1
|
Shen H, Hou Y, Wang X, Li Y, Wu J, Lou H. Genome-Wide Identification, Expression Analysis under Abiotic Stress and Co-Expression Analysis of MATE Gene Family in Torreya grandis. Int J Mol Sci 2024; 25:3859. [PMID: 38612669 PMCID: PMC11012001 DOI: 10.3390/ijms25073859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis.
Collapse
Affiliation(s)
| | | | | | | | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
| |
Collapse
|
2
|
Gajjar P, Ismail A, Islam T, Moniruzzaman M, Darwish AG, Dawood AS, Mohamed AG, Haikal AM, El-Saady AM, El-Kereamy A, Sherif SM, Abazinge MD, Kambiranda D, El-Sharkawy I. Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock 'Ruggeri' throughout Salinity. PLANTS (BASEL, SWITZERLAND) 2024; 13:837. [PMID: 38592889 PMCID: PMC10974295 DOI: 10.3390/plants13060837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Salinity is one of the substantial threats to plant productivity and could be escorted by other stresses such as heat and drought. It impairs critical biological processes, such as photosynthesis, energy, and water/nutrient acquisition, ultimately leading to cell death when stress intensity becomes uncured. Therefore, plants deploy several proper processes to overcome such hostile circumstances. Grapevine is one of the most important crops worldwide that is relatively salt-tolerant and preferentially cultivated in hot and semi-arid areas. One of the most applicable strategies for sustainable viticulture is using salt-tolerant rootstock such as Ruggeri (RUG). The rootstock showed efficient capacity of photosynthesis, ROS detoxification, and carbohydrate accumulation under salinity. The current study utilized the transcriptome profiling approach to identify the molecular events of RUG throughout a regime of salt stress followed by a recovery procedure. The data showed progressive changes in the transcriptome profiling throughout salinity, underpinning the involvement of a large number of genes in transcriptional reprogramming during stress. Our results established a considerable enrichment of the biological process GO-terms related to salinity adaptation, such as signaling, hormones, photosynthesis, carbohydrates, and ROS homeostasis. Among the battery of molecular/cellular responses launched upon salinity, ROS homeostasis plays the central role of salt adaptation.
Collapse
Affiliation(s)
- Pranavkumar Gajjar
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
| | - Ahmed Ismail
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Tabibul Islam
- Plant Sciences Department, University of Tennessee, Knoxville, TN 37996, USA
| | - Md Moniruzzaman
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
| | - Ahmed G Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia 61519, Egypt
| | - Ahmed S Dawood
- Horticulture Department, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed G Mohamed
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
| | - Amr M Haikal
- Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | | | - Ashraf El-Kereamy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Sherif M Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA
| | - Michael D Abazinge
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA
| | - Devaiah Kambiranda
- Department of Plant and Soil Sciences, Southern University Agricultural Research and Extension Center, Baton Rouge, LA 70813, USA
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA
| |
Collapse
|
3
|
Budnick A, Franklin MJ, Utley D, Edwards B, Charles M, Hornstein ED, Sederoff H. Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus. THE PLANT GENOME 2024; 17:e20429. [PMID: 38243772 DOI: 10.1002/tpg2.20429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/21/2024]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.
Collapse
Affiliation(s)
- Asa Budnick
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Megan J Franklin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Delecia Utley
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Brianne Edwards
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Melodi Charles
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Eli D Hornstein
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
4
|
Gélinas Bélanger J, Copley TR, Hoyos-Villegas V, O'Donoughue L. Dissection of the E8 locus in two early maturing Canadian soybean populations. FRONTIERS IN PLANT SCIENCE 2024; 15:1329065. [PMID: 38390301 PMCID: PMC10881665 DOI: 10.3389/fpls.2024.1329065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.
Collapse
Affiliation(s)
- Jérôme Gélinas Bélanger
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
- Department of Plant Science, McGill University, Montréal, QC, Canada
| | - Tanya Rose Copley
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
| | | | - Louise O'Donoughue
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
| |
Collapse
|
5
|
Shen J, Wang X, Song H, Wang M, Niu T, Lei H, Qin C, Liu A. Physiology and transcriptomics highlight the underlying mechanism of sunflower responses to drought stress and rehydration. iScience 2023; 26:108112. [PMID: 37860690 PMCID: PMC10583116 DOI: 10.1016/j.isci.2023.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/15/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Drought can adversely influence the crop growth and production. Accordingly, sunflowers have strong adaptability to drought; hence, we conducted analyses for sunflower seedlings with drought stress and rehydration drought acclimation through physiological measurements and transcriptomics. It showed that drought can cause the accumulation of ROS and enhance the activity of antioxidant enzymes and the content of osmolytes. After rehydration, the contents of ROS and MDA were significantly reduced concomitant with increased antioxidant activity and osmotic adjustment. Totally, 2,589 DEGs were identified among treatments. Functional enrichment analysis showed that DEGs were mainly involved in plant hormone signal transduction, MAPK signaling, and biosynthesis of secondary metabolites. Comparison between differentially spliced genes and DEGs indicated that bHLH025, NAC53, and SINAT3 may be pivotal genes involved in sunflower drought resistance. Our results not only highlight the underlying mechanism of drought stress and rehydration in sunflower but also provide a theoretical basis for crop genetic breeding.
