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Marash I, Leibman-Markus M, Gupta R, Israeli A, Teboul N, Avni A, Ori N, Bar M. Abolishing ARF8A activity promotes disease resistance in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112064. [PMID: 38492890 DOI: 10.1016/j.plantsci.2024.112064] [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: 01/07/2024] [Revised: 02/18/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Auxin response factors (ARFs) are a family of transcription factors that regulate auxin-dependent developmental processes. Class A ARFs function as activators of auxin-responsive gene expression in the presence of auxin, while acting as transcriptional repressors in its absence. Despite extensive research on the functions of ARF transcription factors in plant growth and development, the extent, and mechanisms of their involvement in plant resistance, remain unknown. We have previously reported that mutations in the tomato AUXIN RESPONSE FACTOR8 (ARF8) genes SlARF8A and SlARF8B result in the decoupling of fruit development from pollination and fertilization, leading to partial or full parthenocarpy and increased yield under extreme temperatures. Here, we report that fine-tuning of SlARF8 activity results in increased resistance to fungal and bacterial pathogens. This resistance is mostly preserved under fluctuating temperatures. Thus, fine-tuning SlARF8 activity may be a potent strategy for increasing overall growth and yield.
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Affiliation(s)
- Iftah Marash
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel; School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Alon Israeli
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Teboul
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Avni
- School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Naomi Ori
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel.
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2
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Boucher JJ, Ireland HS, Wang R, David KM, Schaffer RJ. The genetic control of herkogamy. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23315. [PMID: 38687848 DOI: 10.1071/fp23315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/14/2024] [Indexed: 05/02/2024]
Abstract
Herkogamy is the spatial separation of anthers and stigmas within complete flowers, and is a key floral trait that promotes outcrossing in many angiosperms. The degree of separation between pollen-producing anthers and receptive stigmas has been shown to influence rates of self-pollination amongst plants, with a reduction in herkogamy increasing rates of successful selfing in self-compatible species. Self-pollination is becoming a critical issue in horticultural crops grown in environments where biotic pollinators are limited, absent, or difficult to utilise. In these cases, poor pollination results in reduced yield and misshapen fruit. Whilst there is a growing body of work elucidating the genetic basis of floral organ development, the genetic and environmental control points regulating herkogamy are poorly understood. A better understanding of the developmental and regulatory pathways involved in establishing varying degrees of herkogamy is needed to provide insights into the production of flowers more adept at selfing to produce consistent, high-quality fruit. This review presents our current understanding of herkogamy from a genetics and hormonal perspective.
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Affiliation(s)
- Jacques-Joseph Boucher
- The New Zealand Institute for Plant and Food Research Ltd, 55 Old Mill Road, Motueka 7198, New Zealand; and School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Hilary S Ireland
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland 1142, New Zealand
| | - Ruiling Wang
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland 1142, New Zealand
| | - Karine M David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Robert J Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, 55 Old Mill Road, Motueka 7198, New Zealand; and School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Luo H, Li T, Guan Y, Zhang Z, Zhang Z, Zhang Z, Li H. FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1130-1147. [PMID: 37967025 DOI: 10.1111/tpj.16544] [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: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.
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Affiliation(s)
- He Luo
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tianyu Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuhan Guan
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhuo Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zihui Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
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Hua B, Wu J, Han X, Bian X, Xu Z, Sun C, Wang R, Zhang W, Liang F, Zhang H, Li S, Li Z, Wu S. Auxin homeostasis is maintained by sly-miR167-SlARF8A/B-SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits. THE NEW PHYTOLOGIST 2024; 241:1177-1192. [PMID: 37985404 DOI: 10.1111/nph.19391] [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: 11/28/2022] [Accepted: 10/20/2023] [Indexed: 11/22/2023]
Abstract
The locular gel, produced by the placenta, is important for fruit flavor and seed development in tomato. However, the mechanism underlying locule and placenta development is not fully understood yet. Here, we show that two SlARF transcription factors, SlARF8B and SlARF8A (SlARF8A/B), promote the development of locular and placenta tissues. The expression of both SlARF8A and SlARF8B is repressed by sly-microRNA167 (sly-miR167), allowing for the activation of auxin downstream genes. In slarf8a, slarf8b, and slarf8a/b mutants, the auxin (IAA) levels are decreased, whereas the levels of inactive IAA conjugates including IAA-Ala, IAA-Asp, and IAA-Glu are increased. We further find that SlARF8B directly inhibits the expression of SlGH3.4, an acyl acid amino synthetase that conjugates the amino acids to IAA. Disruption of such auxin balance by the increased expression of SlGH3.4 or SlGH3.2 results in defective locular and placental tissues. Taken together, our findings reveal an important regulatory module constituted by sly-miR167-SlARF8A/B-SlGH3.4 during the development of locular and placenta tissues of tomato fruits.
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Affiliation(s)
- Bing Hua
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Junqing Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoqian Han
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinxin Bian
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhijing Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Sun
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Renyin Wang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenyan Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Huimin Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Shuang Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Wang T, Long C, Chang M, Wu Y, Su S, Wei J, Jiang S, Wang X, He J, Xing D, He Y, Ran Y, Li W. Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening. Sci Rep 2024; 14:2226. [PMID: 38278802 PMCID: PMC10817905 DOI: 10.1038/s41598-023-51080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/30/2023] [Indexed: 01/28/2024] Open
Abstract
In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.
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Affiliation(s)
- Tao Wang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Meixia Chang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yuan Wu
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Shixian Su
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjiang Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
| | - Suyan Jiang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xiujun Wang
- College of Brewing and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Jianwen He
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Dan Xing
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yangbo He
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yaoqi Ran
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China.
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China.
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Arpita K, Sharma S, Srivastava H, Kumar K, Mushtaq M, Gupta P, Jain R, Gaikwad K. Genome-wide survey, molecular evolution and expression analysis of Auxin Response Factor (ARF) gene family indicating their key role in seed number per pod in pigeonpea (C. cajan L. Millsp.). Int J Biol Macromol 2023; 253:126833. [PMID: 37709218 DOI: 10.1016/j.ijbiomac.2023.126833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Auxin Response Factors (ARF) are a family of transcription factors that mediate auxin signalling and regulate multiple biological processes. Their crucial role in increasing plant biomass/yield influenced this study, where a systematic analysis of ARF gene family was carried out to identify the key proteins controlling embryo/seed developmental pathways in pigeonpea. A genome-wide scan revealed the presence of 12 ARF genes in pigeonpea, distributed across the chromosomes 1, 3, 4, 8 and 11. Domain analysis of ARF proteins showed the presence of B3 DNA binding, AUX response, and IAA domains. Majority of them are of nuclear origin, and do not exhibit the level of genomic expansion as observed in Glycine max (51 members). The duplication events seem to range from 31.6 to 42.3 million years ago (mya). Promoter analysis revealed the presence of multiple cis-acting elements related to stress responses, hormone signalling and other development processes. The expression atlas data highlighted the expression of CcARF8 in hypocotyl, bud and flower whereas, CcARF7 expression was significantly high in pod. The real-time expression of CcARF2, CcARF3 and CcARF18 was highest in genotypes with high seed number indicating their key role in regulating embryo development and determining seed set in pigeonpea.
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Affiliation(s)
- Kumari Arpita
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
| | - Harsha Srivastava
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India
| | - Muntazir Mushtaq
- Shoolini Univeristy of Biotechnology and Management Sciences, Himachal Pradesh 173229, India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Rishu Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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Jobert F, Yadav S, Robert S. Auxin as an architect of the pectin matrix. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6933-6949. [PMID: 37166384 PMCID: PMC10690733 DOI: 10.1093/jxb/erad174] [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: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.
