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Dong Y, Huang L, Liu J, Nong H, Li H, Zhang W, Zheng H, Tao J. Genome-wide identified VvOFP genes family and VvOFP4 functional characterization provide insight into fruit shape in grape. Int J Biol Macromol 2024; 276:133880. [PMID: 39025176 DOI: 10.1016/j.ijbiomac.2024.133880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Ovate Family Proteins (OFPs) are emerging as novel transcriptional regulators of fruit shape. Despite their established role in various species, their involvement in regulating grape fruit shape remains understudied. This study encompassed a comprehensive evaluation of 16 grape OFP genes in total at the whole genome level. Phylogenetic and synteny analyses established a close relationship between grape VvOFP genes and their tomato counterparts. Expression profiling post-treatment with gibberellic acid (GA3) and thidiazuron (TDZ) revealed that certain OFP genes responded to these regulators, with VvOFP4 showing peak expression three days post-anthesis. Functional assays via overexpression of VvOFP4 in tobacco and tomato altered the morphology of both vegetative and reproductive organs, including leaves, stamens, and fruits/pods. Paraffin sections of transgenic tobacco stems and tomato fruits demonstrated that VvOFP4 overexpression modifies cell dimensions, leading to changes in organ morphology. Additionally, treatments with GA3 and TDZ similarly influenced the shape of grape pulp cells and thereby the overall fruit morphology. These findings suggest that the VvOFP4 gene plays a crucial role in fruit shape determination by modulating cell shape and presents a potential target for future grape breeding programs aimed at diversifying fruit shapes.
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Affiliation(s)
- Yang Dong
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liyuan Huang
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Liu
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huilan Nong
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haoran Li
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Zhang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China
| | - Huan Zheng
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Tao
- Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China.
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2
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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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3
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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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4
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Baranov D, Dolgov S, Timerbaev V. New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:359. [PMID: 38337892 PMCID: PMC10856997 DOI: 10.3390/plants13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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5
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Katuuramu DN, Levi A, Wechter WP. Genome-wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon. THE PLANT GENOME 2023; 16:e20391. [PMID: 37718629 DOI: 10.1002/tpg2.20391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Fruit quality traits are crucial determinants of consumers' willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via whole-genome resequencing. A total of 2,126,759 genome-wide SNP markers were used to uncover marker-trait associations using single and multi-locus GWAS models. High broad-sense heritability for fruit quality traits was detected. Correlation analysis among traits revealed positive relationships, with the exception of fruit diameter and fruit shape index (ratio of fruit length to fruit diameter), which was negative. A total of 37 significant SNP markers associated with soluble solids content, flesh color, fruit length, fruit diameter, and fruit shape index traits were uncovered. These peak SNPs accounted for 2.1%-23.4% of the phenotypic variation explained showing the quantitative inheritance nature of the evaluated traits. Candidate genes relevant to fruit quality traits were uncovered on chromosomes Ca01, Ca03, Ca06, and Ca07. These significant molecular markers and candidate genes will be useful in marker-assisted breeding of fruit quality traits in watermelon.
