University, Baoding, Hebei 071000, China
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Nonaka S, Ito M, Ezura H. Targeted modification of CmACO1 by CRISPR/Cas9 extends the shelf-life of Cucumis melo var. reticulatus melon. Front Genome Ed 2023; 5:1176125. [PMID: 37304010 PMCID: PMC10249633 DOI: 10.3389/fgeed.2023.1176125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
The gaseous plant hormone ethylene is a regulator of fruit shelf-life, one of the essential traits in fruits. Extending fruit shelf-life reduces food loss, thereby expected to contribute to food security. The enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) is the final step of the ethylene production pathway. Its suppression via antisense technology has been demonstrated to extend the shelf-life of melon, apple, and papaya. Genome editing technology is an innovative technique for plant breeding. Because the genome editing technology would not leave the exogenous genes in the final crop products, the crops via genome editing can be considered non-genetically modified yields; compared to conventional breeding, such as mutation breeding, the breeding term would be expected to be relatively short. These points include the advantage of this technique in utilization for commercial applications. We attempted to extend the shelf-life of the Japanese luxury melon (Cucumis melo var. reticulatus, 'Harukei-3') via modification of the ethylene synthesis pathway with the genome editing technology, CRISPR/Cas9 system. The Melonet-DB (https://melonet-db.dna.affrc.go.jp/ap/top) showed that the melon genome had the five CmACOs and the gene CmACO1 predominantly expressed in harvested fruits. From this information, CmACO1 was expected to be a key gene for shelf-life in melons. Based on this information, the CmACO1 was selected as the target of the CRISPR/Cas9 system and introduced the mutation. The final product of this melon did not have any exogenous genes. The mutation was inherited for at least two generations. In the T2 generation, the fruit phenotypes 14 days after harvest were as follows: ethylene production was reduced to one-tenth that of the wild type, pericarp colour remained green, and higher fruit firmness. Early fermentation of the fresh fruit was observed in the wild-type fruit but not in the mutant. These results show that CmACO1 knockout via CRISPR/Cas9 extended the melon's shelf-life. Moreover, our results suggest that genome editing technology would reduce food loss and contribute to food security.
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Affiliation(s)
- Satoko Nonaka
- Tskuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Agricultural Sciences, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Maki Ito
- College of Agro-Biological Resources, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroshi Ezura
- Tskuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Agricultural Sciences, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Xie Y, Liu X, Sun C, Song X, Li X, Cui H, Guo J, Liu L, Ying A, Zhang Z, Zhu X, Yan L, Zhang X. CsTRM5 regulates fruit shape via mediating cell division direction and cell expansion in cucumber. HORTICULTURE RESEARCH 2023; 10:uhad007. [PMID: 36960430 PMCID: PMC10028494 DOI: 10.1093/hr/uhad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Fruit shape and size are important appearance and yield traits in cucumber, but the underlying genes and their regulatory mechanisms remain poorly understood. Here we identified a mutant with spherical fruits from an Ethyl Methane Sulfonate (EMS)-mutagenized library, named the qiu mutant. Compared with the cylindrical fruit shape in 32X (wild type), the fruit shape in qiu was round due to reduced fruit length and increased fruit diameter. MutMap analysis narrowed the candidate gene in the 6.47 MB range on Chr2, harboring the FS2.1 locus reported previously. A single-nucleotide polymorphism (SNP) (11359603) causing a truncated protein of CsaV3_2G013800, the homolog of tomato fruit shape gene SlTRM5, may underlie the fruit shape variation in the qiu mutant. Knockout of CsTRM5 by the CRISPR-Cas9 system confirmed that CsaV3_2G013800/CsTRM5 was the causal gene responsible for qiu. Sectioning analysis showed that the spherical fruit in qiu resulted mainly from increased and reduced cell division along the transverse and longitudinal directions, respectively. Meanwhile, the repressed cell expansion contributed to the decreased fruit length in qiu. Transcriptome profiling showed that the expression levels of cell-wall-related genes and abscisic acid (ABA) pathway genes were significantly upregulated in qiu. Hormone measurements indicated that ABA content was greatly increased in the qiu mutant. Exogenous ABA application reduced fruit elongation by inhibiting cell expansion in cucumber. Taken together, these data suggest that CsTRM5 regulates fruit shape by affecting cell division direction and cell expansion, and that ABA participates in the CsTRM5-mediated cell expansion during fruit elongation in cucumber.
