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Ding T, Li W, Li F, Ren M, Wang W. microRNAs: Key Regulators in Plant Responses to Abiotic and Biotic Stresses via Endogenous and Cross-Kingdom Mechanisms. Int J Mol Sci 2024; 25:1154. [PMID: 38256227 PMCID: PMC10816238 DOI: 10.3390/ijms25021154] [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: 11/09/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Dramatic shifts in global climate have intensified abiotic and biotic stress faced by plants. Plant microRNAs (miRNAs)-20-24 nucleotide non-coding RNA molecules-form a key regulatory system of plant gene expression; playing crucial roles in plant growth; development; and defense against abiotic and biotic stress. Moreover, they participate in cross-kingdom communication. This communication encompasses interactions with other plants, microorganisms, and insect species, collectively exerting a profound influence on the agronomic traits of crops. This article comprehensively reviews the biosynthesis of plant miRNAs and explores their impact on plant growth, development, and stress resistance through endogenous, non-transboundary mechanisms. Furthermore, this review delves into the cross-kingdom regulatory effects of plant miRNAs on plants, microorganisms, and pests. It proceeds to specifically discuss the design and modification strategies for artificial miRNAs (amiRNAs), as well as the protection and transport of miRNAs by exosome-like nanovesicles (ELNVs), expanding the potential applications of plant miRNAs in crop breeding. Finally, the current limitations associated with harnessing plant miRNAs are addressed, and the utilization of synthetic biology is proposed to facilitate the heterologous expression and large-scale production of miRNAs. This novel approach suggests a plant-based solution to address future biosafety concerns in agriculture.
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Affiliation(s)
- Tianze Ding
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.D.); (W.L.); (F.L.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wenkang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.D.); (W.L.); (F.L.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.D.); (W.L.); (F.L.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Maozhi Ren
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.D.); (W.L.); (F.L.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wenjing Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.D.); (W.L.); (F.L.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Zhu X, Kuang Y, Chen Y, Shi J, Cao Y, Hu J, Yu C, Yang F, Tian F, Chen H. miR2118 Negatively Regulates Bacterial Blight Resistance through Targeting Several Disease Resistance Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3815. [PMID: 38005712 PMCID: PMC10675396 DOI: 10.3390/plants12223815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Plant miRNAs are a class of noncoding RNA with a length of 21-24 nt that play an important role in plant responses to biotic and abiotic stresses. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious bacterial diseases in rice. Our previous work showed that osa-miR2118b/n was induced by Xoo infection. However, the biological function of miR2118 has not yet been characterized in experiments. Herein, we constructed MIR2118b OE, as well as single and double mutants of MIR2118b/n using CRISPR/Cas9. Further results showed that osa-MIR2118b OE plants exhibited longer lesion lengths than the wild type after Xoo inoculation, while MIR2118 CRISPR plants exhibited shorter lesion lengths than the wild type after Xoo inoculation. Co-transformation experiments in rice protoplasts indicated that osa-miR2118 negatively regulated the transcripts of three nucleotide-binding sites and leucine-rich repeat (NLR) genes (LOC_Os08g42700.1, LOC_Os01g05600.1, and LOC_Os12g37290.1) which are predicted target genes of miR2118, but not the mutated NLR genes with a 3 bp insertion at the center of the binding sites. The transcriptional level of the three NLR genes was reversed relative to osa-miR2118 in the MIR2118b OE and MIR2118b CRISPR plants. The above results demonstrate that osa-miR2118b/n negatively regulates the resistance to bacterial blight through negatively regulating several NLR genes.
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Affiliation(s)
- Xiumei Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yongjie Kuang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yutong Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Jia Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yaqian Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Jixiang Hu
- Jiangsu Coastal Areas Institute of Agricultural Science, Jiangsu Academy of Agricultural Sciences, Yancheng 224002, China;
| | - Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
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3
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Dai H, Yang J, Teng L, Wang Z, Liang T, Khan WA, Yang R, Qiao B, Zhang Y, Yang C. Mechanistic basis for mitigating drought tolerance by selenium application in tobacco ( Nicotiana tabacum L.): a multi-omics approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1255682. [PMID: 37799555 PMCID: PMC10548829 DOI: 10.3389/fpls.2023.1255682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
The lack of irrigation water in agricultural soils poses a significant constraint on global crop production. In-depth investigation into microRNAs (miRNAs) has been widely used to achieve a comprehensive understanding of plant defense mechanisms. However, there is limited knowledge on the association of miRNAs with drought tolerance in cigar tobacco. In this study, a hydroponic experiment was carried out to identify changes in plant physiological characteristics, miRNA expression and metabolite profile under drought stress, and examine the mitigating effects of selenium (Se) application. The shoot dry weight of drought-stressed plants was approximately half (50.3%) of that in non-stressed (control) conditions. However, plants supplied with Se attained 38.8% greater shoot dry weight as compared to plants with no Se supply under drought stress. Thirteen miRNAs were identified to be associated with drought tolerance. These included 7 known (such as nta-miR156b and nta-miR166a) and 6 novel miRNAs (such as novel-nta-miR156-5p and novel-nta-miR209-5p) with the target genes of squamosa promoter-binding-like protein 4 (SPL4), serine/threonine protein phosphatase 2A (PPP2A), cation/calcium exchanger 4-like (CCX4), extensin-1-like (EXT1) and reduced wall acetylation 2 (RWA2). Further investigation revealed that the expression levels of Ext1 and RWA2 were significantly decreased under drought stress but increased with Se addition. Moreover, key metabolites such as catechin and N-acetylneuraminic acid were identified, which may play a role in the regulation of drought tolerance. The integrated analysis of miRNA sequencing and metabolome highlighted the significance of the novel-nta-miR97-5p- LRR-RLK- catechin pathway in regulating drought tolerance. Our findings provide valuable insights into the molecular mechanisms underlying drought tolerance and Se-induced stress alleviation in cigar tobacco.
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Affiliation(s)
- Huaxin Dai
- Department of Tobacco Agriculture, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Jinpeng Yang
- Department of Research Center on Tobacco Cultivating and Curing, Tobacco Research Institute of Hubei, Wuhan, China
| | - Lidong Teng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Taibo Liang
- Department of Tobacco Agriculture, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Waleed Amjad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ruiwei Yang
- Department of Research Center on Tobacco Cultivating and Curing, Tobacco Research Institute of Hubei, Wuhan, China
| | - Baoming Qiao
- Department of Research Center on Tobacco Cultivating and Curing, Tobacco Research Institute of Hubei, Wuhan, China
| | - Yanling Zhang
- Department of Tobacco Agriculture, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Chunlei Yang
- Department of Research Center on Tobacco Cultivating and Curing, Tobacco Research Institute of Hubei, Wuhan, China
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Huertas R, Torres-Jerez I, Curtin SJ, Scheible W, Udvardi M. Medicago truncatula PHO2 genes have distinct roles in phosphorus homeostasis and symbiotic nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2023; 14:1211107. [PMID: 37409286 PMCID: PMC10319397 DOI: 10.3389/fpls.2023.1211107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Three PHO2-like genes encoding putative ubiquitin-conjugating E2 enzymes of Medicago truncatula were characterized for potential roles in phosphorous (P) homeostasis and symbiotic nitrogen fixation (SNF). All three genes, MtPHO2A, B and C, contain miR399-binding sites characteristic of PHO2 genes in other plant species. Distinct spatiotemporal expression patterns and responsiveness of gene expression to P- and N-deprivation in roots and shoots indicated potential roles, especially for MtPHO2B, in P and N homeostasis. Phenotypic analysis of pho2 mutants revealed that MtPHO2B is integral to Pi homeostasis, affecting Pi allocation during plant growth under nutrient-replete conditions, while MtPHO2C had a limited role in controlling Pi homeostasis. Genetic analysis also revealed a connection between Pi allocation, plant growth and SNF performance. Under N-limited, SNF conditions, Pi allocation to different organs was dependent on MtPHO2B and, to a lesser extent, MtPHO2C and MtPHO2A. MtPHO2A also affected Pi homeostasis associated with nodule formation. Thus, MtPHO2 genes play roles in systemic and localized, i.e., nodule, P homeostasis affecting SNF.