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Affiliation(s)
| | - Amnon Levi
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - William P Wechter
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
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6
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Liu Z, Liang T, Kang C. Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities. PLANT PHYSIOLOGY 2023; 193:900-914. [PMID: 37399254 DOI: 10.1093/plphys/kiad376] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Tong Liang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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7
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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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8
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Riekötter J, Oklestkova J, Muth J, Twyman RM, Epping J. Transcriptomic analysis of Chinese yam ( Dioscorea polystachya Turcz.) variants indicates brassinosteroid involvement in tuber development. Front Nutr 2023; 10:1112793. [PMID: 37215221 PMCID: PMC10196131 DOI: 10.3389/fnut.2023.1112793] [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: 11/30/2022] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Dioscorea is an important but underutilized genus of flowering plants that grows predominantly in tropical and subtropical regions. Several species, known as yam, develop large underground tubers and aerial bulbils that are used as food. The Chinese yam (D. polystachya Turcz.) is one of the few Dioscorea species that grows well in temperate regions and has been proposed as a climate-resilient crop to enhance food security in Europe. However, the fragile, club-like tubers are unsuitable for mechanical harvesting, which is facilitated by shorter and thicker storage organs. Brassinosteroids (BRs) play a key role in plant cell division, cell elongation and proliferation, as well as in the gravitropic response. We collected RNA-Seq data from the head, middle and tip of two tuber shape variants: F60 (long, thin) and F2000 (short, thick). Comparative transcriptome analysis of F60 vs. F2000 revealed 30,229 differentially expressed genes (DEGs), 1,393 of which were differentially expressed in the growing tip. Several DEGs are involved in steroid/BR biosynthesis or signaling, or may be regulated by BRs. The quantification of endogenous BRs revealed higher levels of castasterone (CS), 28-norCS, 28-homoCS and brassinolide in F2000 compared to F60 tubers. The highest BR levels were detected in the growing tip, and CS was the most abundant (439.6 ± 196.41 pmol/g in F2000 and 365.6 ± 112.78 pmol/g in F60). Exogenous 24-epi-brassinolide (epi-BL) treatment (20 nM) in an aeroponic system significantly increased the width-to-length ratio (0.045 ± 0.002) compared to the mock-treated plants (0.03 ± 0.002) after 7 weeks, indicating that exogenous epi-BL produces shorter and thicker tubers. In this study we demonstrate the role of BRs in D. polystachya tuber shape, providing insight into the role of plant hormones in yam storage organ development. We found that BRs can influence tuber shape in Chinese yam by regulating the expression of genes involved cell expansion. Our data can help to improve the efficiency of Chinese yam cultivation, which could provide an alternative food source and thus contribute to future food security in Europe.
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Affiliation(s)
- Jenny Riekötter
- Department of Biology, Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Jana Oklestkova
- Laboratory of Growth Regulators, The Czech Academy of Science, Institute of Experimental Botany and Palacký University, Faculty of Science, Olomouc, Czechia
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | | | - Janina Epping
- Department of Biology, Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
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9
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Hsiao AS, Huang JY. Microtubule Regulation in Plants: From Morphological Development to Stress Adaptation. Biomolecules 2023; 13:biom13040627. [PMID: 37189374 DOI: 10.3390/biom13040627] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/09/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
Microtubules (MTs) are essential elements of the eukaryotic cytoskeleton and are critical for various cell functions. During cell division, plant MTs form highly ordered structures, and cortical MTs guide the cell wall cellulose patterns and thus control cell size and shape. Both are important for morphological development and for adjusting plant growth and plasticity under environmental challenges for stress adaptation. Various MT regulators control the dynamics and organization of MTs in diverse cellular processes and response to developmental and environmental cues. This article summarizes the recent progress in plant MT studies from morphological development to stress responses, discusses the latest techniques applied, and encourages more research into plant MT regulation.
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10
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Uyehara AN, Rasmussen CG. Redundant mechanisms in division plane positioning. Eur J Cell Biol 2023; 102:151308. [PMID: 36921356 DOI: 10.1016/j.ejcb.2023.151308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/05/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
Redundancies in plant cell division contribute to the maintenance of proper division plane orientation. Here we highlight three types of redundancy: 1) Temporal redundancy, or correction of earlier defects that results in proper final positioning, 2) Genetic redundancy, or functional compensation by homologous genes, and 3) Synthetic redundancy, or redundancy within or between pathways that contribute to proper division plane orientation. Understanding the types of redundant mechanisms involved provides insight into current models of division plane orientation and opens up new avenues for exploration.
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Affiliation(s)
- Aimee N Uyehara
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, USA
| | - Carolyn G Rasmussen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, USA.