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Affiliation(s)
| | | | | | - Xiaofei Song
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Xiaoli Li
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Haonan Cui
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Jingyu Guo
- State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Liu Liu
- State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Ao Ying
- State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Zeqin Zhang
- State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Xueyun Zhu
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
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Chen J, Pan B, Li Z, Xu Y, Cao X, Jia J, Shen H, Sun L. Fruit shape loci sun, ovate, fs8.1 and their interactions affect seed size and shape in tomato. FRONTIERS IN PLANT SCIENCE 2023; 13:1091639. [PMID: 36714752 PMCID: PMC9879704 DOI: 10.3389/fpls.2022.1091639] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Seed size and shape are not only critical for plant reproduction and dispersal, but also important agronomic traits. Tomato fruit shape loci sun, ovate and fs8.1 regulate the morphology of fruit, flower, leaf and stem, and recently their functions in seed morphogenesis have also been noticed. However, mechanism underlying seed morphology variation has not been systematically investigated yet. Thus, using the near isogenic lines (NILs) harboring one, two or three of the fruit shape loci, histological, physiological and transcriptional bases of seed morphology change have been studied. sun and ovate showed potential abilities in decreasing seed size, whereas, fs8.1 had a potential ability in increasing this parameter. Interactions between two loci and the interaction among three loci all led to significant decrease of seed size. All the loci significantly down-regulated seed shape index (SSI), except for sun/fs8.1 double NIL, which resulted in the reductions in both seed length and width and finally led to a decreased trend of SSI. Histologically, seed morphological changes were mainly attributed to the cell number variations. Transcriptional and physiological analyses discovered that phytohormone-, cytoskeleton- as well as sugar transportation- and degradation-related genes were involved in the regulation of seed morphology by the fruit shape loci.
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Affiliation(s)
- Jie Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Bingqing Pan
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zixiong Li
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Yue Xu
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaomeng Cao
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Jingjing Jia
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Huolin Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Liang Sun
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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Amanullah S, Li S, Osae BA, Yang T, Abbas F, Gao M, Wang X, Liu H, Gao P, Luan F. Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon ( Citrullus lanatus L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1034952. [PMID: 36714694 PMCID: PMC9877429 DOI: 10.3389/fpls.2022.1034952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32-25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
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Affiliation(s)
- Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Benjamin Agyei Osae
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Farhat Abbas
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
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Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean ( Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms). Genes (Basel) 2022; 13:genes13122350. [PMID: 36553617 PMCID: PMC9777823 DOI: 10.3390/genes13122350] [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: 10/05/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/16/2022] Open
Abstract
Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5-10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.
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Zheng Q, Takei-Hoshi R, Okumura H, Ito M, Kawaguchi K, Otagaki S, Matsumoto S, Luo Z, Zhang Q, Shiratake K. Genome editing of SlMYB3R3, a cell cycle transcription factor gene of tomato, induces elongated fruit shape. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7312-7325. [PMID: 36070755 PMCID: PMC9730800 DOI: 10.1093/jxb/erac352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Fruit shape is an important trait that attracts consumers, and the regulation of genes related to cell division is crucial for shaping multicellular organs. In Arabidopsis, MYB3R transcription factors, which harbor three imperfect repeats in the N-terminus, control organ growth by regulating cell division. However, the function of MYB3Rs in tomato remains unknown. Here, we characterized tomato SlMYB3R3, which was preferentially expressed in flowers and placed in a subclade with two Arabidopsis cell cycle suppressors (MYB3R3/5). slmyb3r3 knockout mutants were generated using the CRISPR/Cas9 system. Morphological observation of the slmyb3r3 mutants showed that fruits that were elongated and occasionally peanut-like in shape were formed, which was caused by significantly increased cell numbers in the longitudinal direction. Transcriptome and yeast one-hybrid assay results suggested that SlMYB3R3 acted as a suppressor of cell-cycle-related genes by binding to the mitosis-specific activator (MSA) motifs in their promoters. Taken together, knock out of the suppressor SlMYB3R3 leads to elongated fruit, which results from the altered cell division pattern at the ovary stage, by regulating cell-cycle-related genes in an MSA-dependent manner. Our results suggest that SlMYB3R3 and its orthologs have the potential to change fruit shape as part of the molecular breeding of fruit crops.
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Affiliation(s)
- Qingyou Zheng
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
| | - Rie Takei-Hoshi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hitomi Okumura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Kohei Kawaguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
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12
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Cao Y, Zhang K, Yu H, Chen S, Xu D, Zhao H, Zhang Z, Yang Y, Gu X, Liu X, Wang H, Jing Y, Mei Y, Wang X, Lefebvre V, Zhang W, Jin Y, An D, Wang R, Bosland P, Li X, Paran I, Zhang B, Giuliano G, Wang L, Cheng F. Pepper variome reveals the history and key loci associated with fruit domestication and diversification. MOLECULAR PLANT 2022; 15:1744-1758. [PMID: 36176193 DOI: 10.1016/j.molp.2022.09.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
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Affiliation(s)
- Yacong Cao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kang Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hailong Yu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Shumin Chen
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Donghui Xu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hong Zhao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhenghai Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yinqing Yang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaozhen Gu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xinyan Liu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Haiping Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yaxin Jing
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yajie Mei
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiang Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Véronique Lefebvre
- INRAE, GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, 84140 Montfavet, France
| | - Weili Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Jin
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Dongliang An
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Risheng Wang
- Institute of Vegetables, Academy of Agricultural Sciences of Guangxi, 174 Daxue East Road, Nanning 53007, P. R. China
| | - Paul Bosland
- Department of Plant and Environmental Sciences, NMSU, Las Cruces, NM 88003, USA
| | - Xixiang Li
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ilan Paran
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Baoxi Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Giovanni Giuliano
- Biotechnology and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese, 301-00123 Roma, Italy.