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Affiliation(s)
- François Jobert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- CRRBM, Université de Picardie Jules Verne, 80000, Amiens, France
| | - Sandeep Yadav
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
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Molesini B, Pennisi F, Vitulo N, Pandolfini T. MicroRNAs associated with AGL6 and IAA9 function in tomato fruit set. BMC Res Notes 2023; 16:242. [PMID: 37777779 PMCID: PMC10544166 DOI: 10.1186/s13104-023-06510-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
OBJECTIVE Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). In a recent work, we developed a method to silence IAA9 and AGL6 in tomato ovaries using exogenous dsRNAs. We also produced small RNA libraries from IAA9- and AGL6-silenced ovaries to confirm the presence of siRNAs, derived from exogenous dsRNA, targeting IAA9 and AGL6. The objective of this work is to exploit these sRNA libraries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries. RESULTS We identified by RNA sequencing 125 and 104 known and 509 and 516 novel miRNAs from reads mapped to mature or hairpin sequences, respectively. Of the known miRNAs, 7 and 45 were differentially expressed in IAA9- and AGL6-silenced ovaries compared to control ones, respectively. Six miRNAs were common to both datasets, suggesting their importance in the fruit set process. The expression pattern of two of these (miR393 and miR482e-5p) was verified by stem-loop qRT-PCR. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.
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Affiliation(s)
- Barbara Molesini
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Federica Pennisi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Tiziana Pandolfini
- Department of Biotechnology, University of Verona, Verona, 37134, Italy.
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Kyndt T. Loss of susceptibility, an underexplored approach for durable resistance to plant-parasitic nematodes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5422-5425. [PMID: 37773262 DOI: 10.1093/jxb/erad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
This article comments on:
Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. 2023. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. Journal of Experimental Botany 74, 5752–5766.
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Affiliation(s)
- Tina Kyndt
- Department Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
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10
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Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5752-5766. [PMID: 37310189 DOI: 10.1093/jxb/erad208] [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: 11/23/2022] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKN) from the genus Meloidogyne induce the dedifferentiation of root vascular cells into giant multinucleate feeding cells. These feeding cells result from an extensive reprogramming of gene expression, and auxin is known to be a key player in their development. However, little is known about how the auxin signal is transmitted during giant cell development. Integrative analyses combining transcriptome and small non-coding RNA datasets with the specific sequencing of cleaved transcripts identified genes targeted by miRNAs in tomato (Solanum lycopersicum) galls. The two auxin-responsive transcription factors ARF8A and ARF8B, and their miRNA167 regulators, were identified as robust gene-miRNA pair candidates to be involved in the tomato response to M. incognita. Spatiotemporal expression analysis using promoter-β-glucuronidase (GUS) fusions showed the up-regulation of ARF8A and ARF8B in RKN-induced feeding cells and surrounding cells. The generation and phenotyping of CRISPR (clustered regularly interspaced palindromic repeats) mutants demonstrated the role of ARF8A and ARF8B in giant cell development and allowed the characterization of their downstream regulated genes.
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Affiliation(s)
- Yara Noureddine
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Martine da Rocha
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Jing An
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Clémence Médina
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Joffrey Mejias
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Karine Mulet
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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11
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Teng C, Zhang C, Guo F, Song L, Fang Y. Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs. Life (Basel) 2023; 13:1917. [PMID: 37763320 PMCID: PMC10533097 DOI: 10.3390/life13091917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs.
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Affiliation(s)
| | | | | | | | - Yanni Fang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (C.T.); (C.Z.); (F.G.)
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12
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Chen X, Liu Y, Zhang X, Zheng B, Han Y, Zhang RX. PpARF6 acts as an integrator of auxin and ethylene signaling to promote fruit ripening in peach. HORTICULTURE RESEARCH 2023; 10:uhad158. [PMID: 37719277 PMCID: PMC10500152 DOI: 10.1093/hr/uhad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 09/19/2023]
Abstract
Although auxin is known to induce ethylene biosynthesis in some Rosaceae fruit crops, the mechanisms underlying the auxin-ethylene interaction during fruit ripening remain largely unknown. Here, the regulatory role of an auxin response factor, PpARF6, in fruit ripening was investigated in peach. Peach fruits showed accelerated ripening after treatment with auxin and PpARF6 was found to be significantly induced. PpARF6 not only could induce ethylene synthesis by directly activating the transcription of ethylene biosynthetic genes, but also competed with EIN3-binding F-box proteins PpEBF1/2 for binding to ethylene-insensitive3-like proteins PpEIL2/3, thereby keeping PpEIL2/3 active. Moreover, PpARF6 showed an interaction with PpEIL2/3 to enhance the PpEIL2/3-activated transcription of ethylene biosynthetic genes. Additionally, ectopic overexpression of PpARF6 in tomato accelerated fruit ripening by promoting the expression of genes involved in ethylene synthesis and fruit texture. In summary, our results revealed a positive regulatory role of PpARF6 in peach fruit ripening via integrating auxin and ethylene signaling.
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Affiliation(s)
- Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yudi Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xian Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ruo-Xi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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13
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Israeli A, Schubert R, Man N, Teboul N, Serrani Yarce JC, Rosowski EE, Wu MF, Levy M, Efroni I, Ljung K, Hause B, Reed JW, Ori N. Modulating auxin response stabilizes tomato fruit set. PLANT PHYSIOLOGY 2023; 192:2336-2355. [PMID: 37032117 PMCID: PMC10315294 DOI: 10.1093/plphys/kiad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/01/2023]
Abstract
Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here, we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Ramona Schubert
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Nave Man
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Naama Teboul
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | | | - Emily E Rosowski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Miin-Feng Wu
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Matan Levy
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Jason W Reed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
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14
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Hu J, Li X, Sun TP. Four class A AUXIN RESPONSE FACTORs promote tomato fruit growth despite suppressing fruit set. NATURE PLANTS 2023; 9:706-719. [PMID: 37037878 DOI: 10.1038/s41477-023-01396-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/14/2023] [Indexed: 05/23/2023]
Abstract
In flowering plants, auxin produced in seeds after fertilization promotes fruit initiation. The application of auxin to unpollinated ovaries can also induce parthenocarpy (seedless fruit production). Previous studies have shown that auxin signalling components SlIAA9 and SlARF7 (a class A AUXIN RESPONSE FACTOR (ARF)) are key repressors of fruit initiation in tomato (Solanum lycopersicum). A similar repressive role of class A ARFs in fruit set has also been observed in other plant species. However, evidence is lacking for a role of any class A ARF in promoting fruit development as predicted in the current auxin signalling model. Here we generated higher-order tomato mutants of four class A SlARFs (SlARF5, SlARF7, SlARF8A and SlARF8B) and uncovered their precise combinatorial roles that lead to suppressing and promoting fruit development. All four class A SlARFs together with SlIAA9 inhibited fruit initiation but promoted subsequent fruit growth. Transgenic tomato lines expressing truncated SlARF8A/8B lacking the IAA9-interacting PB1 domain displayed strong parthenocarpy, further confirming the promoting role of SlARF8A/8B in fruit growth. Altering the doses of these four SlARFs led to biphasic fruit growth responses, showing their versatile dual roles as both negative and positive regulators. RNA-seq and chromatin immunoprecipitation-quantitative PCR analyses further identified SlARF8A/8B target genes, including those encoding MADS-BOX transcription factors (AG1, MADS2 and AGL6) that are key repressors of fruit set. These results support the idea that SlIAA9/SlARFs directly regulate the transcription of these MADS-BOX genes to inhibit fruit set. Our study reveals the previously unknown dual function of four class A SlARFs in tomato fruit development and illuminates the complex combinatorial effects of multiple ARFs in controlling auxin-mediated fruit set and fruit growth.