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11
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Zhang B, Li Q, Keyhaninejad N, Taitano N, Sapkota M, Snouffer A, van der Knaap E. A combinatorial TRM-OFP module bilaterally fine-tunes tomato fruit shape. THE NEW PHYTOLOGIST 2023; 238:2393-2409. [PMID: 36866711 DOI: 10.1111/nph.18855] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/18/2023] [Indexed: 05/16/2023]
Abstract
The mechanisms that regulate the vast diversity of plant organ shapes such as the fruit remain to be fully elucidated. TONNEAU1 Recruiting Motif proteins (TRMs) have been implicated in the control of organ shapes in a number of plant species, including tomato. However, the role of many of them is unknown. TRMs interact with Ovate Family Proteins (OFPs) via the M8 domain. However, the in planta function of the TRM-OFP interaction in regulating shape is unknown. We used CRISPR/Cas9 to generate knockout mutants in TRM proteins from different subclades and in-frame mutants within the M8 domain to investigate their roles in organ shape and interactions with OFPs. Our findings indicate that TRMs impact organ shape along both the mediolateral and proximo-distal axes of growth. Mutations in Sltrm3/4 and Sltrm5 act additively to rescue the elongated fruit phenotype of ovate/Slofp20 (o/s) to a round shape. Contrary, mutations in Sltrm19 and Sltrm17/20a result in fruit elongation and further enhance the obovoid phenotype in the o/s mutant. This study supports a combinatorial role of the TRM-OFP regulon where OFPs and TRMs expressed throughout development have both redundant and opposing roles in regulating organ shape.
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Affiliation(s)
- Biyao Zhang
- National Genomics Data Center, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qiang Li
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Neda Keyhaninejad
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
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12
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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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13
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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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14
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Machado SR, de Deus Bento KB, Canaveze Y, Rodrigues TM. Peltate trichomes in the dormant shoot apex of Metrodorea nigra, a Rutaceae species with rhythmic growth. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:161-175. [PMID: 36278887 DOI: 10.1111/plb.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
In Metrodorea nigra, a Rutaceae species with rhythmic growth, the shoot apex in the dormant stage is enclosed by modified stipules. The young organs are fully covered with peltate secretory trichomes, and these structures remain immersed in a hyaline exudate within a hood-shaped structure. Our study focused on the morpho-functional characterization of the peltate trichomes and cytological events associated with secretion. Shoot apices were collected during both dormant and active stages and processed for anatomical, cytochemical and ultrastructural studies. Trichomes initiate secretion early on, remain active throughout leaf development, but collapse as the leaves expand; at which time secretory cavities start differentiation in the mesophyll and secretion increases as the leaf reaches full expansion. The subcellular apparatus of the trichome head cells is consistent with hydrophilic and lipophilic secretion. Secretion involves two vesicle types: the smaller vesicles are PATAg-positive (periodic acid/thiocarbohydrazide/silver proteinate) for carbohydrates and the larger ones are PATAg-negative. In the first phase of secretory activity, the vesicles containing polysaccharides discharge their contents through exocytosis with the secretion accumulating beneath the cuticle, which detaches from the cell wall. Later, a massive discharge of lipophilic substances (lipids and terpenes/phenols) results in their accumulation between the wall and cuticle. Release of the secretions occurs throughout the cuticular microchannels. Continued protection of the leaves throughout shoot development is ensured by replacement of the collapsed secretory trichomes by oil-secreting cavities. Our findings provide new perspectives for understanding secretion regulation in shoot apices of woody species with rhythmic growth.