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Affiliation(s)
- Raul Huertas
- Noble Research Institute LLC, Ardmore, OK, United States
| | | | - Shaun J. Curtin
- United States Department of Agriculture, Plant Science Research Unit, St. Paul, MN, United States
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | - Wolf Scheible
- Noble Research Institute LLC, Ardmore, OK, United States
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Wang X, Yuan D, Liu Y, Liang Y, He J, Yang X, Hang R, Jia H, Mo B, Tian F, Chen X, Liu L. INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize. THE PLANT CELL 2023; 35:2208-2231. [PMID: 36943781 PMCID: PMC10226601 DOI: 10.1093/plcell/koad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/30/2023]
Abstract
The macronutrient phosphorus is essential for plant growth and development. Plants have evolved multiple strategies to increase the efficiency of phosphate (Pi) acquisition to protect themselves from Pi starvation. However, the crosstalk between Pi homeostasis and plant development remains to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize (Zea mays) is associated with premature senescence after pollination. Knockout of ZmPHO2 (Phosphate 2), a miR399 target, resulted in a similar premature senescence phenotype. Strikingly, we discovered that INDETERMINATE1 (ID1), a floral transition regulator, inhibits the transcription of ZmMIR399 genes by directly binding to their promoters, alleviating the repression of ZmPHO2 by miR399 and ultimately contributing to the maintenance of Pi homeostasis in maize. Unlike ZmMIR399 genes, whose expression is induced by Pi deficiency, ID1 expression was independent of the external inorganic orthophosphate status, indicating that ID1 is an autonomous regulator of Pi homeostasis. Furthermore, we show that ZmPHO2 was under selection during maize domestication and cultivation, resulting in a more sensitive response to Pi starvation in temperate maize than in tropical maize. Our study reveals a direct functional link between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1.
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Affiliation(s)
- Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Dan Yuan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yanchun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Runlai Hang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hong Jia
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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Saputra TI, Maryanto SD, Tanjung ZA, Utomo C, Liwang T. Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.). Mol Biol Rep 2023:10.1007/s11033-023-08484-4. [PMID: 37171552 DOI: 10.1007/s11033-023-08484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. METHOD The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. RESULTS In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. CONCLUSIONS The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.
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Affiliation(s)
- Tengku Imam Saputra
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia.
| | - Sigit Dwi Maryanto
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Zulfikar Achmad Tanjung
- Bioinformatics Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Condro Utomo
- Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Tony Liwang
- Division of Plant Production and Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
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Pazhamala LT, Giri J. Plant phosphate status influences root biotic interactions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2829-2844. [PMID: 36516418 DOI: 10.1093/jxb/erac491] [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: 07/29/2022] [Accepted: 12/09/2022] [Indexed: 06/06/2023]
Abstract
Phosphorus (P) deficiency stress in combination with biotic stress(es) severely impacts crop yield. Plant responses to P deficiency overlapping with that of other stresses exhibit a high degree of complexity involving different signaling pathways. On the one hand, plants engage with rhizosphere microbiome/arbuscular mycorrhizal fungi for improved phosphate (Pi) acquisition and plant stress response upon Pi deficiency; on the other hand, this association is gets disturbed under Pi sufficiency. This nutrient-dependent response is highly regulated by the phosphate starvation response (PSR) mediated by the master regulator, PHR1, and its homolog, PHL. It is interesting to note that Pi status (deficiency/sufficiency) has a varying response (positive/negative) to different biotic encounters (beneficial microbes/opportunistic pathogens/insect herbivory) through a coupled PSR-PHR1 immune system. This also involves crosstalk among multiple players including transcription factors, defense hormones, miRNAs, and Pi transporters, among others influencing the plant-biotic-phosphate interactions. We provide a comprehensive view of these key players involved in maintaining a delicate balance between Pi homeostasis and plant immunity. Finally, we propose strategies to utilize this information to improve crop resilience to Pi deficiency in combination with biotic stresses.
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Affiliation(s)
- Lekha T Pazhamala
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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Zhong Y, Tian J, Li X, Liao H. Cooperative interactions between nitrogen fixation and phosphorus nutrition in legumes. THE NEW PHYTOLOGIST 2023; 237:734-745. [PMID: 36324147 DOI: 10.1111/nph.18593] [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: 07/26/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Legumes such as soybean are considered important crops as they provide proteins and oils for humans and livestock around the world. Different from other crops, leguminous crops accumulate nitrogen (N) for plant growth through symbiotic nitrogen fixation (SNF) in coordination with rhizobia. A number of studies have shown that efficient SNF requires the cooperation of other nutrients, especially phosphorus (P), a nutrient deficient in most soils. During the last decades, great progress has been made in understanding the molecular mechanisms underlying the interactions between SNF and P nutrition, specifically through the identification of transporters involved in P transport to nodules and bacteroids, signal transduction, and regulation of P homeostasis in nodules. These studies revealed a distinct N-P interaction in leguminous crops, which is characterized by specific signaling cross talk between P and SNF. This review aimed to present an updated picture of the cross talk between N fixation and P nutrition in legumes, focusing on soybean as a model crop, and Medicago truncatula and Lotus japonicus as model plants. We also discuss the possibilities for enhancing SNF through improving P nutrition, which are important for high and sustainable production of leguminous crops.
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Affiliation(s)
- Yongjia Zhong
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiang Tian
- Root Biology Center, South China Agricultural University, Guangzhou, 510642, China
| | - Xinxin Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Du K, Yang Y, Li J, Wang M, Jiang J, Wu J, Fang Y, Xiang Y, Wang Y. Functional Analysis of Bna-miR399c- PHO2 Regulatory Module Involved in Phosphorus Stress in Brassica napus. Life (Basel) 2023; 13:life13020310. [PMID: 36836667 PMCID: PMC9965056 DOI: 10.3390/life13020310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Phosphorus stress is one of the important factors restricting plant growth and development, and the microRNA (miRNA) family is involved in the regulation of the response to plant nutrient stress by repressing the expression of target genes at the post-transcriptional or translational level. miR399 is involved in the transportation of phosphate in multiple plants by improving tolerance to low Pi conditions. However, the effect of miR399 on the response of low Pi stress in rapeseed (Brassica napus L.) is unclear. The present study showed a significant increase in taproot length and lateral root number of plants overexpressing Bna-miR399c, while the biomass and Pi accumulation in shoots and roots increased, and the anthocyanin content decreased and chlorophyll content improved under low Pi stress. The results illustrate that Bna-miR399c could enhance the uptake and transportation of Pi in soil, thus making B. napus more tolerant to low Pi stress. Furthermore, we confirmed that BnPHO2 is one of the targets of Bna-miR399c, and the rejection of Pi in rapeseed seedlings increased due to the overexpression of BnPHO2. Hence, we suggest that miR399c-PHO2 module can effectively regulate the homeostasis of Pi in B. napus. Our study can also provide the theoretical basis for germplasm innovation and the design of intelligent crops with low nutrient input and high yield to achieve the dual objectives of income and yield increase and environmental protection in B. napus.