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Affiliation(s)
- Jianhong Hu
- Department of Biology, Duke University, Durham, NC, USA
| | - Xiao Li
- Department of Biology, Duke University, Durham, NC, USA
- School of Grassland Science, Beijing Forestry University, Beijing, P. R. China
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC, USA.
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15
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D’Esposito D, Guadagno A, Amoroso CG, Cascone P, Cencetti G, Michelozzi M, Guerrieri E, Ercolano MR. Genomic and metabolic profiling of two tomato contrasting cultivars for tolerance to Tuta absoluta. PLANTA 2023; 257:47. [PMID: 36708391 PMCID: PMC9884263 DOI: 10.1007/s00425-023-04073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Dissimilar patterns of variants affecting genes involved in response to herbivory, including those leading to difference in VOC production, were identified in tomato lines with contrasting response to Tuta absoluta. Tuta absoluta is one of the most destructive insect pest affecting tomato production, causing important yield losses both in open field and greenhouse. The selection of tolerant varieties to T. absoluta is one of the sustainable approaches to control this invasive leafminer. In this study, the genomic diversity of two tomato varieties, one tolerant and the other susceptible to T. absoluta infestation was explored, allowing us to identify chromosome regions with highly dissimilar pattern. Genes affected by potential functional variants were involved in several processes, including response to herbivory and secondary metabolism. A metabolic analysis for volatile organic compounds (VOCs) was also performed, highlighting a difference in several classes of chemicals in the two genotypes. Taken together, these findings can aid tomato breeding programs aiming to develop tolerant plants to T. absoluta.
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Affiliation(s)
- Daniela D’Esposito
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, NA Italy
| | - Anna Guadagno
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, NA Italy
| | - Ciro Gianmaria Amoroso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, NA Italy
| | - Pasquale Cascone
- Institute for Sustainable Plant Protection, National Research Council of Italy, 80055 Portici, NA Italy
| | - Gabriele Cencetti
- Institute of Biosciences and Bioresources, National Research Council of Italy, 50019 Sesto Fiorentino, FI Italy
| | - Marco Michelozzi
- Institute of Biosciences and Bioresources, National Research Council of Italy, 50019 Sesto Fiorentino, FI Italy
| | - Emilio Guerrieri
- Institute for Sustainable Plant Protection, National Research Council of Italy, 80055 Portici, NA Italy
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16
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Li J, Li M, Wang W, Wang D, Hu Y, Zhang Y, Zhang X. Morphological and physiological mechanism of cytoplasmic inheritance stigma exsertion trait expression in tobacco (Nicotiana tabacum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111528. [PMID: 36332767 DOI: 10.1016/j.plantsci.2022.111528] [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: 07/02/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Stigma exsertion is an essential outcrossing trait that can improve hybrid seed production efficiencies. In this study, the morphological and physiological mechanisms of cytoplasmic inheritance stigma exsertion trait expression in a tobacco line (MSK326SE) which generated from a stigma exsertion tobacco mutant through continuous backcross were investigated. Compared with its homonuclear-heteroplasmic lines (MSK326 and K326 with inserted stigmas), the exserted stigma phenotype of MSK326SE was mainly caused by corolla shortening, while was stable under different environmental temperature. The different responses of mainly endogenous hormones and expression of cell division- and expansion-related genes caused the differences in cell division and expansion in different flower organs, which further determined the lengths of the corolla. Furthermore, the significant decrease of MSK326SE corolla epidermal cell size caused corolla shortening and finally resulting in stigma exsertion. Exogenous JA could shorten the corolla and more effective increased stigma exsertion degree of MSK326SE, suggesting a potential relationship between stigma exsertion and high JA levels during early bud development. The hybrid seed production efficiency could be improved in tobacco. Our results provide a basis for elucidating the cytoplasmic inheritance stigma exsertion trait expression in tobacco while helping to improve hybrid seed production efficiency.
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Affiliation(s)
- Juxu Li
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Man Li
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Weimin Wang
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou 310024, China
| | - Dong Wang
- Henan Provincial Branch of China National Tobacco Corporation, Zhengzhou 450046, China
| | - Yuwei Hu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yunyun Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoquan Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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17
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Cheng Z, Song W, Zhang X. Genic male and female sterility in vegetable crops. HORTICULTURE RESEARCH 2022; 10:uhac232. [PMID: 36643746 PMCID: PMC9832880 DOI: 10.1093/hr/uhac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato (Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.
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Affiliation(s)
- Zhihua Cheng
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiyuan Song
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
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18
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Hu M, Qi Z, Ren Z, Tong J, Wang B, Wu Z, Hao J, Liu N. Genome-Wide Analysis of Auxin Response Factors in Lettuce ( Lactuca sativa L.) Reveals the Positive Roles of LsARF8a in Thermally Induced Bolting. Int J Mol Sci 2022; 23:13509. [PMID: 36362292 PMCID: PMC9653848 DOI: 10.3390/ijms232113509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Warm temperatures induce plant bolting accompanied by flower initiation, where endogenous auxin is dynamically associated with accelerated growth. Auxin signaling is primarily regulated by a family of plant-specific transcription factors, AUXIN RESPONSE FACTORS (ARFs), which either activate or repress the expression of downstream genes in response to developmental and environmental cues. However, the relationship between ARFs and bolting has not been completely understood in lettuce yet. Here, we identified 24 LsARFs (Lactuca sativa ARFs) in the lettuce genome. The phylogenetic tree indicated that LsARFs could be classified into three clusters, which was well supported by the analysis of exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis revealed that more than half of the LsARFs were ubiquitously expressed in all tissues examined, whereas a small number of LsARFs responded to UV or cadmium stresses. qRT-PCR analysis indicated that the expression of most LsARFs could be activated by more than one phytohormone, underling their key roles as integrative hubs of different phytohormone signaling pathways. Importantly, the majority of LsARFs displayed altered expression profiles under warm temperatures, implying that their functions were tightly associated with thermally accelerated bolting in lettuce. Importantly, we demonstrated that silencing of LsARF8a, expression of which was significantly increased by elevated temperatures, resulted in delayed bolting under warm temperatures, suggesting that LsARF8a might conduce to the thermally induced bolting. Together, our results provide molecular insights into the LsARF gene family in lettuce, which will facilitate the genetic improvement of the lettuce in an era of global warming.