| | - Lihao Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Feng Cheng
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
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Phenotypic Characterization and Fine Mapping of a Major-Effect Fruit Shape QTL FS5.2 in Cucumber, Cucumis sativus L., with Near-Isogenic Line-Derived Segregating Populations. Int J Mol Sci 2022; 23:ijms232113384. [DOI: 10.3390/ijms232113384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Cucumber (Cucumis sativus L.) fruit size/shape (FS) is an important yield and quality trait that is quantitatively inherited. Many quantitative trait loci (QTLs) for fruit size/shape have been identified, but very few have been fine-mapped or cloned. In this study, through marker-assisted foreground and background selections, we developed near-isogenic lines (NILs) for a major-effect fruit size/shape QTL FS5.2 in cucumber. Morphological and microscopic characterization of NILs suggests that the allele of fs5.2 from the semi-wild Xishuangbanna (XIS) cucumber (C. s. var. xishuangbannesis) reduces fruit elongation but promotes radial growth resulting in shorter but wider fruit, which seems to be due to reduced cell length, but increased cellular layers. Consistent with this, the NIL carrying the homozygous XIS allele (fs5.2) had lower auxin/IAA contents in both the ovary and the developing fruit. Fine genetic mapping with NIL-derived segregating populations placed FS5.2 into a 95.5 kb region with 15 predicted genes, and a homolog of the Arabidopsis CRABS CLAW (CsCRC) appeared to be the most possible candidate for FS5.2. Transcriptome profiling of NIL fruits at anthesis identified differentially expressed genes enriched in the auxin biosynthesis and signaling pathways, as well as genes involved in cell cycle, division, and cell wall processes. We conclude that the major-effect QTL FS5.2 controls cucumber fruit size/shape through regulating auxin-mediated cell division and expansion for the lateral and longitudinal fruit growth, respectively. The gibberellic acid (GA) signaling pathway also plays a role in FS5.2-mediated fruit elongation.
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Borah P, Ni F, Ying W, Zhuang H, Chong SL, Hu XG, Yang J, Lin EP, Huang H. Genome-wide identification and characterization of OVATE family proteins in Betula luminifera reveals involvement of BlOFP3 and BlOFP5 genes in leaf development. FRONTIERS IN PLANT SCIENCE 2022; 13:950936. [PMID: 36311104 PMCID: PMC9613114 DOI: 10.3389/fpls.2022.950936] [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: 05/23/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Ovate family proteins (OFP) are plant-specific transcription factors involved in regulating morphologies of the lateral organs, plant growth and development. However, the functional roles of OFP genes in Betula luminifera, an important timber tree species, are not well studied. In this study, we identified 20 BlOFP genes and analyzed their phylogenetic relationship, gene structure, conserved motifs, and cis-elements. Further, expression analysis indicates that BlOFP genes were up-regulated in leaves on the one-year-old branch compared to leaves on the current-year branch and bract, except BlOFP7, BlOFP11, BlOFP14 and BlOFP12. The overexpression of BlOFP3 and BlOFP5 in Arabidopsis thaliana not only resulted in a slower growth rate but also produced sawtooth shape, flatter and darker green rosette leaves. Further investigation showed that the leaf thickness of the transgenic plants was more than double that of the wild type, which was caused by the increasement in the number and size of palisade tissue cells. Furthermore, the expression analysis also indicated that the expressions of several genes related to leaf development were significantly changed in the transgene plants. These results suggested the significant roles of BlOFP3 and BlOFP5 in leaf development. Moreover, protein-protein interaction studies showed that BlOFP3 interacts with BlKNAT5, and BlOFP5 interacts with BlKNAT5, BlBLH6 and BlBLH7. In conclusion, our study demonstrates that BlOFP3 and BlOFP5 were involved in leaf shape and thickness regulation by forming a complex with BlKNAT5, BlBLH6 and BlBLH7. In addition, our study serves as a guide for future functional genomic studies of OFP genes of the B. luminifera.