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Affiliation(s)
- Kun Du
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yang Yang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jinping Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Ming Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jian Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yujie Fang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-514-87997303; Fax: +86-514-87991747
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11
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Ou S, Xu Z, Mai C, Li B, Wang J. Ectopic expression of GmNF-YA8 in Arabidopsis delays flowering via modulating the expression of gibberellic acid biosynthesis- and flowering-related genes and promotes lateral root emergence in low phosphorus conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:1033938. [PMID: 36340418 PMCID: PMC9630906 DOI: 10.3389/fpls.2022.1033938] [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: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
NUCLEAR FACTOR Y subunit alpha (NF-YA), together with NF-YB and NF-YC, regulates plant growth and development, as well as plant responses to biotic and abiotic stresses. Although extensive studies have examined the functions of NF-YAs in Arabidopsis thaliana, the roles of NF- YAs in Glycinme max are poorly understood. In this study, we identified a phosphorus (P) starvation-responsive NF-YA8 in soybean. The expression of GmNF-YA8 is induced by low P or low nitrogen in leaves, but not by potassium or iron starvation, respectively. GmNF-YA8 is localized in the nucleus and plasma membrane. Ectopic expression of GmNF-YA8 inhibits plant growth and delayed flowering in Arabidopsis. Exogenous application of gibberellic acid (GA) rescues the delayed flowering phenotype in Arabidopsis overexpressing GmNF-YA8 lines GmNF-YA8OE-05 and GmNF-YA8OE-20. Moreover, quantitative real time PCR (qRT-PCR) verified that overexpression of GmNF-YA8 downregulates GA20ox2 and GA3ox2 expression, but upregulates GA2ox2 and GA2ox3 that encode enzymes, which inactive bioactive GAs. Consistent with the late flowering phenotype of Arabidopsis trangenic lines that overexpress GmNF-YA8, the transcript levels of flowering-promoting genes AP1, CO, LFY, and SOC1 are reduced. In addition, overexpression of GmNF-YA8 promotes the emergence of lateral root (LR) primordium from epidermis rather than the initiation of LR in low P, and increases the LR density in low nitrogen. Our results provide insights into the roles of GmNF-YA8.
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Affiliation(s)
- Siyan Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Zhihao Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Cuishan Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Bodi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
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12
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Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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Li Z, Tong Z, He F, Li X, Sun J. Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa. FRONTIERS IN PLANT SCIENCE 2022; 13:989048. [PMID: 36176687 PMCID: PMC9513243 DOI: 10.3389/fpls.2022.989048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/24/2022] [Indexed: 05/31/2023]
Abstract
The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.
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Affiliation(s)
- Zhenyi Li
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Sun
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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14
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [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: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
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15
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Wang D, Dong W, Murray J, Wang E. Innovation and appropriation in mycorrhizal and rhizobial Symbioses. THE PLANT CELL 2022; 34:1573-1599. [PMID: 35157080 PMCID: PMC9048890 DOI: 10.1093/plcell/koac039] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/20/2023]
Abstract
Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.
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Affiliation(s)
- Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Ertao Wang
- Authors for correspondence: (E.W) and (J.M.)
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16
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Chang H, Zhang H, Zhang T, Su L, Qin QM, Li G, Li X, Wang L, Zhao T, Zhao E, Zhao H, Liu Y, Stacey G, Xu D. A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans. FRONTIERS IN PLANT SCIENCE 2022; 13:860791. [PMID: 35463453 PMCID: PMC9021755 DOI: 10.3389/fpls.2022.860791] [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: 01/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Although growing evidence shows that microRNA (miRNA) regulates plant growth and development, miRNA regulatory networks in plants are not well understood. Current experimental studies cannot characterize miRNA regulatory networks on a large scale. This information gap provides an excellent opportunity to employ computational methods for global analysis and generate valuable models and hypotheses. To address this opportunity, we collected miRNA-target interactions (MTIs) and used MTIs from Arabidopsis thaliana and Medicago truncatula to predict homologous MTIs in soybeans, resulting in 80,235 soybean MTIs in total. A multi-level iterative bi-clustering method was developed to identify 483 soybean miRNA-target regulatory modules (MTRMs). Furthermore, we collected soybean miRNA expression data and corresponding gene expression data in response to abiotic stresses. By clustering these data, 37 MTRMs related to abiotic stresses were identified, including stress-specific MTRMs and shared MTRMs. These MTRMs have gene ontology (GO) enrichment in resistance response, iron transport, positive growth regulation, etc. Our study predicts soybean MTRMs and miRNA-GO networks under different stresses, and provides miRNA targeting hypotheses for experimental analyses. The method can be applied to other biological processes and other plants to elucidate miRNA co-regulation mechanisms.
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Affiliation(s)
- Haowu Chang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Hao Zhang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Tianyue Zhang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Lingtao Su
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- College of Computer Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Qing-Ming Qin
- College of Plant Sciences and Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Jilin, China
| | - Guihua Li
- College of Plant Sciences and Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Jilin, China
| | - Xueqing Li
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Li Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Tianheng Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Enshuang Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Hengyi Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Yuanning Liu
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Division of Plant Sciences and Technology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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17
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Li C, Nong W, Zhao S, Lin X, Xie Y, Cheung MY, Xiao Z, Wong AYP, Chan TF, Hui JHL, Lam HM. Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. BMC Genomics 2022; 23:65. [PMID: 35057741 PMCID: PMC8780314 DOI: 10.1186/s12864-022-08308-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood. RESULTS Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. CONCLUSIONS This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Shancen Zhao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, P.R. China
| | - Xiao Lin
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yichun Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Zhixia Xiao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Annette Y P Wong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
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18
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The Evolution and Functional Roles of miR408 and Its Targets in Plants. Int J Mol Sci 2022; 23:ijms23010530. [PMID: 35008962 PMCID: PMC8745667 DOI: 10.3390/ijms23010530] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.
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19
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Chen J, Han X, Ye S, Liu L, Yang B, Cao Y, Zhuo R, Yao X. Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2022; 13:932926. [PMID: 35979079 PMCID: PMC9377520 DOI: 10.3389/fpls.2022.932926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/11/2022] [Indexed: 05/02/2023]
Abstract
Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.
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Affiliation(s)
- Juanjuan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Forestry Faculty, Nanjing Forestry University, Nanjing, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Sicheng Ye
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Linxiu Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Bingbing Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yongqing Cao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- *Correspondence: Renying Zhuo,
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Xiaohua Yao,
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20
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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21
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Jiang W, He P, Zhou M, Lu X, Chen K, Liang C, Tian J. Soybean responds to phosphate starvation through reversible protein phosphorylation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:222-234. [PMID: 34371392 DOI: 10.1016/j.plaphy.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate (Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated. Among them, a nitrate reductase, GmNR4 exhibiting increased phosphorylation levels under low Pi conditions, was further selected to evaluate the effects of phosphorylation on its nitrate reductase activity and subcellular localization. Mutations of GmNR4 phosphorylation levels significantly influenced its activity in vitro, but not for its subcellular localization. Taken together, identification of differential phosphoproteins reveled the complex regulatory pathways for soybean adaptation to Pi starvation through reversible protein phosphorylation.