Collapse
Affiliation(s)
- Jie Shen
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiying Lei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Cheng Qin
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| |
Collapse
|
6
|
Liu H, Chong P, Yan S, Liu Z, Bao X, Tan B. Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3542. [PMID: 37896006 PMCID: PMC10609793 DOI: 10.3390/plants12203542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
This work aims at studying the molecular mechanisms underlying the response of Reaumuria soongorica to salt stress. We used RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) techniques to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in R. soongorica leaves treated with 0, 200, and 500 mM NaCl for 72 h. The results indicated that compared with the 0 mM NaCl treatment group, 2391 and 6400 DEGs were identified in the 200 and 500 mM NaCl treatment groups, respectively, while 47 and 177 DEPs were also identified. Transcriptome and proteome association analysis was further performed on R. soongorica leaves in the 0/500 mM NaCl treatment group, and 32 genes with consistent mRNA and protein expression trends were identified. SYP71, CS, PCC13-62, PASN, ZIFL1, CHS2, and other differential genes are involved in photosynthesis, vesicle transport, auxin transport, and other functions of plants, and might play a key role in the salt tolerance of R. soongorica. In this study, transcriptome and proteome association techniques were used to screen candidate genes associated with salt tolerance in R. soongorica, which provides an important theoretical basis for understanding the molecular mechanism of salt tolerance in R. soongorica and breeding high-quality germplasm resources.
Collapse
Affiliation(s)
- Hanghang Liu
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Peifang Chong
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Shipeng Yan
- School of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Zehua Liu
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Xinguang Bao
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Bingbing Tan
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| |
Collapse
|
7
|
Spielmann J, Fanara S, Cotelle V, Vert G. Multilayered regulation of iron homeostasis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1250588. [PMID: 37841618 PMCID: PMC10570522 DOI: 10.3389/fpls.2023.1250588] [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: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023]
Abstract
Iron (Fe) is an essential micronutrient for plant growth and development due to its role in crucial processes such as photosynthesis and modulation of the redox state as an electron donor. While Fe is one of the five most abundant metals in the Earth's crust, it is poorly accessible to plants in alkaline soils due to the formation of insoluble complexes. To limit Fe deficiency symptoms, plant have developed a highly sophisticated regulation network including Fe sensing, transcriptional regulation of Fe-deficiency responsive genes, and post-translational modifications of Fe transporters. In this mini-review, we detail how plants perceive intracellular Fe status and how they regulate transporters involved in Fe uptake through a complex cascade of transcription factors. We also describe the current knowledge about intracellular trafficking, including secretion to the plasma membrane, endocytosis, recycling, and degradation of the two main Fe transporters, IRON-REGULATED TRANSPORTER 1 (IRT1) and NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN 1 (NRAMP1). Regulation of these transporters by their non-Fe substrates is discussed in relation to their functional role to avoid accumulation of these toxic metals during Fe limitation.
Collapse
Affiliation(s)
- Julien Spielmann
- Plant Science Research Laboratory (LRSV), University of Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Valérie Cotelle
- Plant Science Research Laboratory (LRSV), University of Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Grégory Vert
- Plant Science Research Laboratory (LRSV), University of Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| |
Collapse
|
8
|
George S, Rafi M, Aldarmaki M, ElSiddig M, Nuaimi MA, Sudalaimuthuasari N, Nath VS, Mishra AK, Hazzouri KM, Shah I, Amiri KMA. Ticarcillin degradation product thiophene acetic acid is a novel auxin analog that promotes organogenesis in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1182074. [PMID: 37731982 PMCID: PMC10507259 DOI: 10.3389/fpls.2023.1182074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 09/22/2023]
Abstract
Efficient regeneration of transgenic plants from explants after transformation is one of the crucial steps in developing genetically modified plants with desirable traits. Identification of novel plant growth regulators and developmental regulators will assist to enhance organogenesis in culture. In this study, we observed enhanced shoot regeneration from tomato cotyledon explants in culture media containing timentin, an antibiotic frequently used to prevent Agrobacterium overgrowth after transformation. Comparative transcriptome analysis of explants grown in the presence and absence of timentin revealed several genes previously reported to play important roles in plant growth and development, including Auxin Response Factors (ARFs), GRF Interacting Factors (GIFs), Flowering Locus T (SP5G), Small auxin up-regulated RNAs (SAUR) etc. Some of the differentially expressed genes were validated by quantitative real-time PCR. We showed that ticarcillin, the main component of timentin, degrades into thiophene acetic acid (TAA) over time. TAA was detected in plant tissue grown in media containing timentin. Our results showed that TAA is indeed a plant growth regulator that promotes root organogenesis from tomato cotyledons in a manner similar to the well-known auxins, indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA). In combination with the cytokinin 6-benzylaminopurine (BAP), TAA was shown to promote shoot organogenesis from tomato cotyledon in a concentration-dependent manner. To the best of our knowledge, the present study reports for the first time demonstrating the function of TAA as a growth regulator in a plant species. Our work will pave the way for future studies involving different combinations of TAA with other plant hormones which may play an important role in in vitro organogenesis of recalcitrant species. Moreover, the differentially expressed genes and long noncoding RNAs identified in our transcriptome studies may serve as contender genes for studying molecular mechanisms of shoot organogenesis.
Collapse
Affiliation(s)
- Suja George
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Mohamed ElSiddig
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | - Vishnu Sukumari Nath
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Ajay Kumar Mishra
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| |
Collapse
|
9
|
Vranić M, Perochon A, Doohan FM. Transcriptional Profiling Reveals the Wheat Defences against Fusarium Head Blight Disease Regulated by a NAC Transcription Factor. PLANTS (BASEL, SWITZERLAND) 2023; 12:2708. [PMID: 37514322 PMCID: PMC10383764 DOI: 10.3390/plants12142708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
The wheat NAC transcription factor TaNACL-D1 enhances resistance to the economically devastating Fusarium head blight (FHB) disease. The objective of this study was to decipher the alterations in gene expression, pathways and biological processes that led to enhanced resistance as a result of the constitutive expression of TaNACL-D1 in wheat. Transcriptomic analysis was used to determine the genes and processes enhanced in wheat due to TaNACL-D1 overexpression, both in the presence and absence of the causal agent of FHB, Fusarium graminearum (0- and 1-day post-treatment). The overexpression of TaNACL-D1 resulted in more pronounced transcriptional reprogramming as a response to fungal infection, leading to the enhanced expression of genes involved in detoxification, immune responses, secondary metabolism, hormone biosynthesis, and signalling. The regulation and response to JA and ABA were differentially regulated between the OE and the WT. Furthermore, the results suggest that the OE may more efficiently: (i) regulate the oxidative burst; (ii) modulate cell death; and (iii) induce both the phenylpropanoid pathway and lignin synthesis. Thus, this study provides insights into the mode of action and downstream target pathways for this novel NAC transcription factor, further validating its potential as a gene to enhance FHB resistance in wheat.