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Affiliation(s)
- Priyanka Borah
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Fei Ni
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiyang Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Hebi Zhuang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Sun-Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Xian-Ge Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Er-pei Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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15
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Ectopic Expression of CsSUN in Tomato Results in Elongated Fruit Shape via Regulation of Longitudinal Cell Division. Int J Mol Sci 2022; 23:ijms23179973. [PMID: 36077369 PMCID: PMC9456224 DOI: 10.3390/ijms23179973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Fruit shape, an important agronomic trait of cucumber (Cucumis sativus L.), is tightly controlled by a series of genes such as CsSUN, a homologue of SlSUN that is responsible for the tomato (Solanum lycopersicum) fruit shape via the modulation of cell division. However, the direct genetic evidence about the CsSUN-mediated regulation of fruit shape is still scarce, limiting our mechanistic understanding of the biological functions of CsSUN. Here, we introduced CsSUN into the round-fruited tomato inbred line ‘SN1′ (wild type, WT) via the Agrobacterium tumefaciens-mediated method. The high and constitutive expression of CsSUN was revealed by real-time PCR in all the tested tissues of the transgenic plants, especially in the fruits and ovaries. Phenotypic analyses showed that the ectopic expression of CsSUN increased fruit length while it decreased fruit diameter, thus leading to the enhanced fruit shape index in the transgenic tomato lines relative to the WT. Additionally, the reduction in the seed size and seed-setting rate and the stimulation of seed germination were observed in the CsSUN-expressed tomato. A histological survey demonstrated that the elongated fruits were mainly derived from the significant increasing of the longitudinal cell number, which compensated for the negative effects of decreased cell area in the central columellae. These observations are different from action mode of SlSUN, thus shedding new insights into the SUN-mediated regulation of fruit shape.
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16
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Wang L, Liu X, Li Q, Xu N, He C. A lineage-specific arginine in POS1 is required for fruit size control in Physaleae (Solanaceae) via gene co-option. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:183-204. [PMID: 35481627 DOI: 10.1111/tpj.15786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Solanaceae have important economic value mainly due to their edible fruits. Physalis organ size 1/cytokinin response factor 3 (POS1/CRF3), a unique gene in Solanaceae, is involved in fruit size variation in Physalis but not in Solanum. However, the underlying mechanisms remain elusive. Here, we found that POS1/CRF3 was likely created via the fusion of CRF7 and CRF8 duplicates. Multiple genetic manipulations revealed that only POS1 and Capsicum POS1 (CaPOS1) functioned in fruit size control via the positive regulation of cell expansion. Comparative studies in a phylogenetic framework showed the directional enhancement of POS1-like expression in the flowers and fruits of Physaleae and the specific gain of certain interacting proteins associated with cell expansion by POS1 and CaPOS1. A lineage-specific single nucleotide polymorphism (SNP) caused the 68th amino acid histidine in the POS1 orthologs of non-Physaleae (Nicotiana and Solanum) to change to arginine in Physaleae (Physalis and Capsicum). Substituting the arginine in Physaleae POS1-like by histidine completely abolished their function in the fruits and the protein-protein interaction (PPI) with calreticulin-3. Transcriptomic comparison revealed the potential downstream pathways of POS1, including the brassinosteroid biosynthesis pathway. However, POS1-like may have functioned ancestrally in abiotic stress within Solanaceae. Our work demonstrated that heterometric expression and a SNP caused a single amino acid change to establish new PPIs, which contributed to the co-option of POS1 in multiple regulatory pathways to regulate cell expansion and thus fruit size in Physaleae. These results provide new insights into fruit morphological evolution and fruit yield control.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
| | - Xueyang Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Qiaoru Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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17
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Zhao P, Wang F, Deng Y, Zhong F, Tian P, Lin D, Deng J, Zhang Y, Huang T. Sly-miR159 regulates fruit morphology by modulating GA biosynthesis in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:833-845. [PMID: 34882929 PMCID: PMC9055814 DOI: 10.1111/pbi.13762] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/28/2021] [Indexed: 05/29/2023]
Abstract
Fruit morphology is an important agronomical trait of many crops. Here, we identify Sly-miR159 as an important regulator of fruit morphology in tomato, a model species of fleshy-fruit development. We show that Sly-miR159 functions through its target SlGAMYB2 to control fruit growth. Suppression of Sly-miR159 and overexpression of SlGAMYB2 result in larger fruits with a reduced length/width ratio, while loss of function of SlGAMYB2 leads to the formation of smaller and more elongated fruits. Gibberellin (GA) is a major phytohormone that regulates fruit development in tomato. We show the Sly-miR159-SlGAMYB2 pathway controls fruit morphology by modulating GA biosynthesis. In particular, we demonstrate that Sly-miR159 promotes GA biosynthesis largely through the direct repression of the GA biosynthetic gene SlGA3ox2 by SlGAMYB2. Together, our findings reveal the action of Sly-miR159 on GA biosynthesis as a previously unidentified mechanism that controls fruit morphology in tomato. Modulating this pathway may have potential applications in tomato breeding for manipulating fruit growth and facilitating the process of fruit improvement.
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Affiliation(s)
- Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Fengpan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Yinjiao Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Fanjia Zhong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Juhui Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
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18
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Amanullah S, Osae BA, Yang T, Abbas F, Liu S, Liu H, Wang X, Gao P, Luan F. Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers. Mol Biol Rep 2022; 49:5459-5472. [PMID: 35235158 DOI: 10.1007/s11033-022-07263-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding. METHODS AND RESULTS In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively. CONCLUSION In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.
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Affiliation(s)
- Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Benjamin Agyei Osae
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Farhat Abbas
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, People's Republic of China
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China.
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China.