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Affiliation(s)
- Weizhen Jiang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; School of Traditional Chinese Medicine Resources, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Panmin He
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Zhou
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kang Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
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22
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Srivastava S, Suprasanna P. MicroRNAs: Tiny, powerful players of metal stress responses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:928-938. [PMID: 34246107 DOI: 10.1016/j.plaphy.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/14/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.
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Affiliation(s)
- Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, Maharashtra, India
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23
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Fan K, Wong-Bajracharya J, Lin X, Ni M, Ku YS, Li MW, Tian CF, Chan TF, Lam HM. Differentially expressed microRNAs that target functional genes in mature soybean nodules. THE PLANT GENOME 2021; 14:e20103. [PMID: 33973410 DOI: 10.1002/tpg2.20103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr.], we identified high-confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium-inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA-seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high-affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole-plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole-plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi-nitrogen balance to promote SNF in nodules.
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Affiliation(s)
- Kejing Fan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Johanna Wong-Bajracharya
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Xiao Lin
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Meng Ni
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Yee-Shan Ku
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting-Fung Chan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
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24
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Kumar J, Sen Gupta D, Djalovic I, Kumar S, Siddique KHM. Root-omics for drought tolerance in cool-season grain legumes. PHYSIOLOGIA PLANTARUM 2021; 172:629-644. [PMID: 33314181 DOI: 10.1111/ppl.13313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ivica Djalovic
- Maize Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
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25
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Zhang M, Su H, Gresshoff PM, Ferguson BJ. Shoot-derived miR2111 controls legume root and nodule development. PLANT, CELL & ENVIRONMENT 2021; 44:1627-1641. [PMID: 33386621 DOI: 10.1111/pce.13992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Legumes control their nodule numbers through the autoregulation of nodulation (AON). Rhizobia infection stimulates the production of root-derived CLE peptide hormones that are translocated to the shoot where they regulate a new signal. We used soybean to demonstrate that this shoot-derived signal is miR2111, which is transported via phloem to the root where it targets transcripts of Too Much Love (TML), a negative regulator of nodulation. Shoot perception of rhizobia-induced CLE peptides suppresses miR2111 expression, resulting in TML accumulation in roots and subsequent inhibition of nodule organogenesis. Feeding synthetic mature miR2111 via the petiole increased nodule numbers per plant. Likewise, elevating miR2111 availability by over-expression promoted nodulation, while target mimicry of TML induced the opposite effect on nodule development in wild-type plants and alleviated the supernodulating and stunted root growth phenotypes of AON-defective mutants. Additionally, in non-nodulating wild-type plants, ectopic expression of miR2111 significantly enhanced lateral root emergence with a decrease in lateral root length and average root diameter. In contrast, hairy roots constitutively expressing the target mimic construct exhibited reduced lateral root density. Overall, these findings demonstrate that miR2111 is both the critical shoot-to-root factor that positively regulates root nodule development and also acts to shape root system architecture.
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Affiliation(s)
- Mengbai Zhang
- Integrative Legume Research Group, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Huanan Su
- Integrative Legume Research Group, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
- National Navel Orange Engineering Research Centre, College of Life Science, Gannan Normal University, Ganzhou, China
| | - Peter M Gresshoff
- Integrative Legume Research Group, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Brett J Ferguson
- Integrative Legume Research Group, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
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26
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Nguyen NNT, Clua J, Vetal PV, Vuarambon DJ, De Bellis D, Pervent M, Lepetit M, Udvardi M, Valentine AJ, Poirier Y. PHO1 family members transport phosphate from infected nodule cells to bacteroids in Medicago truncatula. PLANT PHYSIOLOGY 2021; 185:196-209. [PMID: 33631809 PMCID: PMC8133656 DOI: 10.1093/plphys/kiaa016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/14/2020] [Indexed: 05/20/2023]
Abstract
Legumes play an important role in the soil nitrogen availability via symbiotic nitrogen fixation (SNF). Phosphate (Pi) deficiency severely impacts SNF because of the high Pi requirement of symbiosis. Whereas PHT1 transporters are involved in Pi uptake into nodules, it is unknown how Pi is transferred from the plant infected cells to nitrogen-fixing bacteroids. We hypothesized that Medicago truncatula genes homologous to Arabidopsis PHO1, encoding a vascular apoplastic Pi exporter, are involved in Pi transfer to bacteroids. Among the seven MtPHO1 genes present in M. truncatula, we found that two genes, namely MtPHO1.1 and MtPHO1.2, were broadly expressed across the various nodule zones in addition to the root vascular system. Expressions of MtPHO1.1 and MtPHO1.2 in Nicotiana benthamiana mediated specific Pi export. Plants with nodule-specific downregulation of both MtPHO1.1 and MtPHO1.2 were generated by RNA interference (RNAi) to examine their roles in nodule Pi homeostasis. Nodules of RNAi plants had lower Pi content and a three-fold reduction in SNF, resulting in reduced shoot growth. Whereas the rate of 33Pi uptake into nodules of RNAi plants was similar to control, transfer of 33Pi from nodule cells into bacteroids was reduced and bacteroids activated their Pi-deficiency response. Our results implicate plant MtPHO1 genes in bacteroid Pi homeostasis and SNF via the transfer of Pi from nodule infected cells to bacteroids.
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Affiliation(s)
- Nga N T Nguyen
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Joaquin Clua
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Pallavi V Vetal
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Dominique Jacques Vuarambon
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Damien De Bellis
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
- Electron Microscopy Facility, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR 1342 INRAE-IRD-CIRAD-UM-Montpellier SupAgro, Montpellier, France
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR 1342 INRAE-IRD-CIRAD-UM-Montpellier SupAgro, Montpellier, France
| | - Michael Udvardi
- The Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, USA
| | - Alexander J Valentine
- Botany & Zoology Department, University of Stellenbosch, Matieland 7602, South Africa
| | - Yves Poirier
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
- Author for communication:
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27
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Zhang J, Lin Y, Wu F, Zhang Y, Cheng L, Huang M, Tong Z. Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera. Front Genet 2021; 12:552454. [PMID: 33584823 PMCID: PMC7876418 DOI: 10.3389/fgene.2021.552454] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 01/06/2021] [Indexed: 01/14/2023] Open
Abstract
Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA-target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the "ascorbate and aldarate metabolism" pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA-target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.
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Affiliation(s)
- Junhong Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Bio-Technology, Zhejiang A&F University, Hangzhou, China
| | | | | | | | | | | | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Bio-Technology, Zhejiang A&F University, Hangzhou, China
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28
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Cheng L, Min W, Li M, Zhou L, Hsu CC, Yang X, Jiang X, Ruan Z, Zhong Y, Wang ZY, Wang W. Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L. Int J Mol Sci 2021; 22:E920. [PMID: 33477636 PMCID: PMC7831476 DOI: 10.3390/ijms22020920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/24/2022] Open
Abstract
Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes.