Collapse
Affiliation(s)
- Monika Vranić
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
| |
Collapse
|
10
|
Xu D, Tang Q, Xu P, Schäffner AR, Leister D, Kleine T. Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought. FRONTIERS IN PLANT SCIENCE 2023; 14:1220928. [PMID: 37528975 PMCID: PMC10387551 DOI: 10.3389/fpls.2023.1220928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 08/03/2023]
Abstract
Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used RNA-sequencing after ribosomal RNA depletion to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0. Concerning the changes detected in the organellar transcriptomes, chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Conversely, alternative splicing (AS) affected nearly 1,500 genes (9% of expressed nuclear genes). Of these, 42% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Moreover, we identified 927 isoform switching events. We provide a table of the most interesting candidates, and as proof of principle, increased drought tolerance of the carbonic anhydrase ca1 and ca2 mutants is shown. In addition, altering the relative contributions of the spliced isoforms could increase drought resistance. For example, our data suggest that the accumulation of a nonfunctional FLM (FLOWERING LOCUS M) isoform and not the ratio of FLM-ß and -δ isoforms may be responsible for the phenotype of early flowering under long-day drought conditions. In sum, our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought.
Collapse
Affiliation(s)
- Duorong Xu
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Qian Tang
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Ping Xu
- Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, München, Germany
| | - Anton R. Schäffner
- Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, München, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| |
Collapse
|
11
|
Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. OBJECTIVES To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. METHODS Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. RESULTS Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. CONCLUSION Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
Collapse
Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
12
|
Hazra A, Pal A, Kundu A. Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]. Funct Integr Genomics 2023; 23:144. [PMID: 37133618 DOI: 10.1007/s10142-023-01066-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.
Collapse
Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, 700091, India.
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
| |
Collapse
|
13
|
Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. THE NEW PHYTOLOGIST 2023; 238:1722-1732. [PMID: 36751910 PMCID: PMC10952736 DOI: 10.1111/nph.18799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Understanding the evolutionary conservation of complex eukaryotic transcriptomes significantly illuminates the physiological relevance of alternative splicing (AS). Examining the evolutionary depth of a given AS event with ordinary homology searches is generally challenging and time-consuming. Here, we present Catsnap, an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by AS. It employs a machine learning approach following a database search with the provided pair of protein sequences. We used the Catsnap algorithm for analyzing the conservation of emerging experimentally characterized alternative proteins from plants and animals. Indeed, most of them are conserved among other species. Catsnap can detect the conserved functional protein isoforms regardless of the AS type by which they are generated. Notably, we found that while the primary amino acid sequence is maintained, the type of AS determining the inclusion or exclusion of protein regions varies throughout plant phylogenetic lineages in these proteins. We also document that this phenomenon is less seen among animals. In sum, our algorithm highlights the presence of unexpectedly frequent hotspots where protein isoforms recurrently arise to carry physiologically relevant functions. The user web interface is available at https://catsnap.cesnet.cz/.
Collapse
Affiliation(s)
- Ksenia Timofeyenko
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental BotanyCzech Academy of Sciences165 02Prague 6Czech Republic
- Functional Genomics and Proteomics of Plants and National Centre for Biomolecular ResearchMasaryk University625 00BrnoCzech Republic
| | | | - Panagiotis Alexiou
- Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant BiologyUniversity of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental BotanyCzech Academy of Sciences165 02Prague 6Czech Republic
| |
Collapse
|
14
|
Muhammad S, Xu X, Zhou W, Wu L. Alternative splicing: An efficient regulatory approach towards plant developmental plasticity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1758. [PMID: 35983878 DOI: 10.1002/wrna.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 05/13/2023]
Abstract
Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
Collapse
Affiliation(s)
- Sajid Muhammad
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoli Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weijun Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liang Wu
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
15
|
Srivastava R, Kobayashi Y, Koyama H, Sahoo L. Cowpea NAC1/NAC2 transcription factors improve growth and tolerance to drought and heat in transgenic cowpea through combined activation of photosynthetic and antioxidant mechanisms. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:25-44. [PMID: 36107155 DOI: 10.1111/jipb.13365] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
NAC (NAM/ATAF1/2/CUC2) transcription factors are central switches of growth and stress responses in plants. However, unpredictable interspecies conservation of function and regulatory targets makes the well-studied NAC orthologs inapt for pulse engineering. The knowledge of suitable NAC candidates in hardy pulses like cowpea (Vigna unguiculata (L.) Walp.) is still in infancy, hence warrants immediate biotechnological intervention. Here, we showed that overexpression of two native NAC genes (VuNAC1 and VuNAC2) promoted germinative, vegetative, and reproductive growth and conferred multiple abiotic stress tolerance in a commercial cowpea variety. The transgenic lines displayed increased leaf area, thicker stem, nodule-rich denser root system, early flowering, higher pod production (∼3.2-fold and ∼2.1-fold), and greater seed weight (10.3% and 6.0%). In contrast, transient suppression of VuNAC1/2 caused severe growth retardation and flower inhibition. The overexpressor lines showed remarkable tolerance to major yield-declining terminal stresses, such as drought, salinity, heat, and cold, and recovered growth and seed production by boosting photosynthetic activity, water use efficiency, membrane integrity, Na+ /K+ homeostasis, and antioxidant activity. The comparative transcriptome study indicated consolidated activation of genes involved in chloroplast development, photosynthetic complexes, cell division and expansion, cell wall biogenesis, nutrient uptake and metabolism, stress response, abscisic acid, and auxin signaling. Unlike their orthologs, VuNAC1/2 direct synergistic transcriptional tuning of stress and developmental signaling to avoid unwanted trade-offs. Their overexpression governs the favorable interplay of photosynthesis and reactive oxygen species regulation to improve stress recovery, nutritional sufficiency, biomass, and production. This unconventional balance of strong stress tolerance and agronomic quality is useful for translational crop research and molecular breeding of pulses.