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19
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Liu L, Zheng Y, Feng S, Yu L, Li Y, Zong Y, Chen W, Liao F, Yang L, Guo W. Transcriptomic and Physiological Analysis Reveals the Responses to Auxin and Abscisic Acid Accumulation During Vaccinium corymbosum Flower Bud and Fruit Development. FRONTIERS IN PLANT SCIENCE 2022; 13:818233. [PMID: 35242154 PMCID: PMC8886112 DOI: 10.3389/fpls.2022.818233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Blueberry (Vaccinium corymbosum) is reputed as a rich source of health-promoting phytonutrients, which contributes to its burgeoning consumer demand and production. However, blueberries are much smaller and have lower yields than most domesticated berries, and the inherent regulatory mechanisms remain elusive. In this study, the cytological and physiological changes, as well as comparative transcriptomic analysis throughout flower and fruit development in the southern highbush blueberry cultivar 'O'Neal' were performed. 'O'Neal' hypanthium and fruit exhibited a distinctive cell proliferation pattern, and auxin accumulation was unusual throughout development, while abscisic acid (ABA) levels rapidly increased in association with anthocyanin accumulation, total phenolic reduction and fruit maturation. Transcriptomic data showed that many differentially expressed genes (DEGs) were specifically expressed at each flower bud and fruit developmental stage. Further weighted gene co-expression network analysis (WGCNA) revealed numerous DEGs that correlated with the cell numbers of outer mesocarp and columella, showed two distinctive expression patterns. Most of the DEGs involved in auxin biosynthesis, transportation and signal transduction were upregulated, and this upregulation was accompanied by cell expansion, and flower bud and fruit development. However, individual members of VcSAUR50 and VcIAA9 families might be insensitive to auxin, suggesting that these genes play a distinctive role in the growth and development of blueberry fruits. These results will support future research to better understand the flower and fruit development of southern highbush blueberry.
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Affiliation(s)
- Liangmiao Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Yiqi Zheng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Shiji Feng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Lei Yu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Yongqiang Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Yu Zong
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Wenrong Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Fanglei Liao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Li Yang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Weidong Guo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
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20
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Genetic and Molecular Regulation Mechanisms in the Formation and Development of Vegetable Fruit Shape. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vegetable crops have a long history of cultivation worldwide and rich germplasm resources. With its continuous development and progress, molecular biology technology has been applied to various fields of vegetable crop research. Fruit is an important organ in vegetable crops, and fruit shape can affect the yield and commercialization of vegetables. In nature, fruits show differences in size and shape. Based on fruit shape diversity, the growth direction and coordination mechanism of fruits remain unclear. In this review, we discuss the latest research on fruit shape. In addition, we compare the current theories on the molecular mechanisms that regulate fruit growth, size, and shape in different vegetable families.
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21
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Li C, Dong N, Shen L, Lu M, Zhai J, Zhao Y, Chen L, Wan Z, Liu Z, Ren H, Wu S. Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola. PeerJ 2022; 9:e12558. [PMID: 35036123 PMCID: PMC8740515 DOI: 10.7717/peerj.12558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
Background Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available. Methods In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed. Results Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.
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Affiliation(s)
- Chengru Li
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Na Dong
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Liming Shen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Meng Lu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junwen Zhai
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yamei Zhao
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lei Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhiting Wan
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongjian Liu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hui Ren
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Shasha Wu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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22
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Borovsky Y, Raz A, Doron-Faigenboim A, Zemach H, Karavani E, Paran I. Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20. FRONTIERS IN PLANT SCIENCE 2022; 12:815589. [PMID: 35058962 PMCID: PMC8763684 DOI: 10.3389/fpls.2021.815589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 05/28/2023]
Abstract
Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.
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23
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Xu P, Wang Y, Sun F, Wu R, Du H, Wang Y, Jiang L, Wu X, Wu X, Yang L, Xing N, Hu Y, Wang B, Huang Y, Tao Y, Gao Q, Liang C, Li Y, Lu Z, Li G. Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:956-968. [PMID: 34043857 DOI: 10.1111/tpj.15358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.
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Affiliation(s)
- Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengshuo Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, USA
| | - Huilong Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuhong Wang
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nailin Xing
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Yaowen Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yunping Huang
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Ye Tao
- Biozeron Biotechnology Co., Ltd, Shanghai, China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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Beauchet A, Gévaudant F, Gonzalez N, Chevalier C. In search of the still unknown function of FW2.2/CELL NUMBER REGULATOR, a major regulator of fruit size in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5300-5311. [PMID: 33974684 DOI: 10.1093/jxb/erab207] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
The FW2.2 gene is associated with the major quantitative trait locus (QTL) governing fruit size in tomato, and acts by negatively controlling cell division during fruit development. FW2.2 belongs to a multigene family named the CELL NUMBER REGULATOR (CNR) family. CNR proteins harbour the uncharacterized PLAC8 motif made of two conserved cysteine-rich domains separated by a variable region that are predicted to be transmembrane segments, and indeed FW2.2 localizes to the plasma membrane. Although FW2.2 was cloned more than two decades ago, the molecular mechanisms of action remain unknown. In particular, how FW2.2 functions to regulate cell cycle and fruit growth, and thus fruit size, is as yet not understood. Here we review current knowledge on PLAC8-containing CNR/FWL proteins in plants, which are described to participate in organogenesis and the regulation of organ size, especially in fruits, and in cadmium resistance, ion homeostasis, and/or Ca2+ signalling. Within the plasma membrane FW2.2 and some CNR/FWLs are localized in microdomains, which is supported by recent data from interactomics studies. Hence FW2.2 and CNR/FWL could be involved in a transport function of signalling molecules across membranes, influencing organ growth via a cell to cell trafficking mechanism.