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Affiliation(s)
- Ling Cheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (X.J.); (Z.R.)
| | - Wanling Min
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.M.); (M.L.); (L.Z.)
| | - Man Li
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.M.); (M.L.); (L.Z.)
| | - Lili Zhou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.M.); (M.L.); (L.Z.)
| | - Chuan-Chih Hsu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; (C.-C.H.); (X.Y.); (Z.-Y.W.)
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Xuelian Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; (C.-C.H.); (X.Y.); (Z.-Y.W.)
| | - Xue Jiang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (X.J.); (Z.R.)
| | - Zhijie Ruan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (X.J.); (Z.R.)
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; (C.-C.H.); (X.Y.); (Z.-Y.W.)
| | - Wenfei Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (X.J.); (Z.R.)
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29
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Ding N, Huertas R, Torres‐Jerez I, Liu W, Watson B, Scheible W, Udvardi M. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. PLANT, CELL & ENVIRONMENT 2021; 44:186-202. [PMID: 32822068 PMCID: PMC7821211 DOI: 10.1111/pce.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 05/10/2023]
Abstract
Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.
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Affiliation(s)
- Na Ding
- Noble Research Institute LLCArdmoreOklahomaUSA
| | | | | | - Wei Liu
- Noble Research Institute LLCArdmoreOklahomaUSA
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30
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Pyo Y, Kim GM, Choi SW, Song CY, Yang SW, Jung IL. Strontium stress disrupts miRNA biogenesis by reducing HYL1 protein levels in Arabidopsis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111056. [PMID: 32763566 DOI: 10.1016/j.ecoenv.2020.111056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 05/20/2023]
Abstract
Strontium (Sr) is an emerging environmental pollutant that has become a major global concern after the nuclear accident at the Fukushima Daiichi Nuclear Power Plant in 2011. Although many studies have demonstrated the harmful effects of Sr on plant growth and development at the physiological level, knowledge regarding how plants sense and respond to Sr stress at the molecular level is limited. Recent studies have suggested that microRNAs (miRNAs) function as key regulators of plant growth and development as well as in the responses of plants to environmental stresses, including salinity, drought, cold, nutrient starvation, and heavy metals. In this study, we examined the global expression profile of miRNAs under Sr stress using small RNA sequencing analysis in Arabidopsis to better understand the molecular basis of plant responses to Sr stress. To identify specific Sr-responsive miRNAs, we performed comparative miRNA expression profiling analysis using control, CaCl2-, and SrCl2-treated seedlings. Compared to the control treatment, the expressions of most miRNAs were considerably decreased in the Sr-treated seedlings. However, under Sr stress, the expressions of primary miRNAs (pri-miRNAs) and their target genes were significantly increased; the protein levels of HYPONASTIC LEAVES 1 (HYL1), one of the core components of the microprocessor complex, were strongly reduced despite the increased HYL1 mRNA expression. In addition, hyl1-2 mutant plants were shown to be more sensitive to Sr stress than wild-type plants. Collectively, our results strongly suggested that Sr stress may be associated with the disruption of miRNA biogenesis by reducing the protein level of HYL1, which is required to maintain proper growth and development for plants. Our findings further indicated that some miRNAs may play important roles in plant responses to Sr stress.
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Affiliation(s)
- Youngjae Pyo
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea
| | - Gu Min Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suk Won Choi
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Yeob Song
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, 2000, Frederiksberg, Copenhagen, Denmark.
| | - Il Lae Jung
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Liu X, Chu S, Sun C, Xu H, Zhang J, Jiao Y, Zhang D. Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing. Funct Integr Genomics 2020; 20:825-838. [PMID: 33009591 DOI: 10.1007/s10142-020-00754-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype), were used for the construction of RNA sequencing (RNA-seq) libraries under low/normal-P treatment by high-throughput sequencing. In total, 603 existing miRNAs and 1699 novel miRNAs belonging to 248 and 1582 families in all samples were identified, respectively. Among these miRNAs, 777 miRNAs were differentially expressed (DE) across different P levels and genotypes. Furthermore, putative targets of DE miRNAs were predicted, and these miRNAs mainly targeted ERF (ethylene responsive factor), auxin response factors (ARF), zinc finger protein, MYB, and NAC domain transcription factors. Gene ontology (GO) analysis showed that targets of DE miRNAs were significantly enriched in binding, metabolic processes, biological regulation, response to stress, and phosphorus metabolic processes. In addition, the expression profiles of chosen P-responsive miRNAs and target genes were validated by quantitative real-time PCR (qRT-PCR). Our study focused on genome-wide miRNA identification in two representative soybean genotypes under low-P stress. Overall, the DE miRNAs across different P levels and genotypes and their putative target genes will provide useful information for further study of miRNAs mediating low-P response and facilitate improvements in soybean breeding.
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Affiliation(s)
- Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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Zhao Y, Xu K, Liu G, Li S, Zhao S, Liu X, Yang X, Xiao K. Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.). Sci Rep 2020; 10:15812. [PMID: 32978439 PMCID: PMC7519128 DOI: 10.1038/s41598-020-72642-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/18/2020] [Indexed: 12/25/2022] Open
Abstract
Potassium (K) is essential for plant growth and stress responses. MicroRNAs (miRNAs) are involved in adaptation to nutrient deprivation through modulating gene expression. Here, we identified the miRNAs responsive to K deficiency in Triticum aestivum based on high-throughput small RNA sequencing analyses. Eighty-nine miRNAs, including 68 previously reported ones and 21 novel ones, displayed differential expression under K deficiency. In Gene Ontology and Kyoto Encyclopedia and Genome analyses, the putative target genes of the differentially expressed miRNAs were categorized into functional groups associated with ADP-binding activity, secondary metabolic pathways, and biosynthesis and metabolism. Functional characterization of tae-miR408, an miRNA significantly down-regulated under K deficiency, revealed its important role in mediating low-K tolerance. Compared with wild type, transgenic tobacco lines overexpressing tae-miR408 showed significantly improved K uptake, biomass, photosynthesis, and reactive oxygen species scavenging under K deficiency. These results show that distinct miRNAs function in the plant response to K deficiency through regulating target genes involved in energy metabolism and various secondary metabolic pathways. Our findings shed light on the plant response to K deficiency mediated by miRNAs in T. aestivum. Distinct miRNAs, such as tae-miR408, are valuable targets for generating crop varieties with improved K-use efficiency.
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Affiliation(s)
- Yong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Ke Xu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Gaoran Liu
- College of Life Sciences, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Shanshan Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Sihang Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xiaowei Liu
- College of Resources and Environment Science, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xueju Yang
- College of Life Sciences, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China.