Collapse
Affiliation(s)
- Richa Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu, 501-1193,, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu, 501-1193,, Japan
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| |
Collapse
|
16
|
Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023; 32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.
Collapse
Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - DongLei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| |
Collapse
|
17
|
Salgado FF, da Silva TLC, Vieira LR, Silva VNB, Leão AP, Costa MMDC, Togawa RC, de Sousa CAF, Grynberg P, Souza MT. The early response of oil palm ( Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress. FRONTIERS IN PLANT SCIENCE 2022; 13:970113. [PMID: 36212369 PMCID: PMC9539919 DOI: 10.3389/fpls.2022.970113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/25/2022] [Indexed: 06/09/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a oilseed crop of great economic importance drastically affected by abiotic stresses. MicroRNAs (miRNAs) play crucial roles in transcription and post-transcription regulation of gene expression, being essential molecules in the response of plants to abiotic stress. To better understand the molecular mechanisms behind the response of young oil palm plants to drought stress, this study reports on the prediction and characterization of miRNAs and their putative target genes in the apical leaf of plants subjected to 14 days of water deprivation. Then, the data from this study were compared to the data from a similar study that focused on salinity stress. Both, the drought-and salt-responsive miRNAs and their putative target genes underwent correlation analysis to identify similarities and dissimilarities among them. Among the 81 identified miRNAs, 29 are specific for oil palm, including two (egu-miR28ds and egu-miR29ds) new ones - described for the first time. As for the expression profile, 62 miRNAs were significantly differentially expressed under drought stress, being five up-regulated (miR396e, miR159b, miR529b, egu-miR19sds, and egu-miR29ds) and 57 down-regulated. Transcription factors, such as MYBs, HOXs, and NF-Ys, were predicted as putative miRNA-target genes in oil palm under water deprivation; making them the most predominant group of such genes. Finally, the correlation analysis study revealed a group of putative target genes with similar behavior under salt and drought stresses. Those genes that are upregulated by these two abiotic stresses encode lncRNAs and proteins linked to stress tolerance, stress memory, modulation of ROS signaling, and defense response regulation to abiotic and biotic stresses. In summary, this study provides molecular evidence for the possible involvement of miRNAs in the drought stress response in oil palm. Besides, it shows that, at the molecular level, there are many similarities in the response of young oil palm plants to these two abiotic stresses.
Collapse
Affiliation(s)
| | | | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil
| | | | - André Pereira Leão
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, Brazil
| | - Marcos Mota do Carmo Costa
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Roberto Coiti Togawa
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | | | - Priscila Grynberg
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, Brazil
| |
Collapse
|
18
|
Cabezas-Fuster A, Micol-Ponce R, Fontcuberta-Cervera S, Ponce M. Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites. Nucleic Acids Res 2022; 50:5513-5527. [PMID: 35639749 PMCID: PMC9177961 DOI: 10.1093/nar/gkac338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022] Open
Abstract
Efficient splicing requires a balance between high-fidelity splice-site (SS) selection and speed. In Saccharomyces cerevisiae, Pre-mRNA processing factor 8 (Prp8) helps to balance precise SS selection and rapid, efficient intron excision and exon joining. argonaute1-52 (ago1-52) and incurvata13 (icu13) are hypomorphic alleles of the Arabidopsis thaliana genes ARGONAUTE1 (AGO1) and AUXIN RESISTANT6 (AXR6) that harbor point mutations creating a novel 3'SS and 5'SS, respectively. The spliceosome recognizes these novel SSs, as well as the intact genuine SSs, producing a mixture of wild-type and aberrant mature mRNAs. Here, we characterized five novel mutant alleles of PRP8 (one of the two Arabidopsis co-orthologs of yeast Prp8), naming these alleles morphology of ago1-52 suppressed5 (mas5). In the mas5-1 background, the spliceosome preferentially recognizes the intact genuine 3'SS of ago1-52 and 5'SS of icu13. Since point mutations that damage genuine SSs make the spliceosome prone to recognizing cryptic SSs, we also tested alleles of four genes carrying damaged genuine SSs, finding that mas5-1 did not suppress their missplicing. The mas5-1 and mas5-3 mutations represent a novel class of missplicing suppressors that increase splicing fidelity by hampering the use of novel SSs, but do not alter general pre-mRNA splicing.
Collapse
Affiliation(s)
- Adrián Cabezas-Fuster
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Sara Fontcuberta-Cervera
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| |
Collapse
|
19
|
Ankit A, Kamali S, Singh A. Genomic & structural diversity and functional role of potassium (K +) transport proteins in plants. Int J Biol Macromol 2022; 208:844-857. [PMID: 35367275 DOI: 10.1016/j.ijbiomac.2022.03.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/03/2023]
Abstract
Potassium (K+) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K+ availability is sensed by plant roots, consequently K+ transport proteins are activated to optimize K+ uptake. In addition to K+ uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na+/K+ ratio and stomata movement during abiotic stress responses. K+ transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K+ uptake and transport and thus, provide functional diversity. Most K+ transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K+ transporters/channels could be a prominent strategy for improving K+ utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K+ transport proteins in plants. Also, an update on the function of K+ transport proteins and their regulatory mechanism in response to variable K+ availability, in improving KUE, biotic and abiotic stresses is provided.