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Affiliation(s)
- Arthur Beauchet
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Frédéric Gévaudant
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
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25
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Barchi L, Rabanus‐Wallace MT, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino GL, Stein N, Lanteri S, Giuliano G. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:579-596. [PMID: 33964091 PMCID: PMC8453987 DOI: 10.1111/tpj.15313] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | | | - Jaime Prohens
- COMAVUniversitat Politècnica de ValènciaCamino de Vera 14Valencia46022Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
| | - Ezio Portis
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
- Department of Crop SciencesCenter for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Sergio Lanteri
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
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Yang L, Liu L, Wang Z, Zong Y, Yu L, Li Y, Liao F, Chen M, Cai K, Guo W. Comparative anatomical and transcriptomic insights into Vaccinium corymbosum flower bud and fruit throughout development. BMC PLANT BIOLOGY 2021; 21:289. [PMID: 34167466 PMCID: PMC8223347 DOI: 10.1186/s12870-021-03067-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/17/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Blueberry (Vaccinium spp.) is characterized by the production of berries that are smaller than most common fruits, and the underlying mechanisms of fruit size in blueberry remain elusive. V. corymbosum 'O'Neal' and 'Bluerain' are commercial southern highbush blueberry cultivars with large- and small-size fruits, respectively, which mature 'O'Neal' fruits are 1 ~ 2-fold heavier than those of 'Bluerain'. In this study, the ontogenetical patterns of 'O'Neal' and 'Bluerain' hypanthia and fruits were compared, and comparative transcriptomic analysis was performed during early fruit development. RESULTS V. corymbosum 'O'Neal' and 'Bluerain' hypanthia and fruits exhibited intricate temporal and spatial cell proliferation and expansion patterns. Cell division before anthesis and cell expansion after fertilization were the major restricting factors, and outer mesocarp was the key tissue affecting fruit size variation among blueberry genotypes. Comparative transcriptomic and annotation analysis of differentially expressed genes revealed that the plant hormone signal transduction pathway was enriched, and that jasmonate-related TIFYs genes might be the key components orchestrating other phytohormones and influencing fruit size during early blueberry fruit development. CONCLUSIONS These results provided detailed ontogenetic evidence for determining blueberry fruit size, and revealed the important roles of phytohormone signal transductions involving in early fruit development. The TIFY genes could be useful as markers for large-size fruit selection in the current breeding programs of blueberry.
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Affiliation(s)
- Li Yang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China.
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China.
| | - Liangmiao Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Zhuoyi Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Yu Zong
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Lei Yu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Yongqaing Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Fanglei Liao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Manman Chen
- Zhejiang College of Security Technology, Wenzhou, Zhejiang, 325000, P. R. China
| | - Kailing Cai
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China
| | - Weidong Guo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China.
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang, 321004, P. R. China.
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Wang Y, Wang J, Guo S, Tian S, Zhang J, Ren Y, Li M, Gong G, Zhang H, Xu Y. CRISPR/Cas9-mediated mutagenesis of ClBG1 decreased seed size and promoted seed germination in watermelon. HORTICULTURE RESEARCH 2021; 8:70. [PMID: 33790265 PMCID: PMC8012358 DOI: 10.1038/s41438-021-00506-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 05/11/2023]
Abstract
Abscisic acid (ABA) is a critical regulator of seed development and germination. β-glucosidases (BGs) have been suggested to be contributors to increased ABA content because they catalyze the hydrolysis of ABA-glucose ester to release free ABA. However, whether BGs are involved in seed development is unclear. In this study, a candidate gene, ClBG1, in watermelon was selected for targeted mutagenesis via the CRISPR/Cas9 system. Seed size and weight were significantly reduced in the Clbg1-mutant watermelon lines, which was mainly attributed to decreased cell number resulting from decreased ABA levels. A transcriptome analysis showed that the expression of 1015 and 1429 unique genes was changed 10 and 18 days after pollination (DAP), respectively. Cytoskeleton- and cell cycle-related genes were enriched in the differentially expressed genes of wild type and Clbg1-mutant lines during seed development. Moreover, the expression of genes in the major signaling pathways of seed size control was also changed. In addition, seed germination was promoted in the Clbg1-mutant lines due to decreased ABA content. These results indicate that ClBG1 may be critical for watermelon seed size regulation and germination mainly through the modulation of ABA content and thereby the transcriptional regulation of cytoskeleton-, cell cycle- and signaling-related genes. Our results lay a foundation for dissecting the molecular mechanisms of controlling watermelon seed size, a key agricultural trait of significant economic importance.