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Patil PG, Singh NV, Parashuram S, Bohra A, Mundewadikar DM, Sangnure VR, Babu KD, Sharma J. Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate ( Punica granatum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:683-696. [PMID: 32255932 PMCID: PMC7113349 DOI: 10.1007/s12298-020-00790-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/13/2020] [Accepted: 02/25/2020] [Indexed: 05/21/2023]
Abstract
A total of 17,439 mature miRNAs (~ 21 nt) earlier generated through RNA seq in the pomegranate were used for in silico analysis. After complexity reduction, a total of 1922 representative mature miRNAs were selected and used as query sequences against pomegranate genome to retrieve 2540 homologous contigs with flanking regions (~ 800). By using pre-miRNA prediction web server, a total of 1028 true contigs harbouring pri-miRNAs encoding 1162 pre-miRNAs were identified. Survey of these sequences for SSRs yielded a total of 1358 and 238 SSRs specific to pri-miRNA and pre-miRNAs, respectively. Of these, primer pairs were designed for 897 pri-miRNA and 168 pre-miRNA SSRs. In pri-miRNA sequences, hexa-nucleotides repeats were found to be most abundant (44.18%) followed by mono- (18.41%) and di-nucleotide (17.01%), which is also observed in pre-miRNA sequences. Further, a set of 51 randomly selected pre-miRNA-SSRs was examined for marker polymorphism. The experimental validation of these markers on eight pomegranate genotypes demonstrated 92.15% polymorphism. Utility of these functional markers was confirmed via examination of genetic diversity of 18 pomegranate genotypes using 15 miRNA-SSRs. Further, potential application of miRNA-SSRs for discovery of trait specific candidate genes was showed by validating 51 mature miRNA against publically available 2047 EST sequences of pomegranate by target and network analysis. In summary, the current study offers novel functional molecular markers for pomegranate genetic improvement.
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Affiliation(s)
- Prakash G. Patil
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - N. V. Singh
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 Uttar Pradesh India
| | | | - Vipul R. Sangnure
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - K. Dhinesh Babu
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
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Hu XG, Zhou SS, Yang Y, Liu H, Anil S, Wang Q, Zhao W, Gao Q, El-Kassaby YA, Wang T, Li Y, Mao JF. Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis. J Biosci 2020. [DOI: 10.1007/s12038-020-0002-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Rao S, Balyan S, Jha S, Mathur S. Novel insights into expansion and functional diversification of MIR169 family in tomato. PLANTA 2020; 251:55. [PMID: 31974682 DOI: 10.1007/s00425-020-03346-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 05/23/2023]
Abstract
MAIN CONCLUSION Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increase the functional diversification of MIR169 in tomato. MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.
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Affiliation(s)
- Sombir Rao
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Sonia Balyan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Sarita Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India.
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Hu XG, Zhou SS, Yang Y, Liu H, Anil S, Wang Q, Zhao W, Gao Q, El-Kassaby Y, Wang T, Li Y, Mao JF. Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis. J Biosci 2020; 45:41. [PMID: 32098920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18-30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species' stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.
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Affiliation(s)
- Xian-Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Zeng W, Sun Z, Lai Z, Yang S, Chen H, Yang X, Tao J, Tang X. Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing. Int J Mol Sci 2019; 20:E2966. [PMID: 31216642 PMCID: PMC6628378 DOI: 10.3390/ijms20122966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/05/2023] Open
Abstract
Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean's defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on-as well as their negatively regulated differentially expressed target genes-may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.
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Affiliation(s)
- Weiying Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zudong Sun
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zhenguang Lai
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Shouzhen Yang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Huaizhu Chen
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Jiangrong Tao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Xiangmin Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
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Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa. Funct Integr Genomics 2019; 19:953-972. [PMID: 31177404 DOI: 10.1007/s10142-019-00692-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 11/02/2018] [Accepted: 05/17/2019] [Indexed: 12/16/2022]
Abstract
miRNAs (microRNAs) are ~ 21-nt non-coding small RNAs (sRNAs) that play crucial regulatory roles in plant biotic and abiotic stress responses. Phosphorus (Pi) deficiency constrains plant growth and reduces yields worldwide. To identify tree miRNAs and evaluate their functions in the response to low Pi, we identified 261 known and 31 candidate novel miRNA families from three sRNA libraries constructed from Populus tomentosa subjected to sufficient or Pi deficiency condition or to restoration of a sufficient Pi level after Pi deficiency. Pi deficiency resulted in significant changes in the abundance of TPM (transcript per million) of 65 known and 3 novel miRNAs. Interestingly, four miRNAs responsive to low N-miR167, miR394, miR171, and miR857-were found to be involved in the response to low Pi. Thirty-five known and one novel miRNAs responded dynamically to Pi fluctuations, suggesting their involvement in the response to Pi deficiency. miRNA clusters comprising 36 miRNAs were identified in 10 chromosomes. Intriguingly, nine pairs of sense and antisense miRNAs transcribed from the same loci were detected in P. tomentosa, which is the first such report in woody plants. Moreover, target genes of the known miRNAs and novel miRNA candidates with significantly changed abundance were predicted, and their functions were annotated. Degradome sequencing supported the identified targets of miRNAs in P. tomentosa. These findings will enhance our understanding of universal and specific molecular regulatory mechanisms of trees under nutrition stress and may facilitate improvement of the Pi utilization efficiency of woody plants.
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Mo X, Zhang M, Liang C, Cai L, Tian J. Integration of metabolome and transcriptome analyses highlights soybean roots responding to phosphorus deficiency by modulating phosphorylated metabolite processes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:697-706. [PMID: 31054472 DOI: 10.1016/j.plaphy.2019.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 05/22/2023]
Abstract
Phosphorus (P) is a major constituent of biomolecules in plant cells, and is an essential plant macronutrient. Low phosphate (Pi) availability in soils is a major constraint on plant growth. Although a complex variety of plant responses to Pi starvation has been well documented, few studies have integrated both global transcriptome and metabolome analyses to shed light on molecular mechanisms underlying metabolic responses to P deficiency. This study is the first time to investigate global profiles of metabolites and transcripts in soybean (Glycine max) roots subjected to Pi starvation through targeted liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS/MS) and RNA-sequencing analyses. This integrated analysis allows for assessing coordinated transcriptomic and metabolic responses in terms of both pathway enzyme expression and regulatory levels. Between two Pi availability treatments, a total of 155 metabolites differentially accumulated in soybean roots, of which were phosphorylated metabolites, flavonoids and amino acids. Meanwhile, a total of 1644 differentially expressed genes (DEGs) were identified in soybean roots, including 1199 up-regulated and 445 down-regulated genes. Integration of metabolome and transcriptome analyses revealed Pi starvation responsive connection between specific metabolic processes in soybean roots, especially metabolic processes involving phosphorylated metabolites (e.g., phosphorylated lipids and nucleic acids). Taken together, this study suggests that complex molecular responses scavenging internal Pi from phosphorylated metabolites are typical adaptive strategies soybean roots employ as responses to Pi starvation. Identified DEGs will provide potential target region for future efforts to develop P-efficient soybean cultivars.
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Affiliation(s)
- Xiaohui Mo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Mengke Zhang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Luyu Cai
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China.
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Fei Y, Luo C, Tang W. Differential Expression of MicroRNAs During Root Formation in Taxus Chinensis Var. mairei Cultivars. Open Life Sci 2019; 14:97-109. [PMID: 33817141 PMCID: PMC7874753 DOI: 10.1515/biol-2019-0011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 11/15/2022] Open
Abstract
MicroRNAs (miRNAs) have been shown to play key roles in the regulation of plant growth and development by modifying the expression of their target genes. However, the influence of miRNAs on root formation and development in woody plants, such as Taxus chinensis, remains largely unknown. In the current study, we explored the phytohormone-response and nutrition-response miRNA expression profiles during T. chinensis rooting by quantitative real-time PCR (qPCR). We identified six phytohormone-response miRNAs, namely, miR164a, miR165, miR167a, miR171b, miR319, and miR391, and eight nutrition-response miRNAs, namely, miR169b, miR395a, miR399c, miR408, miR826, miR827, miR857, and miR2111a, that were differentially expressed at different rooting phases of T. chinensis. Using northern blot analysis of the putative target genes of these miRNAs, we detected the relative gene expression changes of the target genes. Taken together, our results suggest that miRNAs are involved in root formation of T. chinensis and that miRNAs may play important regulatory roles in primary root, crown root, and root hair formation by targeting phytohormone and/or nutrition response genes in T. chinensis. For the first time, these results expand our understanding of the molecular mechanisms of plant root formation and development in a conifer species.