Collapse
Affiliation(s)
- Ankit Ankit
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi 110067, India.
| |
Collapse
|
20
|
Sun G, Xia M, Li J, Ma W, Li Q, Xie J, Bai S, Fang S, Sun T, Feng X, Guo G, Niu Y, Hou J, Ye W, Ma J, Guo S, Wang H, Long Y, Zhang X, Zhang J, Zhou H, Li B, Liu J, Zou C, Wang H, Huang J, Galbraith DW, Song CP. The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata. THE PLANT CELL 2022; 34:1890-1911. [PMID: 35166333 PMCID: PMC9048877 DOI: 10.1093/plcell/koac047] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/28/2022] [Indexed: 05/26/2023]
Abstract
The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these responses is critical for improving food security. We have developed a planta platform of single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it to identify cell types in mature and developing stomata from 33,098 nuclei of the maize epidermis-enriched tissues. Guard cells (GCs) and subsidiary cells (SCs) displayed differential expression of genes, besides those encoding transporters, involved in the abscisic acid, CO2, Ca2+, starch metabolism, and blue light signaling pathways, implicating coordinated signal integration in speedy stomatal responses, and of genes affecting cell wall plasticity, implying a more sophisticated relationship between GCs and SCs in stomatal development and dumbbell-shaped guard cell formation. The trajectory of stomatal development identified in young tissues, and by comparison to the bulk RNA-seq data of the MUTE defective mutant in stomatal development, confirmed known features, and shed light on key participants in stomatal development. Our study provides a valuable, comprehensive, and fundamental foundation for further insights into grass stomatal function.
Collapse
Affiliation(s)
- Guiling Sun
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Mingzhang Xia
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Jieping Li
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Wen Ma
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Qingzeng Li
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Jinjin Xie
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Shenglong Bai
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Shanshan Fang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Ting Sun
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Xinlei Feng
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Guanghui Guo
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Yanli Niu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Jingyi Hou
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Wenling Ye
- School of Medicine, Key Laboratory of Receptors-Mediated Gene Regulation and Drug Discovery, Henan University, Kaifeng 475004, China
| | - Jianchao Ma
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Siyi Guo
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Hongliang Wang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Yu Long
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Xuebin Zhang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Junli Zhang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Hui Zhou
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Baozhu Li
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Jiong Liu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Changsong Zou
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
| | - Hai Wang
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jinling Huang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475004, China
- Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
| | | | | |
Collapse
|
21
|
Lee JS, Jahani M, Huang K, Mandel JR, Marek LF, Burke JM, Langlade NB, Owens GL, Rieseberg LH. Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower. J Adv Res 2022; 42:83-98. [PMID: 36513422 PMCID: PMC9788961 DOI: 10.1016/j.jare.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/01/2022] [Accepted: 04/16/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood. OBJECTIVES This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments. METHODS Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F1 hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing. RESULTS Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses. CONCLUSION Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.
Collapse
Affiliation(s)
- Joon Seon Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer R. Mandel
- Department of Biological Sciences and Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Laura F. Marek
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens 30602, Georgia
| | | | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada,Corresponding author.
| |
Collapse
|
22
|
Perlikowski D, Lechowicz K, Pawłowicz I, Arasimowicz-Jelonek M, Kosmala A. Scavenging of nitric oxide up-regulates photosynthesis under drought in Festuca arundinacea and F. glaucescens but reduces their drought tolerance. Sci Rep 2022; 12:6500. [PMID: 35444199 PMCID: PMC9021232 DOI: 10.1038/s41598-022-10299-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/06/2022] [Indexed: 12/18/2022] Open
Abstract
Nitric oxide (NO) has been proven to be involved in the regulation of many physiological processes in plants. Though the contribution of NO in plant response to drought has been demonstrated in numerous studies, this phenomenon remains still not fully recognized. The research presented here was performed to decipher the role of NO metabolism in drought tolerance and the ability to recover after stress cessation in two closely related species of forage grasses, important for agriculture in European temperate regions: Festuca arundinacea and F. glaucescens. In both species, two genotypes with distinct levels of drought tolerance were selected to compare their physiological reactions to simulated water deficit and further re-watering, combined with a simultaneous application of NO scavenger, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). The results clearly indicated a strong relationship between scavenging of NO in leaves and physiological response of both analyzed grass species to water deficit and re-watering. It was revealed that NO generated under drought was mainly located in mesophyll cells. In plants with reduced NO level a higher photosynthetic capacity and delay in stomatal closure under drought, were observed. Moreover, NO scavenging resulted also in the increased membrane permeability and higher accumulation of ROS in cells of analyzed plants both under drought and re-watering. This phenomena indicate that lower NO level might reduce drought tolerance and the ability of F. arundinacea and F. glaucescens to recover after stress cessation.
Collapse
Affiliation(s)
- Dawid Perlikowski
- Plant Physiology Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland.
| | - Katarzyna Lechowicz
- Plant Physiology Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Izabela Pawłowicz
- Plant Physiology Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Arkadiusz Kosmala
- Plant Physiology Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| |
Collapse
|
23
|
Islam MR, Naveed SA, Zhang Y, Li Z, Zhao X, Fiaz S, Zhang F, Wu Z, Hu Z, Fu B, Shi Y, Shah SM, Xu J, Wang W. Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses. Front Genet 2022; 13:822516. [PMID: 35281797 PMCID: PMC8905349 DOI: 10.3389/fgene.2022.822516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.
Collapse
Affiliation(s)
- Mohammad Rafiqul Islam
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqing Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shahid Masood Shah
- Department of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, Abbottabad, Pakistan
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| |
Collapse
|
24
|
Singh D, Singh CK, Taunk J, Gaikwad K, Singh V, Sanwal SK, Karwa S, Singh D, Sharma PC, Yadav RK, Pal M. Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus). BMC PLANT BIOLOGY 2022; 22:99. [PMID: 35247970 PMCID: PMC8897830 DOI: 10.1186/s12870-022-03489-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. RESULTS PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes' accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. CONCLUSIONS Phyto-hormones biosynthesis-predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.