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Affiliation(s)
- Manman Hu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhengyang Qi
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jing Tong
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Baoju Wang
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhanhui Wu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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19
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Xu X, Zhang Q, Gao X, Wu G, Wu M, Yuan Y, Zheng X, Gong Z, Hu X, Gong M, Qi T, Li H, Luo Z, Li Z, Deng W. Auxin and abscisic acid antagonistically regulate ascorbic acid production via the SlMAPK8-SlARF4-SlMYB11 module in tomato. THE PLANT CELL 2022; 34:4409-4427. [PMID: 36000899 PMCID: PMC9614483 DOI: 10.1093/plcell/koac262] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/11/2022] [Indexed: 06/01/2023]
Abstract
Ascorbic acid (AsA) is a multifunctional phytonutrient that is essential for the human diet as well as plant development. While much is known about AsA biosynthesis in plants, how this process is regulated in tomato (Solanum lycopersicum) fruits remains unclear. Here, we found that auxin treatment inhibited AsA accumulation in the leaves and pericarps of tomato. The auxin response factor gene SlARF4 is induced by auxin to mediate auxin-induced inhibition of AsA accumulation. Specifically, SlARF4 transcriptionally inhibits the transcription factor gene SlMYB11, thereby modulating AsA accumulation by regulating the transcription of the AsA biosynthesis genes l-galactose-1-phosphate phosphatase, l-galactono-1,4-lactone dehydrogenase, and dehydroascorbate. By contrast, abscisic acid (ABA) treatment increased AsA accumulation in tomato under drought stress. ABA induced the expression of the mitogen-activated protein kinase gene SlMAPK8. We demonstrate that SlMAPK8 phosphorylates SlARF4 and inhibits its transcriptional activity, whereas SlMAPK8 phosphorylates SlMYB11 and activates its transcriptional activity. SlMAPK8 functions in ABA-induced AsA accumulation and drought stress tolerance. Moreover, ABA antagonizes the effects of auxin on AsA biosynthesis. Therefore, auxin- and ABA-induced regulation of AsA accumulation is mediated by the SlMAPK8-SlARF4-SlMYB11 module in tomato during fruit development and drought stress responses, shedding light on the roles of phytohormones in regulating AsA accumulation to mediate stress tolerance.
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Affiliation(s)
- Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Qiongdan Zhang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Xueli Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Guanle Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Mengbo Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Yujin Yuan
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Xianzhe Zheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Zehao Gong
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Xiaowei Hu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Min Gong
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Tiancheng Qi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Honghai Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China
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20
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Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
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21
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Identification and Characterization of AUXIN Response Factor Gene Family Reveals Their Regulatory Network to Respond the Multi-Hormones Crosstalk during GA-Induced Grape Parthenocarpic Berry. Int J Mol Sci 2022; 23:ijms231911108. [PMID: 36232409 PMCID: PMC9569648 DOI: 10.3390/ijms231911108] [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: 06/15/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Exogenous gibberellin (GA) was widely used to improve berry quality through inducing parthenocarpic seedless berries in grapes. We revealed that auxin response factors (ARFs), the key transcription factors in response to auxin, might respond to GA involving modulation of grape parthenocarpy. However, the underlying molecular mechanism in this process remains yet unclear. Here, a total of 19 VvARF members were identified in the ovaries during GA-induced grapes’ parthenocarpy. Interestingly, almost all members were GA-responsive factors, of which 9 could be classified in plant hormone signal transduction (KO04075) and involved in the tryptophan metabolic pathway (K14486). Moreover, VvARFs were predicted to have 310 interacted proteins involved in 19 KEGG pathways. Of them, 32 interacted proteins participated in the KO04075 pathway, including auxin (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signaling pathways by responding to GA-mediated multi-hormone crosstalk. Further analysis demonstrated that VvARF4-2 might be the major factor in the modulation of GA-induced parthenocarpy via the crosstalk of IAA, CTK, SA, and ethylene signaling, followed by VvARF6-1 and VvARF9 involved in SA and ABA signaling pathways, respectively. Finally, we developed a VvARFs-mediated regulatory network by responding to GA-mediated multi-hormone crosstalk during grape parthenocarpy. Collectively, our findings provided novel insights into the regulatory network of VvARFs in GA-guided multi-hormone signaling to modulate grape parthenocarpy, which has great implications for the molecular breeding of high quality seedless grape berries.
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Li Y, Zhu J, Feng Y, Li Z, Ren Z, Liu N, Liu C, Hao J, Han Y. LsARF3 mediates thermally induced bolting through promoting the expression of LsCO in lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:958833. [PMID: 36160965 PMCID: PMC9498183 DOI: 10.3389/fpls.2022.958833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable whose edible organs usually are leaf or stems, and thus high-temperature induced bolting followed by flower initiation is an undesirable trait in lettuce production. However, the molecular mechanism that controls lettuce bolting and flowering upon thermal treatments is largely unknown. Here, we identified a Lettuce auxin response factor 3 (LsARF3), the expression of which was enhanced by heat and auxin treatments. Interestingly, LsARF3 is preferentially expressed in stem apex, suggesting it might be associated with lettuce bolting. Transgenic lettuce overexpressing LsARF3 displayed early bolting and flowering, whereas knockout of LsARF3 dramatically delayed bolting and flowering in lettuce under normal or high temperature conditions. Furthermore, Exogenous application of IAA failed to rescue the late-bolting and -flowering phenotype of lsarf3 mutants. Several floral integrator genes including LsCO, LsFT, and LsLFY were co-expressed with LsARF3 in the overexpression and knockout lettuce plants. Yeast one-hybrid (Y1H) experiments suggested that LsARF3 could physically interact with the LsCO promoter, which was further confirmed by a dual luciferase assay in tobacco leaves. The results indicated that LsARF3 might directly modulate the expression of LsCO in lettuce. Therefore, these results demonstrate that LsARF3 could promote lettuce bolting in response to the high temperature by directly or indirectly activating the expression of floral genes such as LsCO, which provides new insights into lettuce bolting in the context of ARFs signaling and heat response.
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Affiliation(s)
- Yunfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiaqi Zhu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yixuan Feng
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zhenfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chaojie Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
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23
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Zhang C, Zhang K, Chai Z, Song Y, Wang X, Duan Y, Zhang M. Identification of miRNAs and Target Genes at Key Stages of Sexual Differentiation in Androdioecious Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms231810386. [PMID: 36142310 PMCID: PMC9499476 DOI: 10.3390/ijms231810386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022] Open
Abstract
Androdioecy is the crucial transition state in the evolutionary direction of hermaphroditism to dioecy, however, the molecular mechanisms underlying the formation of this sex system remain unclear. While popular in China for its ornamental and cultural value, Osmanthus fragrans has an extremely rare androdioecy breeding system, meaning that there are both male and hermaphroditic plants in a population. To unravel the mechanisms underlying the formation of androdioecy, we performed small RNA sequencing studies on male and hermaphroditic O. fragrans. A total of 334 miRNAs were identified, of which 59 were differentially expressed. Functional categorization revealed that the target genes of differentially expressed miRNAs were mainly involved in the biological processes of reproductive development and the hormone signal transduction pathway. We speculated that the miRNA160, miRNA167, miRNA393 and miRNA396 families may influence the sex differentiation in O. fragrans. Overall, our study is the first exploration of miRNAs in the growth and development process of O. fragrans, and is also the first study of androdioecious plants from the miRNA sequencing perspective. The analysis of miRNAs and target genes that may be involved in the sex differentiation process lay a foundation for the ultimate discovery of the androdioecious molecular mechanism in O. fragrans.
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Ren H, Xu Y, Lixie H, Kuang J, Wang Y, Jin Q. Integrated Transcriptome and Targeted Metabolite Analysis Reveal miRNA-mRNA Networks in Low-Light-Induced Lotus Flower Bud Abortion. Int J Mol Sci 2022; 23:9925. [PMID: 36077323 PMCID: PMC9456346 DOI: 10.3390/ijms23179925] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Most Nelumbo nucifera (lotus) flower buds were aborted during the growing season, notably in low-light environments. How lotus produces so many aborted flower buds is largely unknown. An integrated transcriptome and targeted metabolite analysis was performed to reveal the genetic regulatory networks underlying lotus flower bud abortion. A total of 233 miRNAs and 25,351 genes were identified in lotus flower buds, including 68 novel miRNAs and 1108 novel genes. Further enrichment analysis indicated that sugar signaling plays a potential central role in regulating lotus flower bud abortion. Targeted metabolite analysis showed that trehalose levels declined the most in the aborting flower buds. A potential regulatory network centered on miR156 governs lotus flower bud abortion, involving multiple miRNA-mRNA pairs related to cell integrity, cell proliferation and expansion, and DNA repair. Genetic analysis showed that miRNA156-5p-overexpressing lotus showed aggravated flower bud abortion phenotypes. Trehalose-6-P synthase 1 (TPS1), which is required for trehalose synthase, had a negative regulatory effect on miR156 expression. TPS1-overexpression lotus showed significantly decreased flower bud abortion rates both in normal-light and low-light environments. Our study establishes a possible genetic basis for how lotus produces so many aborted flower buds, facilitating genetic improvement of lotus' shade tolerance.
