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Edet OU, Ubi BE, Ishii T. Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp. Sci Rep 2024; 14:10654. [PMID: 38724579 PMCID: PMC11082238 DOI: 10.1038/s41598-024-61062-x] [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: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Department of Crop Science, University of Calabar, PMB 1115, Calabar, Cross River State, Nigeria.
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Zhao M, Du C, Zeng J, Gao Z, Zhu Y, Wang J, Zhang Y, Zhu Z, Wang Y, Chen M, Wang Y, Chang J, Yang G, He G, Li Y, Chen X. Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1156514. [PMID: 37360728 PMCID: PMC10288491 DOI: 10.3389/fpls.2023.1156514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/26/2023] [Indexed: 06/28/2023]
Abstract
Partial root-zone drying (PRD) is an effective water-saving irrigation strategy that improves stress tolerance and facilitates efficient water use in several crops. It has long been considered that abscisic acid (ABA)-dependent drought resistance may be involved during partial root-zone drying. However, the molecular mechanisms underlying PRD-mediated stress tolerance remain unclear. It's hypothesized that other mechanisms might contribute to PRD-mediated drought tolerance. Here, rice seedlings were used as a research model and the complex transcriptomic and metabolic reprogramming processes were revealed during PRD, with several key genes involved in osmotic stress tolerance identified by using a combination of physiological, transcriptome, and metabolome analyses. Our results demonstrated that PRD induces transcriptomic alteration mainly in the roots but not in the leaves and adjusts several amino-acid and phytohormone metabolic pathways to maintain the balance between growth and stress response compared to the polyethylene glycol (PEG)-treated roots. Integrated analysis of the transcriptome and metabolome associated the co-expression modules with PRD-induced metabolic reprogramming. Several genes encoding the key transcription factors (TFs) were identified in these co-expression modules, highlighting several key TFs, including TCP19, WRI1a, ABF1, ABF2, DERF1, and TZF7, involved in nitrogen metabolism, lipid metabolism, ABA signaling, ethylene signaling, and stress regulation. Thus, our work presents the first evidence that molecular mechanisms other than ABA-mediated drought resistance are involved in PRD-mediated stress tolerance. Overall, our results provide new insights into PRD-mediated osmotic stress tolerance, clarify the molecular regulation induced by PRD, and identify genes useful for further improving water-use efficiency and/or stress tolerance in rice.
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Affiliation(s)
- Minhua Zhao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jian Zeng
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhihong Gao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yongyong Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Jinfei Wang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yupeng Zhang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zetao Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyuan Chen
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
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Wenndt A, Boyles R, Ackerman A, Sapkota S, Repka A, Nelson R. Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex. PLANT DISEASE 2023; 107:315-325. [PMID: 36800304 DOI: 10.1094/pdis-03-22-0675-re] [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: 06/18/2023]
Abstract
Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.
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Affiliation(s)
- Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Richard Boyles
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Arlyn Ackerman
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634
| | - Ace Repka
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Rebecca Nelson
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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Li Y, Wang W, Ma C, Ming R. Editorial: Genomics-Enabled Crop Genetics. Front Genet 2021; 12:687160. [PMID: 34025725 PMCID: PMC8138204 DOI: 10.3389/fgene.2021.687160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/15/2021] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wenqin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Xianyang, China.,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Xianyang, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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