Collapse
Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Vijayata Singh
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Satish Kumar Sanwal
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Sourabh Karwa
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Depatment of Botany, Meerut College, 250001, Meerut, India
| | - Parbodh Chander Sharma
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, 208002, Kanpur, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| |
Collapse
|
25
|
Ndoye MS, Burridge J, Bhosale R, Grondin A, Laplaze L. Root traits for low input agroecosystems in Africa: Lessons from three case studies. PLANT, CELL & ENVIRONMENT 2022; 45:637-649. [PMID: 35037274 DOI: 10.1111/pce.14256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In many regions across Africa, agriculture is largely based on low-input and small-holder farming systems that use little inorganic fertilisers and have limited access to irrigation and mechanisation. Improving agricultural practices and developing new cultivars adapted to these environments, where production already suffers from climate change, is a major priority for food security. Here, we illustrate how breeding for specific root traits could improve crop resilience in Africa using three case studies covering very contrasting low-input agroecosystems. We first review how greater basal root whorl number and longer and denser root hairs increased P acquisition efficiency and yield in common bean in South East Africa. We then discuss how water-saving strategies, root hair density and deep root growth could be targeted to improve sorghum and pearl millet yield in West Africa. Finally, we evaluate how breeding for denser root systems in the topsoil and interactions with arbuscular mycorrhizal fungi could be mobilised to optimise water-saving alternate wetting and drying practices in West African rice agroecosystems. We conclude with a discussion on how to evaluate the utility of root traits and how to make root trait selection feasible for breeders so that improved varieties can be made available to farmers through participatory approaches.
Collapse
Affiliation(s)
- Mame S Ndoye
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - James Burridge
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Rahul Bhosale
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Alexandre Grondin
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Laurent Laplaze
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| |
Collapse
|
26
|
Stanton C, Sanders D, Krämer U, Podar D. Zinc in plants: Integrating homeostasis and biofortification. MOLECULAR PLANT 2022; 15:65-85. [PMID: 34952215 DOI: 10.1016/j.molp.2021.12.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 05/24/2023]
Abstract
Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn2+ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.
Collapse
Affiliation(s)
| | - Dale Sanders
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Dorina Podar
- Department of Molecular Biology and Biotechnology and Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400084 Cluj-Napoca, Romania.
| |
Collapse
|
27
|
Kashkan I, Timofeyenko K, Růžička K. How alternative splicing changes the properties of plant proteins. QUANTITATIVE PLANT BIOLOGY 2022; 3:e14. [PMID: 37077961 PMCID: PMC10095807 DOI: 10.1017/qpb.2022.9] [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: 11/07/2021] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 05/03/2023]
Abstract
Most plant primary transcripts undergo alternative splicing (AS), and its impact on protein diversity is a subject of intensive investigation. Several studies have uncovered various mechanisms of how particular protein splice isoforms operate. However, the common principles behind the AS effects on protein function in plants have rarely been surveyed. Here, on the selected examples, we highlight diverse tissue expression patterns, subcellular localization, enzymatic activities, abilities to bind other molecules and other relevant features. We describe how the protein isoforms mutually interact to underline their intriguing roles in altering the functionality of protein complexes. Moreover, we also discuss the known cases when these interactions have been placed inside the autoregulatory loops. This review is particularly intended for plant cell and developmental biologists who would like to gain inspiration on how the splice variants encoded by their genes of interest may coordinately work.
Collapse
Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Ksenia Timofeyenko
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Author for correspondence: K. Růžička, E-mail:
| |
Collapse
|
28
|
Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 233:329-343. [PMID: 34637542 DOI: 10.1111/nph.17792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.
Collapse
Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Mónika Hrtyan
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 166 10, Czech Republic
| | - Aswathy Jayasree
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Roberta Filepová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Zuzana Vondráková
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Sibu Simon
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg, 3400, Austria
| | - Jan Petrášek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| |
Collapse
|
29
|
Meena V, Sharma S, Kaur G, Singh B, Pandey AK. Diverse Functions of Plant Zinc-Induced Facilitator-like Transporter for Their Emerging Roles in Crop Trait Enhancement. PLANTS 2021; 11:plants11010102. [PMID: 35009105 PMCID: PMC8747725 DOI: 10.3390/plants11010102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022]
Abstract
The major facilitator superfamily (MFS) is a large and diverse group of secondary transporters found across all kingdoms of life. Zinc-induced facilitator-like (ZIFL) transporters are the MFS family members that function as exporters driven by the antiporter-dependent processes. The presence of multiple ZIFL transporters was shown in various plant species, as well as in bryophytes. However, only a few ZIFLs have been functionally characterized in plants, and their localization has been suggested to be either on tonoplast or at the plasma membrane. A subset of the plant ZIFLs were eventually characterized as transporters due to their specialized role in phytosiderophores efflux and auxin homeostasis, and they were also proven to impart tolerance to micronutrient deficiency. The emerging functions of ZIFL proteins highlight their role in addressing important traits in crop species. This review aims to provide insight into and discuss the importance of plant ZIFL in various tissue-specific functions. Furthermore, a spotlight is placed on their role in mobilizing essential micronutrients, including iron and zinc, from the rhizosphere to support plant survival. In conclusion, in this paper, we discuss the functional redundancy of ZIFL transporters to understand their roles in developing specific traits in crop.
Collapse
Affiliation(s)
- Varsha Meena
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar 140306, India; (V.M.); (S.S.); (G.K.)
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Shivani Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar 140306, India; (V.M.); (S.S.); (G.K.)
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar 140306, India; (V.M.); (S.S.); (G.K.)
| | - Bhupinder Singh
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-IARI, New Delhi 110002, India;
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar 140306, India; (V.M.); (S.S.); (G.K.)