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Affiliation(s)
- S R Machado
- Center of Electron Microscopy (CME), Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu City, SP, Brazil
| | - K B de Deus Bento
- Postgraduate Program in Plant Biology Interunits, Paulo State University (UNESP), Botucatu City, SP, Brazil
| | - Y Canaveze
- Department of Botany, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro City, RJ, Brazil
| | - T M Rodrigues
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences - IBB, São Paulo State University - UNESP, Botucatu City, SP, Brazil
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15
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Feng Z, Wu X, Wang J, Wu X, Wang B, Lu Z, Ye Z, Li G, Wang Y. Identification of Bottle Gourd ( Lagenaria siceraria) OVATE Family Genes and Functional Characterization of LsOVATE1. Biomolecules 2022; 13:biom13010085. [PMID: 36671470 PMCID: PMC9855390 DOI: 10.3390/biom13010085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The OVATE gene family is a class of conserved transcription factors that play significant roles in plant growth, development, and abiotic stress, and also affect fruit shape in vegetable crops. Bottle gourd (Lagenaria siceraria), commonly known as calabash or gourd, is an annual climber belonging to the Cucurbitaceae family. Studies on bottle gourd OVATE genes are limited. In this study, we performed genome-wide identification of the OVATE gene family in bottle gourd, and identified a total of 20 OVATE family genes. The identified genes were unevenly distributed across 11 bottle gourd chromosomes. We also analyzed the gene homology, amino acid sequence conservation, and three-dimensional protein structure (via prediction) of the 20 OVATE family genes. We used RNA-seq data to perform expression analysis, which found 20 OVATE family genes to be differentially expressed based on spatial and temporal characteristics, suggesting that they have varying functions in the growth and development of bottle gourd. In situ hybridization and subcellular localization analysis showed that the expression characteristics of the LsOVATE1 gene, located on chromosome 7 homologous to OVATE, is a candidate gene for affecting the fruit shape of bottle gourd. In addition, RT-qPCR data from bottle gourd roots, stems, leaves, and flowers showed different spatial expression of the LsOVATE1 gene. The ectopic expression of LsOVATE1 in tomato generated a phenotype with a distinct fruit shape and development. Transgenic-positive plants that overexpressed LsOVATE1 had cone-shaped fruit, calyx hypertrophy, petal degeneration, and petal retention after flowering. Our results indicate that LsOVATE1 could serve important roles in bottle gourd development and fruit shape determination, and provide a basis for future research into the function of LsOVATE1.
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Affiliation(s)
- Zishan Feng
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Zihong Ye
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- Correspondence: ; Tel.: +86-0571-8640-3050
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16
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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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17
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Dou J, Duan S, Umer MJ, Xie K, Wang Y, Kang Q, Yang S, Yang L, Liu D, Liu L, Zhao F. Genome-wide analysis of IQD proteins and ectopic expression of watermelon ClIQD24 in tomato suggests its important role in regulating fruit shape. Front Genet 2022; 13:993218. [PMID: 36186419 PMCID: PMC9515400 DOI: 10.3389/fgene.2022.993218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
The plant-specific IQ67 domain (IQD) is the largest class of calmodulin targets found in plants, and plays an important role in many biological processes, especially fruit development processes. However, the functional role of IQD proteins in the development of watermelon (Citrullus lanatus) shape remains unknown, as the IQD protein family in watermelon has not been systematically characterized. Herein, we elucidated the gene structures, chromosomal locations, evolutionary divergence, and functions of 35 IQD genes in the watermelon genome. The transcript profiles and quantitative real-time PCR analysis at different stages of fruit development showed that the ClIQD24 gene was highly expressed on 0 days after pollination. Furthermore, we found that the ectopic overexpression of ClIQD24 promoted tomato fruit elongation, thereby revealing the significance of ClIQD24 in the progression of watermelon shape. Our study will serve as a reference for further investigations on the molecular mechanisms underlying watermelon fruit shape formation.
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Affiliation(s)
- Junling Dou
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Shixiang Duan
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kuixi Xie
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yinping Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Qishuai Kang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
| | - Fengli Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
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18
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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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19
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Wu Q, Sun J, Fu J, Yu H, Wang X, Wang S, Adhikari PB, Deng X, Xu Q. Genome-wide identification of ovate family in Citrus and functional characterization of CitOFP19. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111328. [PMID: 35696928 DOI: 10.1016/j.plantsci.2022.111328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/14/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Fruit shape is an important trait for fruit appearance and commercial value. Diversity of fruit-shape has been utilized in the breeding of pummelo (Citrus maxima), a basic species in Citrus. However, little is known about genetic basis of fruit shape in citrus. In this study, we identified 16 OVATE family protein (OFP) genes in the pummelo genome. Phylogenetically, they were classified into three subfamilies, which was consistent with the classification of their Arabidopsis orthologs. Synteny analysis suggested that segment and tandem duplications were responsible for their expansion in pummelo. Expression pattern analysis of Citrus OFPs (CitOFPs) showed that CitOFP19 had significantly higher expression level in the ovaries of round pummelo than in those of pear-shaped pummelo. Heterologous overexpression of CitOFP19 in tomato resulted in pear-shaped ovary and fruit shape. Taken together, this study characterized OVATE gene family in Citrus genome and assessed the function of CitOFP19.