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Affiliation(s)
| | | | | | | | | | - Qijiang Jin
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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25
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Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
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Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zhao ZX, Yin XX, Li S, Peng YT, Yan XL, Chen C, Hassan B, Zhou SX, Pu M, Zhao JH, Hu XH, Li GB, Wang H, Zhang JW, Huang YY, Fan J, Li Y, Wang WM. miR167d-ARFs Module Regulates Flower Opening and Stigma Size in Rice. RICE (NEW YORK, N.Y.) 2022; 15:40. [PMID: 35876915 PMCID: PMC9314575 DOI: 10.1186/s12284-022-00587-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Flower opening and stigma exertion are two critical traits for cross-pollination during seed production of hybrid rice (Oryza sativa L.). In this study, we demonstrate that the miR167d-ARFs module regulates stigma size and flower opening that is associated with the elongation of stamen filaments and the cell arrangement of lodicules. The overexpression of miR167d (OX167d) resulted in failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule, resulting in cleistogamy. Blocking miR167d by target mimicry also led to a morphological alteration of the individual floral organs, including a reduction in stigma size and alteration of lodicule cell morphology, but did not show the cleistogamous phenotype. In addition, the four target genes of miR167d, namely ARF6, ARF12, ARF17, and ARF25, have overlapping functions in flower opening and stigma size. The loss-of-function of a single ARF gene did not influence the flower opening and stigma size, but arf12 single mutant showed a reduced plant height and aborted apical spikelets. However, mutation in ARF12 together with mutation in either ARF6, ARF17, or ARF25 led to the same defective phenotypes that were observed in OX167d, including the failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule. These findings indicate that the appropriate expression of miR167d is crucial and the miR167d-ARFs module plays important roles in the regulation of flower opening and stigma size in rice.
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Affiliation(s)
- Zhi-Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Xiao Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Sha Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu-Ting Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiu-Lian Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beenish Hassan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shi-Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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27
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Wang H, Huang H, Shang Y, Song M, Ma H. Identification and characterization of auxin response factor (ARF) family members involved in fig ( Ficus carica L.) fruit development. PeerJ 2022; 10:e13798. [PMID: 35898939 PMCID: PMC9310797 DOI: 10.7717/peerj.13798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
The auxin response factor (ARF) combines with AuxREs cis-acting elements in response to auxin to regulate plant development. To date, no comprehensive analysis of ARF genes expressed during fruit development has been conducted for common fig (Ficus carica L.). In this study, members of the FcARF gene family were screened, identified in the fig genome database and their features characterized using bioinformatics. Twenty FcARF genes were clustered into three classes, with almost similar highly conserved DBD (B3-like DNA binding domain), AUX/IAA (auxin/indole-3-acetic acid gene family) and MR domain structure among class members. Analysis of amino acid species in MR domain revealed 10 potential transcription activators and 10 transcription inhibitors, and 17 FcARF members were predicted to be located in the nucleus. DNA sequence analysis showed that the ARF gene family consisted of 4-25 exons, and the promoter region contained 16 cis-acting elements involved in stress response, hormone response and flavonoid biosynthesis. ARF genes were expressed in most tissues of fig, especially flower and peel. Transcriptomics analysis results showed that FcARF2, FcARF11 and FcARF12, belonging to class-Ia, were stably and highly expressed in the early development stage of flower and peel of 'Purple peel' fig. However, their expression levels decreased after maturity. Expression of class-Ic member FcARF3 conformed to the regularity of fig fruit development. These four potential transcription inhibitors may regulate fruit growth and development of 'Purple Peel' fig. This study provides comprehensive information on the fig ARF gene family, including gene structure, chromosome position, phylogenetic relationship and expression pattern. Our work provides a foundation for further research on auxin-mediated fig fruit development.
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Affiliation(s)
- Haomiao Wang
- College of Horticulture, China Agricultural University, Beijing, Beijing, China
| | - Hantang Huang
- College of Horticulture, China Agricultural University, Beijing, Beijing, China
| | - Yongkai Shang
- College of Horticulture, China Agricultural University, Beijing, Beijing, China
| | - Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, Beijing, China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, Beijing, China
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28
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Integrative Analysis of miRNAs and Their Targets Involved in Ray Floret Growth in Gerbera hybrida. Int J Mol Sci 2022; 23:ijms23137296. [PMID: 35806310 PMCID: PMC9266715 DOI: 10.3390/ijms23137296] [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: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in regulating many aspects of plant growth and development at the post-transcriptional level. Gerbera (Gerbera hybrida) is an important ornamental crop. However, the role of miRNAs in the growth and development of gerbera is still unclear. In this study, we used high-throughput sequencing to analyze the expression profiles of miRNAs in ray floret during inflorescence opening. A total of 164 miRNAs were obtained, comprising 24 conserved miRNAs and 140 novel miRNAs. Ten conserved and 15 novel miRNAs were differentially expressed during ray floret growth, and 607 differentially expressed target genes of these differentially expressed miRNAs were identified using psRNATarget. We performed a comprehensive analysis of the expression profiles of the miRNAs and their targets. The changes in expression of five miRNAs (ghy-miR156, ghy-miR164, ghy-miRn24, ghy-miRn75 and ghy-miRn133) were inversely correlated with the changes in expression of their eight target genes. The miRNA cleavage sites in candidate target gene mRNAs were determined using 5′-RLM-RACE. Several miRNA-mRNA pairs were predicted to regulate ray floret growth and anthocyanin biosynthesis. In conclusion, the results of small RNA sequencing provide valuable information to reveal the mechanisms of miRNA-mediated ray floret growth and anthocyanin accumulation in gerbera.
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29
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Jia Y, Chen C, Gong F, Jin W, Zhang H, Qu S, Ma N, Jiang Y, Gao J, Sun X. An Aux/IAA Family Member, RhIAA14, Involved in Ethylene-Inhibited Petal Expansion in Rose ( Rosa hybrida). Genes (Basel) 2022; 13:1041. [PMID: 35741802 PMCID: PMC9222917 DOI: 10.3390/genes13061041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Flower size, a primary agronomic trait in breeding of ornamental plants, is largely determined by petal expansion. Generally, ethylene acts as an inhibitor of petal expansion, but its effect is restricted by unknown developmental cues. In this study, we found that the critical node of ethylene-inhibited petal expansion is between stages 1 and 2 of rose flower opening. To uncover the underlying regulatory mechanism, we carried out a comparative RNA-seq analysis. Differentially expressed genes (DEGs) involved in auxin-signaling pathways were enriched. Therefore, we identified an auxin/indole-3-acetic acid (Aux/IAA) family gene, RhIAA14, whose expression was development-specifically repressed by ethylene. The silencing of RhIAA14 reduced cell expansion, resulting in diminished petal expansion and flower size. In addition, the expressions of cell-expansion-related genes, including RhXTH6, RhCesA2, RhPIP2;1, and RhEXPA8, were significantly downregulated following RhIAA14 silencing. Our results reveal an Aux/IAA that serves as a key player in orchestrating petal expansion and ultimately contributes to flower size, which provides new insights into ethylene-modulated flower opening and the function of the Aux/IAA transcription regulator.