- Correspondence: or ; Tel.: +91-1724990124
| |
Collapse
|
30
|
Phosphorus Starvation- and Zinc Excess-Induced Astragalus sinicus AsZIP2 Zinc Transporter Is Suppressed by Arbuscular Mycorrhizal Symbiosis. J Fungi (Basel) 2021; 7:jof7110892. [PMID: 34829181 PMCID: PMC8623892 DOI: 10.3390/jof7110892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Zinc (Zn) is one of the most essential micronutrients for plant growth and metabolism, but Zn excess can impair many basic metabolic processes in plant cells. In agriculture, crops often experience low phosphate (Pi) and high Zn double nutrient stresses because of inordinate agro-industrial activities, while the dual benefit of arbuscular mycorrhizal (AM) fungi protects plants from experiencing both deficient and toxic nutrient stresses. Although crosstalk between Pi and Zn nutrients in plants have been extensively studied at the physiological level, the molecular basis of how Pi starvation triggers Zn over-accumulation in plants and how AM plants coordinately modulate the Pi and Zn nutrient homeostasis remains to be elucidated. Here, we report that a novel AsZIP2 gene, a Chinese milk vetch (Astragalus sinicus) member of the ZIP gene family, participates in the interaction between Pi and Zn nutrient homeostasis in plants. Phylogenetic analysis revealed that this AsZIP2 protein was closely related to the orthologous Medicago MtZIP2 and Arabidopsis AtZIP2 transporters. Gene expression analysis indicated that AsZIP2 was highly induced in roots by Pi starvation or Zn excess yet attenuated by arbuscular mycorrhization in a Pi-dependent manner. Subcellular localization and heterologous expression experiments further showed that AsZIP2 encoded a functional plasma membrane-localized transporter that mediated Zn uptake in yeast. Moreover, overexpression of AsZIP2 in A. sinicus resulted in the over-accumulation of Zn concentration in roots at low Pi or excessive Zn concentrations, whereas AsZIP2 silencing lines displayed an even more reduced Zn concentration than control lines under such conditions. Our results reveal that the AsZIP2 transporter functioned in Zn over-accumulation in roots during Pi starvation or high Zn supply but was repressed by AM symbiosis in a Pi-dependent manner. These findings also provide new insights into the AsZIP2 gene acting in the regulation of Zn homeostasis in mycorrhizal plants through Pi signal.
Collapse
|
31
|
O’Rourke JA, Morrisey MJ, Merry R, Espina MJ, Lorenz AJ, Stupar RM, Graham MA. Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean. Int J Mol Sci 2021; 22:11032. [PMID: 34681702 PMCID: PMC8537376 DOI: 10.3390/ijms222011032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022] Open
Abstract
The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.
Collapse
Affiliation(s)
| | | | - Ryan Merry
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Mary Jane Espina
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Aaron J. Lorenz
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Robert M. Stupar
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | | |
Collapse
|
32
|
Snigdha M, Prasath D. Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species. BMC PLANT BIOLOGY 2021; 21:355. [PMID: 34325661 PMCID: PMC8323298 DOI: 10.1186/s12870-021-03108-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Bacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum. Even though ginger (Zingiber officinale) and mango ginger (Curcuma amada) are from the same family Zingiberaceae, the latter is resistant to R. solanacearum infection. MicroRNAs have been identified in many crops which regulates plant-pathogen interaction, either through silencing genes or by blocking mRNA translation. However, miRNA's vital role and its targets in mango ginger in protecting bacterial wilt is not yet studied extensively. In the present study, using the "psRNATarget" server, we analyzed available ginger (susceptible) and mango ginger (resistant) transcriptome to delineate and compare the microRNAs (miRNA) and their target genes (miRTGs). RESULTS A total of 4736 and 4485 differential expressed miRTGs (DEmiRTGs) were identified in ginger and mango ginger, respectively, in response to R. solanacearum. Functional annotation results showed that mango ginger had higher enrichment than ginger in top enriched GO terms. Among the DEmiRTGs, 2105 were common in ginger and mango ginger. However, 2337 miRTGs were expressed only in mango ginger which includes 62 defence related and upregulated miRTGs. We also identified 213 miRTGs upregulated in mango ginger but downregulated in ginger, out of which 23 DEmiRTGS were defence response related. We selected nine miRNA/miRTGs pairs from the data set of common miRTGs of ginger and mango ginger and validated using qPCR. CONCLUSIONS Our data covered the expression information of 9221 miRTGs. We identified nine miRNA/miRTGs key candidate pairs in response to R. solanacearum infection in ginger. This is the first report of the integrated analysis of miRTGs and miRNAs in response to R. solanacearum infection among ginger species. This study is expected to deliver several insights in understanding the miRNA regulatory network in ginger and mango ginger response to bacterial wilt.
Collapse
Affiliation(s)
- Mohandas Snigdha
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Duraisamy Prasath
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India.
| |
Collapse
|
33
|
Liu L, Tang Z, Liu F, Mao F, Yujuan G, Wang Z, Zhao X. Normal, novel or none: versatile regulation from alternative splicing. PLANT SIGNALING & BEHAVIOR 2021; 16:1917170. [PMID: 33882794 PMCID: PMC8205018 DOI: 10.1080/15592324.2021.1917170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Pre-mRNA splicing is a vital step in the posttranscriptional regulation of gene expression. Splicing is catalyzed by the spliceosome, a multidalton RNA-protein complex, through two successive transesterifications to yield mature mRNAs. In Arabidopsis, more than 61% of all transcripts from intron-containing genes are alternatively spliced, thereby resulting in transcriptome and subsequent proteome diversities for cellular processes. Moreover, it is estimated that more alternative splicing (AS) events induced by adverse stimuli occur to confer stress tolerance. Recently, increasing AS variants encoding normal or novel proteins, or degraded by nonsense-mediated decay (NMD) and their corresponding splicing factors or regulators acting at the posttranscriptional level have been functionally characterized. This review comprehensively summarizes and highlights the advances in our understanding of the biological functions and underlying mechanisms of AS events and their regulators in Arabidopsis and provides prospects for further research on AS in crops.