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Affiliation(s)
- Yanping Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Jinfang Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shouwei Tian
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Jie Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Maoying Li
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Guoyi Gong
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Haiying Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
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Li Q, Chakrabarti M, Taitano NK, Okazaki Y, Saito K, Al-Abdallat AM, van der Knaap E. Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1225-1244. [PMID: 33159787 PMCID: PMC7904157 DOI: 10.1093/jxb/eraa518] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/02/2020] [Indexed: 05/21/2023]
Abstract
The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Nathan K Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Department of Horticulture, University of Georgia, Athens, GA, USA
- Correspondence:
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29
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Special Issue on "Fruit Metabolism and Metabolomics". Metabolites 2020; 10:metabo10060230. [PMID: 32503284 PMCID: PMC7344593 DOI: 10.3390/metabo10060230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.
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30
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Snouffer A, Kraus C, van der Knaap E. The shape of things to come: ovate family proteins regulate plant organ shape. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:98-105. [PMID: 31837627 DOI: 10.1016/j.pbi.2019.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 05/14/2023]
Abstract
The shape of produce is an important agronomic trait. The knowledge of the cellular regulation of organ shapes can be implemented in the improvement of a variety of crops. The plant-specific Ovate Family Proteins (OFPs) regulate organ shape in Arabidopsis and many crops including rice, tomato, and melon. Although OFPs were previously described as transcriptional repressors, recent data support a role for the family in organ shape regulation through control of subcellular localization of protein complexes. OFPs interact with TONNEAU1 RECRUITMENT MOTIF (TRMs) and together they regulate cell division patterns in tomato fruit development. OFPs also respond to changes in plant hormones and responses to stress. The OFP-TRM interaction may work in conjunction with additional shape regulators such as IQ67 Domain (IQD) proteins to modulate the response to tissue level cues as well as external stimuli and stressors to form reproducible organ shapes by regulating cytoskeleton activities.
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Affiliation(s)
- Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens GA, 30602 United States
| | - Carmen Kraus
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Rd, Athens GA, 30602 United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens GA, 30602 United States; Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Rd, Athens GA, 30602 United States; Department of Horticulture, University of Georgia, 111 Riverbend Rd, Athens GA, 30602 United States.
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31
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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32
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Maeda H, Akagi T, Onoue N, Kono A, Tao R. Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon. PLANT & CELL PHYSIOLOGY 2019; 60:2464-2477. [PMID: 31350891 PMCID: PMC6839372 DOI: 10.1093/pcp/pcz139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
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Affiliation(s)
- Haruka Maeda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Akagi
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Ryutaro Tao
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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33
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Chu Y, Jang J, Huang Z, van der Knaap E. Tomato locule number and fruit size controlled by natural alleles of lc and fas. PLANT DIRECT 2019; 3:e00142. [PMID: 31312784 PMCID: PMC6607973 DOI: 10.1002/pld3.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/27/2019] [Indexed: 05/22/2023]
Abstract
Improving yield by increasing the size of produce is an important selection criterion during the domestication of fruit and vegetable crops. Genes controlling meristem organization and organ formation work in concert to regulate the size of reproductive organs. In tomato, lc and fas control locule number, which often leads to enlarged fruits compared to the wild progenitors. LC is encoded by the tomato ortholog of WUSCHEL (WUS), whereas FAS is encoded by the tomato ortholog of CLAVATA3 (CLV3). The critical role of the WUS-CLV3 feedback loop in meristem organization has been demonstrated in several plant species. We show that mutant alleles for both loci in tomato led to an expansion of the SlWUS expression domain in young floral buds 2-3 days after initiation. Single and double mutant alleles of lc and fas maintain higher SlWUS expression during the development of the carpel primordia in the floral bud. This augmentation and altered spatial expression of SlWUS provided a mechanistic basis for the formation of multilocular and large fruits. Our results indicated that lc and fas are gain-of-function and partially loss-of-function alleles, respectively, while both mutations positively affect the size of tomato floral meristems. In addition, expression profiling showed that lc and fas affected the expression of several genes in biological processes including those involved in meristem/flower development, patterning, microtubule binding activity, and sterol biosynthesis. Several differentially expressed genes co-expressed with SlWUS have been identified, and they are enriched for functions in meristem regulation. Our results provide new insights into the transcriptional regulation of genes that modulate meristem maintenance and floral organ determinacy in tomato.