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Affiliation(s)
- Qingjiang Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Institute of Horticultural Sciences, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Juan Sun
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jialing Fu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Huiwen Yu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Landscape Plants with Fujian and Taiwan Characteristics of Fujian Colleges and Universities, Minnan Normal University, Zhangzhou 363000, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaohua Wang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China
| | - Prakash Babu Adhikari
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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20
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Boualem A, Berthet S, Devani RS, Camps C, Fleurier S, Morin H, Troadec C, Giovinazzo N, Sari N, Dogimont C, Bendahmane A. Ethylene plays a dual role in sex determination and fruit shape in cucurbits. Curr Biol 2022; 32:2390-2401.e4. [PMID: 35525245 DOI: 10.1016/j.cub.2022.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
Abstract
Shapes of vegetables and fruits are the result of adaptive evolution and human selection. Modules controlling organ shape have been identified. However, little is known about signals coordinating organ development and shape. Here, we describe the characterization of a melon mutation rf1, leading to round fruit. Histological analysis of rf1 flower and fruits revealed fruit shape is determined at flower stage 8, after sex determination and before flower fertilization. Using positional cloning, we identified the causal gene as the monoecy sex determination gene CmACS7, and survey of melon germplasms showed strong association between fruit shape and sexual types. We show that CmACS7-mediated ethylene production in carpel primordia enhances cell expansion and represses cell division, leading to elongated fruit. Cell size is known to rise as a result of endoreduplication. At stage 8 and anthesis, we found no variation in ploidy levels between female and hermaphrodite flowers, ruling out endoreduplication as a factor in fruit shape determination. To pinpoint the gene networks controlling elongated versus round fruit phenotype, we analyzed the transcriptomes of laser capture microdissected carpels of wild-type and rf1 mutant. These high-resolution spatiotemporal gene expression dynamics revealed the implication of two regulatory modules. The first module implicates E2F-DP transcription factors, controlling cell elongation versus cell division. The second module implicates OVATE- and TRM5-related proteins, controlling cell division patterns. Our finding highlights the dual role of ethylene in the inhibition of the stamina development and the elongation of ovary and fruit in cucurbits.
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Affiliation(s)
- Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Serge Berthet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ravi Sureshbhai Devani
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Celine Camps
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Sebastien Fleurier
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Halima Morin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Nathalie Giovinazzo
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Nebahat Sari
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Catherine Dogimont
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France.
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21
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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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22
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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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23
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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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24
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Biswas S, Barma S. A Large-Scale Fully Annotated Low-Cost Cost Microscopy Image Dataset for Deep Learning Framework. IEEE Trans Nanobioscience 2021; 20:507-515. [PMID: 34228624 DOI: 10.1109/tnb.2021.3095151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This work presents a large-scale three-fold annotated, low-cost microscopy image dataset of potato tubers for plant cell analysis in deep learning (DL) framework which has huge potential in the advancement of plant cell biology research. Indeed, low-cost microscopes coupled with new generation smartphones could open new aspects in DL-based microscopy image analysis, which offers several benefits including portability, easy to use, and maintenance. However, its successful implications demand properly annotated large number of diverse microscopy images, which has not been addressed properly- that confines the advanced image processing based plant cell research. Therefore, in this work, a low-cost microscopy image database of potato tuber cells having total 34,657 number of images, has been generated by Foldscope (costs around 1 USD) coupled with a smartphone. This dataset includes 13,369 unstained and 21,288 stained (safranin-o, toluidine blue-o, and lugol's iodine) images with three-fold annotation based on weight, section areas, and tissue zones of the tubers. The physical image quality (e.g., contrast, focus, geometrical attributes, etc.) and its applicability in the DL framework (CNN-based multi-class and multi-label classification) have been examined and results are compared with the traditional microscope image set. The results show that the dataset is highly compatible for the DL framework.