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Affiliation(s)
- Yangchao Jia
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Changxi Chen
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Feifei Gong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Weichan Jin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Hao Zhang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.Z.); (S.Q.)
| | - Suping Qu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.Z.); (S.Q.)
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Yunhe Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (Y.J.); (C.C.); (F.G.); (W.J.); (N.M.); (Y.J.); (J.G.)
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Genome-Wide Identification of Auxin Response Factors in Peanut ( Arachis hypogaea L.) and Functional Analysis in Root Morphology. Int J Mol Sci 2022; 23:ijms23105309. [PMID: 35628135 PMCID: PMC9141974 DOI: 10.3390/ijms23105309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022] Open
Abstract
Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.
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31
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An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.
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32
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Zhao Y, Wang Y, Zhao X, Yan M, Ren Y, Yuan Z. ARF6s Identification and Function Analysis Provide Insights Into Flower Development of Punica granatum L. FRONTIERS IN PLANT SCIENCE 2022; 13:833747. [PMID: 35321445 PMCID: PMC8937018 DOI: 10.3389/fpls.2022.833747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1-14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1-12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers.
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Affiliation(s)
- Yujie Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuying Wang
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xueqing Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ming Yan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuan Ren
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaohe Yuan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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Basnet P, Um T, Roy NS, Cho WS, Park SC, Park KC, Choi IY. Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean. Front Genet 2022; 13:805347. [PMID: 35281824 PMCID: PMC8907156 DOI: 10.3389/fgene.2022.805347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F7 derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.
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Affiliation(s)
- Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Taeyoung Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Woo Suk Cho
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Soo Chul Park
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
- *Correspondence: Ik-Young Choi,
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Auxin Response Factors Are Ubiquitous in Plant Growth and Development, and Involved in Crosstalk between Plant Hormones: A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031360] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Auxin response factors (ARFs) are an important family of transcription factors involved in the exertion of auxin in plants and play a key role in regulating the growth and development of plant nutritional and reproductive organs such as roots, stems, leaves, flowers, fruits, and seeds. Foods of plant origin occupy an important place in the nutritional structure of the human diet, and the main edible parts of different plants vary. In this paper, we review recent research reports on ARFs and summarize its role in the regulation of leaf, flower, root, and fruit growth, as well as other important life activities. We also present the challenges and opportunities that ARFs will present in the future. It will be important to deepen our understanding of the mechanisms by which ARFs interact with other proteins or genes. In addition, it is worth considering that more technical tools should be put into the study of ARFs and that the research should be oriented towards solving practical problems. In the future, it is expected that the nutrition and function of plant-derived foods can be improved through gene editing and other means.
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Gupta C, Salgotra RK. Epigenetics and its role in effecting agronomical traits. FRONTIERS IN PLANT SCIENCE 2022; 13:925688. [PMID: 36046583 PMCID: PMC9421166 DOI: 10.3389/fpls.2022.925688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.
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Zhang M, Cheng W, Yuan X, Wang J, Cheng T, Zhang Q. Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:931454. [PMID: 35937373 PMCID: PMC9355595 DOI: 10.3389/fpls.2022.931454] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/30/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.
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Tang Y, Du G, Xiang J, Hu C, Li X, Wang W, Zhu H, Qiao L, Zhao C, Wang J, Yu S, Sui J. Genome-wide identification of auxin response factor (ARF) gene family and the miR160-ARF18-mediated response to salt stress in peanut (Arachis hypogaea L.). Genomics 2021; 114:171-184. [PMID: 34933069 DOI: 10.1016/j.ygeno.2021.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Auxin response factors (ARFs) are transcription factors that regulate the transcription of auxin-responsive genes during plant growth and development. In this study, 29 and 30 ARF members were identified from the two wild peanut species, A. duranensis and A. ipaensis, respectively. The ARFs, including their classifications, conserved domains and evolutionary relationships were characterized. RNA-seq analyses revealed that some of the ARF genes were responsive to abiotic stress, particularly high salinity. In addition to abiotic stress, the expression of 2 ARF members was also regulated by biotic stress, specifically Bradyrhizobium infection in A. duranensis. The ARF gene Arahy.7DXUOK was predicted to be a potential target of miR160. Overexpression of miR160 could cause degradation of the Arahy.7DXUOK target gene transcript and increased salt tolerance in miR160OX transgenic plants. Therefore, these molecular characterization and expression profile analyses provide comprehensive information on ARF family members and will help to elucidate their functions to facilitate further research on peanuts.
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Affiliation(s)
- Yanyan Tang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Guoning Du
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Jie Xiang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Changli Hu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Xiaoting Li
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Weihua Wang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Lixian Qiao
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Chunmei Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Shanlin Yu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China..
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Wu R, Wu G, Wang L, Wang X, Liu Z, Li M, Tan W, Qing L. Tobacco curly shoot virus Down-Regulated the Expression of nbe-miR167b-3p to Facilitate Its Infection in Nicotiana benthamiana. Front Microbiol 2021; 12:791561. [PMID: 34975814 PMCID: PMC8716884 DOI: 10.3389/fmicb.2021.791561] [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: 10/08/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022] Open
Abstract
Tobacco curly shoot virus (TbCSV) belongs to the genus Begomovirus of the family Geminiviridae, and causes leaf curling and curly shoot symptoms in tobacco and tomato crops. MicroRNAs (miRNAs) are pivotal modulators of plant development and host-virus interactions. However, the relationship between TbCSV infection and miRNAs accumulation has not been well investigated. The present study was conducted to analyze different expressions of miRNAs in Nicotiana benthamiana in response to the infection of TbCSV via small RNAs sequencing. The results showed that 15 up-regulated miRNAs and 12 down-regulated miRNAs were differentially expressed in TbCSV infected N. benthamiana, and nbe-miR167b-3p was down-regulated. To decipher the relationship between nbe-miR167b-3p expression and the accumulations of TbCSV DNA, pCVA mediation of miRNA overexpression and PVX based short tandem target mimic (STTM) were used in this study. It was found that overexpression of nbe-miR167b-3p attenuated leaf curling symptom of TbCSV and decreased viral DNA accumulation, but suppression of nbe-miR167b-3p expression enhanced the symptoms and accumulation of TbCSV. PRCP, the target gene of nbe-miR167b-3p, was silenced in plants using VIGS and this weakened the viral symptoms and DNA accumulation of TbCSV in the plants. Overall, this study clarified the effect of nbe-miR167b-3p on plant defense during TbCSV infection, and provided a framework to reveal the molecular mechanisms of miRNAs between plants and viruses.
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Affiliation(s)
- Rui Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Lyuxin Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Xu Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Zhuoying Liu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Mingjun Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Wanzhong Tan
- College of Tropical Crops Sciences, Yunnan Agricultural University, Kunming, China
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
- *Correspondence: Ling Qing,
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Hou Q, Qiu Z, Wen Z, Zhang H, Li Z, Hong Y, Qiao G, Wen X. Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L. Int J Mol Sci 2021; 22:11968. [PMID: 34769398 PMCID: PMC8584427 DOI: 10.3390/ijms222111968] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhilang Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Huimin Zhang
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Zhengchun Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
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Li P, Ma Q, Qu C, Zhu S, Zhao K, Ma X, Li Z, Zhang X, Gong F, Yin D. Genome-wide identification and expression analysis of auxin response factors in peanut ( Arachis hypogaea L.). PeerJ 2021; 9:e12319. [PMID: 34721990 PMCID: PMC8542371 DOI: 10.7717/peerj.12319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022] Open
Abstract
Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I-VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.