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Affiliation(s)
- Yongjun Fei
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, Jingzhou, People's Republic of China
| | - Caroline Luo
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, Chapel Hill, USA
| | - Wei Tang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, Jingzhou, People's Republic of China
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41
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Noon JB, Hewezi T, Baum TJ. Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1653-1668. [PMID: 30715445 PMCID: PMC6411377 DOI: 10.1093/jxb/erz022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 05/20/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, penetrates soybean roots and migrates to the vascular cylinder where it forms a feeding site called the syncytium. MiRNA396 (miR396) targets growth-regulating factor (GRF) genes, and the miR396-GRF1/3 module is a master regulator of syncytium development in model cyst nematode H. schachtii infection of Arabidopsis. Here, we investigated whether this regulatory system operates similarly in soybean roots and is likewise important for H. glycines infection. We found that a network involving nine MIR396 and 23 GRF genes is important for normal development of soybean roots and that GRF function is specified in the root apical meristem by miR396. All MIR396 genes are down-regulated in the syncytium during its formation phase while, specifically, 11 different GRF genes are up-regulated. The switch to the syncytium maintenance phase coincides with up-regulation of MIR396 and down-regulation of the 11 GRF genes specifically via post-transcriptional regulation by miR396. Furthermore, interference with the miR396-GRF6/8-13/15-17/19 regulatory network, through either overexpression or knockdown experiments, does not affect the number of H. glycines juveniles that enter the vascular cylinder to initiate syncytia, but specifically inhibits efficient H. glycines development to adult females. Therefore, homeostasis in the miR396-GRF6/8-13/15-17/19 regulatory network is essential for productive H. glycines infections.
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Affiliation(s)
- Jason B Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
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Hua Y, Zhang C, Shi W, Chen H. High-throughput sequencing reveals microRNAs and their targets in response to drought stress in wheat (Triticum aestivum L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1586586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Ye Hua
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Cheng Zhang
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Wanxi Shi
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Hong Chen
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
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Jiu S, Leng X, Haider MS, Dong T, Guan L, Xie Z, Li X, Shangguan L, Fang J. Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180735. [PMID: 30800341 PMCID: PMC6366190 DOI: 10.1098/rsos.180735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/24/2018] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development and stress responses. With more copper (Cu) and copper containing compounds used as bactericides and fungicides in plants, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, two small RNA libraries were constructed from Cu-treated and water-treated (Control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, a total of 158 known and 98 putative novel miRNAs were identified in the two libraries. Among these, 100 known and 47 novel miRNAs were identified as differentially expressed under Cu stress. Subsequently, the expression patterns of nine Cu-responsive miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive miRNAs between high throughput sequencing and qRT-PCR assays. The targets prediction of miRNAs indicates that miRNA may regulate some transcription factors, including AP2, SBP, NAC, MYB and ARF during Cu stress. The target genes for two known and two novel miRNAs showed specific cleavage sites at the 10th and/or 11th nucleotide from the 5'-end of the miRNA corresponding to their miRNA complementary sequences. The findings will lay the foundation for exploring the role of the regulation of miRNAs in response to Cu stress and provide valuable gene information for breeding some Cu-tolerant grapevine cultivars.
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Affiliation(s)
- Songtao Jiu
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Le Guan
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Zhenqiang Xie
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaopeng Li
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lingfei Shangguan
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
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miRNA Detection by Stem-Loop RT-qPCR in Studying microRNA Biogenesis and microRNA Responsiveness to Abiotic Stresses. Methods Mol Biol 2019; 1932:131-150. [PMID: 30701497 DOI: 10.1007/978-1-4939-9042-9_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This chapter is devoted to a PCR-based method for analyzing the expression level of mature miRNAs which utilizes the TaqMan® technology. Stem-loop RT-qPCR requires preparation of separate cDNA templates for each analyzed miRNA as reverse transcription occurs in the presence of a miRNA-specific stem-loop reverse primer. In quantitative analysis, SYBR® Green is not used but the more sensitive TaqMan® probe that on 5' end contains a covalently attached fluorophore and on 3' quencher. When quencher and fluorophore are spatially separated due to nucleolytic DNA polymerase activity, the signal is released and quantified. This section provides a detailed and comprehensive protocol allowing for the successful analysis of mature miRNA levels in analyzed sample. Reverse transcription combined with classic real-time PCR as well as ddPCR™ (Droplet Digital™ PCR) will be presented.
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Ferguson BJ, Mens C, Hastwell AH, Zhang M, Su H, Jones CH, Chu X, Gresshoff PM. Legume nodulation: The host controls the party. PLANT, CELL & ENVIRONMENT 2019; 42:41-51. [PMID: 29808564 DOI: 10.1111/pce.13348] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/16/2018] [Indexed: 05/21/2023]
Abstract
Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic relationship that legume plants establish with nitrogen-fixing rhizobia bacteria is central to their advantage. This plant-microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.
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Affiliation(s)
- Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Céline Mens
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - April H Hastwell
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Mengbai Zhang
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Huanan Su
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
- National Navel Orange Engineering Research Center, College of Life and Environmental Science, Gannan Normal University, Ganzhou, China
| | - Candice H Jones
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Xitong Chu
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
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Huen A, Bally J, Smith P. Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5'RACE analysis. BMC Genomics 2018; 19:940. [PMID: 30558535 PMCID: PMC6296076 DOI: 10.1186/s12864-018-5258-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/16/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate. RESULTS This study identified and characterised phosphate starvation-responsive miRNAs in the native Australian tobacco Nicotiana benthamiana. Small RNA libraries were constructed and sequenced from phosphate-starved plant leaves, stems and roots. Twenty-four conserved miRNA families and 36 species-specific miRNAs were identified. The majority of highly phosphate starvation-responsive miRNAs were highly conserved, comprising of members from the miR399, miR827, and miR2111 families. In addition, two miRNA-star species were identified to be phosphate starvation-responsive. A total of seven miRNA targets were confirmed using RLM-5'RACE to be cleaved by five miRNA families, including two confirmed cleavage targets for Nbe-miR399 species, one for Nbe-miR2111, and two for Nbe-miR398. A number of N. benthamiana-specific features for conserved miRNAs were identified, including species-specific miRNA targets predicted or confirmed for miR399, miR827, and miR398. CONCLUSIONS Our results give an insight into the phosphate starvation-responsive miRNAs of Nicotiana benthamiana, and indicate that the phosphate starvation response pathways in N. benthamiana contain both highly conserved and species-specific components.