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25
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Wang L, Liu Y, Liu C, Ge C, Xu F, Luo M. Ectopic expression of GhIQD14 (cotton IQ67 domain-containing protein 14) causes twisted organ and modulates secondary wall formation in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:276-284. [PMID: 33872832 DOI: 10.1016/j.plaphy.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/02/2021] [Indexed: 05/26/2023]
Abstract
In plants, although KNOX genes are known to regulate secondary cell wall (SCW) formation, their protein-regulating mechanisms remain largely unknown. Here, we showed that GhKNL1, which regulates SCW formation and fiber development in cotton, could interact with an IQ67 domain containing protein (GhIQD14) in yeast. Confocal observation showed that GhIQD14 was localized to the microtubules. In Arabidopsis, ectopic expression of GhIQD14 caused hypocotyls to be sensitive to microtubule depolymerization agent, organ twisting of seedlings, trichomes, rosette leaves, and capsules, as well as severely irregular xylem vessels and thicker interfascicular fiber cell walls in the inflorescence stem. Furthermore, we found that GhIQD14 interacted with AtKNAT7 in vivo, and instantaneous co-expression of GhIQD14 and AtKNAT7 in tobacco showed that GhIQD14 weakened the distribution of AtKNAT7 in the nucleus, bringing it into the microtubules, thus affecting the SCW formation related genes expression. Our results suggested that GhIQD14 might be involved in the morphological development and SCW formation in cotton.
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Affiliation(s)
- Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yujie Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chen Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fan Xu
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China
| | - Ming Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China.
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26
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Li Y, Huang Y, Wen Y, Wang D, Liu H, Li Y, Zhao J, An L, Yu F, Liu X. The domain of unknown function 4005 (DUF4005) in an Arabidopsis IQD protein functions in microtubule binding. J Biol Chem 2021; 297:100849. [PMID: 34058197 PMCID: PMC8246641 DOI: 10.1016/j.jbc.2021.100849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
The dynamic responses of microtubules (MTs) to internal and external signals are modulated by a plethora of microtubule-associated proteins (MAPs). In higher plants, many plant-specific MAPs have emerged during evolution as advantageous to their sessile lifestyle. Some members of the IQ67 domain (IQD) protein family have been shown to be plant-specific MAPs. However, the mechanisms of interaction between IQD proteins and MTs remain elusive. Here we demonstrate that the domain of unknown function 4005 (DUF4005) of the Arabidopsis IQD family protein ABS6/AtIQD16 is a novel MT-binding domain. Cosedimentation assays showed that the DUF4005 domain binds directly to MTs in vitro. GFP-labeled DUF4005 also decorates all types of MT arrays tested in vivo. Furthermore, we showed that a conserved stretch of 15 amino acid residues within the DUF4005 domain, which shares sequence similarity with the C-terminal MT-binding domain of human MAP Kif18A, is required for the binding to MTs. Transgenic lines overexpressing the DUF4005 domain displayed a spectrum of developmental defects, including spiral growth and stunted growth at the organismal level. At the cellular level, DUF4005 overexpression caused defects in epidermal pavement cell and trichome morphogenesis, as well as abnormal anisotropic cell elongation in the hypocotyls of dark-grown seedlings. These data establish that the DUF4005 domain of ABS6/AtIQD16 is a new MT-binding domain, overexpression of which perturbs MT homeostasis in plants. Our findings provide new insights into the MT-binding mechanisms of plant IQD proteins.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yujia Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yunze Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Dan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Haofeng Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yuanfeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
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27
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Guo C, Zhou J, Li D. New Insights Into Functions of IQ67-Domain Proteins. FRONTIERS IN PLANT SCIENCE 2021; 11:614851. [PMID: 33679817 PMCID: PMC7930834 DOI: 10.3389/fpls.2020.614851] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/21/2020] [Indexed: 05/31/2023]
Abstract
IQ67-domain (IQD) proteins, first identified in Arabidopsis and rice, are plant-specific calmodulin-binding proteins containing highly conserved motifs. They play a critical role in plant defenses, organ development and shape, and drought tolerance. Driven by comprehensive genome identification and analysis efforts, IQDs have now been characterized in several species and have been shown to act as microtubule-associated proteins, participating in microtubule-related signaling pathways. However, the precise molecular mechanisms underpinning their biological functions remain incompletely understood. Here we review current knowledge on how IQD family members are thought to regulate plant growth and development by affecting microtubule dynamics or participating in microtubule-related signaling pathways in different plant species and propose some new insights.