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Affiliation(s)
- Peipei Li
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Qian Ma
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Chengxin Qu
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Shuliang Zhu
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Kunkun Zhao
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Xingli Ma
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Zhongfeng Li
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Xingguo Zhang
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Fangping Gong
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Dongmei Yin
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
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Hu M, Zhang H, Wang B, Song Z, Gao Y, Yuan C, Huang C, Zhao L, Zhang Y, Wang L, Zou C, Sui X. Transcriptomic analysis provides insights into the AUXIN RESPONSE FACTOR 6-mediated repression of nicotine biosynthesis in tobacco (Nicotiana tabacum L.). PLANT MOLECULAR BIOLOGY 2021; 107:21-36. [PMID: 34302568 DOI: 10.1007/s11103-021-01175-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE NtARF6 overexpression represses nicotine biosynthesis in tobacco. Transcriptome analysis suggests that NtARF6 acts as a regulatory hub that connect different phytohormone signaling pathways to antagonize the jasmonic acid-induced nicotine biosynthesis. Plant specialized metabolic pathways are regulated by a plethora of molecular regulators that form complex networks. In Nicotiana tabacum, nicotine biosynthesis is regulated by transcriptional activators, such as NtMYC2 and the NIC2-locus ERFs. However, the underlying molecular mechanism of the regulatory feedback is largely unknown. Previous research has shown that NbARF1, a nicotine synthesis repressor, reduces nicotine accumulation in N. benthamiana. In this study, we demonstrated that overexpression of NtARF6, an ortholog of NbARF1, was able to reduce pyridine alkaloid accumulation in tobacco. We found that NtARF6 could not directly repress the transcriptional activities of the key nicotine pathway structural gene promoters. Transcriptomic analysis suggested that this NtARF6-induced deactivation of alkaloid biosynthesis might be achieved by the antagonistic effect between jasmonic acid (JA) and other plant hormone signaling pathways, such as ethylene (ETH), salicylic acid (SA), abscisic acid (ABA). The repression of JA biosynthesis is accompanied by the induction of ETH, ABA, and SA signaling and pathogenic infection defensive responses, resulting in counteracting JA-induced metabolic reprogramming and decreasing the expression of nicotine biosynthetic genes in vivo. This study provides transcriptomic evidence for the regulatory mechanism of the NtARF6-mediated repression of alkaloid biosynthesis and indicates that this ARF transcription factor might act as a regulatory hub to connect different hormone signaling pathways in tobacco.
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Affiliation(s)
- Mengyang Hu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongbo Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Bingwu Wang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Zhongbang Song
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Yulong Gao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Cheng Yuan
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Changjun Huang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Lu Zhao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Yihan Zhang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Longchang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Congming Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Xueyi Sui
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.
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Clepet C, Devani RS, Boumlik R, Hao Y, Morin H, Marcel F, Verdenaud M, Mania B, Brisou G, Citerne S, Mouille G, Lepeltier JC, Koussevitzky S, Boualem A, Bendahmane A. The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato. MOLECULAR PLANT 2021; 14:1185-1198. [PMID: 33964458 DOI: 10.1016/j.molp.2021.05.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Fruit set is inhibited by adverse temperatures, with consequences on yield. We isolated a tomato mutant producing fruits under non-permissive hot temperatures and identified the causal gene as SlHB15A, belonging to class III homeodomain leucine-zipper transcription factors. SlHB15A loss-of-function mutants display aberrant ovule development that mimics transcriptional changes occurring in fertilized ovules and leads to parthenocarpic fruit set under optimal and non-permissive temperatures, in field and greenhouse conditions. Under cold growing conditions, SlHB15A is subjected to conditional haploinsufficiency and recessive dosage sensitivity controlled by microRNA 166 (miR166). Knockdown of SlHB15A alleles by miR166 leads to a continuum of aberrant ovules correlating with parthenocarpic fruit set. Consistent with this, plants harboring an Slhb15a-miRNA166-resistant allele developed normal ovules and were unable to set parthenocarpic fruit under cold conditions. DNA affinity purification sequencing and RNA-sequencing analyses revealed that SlHB15A is a bifunctional transcription factor expressed in the ovule integument. SlHB15A binds to the promoters of auxin-related genes to repress auxin signaling and to the promoters of ethylene-related genes to activate their expression. A survey of tomato genetic biodiversity identified pat and pat-1, two historical parthenocarpic mutants, as alleles of SlHB15A. Taken together, our findings demonstrate the role of SlHB15A as a sentinel to prevent fruit set in the absence of fertilization and provide a mean to enhance fruiting under extreme temperatures.
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Affiliation(s)
- Christian Clepet
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Ravi Sureshbhai Devani
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Rachid Boumlik
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Yanwei Hao
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Halima Morin
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Fabien Marcel
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Marion Verdenaud
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Brahim Mania
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Gwilherm Brisou
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | | | | | | | | | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France.
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Zhang Z, Liu J, Huber DJ, Qu H, Yun Z, Li T, Jiang Y. Transcriptome, degradome and physiological analysis provide new insights into the mechanism of inhibition of litchi fruit senescence by melatonin. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110926. [PMID: 34034874 DOI: 10.1016/j.plantsci.2021.110926] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 05/25/2023]
Abstract
Litchi fruit has high commercial value on the international market, but senesces rapidly after harvest. We used weighted gene co-expression network analysis (WGCNA) and degradome technology to investigate the molecular mechanisms of melatonin-mediated delay of litchi fruit senescence through application of exogenous melatonin and p-chlorophenylalanine (p-CPA, an inhibitor of melatonin biosynthesis) treatments. Results demonstrated that exogenous melatonin treatment delayed litchi fruit senescence while p-CPA accelerated senescence. Coupled analyses of transcriptome and physiological parameters of litchi fruit provided the correlation of network modules with dynamic changes in browning index during storage. Additionally, we found that microRNAs (miR858 and miR160a) and their targets were actively involved in melatonin-mediated delay of litchi fruit senescence. Melatonin treatment decreased abscisic acid (ABA) content but increased PP2C and F-box expression levels, suggesting the involvement of ABA signaling in melatonin-mediated antisenescence. The transcriptions of ZAT, NAC and DREB1 were activated by melatonin treatment. Moreover, the major functional genes involved in histone methylation, γ-aminobutyric acid (GABA) metabolism, energy production, reactive oxygen species (ROS) accumulation and cell death were identified in the melatonin-inhibited litchi pericarp browning. Taken together, we first constructed the global map of the important regulators and pathways to delay litchi senescence and pericarp browning mediated by melatonin.