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Affiliation(s)
- Amanda Huen
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, QLD, Brisbane, 4000, Australia
| | - Penelope Smith
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
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Du Q, Wang K, Zou C, Xu C, Li WX. The PILNCR1-miR399 Regulatory Module Is Important for Low Phosphate Tolerance in Maize. PLANT PHYSIOLOGY 2018; 177:1743-1753. [PMID: 29967097 PMCID: PMC6084674 DOI: 10.1104/pp.18.00034] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 05/21/2023]
Abstract
The regulation of adaptive responses to phosphorus (P) deficiency by the microRNA399 (miR399)/PHOSPHATE2 (PHO2) pathway has been well studied in Arabidopsis (Arabidopsis thaliana) but not in maize (Zea mays). Here, we show that miR399 transcripts are strongly induced in maize by phosphate (Pi) deficiency. Transgenic maize plants that overexpressed MIR399b accumulated excessive amounts of P in their shoots and displayed typical Pi-toxicity phenotypes. We reannotated ZmPHO2 with an additional 1,165 bp of the 5' untranslated region. miR399-guided posttranscriptional repression of ZmPHO2 was mainly observed in the P-efficient lines. We identified Pi-deficiency-induced long-noncoding RNA1 (PILNCR1) from our strand-specific RNA libraries. Transient expression assays in Nicotiana benthamiana and maize leaf protoplasts demonstrated that PILNCR1 inhibits ZmmiR399-guided cleavage of ZmPHO2 The abundance of PILNCR1 was significantly higher in P-inefficient lines than in P-efficient lines, which is consistent with the abundance of ZmmiR399 transcripts. These results indicate that the interaction between PILNCR1 and miR399 is important for tolerance to low Pi in maize.
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Affiliation(s)
- Qingguo Du
- Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Zou
- Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Xu
- Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen-Xue Li
- Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yu C, Chen Y, Cao Y, Chen H, Wang J, Bi YM, Tian F, Yang F, Rothstein SJ, Zhou X, He C. Overexpression of miR169o, an Overlapping MicroRNA in Response to Both Nitrogen Limitation and Bacterial Infection, Promotes Nitrogen Use Efficiency and Susceptibility to Bacterial Blight in Rice. PLANT & CELL PHYSIOLOGY 2018; 59:1234-1247. [PMID: 29566243 DOI: 10.1093/pcp/pcy060] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/14/2018] [Indexed: 05/04/2023]
Abstract
Limiting nitrogen (N) supply contributes to improved resistance to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) in susceptible rice (Oryza sativa). To understand the regulatory roles of microRNAs (miRNAs) in this phenomenon, 63 differentially expressed overlapping miRNAs in response to Xoo infection and N limitation stress in rice were identified through deep RNA sequencing and stem-loop quantitative real-time PCR. Among these, miR169o was further assessed as a typical overlapping miRNA through the overexpression of the miR169o primary gene. Osa-miR169o-OX plants were taller, and had more biomass accumulation with significantly increased nitrate and total amino acid contents in roots than the wild type (WT). Transcript level assays showed that under different N supply conditions, miR169o oppositely regulated NRT2, and this is reduced under normal N supply conditions but remarkably induced under N-limiting stress. On the other hand, osa-miR169o-OX plants also displayed increased disease lesion lengths and reduced transcriptional levels of defense gene (PR1b, PR10a, PR10b and PAL) compared with the WT after inoculation with Xoo. In addition, miR169o impeded Xoo-mediated NRT transcription. Therefore, the overlapping miR169o contributes to increase N use efficiency and negatively regulates the resistance to BB in rice. Consistently, transient expression of NF-YA genes in rice protoplasts promoted the transcripts of PR genes and NRT2 genes, while it reduced the transcripts of NRT1 genes. Our results provide novel and additional insights into the co ordinated regulatory mechanisms of cross-talk between Xoo infection and N deficiency responses in rice.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yutong Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaqian Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jichun Wang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chenyang He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Bao D, Ganbaatar O, Cui X, Yu R, Bao W, Falk BW, Wuriyanghan H. Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean. MOLECULAR PLANT PATHOLOGY 2018; 19:948-960. [PMID: 28695996 PMCID: PMC6638018 DOI: 10.1111/mpp.12581] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
Plants protect themselves from virus infections by several different defence mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including the regulation of host defences. Soybean mosaic virus (SMV) is the most common virus in soybean and, in this work, we identified dozens of SMV-responsive miRNAs by microarray analysis in an SMV-susceptible soybean line. Amongst the up-regulated miRNAs, miR168a, miR403a, miR162b and miR1515a predictively regulate the expression of AGO1, AGO2, DCL1 and DCL2, respectively, and miR1507a, miR1507c and miR482a putatively regulate the expression of several NBS-LRR family disease resistance genes. The regulation of target gene expression by these seven miRNAs was validated by both transient expression assays and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) experiments. Transcript levels for AGO1, DCL1, DCL2 and five NBS-LRR family genes were repressed at different time points after SMV infection, whereas the corresponding miRNA levels were up-regulated at these same time points. Furthermore, inhibition of miR1507a, miR1507c, miR482a, miR168a and miR1515a by short tandem target mimic (STTM) technology compromised SMV infection efficiency in soybean. Our results imply that SMV can counteract soybean defence responses by the down-regulation of several RNAi pathway genes and NBS-LRR family resistance genes via the induction of the accumulation of their corresponding miRNA levels.
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Affiliation(s)
- Duran Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Oyunchuluun Ganbaatar
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Xiuqi Cui
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Ruonan Yu
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Wenhua Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Bryce W. Falk
- Department of Plant PathologyUniversity of California DavisDavisCA 95616USA
| | - Hada Wuriyanghan
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
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Huo W, Li B, Kuang J, He P, Xu Z, Wang J. Functional Characterization of the Steroid Reductase Genes GmDET2a and GmDET2b form Glycine max. Int J Mol Sci 2018; 19:E726. [PMID: 29510512 PMCID: PMC5877587 DOI: 10.3390/ijms19030726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
Brassinosteroids are important phytohormones for plant growth and development. In soybean (Glycine max), BR receptors have been identified, but the genes encoding BR biosynthesis-related enzymes remain poorly understood. Here, we found that the soybean genome encodes eight steroid reductases (GmDET2a to GmDET2h). Phylogenetic analysis grouped 105 steroid reductases from moss, fern and higher plants into five subgroups and indicated that the steroid reductase family has experienced purifying selection. GmDET2a and GmDET2b, homologs of the Arabidopsis thaliana steroid 5 α -reductase AtDET2, are proteins of 263 amino acids. Ectopic expression of GmDET2a and GmDET2b rescued the defects of the Atdet2-1 mutant in both darkness and light. Compared to the mutant, the hypocotyl length and plant height of the transgenic lines GmDET2a and GmDET2b increased significantly, in both darkness and light, and the transcript levels of the BR biosynthesis-related genes CPD, DWF4, BR6ox-1 and BR6ox-2 were downregulated in GmDET2aOX-23 and GmDET2bOX-16 lines compared to that in Atdet2-1. Quantitative real-time PCR revealed that GmDET2a and GmDET2b are ubiquitously expressed in all tested soybean organs, including roots, leaves and hypocotyls. Moreover, epibrassinosteroid negatively regulated GmDET2a and GmDET2b expression. Sulfate deficiency downregulated GmDET2a in leaves and GmDET2b in leaves and roots; by contrast, phosphate deficiency upregulated GmDET2b in roots and leaves. Taken together, our results revealed that GmDET2a and GmDET2b function as steroid reductases.
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Affiliation(s)
- Weige Huo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Bodi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Jiebing Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Pingan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Zhihao Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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