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Affiliation(s)
- Chunyue Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
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28
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Oren E, Tzuri G, Dafna A, Meir A, Kumar R, Katzir N, Elkind Y, Freilich S, Schaffer AA, Tadmor Y, Burger J, Gur A. High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1927-1945. [PMID: 32100072 DOI: 10.1007/s00122-020-03567-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/17/2020] [Indexed: 05/06/2023]
Abstract
Melon is an important crop that exhibits broad variation for fruit morphology traits that are the substrate for genetic mapping efforts. In the post-genomic era, the link between genetic maps and physical genome assemblies is key for leveraging QTL mapping results for gene cloning and breeding purposes. Here, using a population of 164 melon recombinant inbred lines (RILs) that were subjected to genotyping-by-sequencing, we constructed and compared high-density sequence- and linkage-based recombination maps that were aligned to the reference melon genome. These analyses reveal the genome-wide variation in recombination frequency and highlight regions of disrupted collinearity between our population and the reference genome. The population was phenotyped over 3 years for fruit size and shape as well as rind netting. Four QTLs were detected for fruit size, and they act in an additive manner, while significant epistatic interaction was found between two neutral loci for this trait. Fruit shape displayed transgressive segregation that was explained by the action of four QTLs, contributed by alleles from both parents. The complexity of rind netting was demonstrated on a collection of 177 diverse accessions. Further dissection of netting in our RILs population, which is derived from a cross of smooth and densely netted parents, confirmed the intricacy of this trait and the involvement of major locus and several other interacting QTLs. A major netting QTL on chromosome 2 co-localized with results from two additional populations, paving the way for future study toward identification of a causative gene for this trait.
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Affiliation(s)
- Elad Oren
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Galil Tzuri
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Asaf Dafna
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Ayala Meir
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Ravindra Kumar
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Yonatan Elkind
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7507101, Rishon LeZiyyon, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Amit Gur
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel.
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29
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Liu Z, Haider MS, Khan N, Fang J. Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine ( Vitis vinifera). Genes (Basel) 2020; 11:genes11020235. [PMID: 32102395 PMCID: PMC7073947 DOI: 10.3390/genes11020235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries.
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Affiliation(s)
- Zhongjie Liu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
| | - Nadeem Khan
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
- Correspondence: ; Tel.: +86-02584395217; Fax: +86-02584395217
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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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Buschmann H, Borchers A. Handedness in plant cell expansion: a mutant perspective on helical growth. THE NEW PHYTOLOGIST 2020; 225:53-69. [PMID: 31254400 DOI: 10.1111/nph.16034] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/04/2019] [Indexed: 06/09/2023]
Abstract
Many plant mutants are known that exhibit some degree of helical growth. This 'twisted' phenotype has arisen frequently in mutant screens of model organisms, but it is also found in cultivars of ornamental plants, including trees. The phenomenon, in many cases, is based on defects in cell expansion symmetry. Any complete model which explains the anisotropy of plant cell growth must ultimately explain how helical cell expansion comes into existence - and how it is normally avoided. While the mutations observed in model plants mainly point to the microtubule system, additional affected components involve cell wall functions, auxin transport and more. Evaluation of published data suggests a two-way mechanism underlying the helical growth phenomenon: there is, apparently, a microtubular component that determines handedness, but there is also an influence arising in the cell wall that feeds back into the cytoplasm and affects cellular handedness. This idea is supported by recent reports demonstrating the involvement of the cell wall integrity pathway. In addition, there is mounting evidence that calcium is an important relayer of signals relating to the symmetry of cell expansion. These concepts suggest experimental approaches to untangle the phenomenon of helical cell expansion in plant mutants.