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Affiliation(s)
- Zhengke Zhang
- College of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Jialiang Liu
- College of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Donald J Huber
- Horticultural Sciences Department, PO Box 110690, IFAS, University of Florida, Gainesville, FL, 32611-0690, USA
| | - Hongxia Qu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ze Yun
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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45
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Iqbal S, Pan Z, Hayat F, Bai Y, Coulibaly D, Ali S, Ni X, Shi T, Gao Z. Comprehensive transcriptome profiling to identify genes involved in pistil abortion of Japanese apricot. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1191-1204. [PMID: 34177144 PMCID: PMC8212332 DOI: 10.1007/s12298-021-01019-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/08/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Flower development exists as a key period in the angiosperms life cycle and the proper development is considered with its reproductive success. Pistil abortion is one of the widely distributed aspects of berry plants and its basic mechanism in Japanese apricot is quite unclear and needs thorough investigation. The present study was carried out to get a deep insight into the pistil abortion mechanism in Japanese apricot using a transcriptomic approach. A large number of DEGs were identified from different development stages of normal and abortive pistils. Pair-wise comparison analysis was performed as LY1 vs DQD1, LY2 vs DQD2, and LY3 vs DQD3 and produced 3590, 2085, and 2286 transcripts, respectively. The Gene Ontology (GO) showed that different metabolic processes, plant hormones, developmental processes, and photosystem-related genes were involved in pistil abortion. The pathway analysis revealed significant enrichment of plant hormone's signal transduction and circadian rhythm pathways. Furthermore, transcription factors such as MYB, MADS-box, and NAC family showed lower expression in abortive pistils. The current study presents a new strategy for advanced research and understanding of the pistil abortion process in Japanese apricot and provides a possible reference for other deciduous fruit trees.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50 Zhongling Street, Nanjing, 210014 China
| | - Zhenpeng Pan
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Daouda Coulibaly
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Sajid Ali
- Department of Horticulture, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Pakistan
| | - Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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46
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Ben-Targem M, Ripper D, Bayer M, Ragni L. Auxin and gibberellin signaling cross-talk promotes hypocotyl xylem expansion and cambium homeostasis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3647-3660. [PMID: 33619529 DOI: 10.1093/jxb/erab089] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/19/2021] [Indexed: 05/04/2023]
Abstract
During secondary growth, the thickening of plant organs, wood (xylem) and bast (phloem) is continuously produced by the vascular cambium. In Arabidopsis hypocotyl and root, we can distinguish two phases of secondary growth based on cell morphology and production rate. The first phase, in which xylem and phloem are equally produced, precedes the xylem expansion phase in which xylem formation is enhanced and xylem fibers differentiate. It is known that gibberellins (GA) trigger this developmental transition via degradation of DELLA proteins and that the cambium master regulator BREVIPEDICELLUS/KNAT1 (BP/KNAT1) and receptor like kinases ERECTA and ERL1 regulate this process downstream of GA. However, our understanding of the regulatory network underlying GA-mediated secondary growth is still limited. Here, we demonstrate that DELLA-mediated xylem expansion in Arabidopsis hypocotyl is mainly achieved through DELLA family members RGA and GAI, which promote cambium senescence. We further show that AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8, which physically interact with DELLAs, specifically repress phloem proliferation and induce cambium senescence during the xylem expansion phase. Moreover, the inactivation of BP in arf6 arf8 background revealed an essential role for ARF6 and ARF8 in cambium establishment and maintenance. Overall, our results shed light on a pivotal hormone cross-talk between GA and auxin in the context of plant secondary growth.
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Affiliation(s)
- Mehdi Ben-Targem
- ZMBP - Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Dagmar Ripper
- ZMBP - Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Martin Bayer
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Laura Ragni
- ZMBP - Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
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47
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Jodder J. Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant. PLANT CELL REPORTS 2021; 40:783-798. [PMID: 33454802 DOI: 10.1007/s00299-020-02660-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.
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Affiliation(s)
- Jayanti Jodder
- School of Biotechnology, Presidency University (Rajarhat Campus), Canal Bank 7 Road, DG Block, Action Area 1D, Newtown, Kolkata, West Bengal, 700156, India.
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Han Y, Zhang Y, Cao G, Shao L, Ding Q, Ma L. Dynamic expression of miRNAs and functional analysis of target genes involved in the response to male sterility of the wheat line YS3038. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:363-377. [PMID: 33730621 DOI: 10.1016/j.plaphy.2021.02.047] [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: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Thermosensitive cytoplasmic male sterile (TCMS) lines play an important role in wheat breeding, heterosis utilization, and germplasm innovation. MicroRNAs (miRNAs) can regulate the expression level of target genes by inhibiting the translation of these genes. YS3038 is a wheat TCMS line. In this study, the fertility conversion mechanism of YS3038 was studied by examining the abortion characteristics of YS3038, the regulation pattern of miRNAs and the target genes of miRNAs in YS3038. MiRNA-seq was performed on three important stages of YS3038 under sterile and fertile conditions. Then, the clean reads were aligned with some databases to filter other ncRNAs and repeats. The known miRNAs and novel miRNAs were predicted by sequence comparison with known miRNAs from miRbase. Differential expression of miRNAs between different stages and between different fertile conditions was analyzed, and functional analysis of target genes with opposite expression patterns as those of the miRNAs was conducted. The Ubisch bodies and microspores of sterile anthers were covered with filamentous materials. The degradation of the tapetum cells, the chloroplast structure of endothecium cells, and the microspore structure were abnormal. Microspore development was hindered from the late uninucleate stage to the binucleate stage. Twenty, 52, and 68 differentially expressed miRNAs (DEmiRs) were identified at the early uninucleate, late uninucleate, and binucleate stages, respectively, and there were 0, 7, and 72 differentially expressed target genes (DETGs), respectively, at these three stages. At the binucleate stage, 29 DEmiRs had 41 target mRNAs in total, and the expression patterns of the 41 target mRNAs were opposite to those of the 29 miRNAs. Fifteen significantly enriched KEGG pathways were associated with the 41 target mRNAs. Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental and physiological processes. Some studies have shown that the expression of LRR-RLKs is related to the differentiation of microsporocytes and tapetum cells and to male sterility. An LRR-RLK (TaeRPK) gene was silenced by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method, and the seed setting rates of the TaeRPK-silenced plants (3.51%) were significantly lower than those of the negative control plants (88.78%) (P < 0.01). Thus, the TaeRPK gene is likely to be involved in the fertility conversion of YS3038.
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Affiliation(s)
- Yucui Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiyang Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guannan Cao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Leilei Shao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Priming by High Temperature Stress Induces MicroRNA Regulated Heat Shock Modules Indicating Their Involvement in Thermopriming Response in Rice. Life (Basel) 2021; 11:life11040291. [PMID: 33805566 PMCID: PMC8067039 DOI: 10.3390/life11040291] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 01/09/2023] Open
Abstract
Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures.
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50
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Genome-Wide Analysis of Ribosomal Protein GhRPS6 and Its Role in Cotton Verticillium Wilt Resistance. Int J Mol Sci 2021; 22:ijms22041795. [PMID: 33670294 PMCID: PMC7918698 DOI: 10.3390/ijms22041795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023] Open
Abstract
Verticillium wilt is threatening the world’s cotton production. The pathogenic fungus Verticillium dahliae can survive in the soil in the form of microsclerotia for a long time, colonize through the root of cotton, and invade into vascular bundles, causing yellowing and wilting of cotton leaves, and in serious cases, leading to plant death. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. In previous studies, proteomic analysis was carried out on different cotton varieties inoculated with V. dahliae strain Vd080. It was found that GhRPS6 was phosphorylated after inoculation, and the phosphorylation level in resistant cultivars was 1.5 times than that in susceptible cultivars. In this study, knockdown of GhRPS6 expression results in the reduction of SA and JA content, and suppresses a series of defensive response, enhancing cotton plants susceptibility to V. dahliae. Overexpression in Arabidopsis thaliana transgenic plants was found to be more resistant to V. dahliae. Further, serines at 237 and 240 were mutated to phenylalanine, respectively and jointly. The transgenic Arabidopsis plants demonstrated that seri-237 compromised the plant resistance to V. dahliae. Subcellular localization in Nicotiana benthamiana showed that GhRPS6 was localized in the nucleus. Additionally, the pathogen inoculation and phosphorylation site mutation did not change its localization. These results indicate that GhRPS6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.
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