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Affiliation(s)
- Yi‐Hsuan Chu
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhio
- Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusOhio
| | - Jyan‐Chyun Jang
- Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusOhio
| | - Zejun Huang
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhio
| | - Esther van der Knaap
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhio
- Institute of Plant Breeding, Genetics and GenomicsUniversity of GeorgiaAthensGeorgia
- Department of HorticultureUniversity of GeorgiaAthensGeorgia
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34
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Wang Y, Clevenger JP, Illa-Berenguer E, Meulia T, van der Knaap E, Sun L. A Comparison of sun, ovate, fs8.1 and Auxin Application on Tomato Fruit Shape and Gene Expression. PLANT & CELL PHYSIOLOGY 2019; 60:1067-1081. [PMID: 30753610 DOI: 10.1093/pcp/pcz024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
Elongated tomato fruit shape is the result of the action of the fruit shape genes possibly in coordination with the phytohormone auxin. To investigate the possible link between auxin and the fruit shape genes, a series of auxin (2,4-D) treatments were performed on the wild-type and the fruit shape near-isogenic lines (NILs) in Solanum pimpinellifolium accession LA1589 background. Morphological and histological analyses indicated that auxin application approximately 3 weeks before anthesis led to elongated pear-shaped ovaries and fruits, which was mainly attributed to the increase of ovary/fruit proximal end caused by the increase of both cell number and cell size. Fruit shape changes caused by SUN, OVATE and fs8.1 were primarily due to the alterations of cell number along different growth axes. Particularly, SUN caused elongation by extending cell number along the entire proximal-distal axis, whereas OVATE caused fruit elongation in the proximal area, which was most similar to the effect of auxin on ovary shape. Expression analysis of flower buds at different stages in fruit shape NILs indicated that SUN had a stronger impact on the transcriptome than OVATE and fs8.1. The sun NIL differentially expressed genes were enriched in several biological processes, such as lipid metabolism, ion transmembrane and actin cytoskeleton organization. Additionally, SUN also shifted the expression of the auxin-related genes, including those involved in auxin biosynthesis, homeostasis, signal transduction and polar transport, indicating that SUN may regulate ovary/fruit shape through modifying the expression of auxin-related genes very early during the formation of the ovary in the developing flower.
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Affiliation(s)
- Yanping Wang
- College of Horticulture, China Agricultural University, Beijing, P.R. China
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P.R. China
| | - Josh P Clevenger
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, Mars Wrigley Confectionery, Athens, GA, USA
| | | | - Tea Meulia
- Department of Plant Pathology, Molecular and Cellular Imaging Center, The Ohio State University/OARDC, Wooster, OH, USA
| | - Esther van der Knaap
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Liang Sun
- College of Horticulture, China Agricultural University, Beijing, P.R. China
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, P.R. China
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Lazzaro MD, Wu S, Snouffer A, Wang Y, van der Knaap E. Plant Organ Shapes Are Regulated by Protein Interactions and Associations With Microtubules. FRONTIERS IN PLANT SCIENCE 2018; 9:1766. [PMID: 30619384 PMCID: PMC6300067 DOI: 10.3389/fpls.2018.01766] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/14/2018] [Indexed: 05/07/2023]
Abstract
Plant organ shape is determined by the spatial-temporal expression of genes that control the direction and rate of cell division and expansion, as well as the mechanical constraints provided by the rigid cell walls and surrounding cells. Despite the importance of organ morphology during the plant life cycle, the interplay of patterning genes with these mechanical constraints and the cytoskeleton is poorly understood. Shapes of harvestable plant organs such as fruits, leaves, seeds and tubers vary dramatically among, and within crop plants. Years of selection have led to the accumulation of mutations in genes regulating organ shapes, allowing us to identify new genetic and molecular components controlling morphology as well as the interactions among the proteins. Using tomato as a model, we discuss the interaction of Ovate Family Proteins (OFPs) with a subset of TONNEAU1-recruiting motif family of proteins (TRMs) as a part of the protein network that appears to be required for interactions with the microtubules leading to coordinated multicellular growth in plants. In addition, SUN and other members of the IQD family also exert their effects on organ shape by interacting with microtubules. In this review, we aim to illuminate the probable mechanistic aspects of organ growth mediated by OFP-TRM and SUN/IQD via their interactions with the cytoskeleton.
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Affiliation(s)
- Mark D. Lazzaro
- Department of Biology, College of Charleston, Charleston, SC, United States
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Yanping Wang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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A common genetic mechanism underlies morphological diversity in fruits and other plant organs. Nat Commun 2018; 9:4734. [PMID: 30413711 PMCID: PMC6226536 DOI: 10.1038/s41467-018-07216-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/18/2018] [Indexed: 11/23/2022] Open
Abstract
Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape. The physical interactions between the members of these two families are necessary for dynamic relocalization of the protein complexes to different cellular compartments when expressed in tobacco leaf cells. Together with data from other domesticated crops and model plant species, the protein interaction studies provide possible mechanistic insights into the regulation of morphological variation in plants and a framework that may apply to organ growth in all plant species. Remarkable organ shape morphological diversity exists in fruits, vegetables and seeds. Here, the authors establish a link between OVATE Family Proteins and TONNEAU1 Recruiting Motif family proteins in the development pathway that governs fruit shape of tomato, melon, and cucumber as well as potato tuber shape.
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