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Affiliation(s)
- Henrik Buschmann
- Botanical Institute, Biology and Chemistry Department, University of Osnabrück, 49076, Osnabrück, Germany
| | - Agnes Borchers
- Botanical Institute, Biology and Chemistry Department, University of Osnabrück, 49076, Osnabrück, Germany
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Vavrdová T, Křenek P, Ovečka M, Šamajová O, Floková P, Illešová P, Šnaurová R, Šamaj J, Komis G. Complementary Superresolution Visualization of Composite Plant Microtubule Organization and Dynamics. FRONTIERS IN PLANT SCIENCE 2020; 11:693. [PMID: 32582243 PMCID: PMC7290007 DOI: 10.3389/fpls.2020.00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 05/04/2023]
Abstract
Microtubule bundling is an essential mechanism underlying the biased organization of interphase and mitotic microtubular systems of eukaryotes in ordered arrays. Microtubule bundle formation can be exemplified in plants, where the formation of parallel microtubule systems in the cell cortex or the spindle midzone is largely owing to the microtubule crosslinking activity of a family of microtubule associated proteins, designated as MAP65s. Among the nine members of this family in Arabidopsis thaliana, MAP65-1 and MAP65-2 are ubiquitous and functionally redundant. Crosslinked microtubules can form high-order arrays, which are difficult to track using widefield or confocal laser scanning microscopy approaches. Here, we followed spatiotemporal patterns of MAP65-2 localization in hypocotyl cells of Arabidopsis stably expressing fluorescent protein fusions of MAP65-2 and tubulin. To circumvent imaging difficulties arising from the density of cortical microtubule bundles, we use different superresolution approaches including Airyscan confocal laser scanning microscopy (ACLSM), structured illumination microscopy (SIM), total internal reflection SIM (TIRF-SIM), and photoactivation localization microscopy (PALM). We provide insights into spatiotemporal relations between microtubules and MAP65-2 crossbridges by combining SIM and ACLSM. We obtain further details on MAP65-2 distribution by single molecule localization microscopy (SMLM) imaging of either mEos3.2-MAP65-2 stochastic photoconversion, or eGFP-MAP65-2 stochastic emission fluctuations under specific illumination conditions. Time-dependent dynamics of MAP65-2 were tracked at variable time resolution using SIM, TIRF-SIM, and ACLSM and post-acquisition kymograph analysis. ACLSM imaging further allowed to track end-wise dynamics of microtubules labeled with TUA6-GFP and to correlate them with concomitant fluctuations of MAP65-2 tagged with tagRFP. All different microscopy modules examined herein are accompanied by restrictions in either the spatial resolution achieved, or in the frame rates of image acquisition. PALM imaging is compromised by speed of acquisition. This limitation was partially compensated by exploiting emission fluctuations of eGFP which allowed much higher photon counts at substantially smaller time series compared to mEos3.2. SIM, TIRF-SIM, and ACLSM were the methods of choice to follow the dynamics of MAP65-2 in bundles of different complexity. Conclusively, the combination of different superresolution methods allowed for inferences on the distribution and dynamics of MAP65-2 within microtubule bundles of living A. thaliana cells.
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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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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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Xanthopoulou A, Montero-Pau J, Mellidou I, Kissoudis C, Blanca J, Picó B, Tsaballa A, Tsaliki E, Dalakouras A, Paris HS, Ganopoulou M, Moysiadis T, Osathanunkul M, Tsaftaris A, Madesis P, Kalivas A, Ganopoulos I. Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits. HORTICULTURE RESEARCH 2019; 6:94. [PMID: 31645952 PMCID: PMC6804688 DOI: 10.1038/s41438-019-0176-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 05/20/2023]
Abstract
Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance.
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Affiliation(s)
- Aliki Xanthopoulou
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki, 54124 Greece
| | - Javier Montero-Pau
- Department of Biochemistry and Molecular Biology, Universitat de València, 46022 Valencia, Spain
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | | | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Eleni Tsaliki
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Athanasios Dalakouras
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Harry S. Paris
- Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishay, Israel
| | - Maria Ganopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and MedicineChiang Mai University, Chiang Mai, Thailand
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
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