Collapse
Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
| | - Ziwei Tang
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Gu Yujuan
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Zhijuan Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, WuhanChina
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
| |
Collapse
|
34
|
The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators. Cells 2021; 10:cells10071665. [PMID: 34359847 PMCID: PMC8303113 DOI: 10.3390/cells10071665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.
Collapse
|
35
|
Britto DT, Coskun D, Kronzucker HJ. Potassium physiology from Archean to Holocene: A higher-plant perspective. JOURNAL OF PLANT PHYSIOLOGY 2021; 262:153432. [PMID: 34034042 DOI: 10.1016/j.jplph.2021.153432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 05/27/2023]
Abstract
In this paper, we discuss biological potassium acquisition and utilization processes over an evolutionary timescale, with emphasis on modern vascular plants. The quintessential osmotic and electrical functions of the K+ ion are shown to be intimately tied to K+-transport systems and membrane energization. Several prominent themes in plant K+-transport physiology are explored in greater detail, including: (1) channel mediated K+ acquisition by roots at low external [K+]; (2) K+ loading of root xylem elements by active transport; (3) variations on the theme of K+ efflux from root cells to the extracellular environment; (4) the veracity and utility of the "affinity" concept in relation to transport systems. We close with a discussion of the importance of plant-potassium relations to our human world, and current trends in potassium nutrition from farm to table.
Collapse
Affiliation(s)
- Dev T Britto
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Devrim Coskun
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation (FSAA), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Herbert J Kronzucker
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| |
Collapse
|
36
|
Abstract
This review highlights the most recent updated information available about Zn phytotoxicity at physiological, biochemical and molecular levels, uptake mechanisms as well as excess Zn homeostasis in plants. Zinc (Zn) is a natural component of soil in terrestrial environments and is a vital element for plant growth, as it performs imperative functions in numerous metabolic pathways. However, potentially noxious levels of Zn in soils can result in various alterations in plants like reduced growth, photosynthetic and respiratory rate, imbalanced mineral nutrition and enhanced generation of reactive oxygen species. Zn enters into soils through various sources, such as weathering of rocks, forest fires, volcanoes, mining and smelting activities, manure, sewage sludge and phosphatic fertilizers. The rising alarm in environmental facet, as well as, the narrow gap between Zn essentiality and toxicity in plants has drawn the attention of the scientific community to its effects on plants and crucial role in agricultural sustainability. Hence, this review focuses on the most recent updates about various physiological and biochemical functions perturbed by high levels of Zn, its mechanisms of uptake and transport as well as molecular aspects of surplus Zn homeostasis in plants. Moreover, this review attempts to understand the mechanisms of Zn toxicity in plants and to present novel perspectives intended to drive future investigations on the topic. The findings will further throw light on various mechanisms adopted by plants to cope with Zn stress which will be of great significance to breeders for enhancing tolerance to Zn contamination.
Collapse
Affiliation(s)
- Harmanjit Kaur
- Department of Botany, Akal University, Bathinda, 151302, Punjab, India
| | - Neera Garg
- Department of Botany, Panjab University, Chandigarh, 160014, India.
| |
Collapse
|
37
|
Lee S, Ricachenevsky FK, Punshon T. Functional overlap of two major facilitator superfamily transporter, ZIF1, and ZIFL1 in zinc and iron homeostasis. Biochem Biophys Res Commun 2021; 560:7-13. [PMID: 33964505 DOI: 10.1016/j.bbrc.2021.04.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Zinc and iron are essential micronutrients for plant growth, and their homeostasis must be tightly regulated. Previously, it has been shown that Zinc-Induced Facilitator 1 (ZIF1) is involved in basal Zn tolerance by controlling the vacuolar storage of nicotianamine (NA). However, knowledge of the functional roles of two ZIF1 paralogs, ZIF-LIKE1 (ZIFL1) and ZIFL2, in metal homeostasis remains limited. Here, we functionally characterized the roles of ZIF1, ZIFL1, and ZIFL2 in Zn and Fe homeostasis. Expression of ZIF1 and ZIFL1 was induced by both excess Zn and Fe-deficiency, and their loss-of-function led to hypersensitivity under excess Zn and Fe-deficiency, suggesting functional overlap between ZIF1 and ZIFL1. By contrast, the disruption of ZIFL2 resulted in no obvious phenotypic alteration under both conditions. Additionally, the expression of ZIFL1, but not that of ZIFL2, in the zif1 mutant partially restored the phenotype under excess Zn, suggesting that ZIF1 and ZIFL1 perform functionally redundant roles in Zn homeostasis.
Collapse
Affiliation(s)
- Sichul Lee
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 43019, South Korea.
| | - Felipe K Ricachenevsky
- Departamento de Botânica, Instituto de Biociências; and Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| |
Collapse
|
38
|
Hu L, Wang P, Long X, Wu W, Zhang J, Pan Y, Cheng T, Shi J, Chen J. The PIN gene family in relic plant L. chinense: Genome-wide identification and gene expression profiling in different organizations and abiotic stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:634-646. [PMID: 33774468 DOI: 10.1016/j.plaphy.2021.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The auxin efflux carrier PIN-FORMED (PIN) proteins are required for the polar transport of auxin between cells through their asymmetric distribution on the plasma membrane, thus mediating the differential distribution of auxin in plants, finally, affecting plant growth and developmental processes. In this study, 11 LcPIN genes were identified. The structural characteristics and evolutionary status of LcPIN genes were thoroughly investigated and interpreted combining physicochemical property analysis, evolutionary analysis, gene structure analysis, chromosomal localization, etc. Multi-species protein sequence analysis showed that angiosperm PIN genes have strong purification options and some functional sites were predicted about PIN protein polarity, trafficking and activity in L. chinense. Further qRT-PCR and transcriptome data analysis indicated that the long LcPINs have highly expressed from globular embryo to plantlet, and the LcPIN6a started upregulated in cotyledon embryo. The LcPIN3 and LcPIN6a are both highly expressed during the development of stamens and petals and the expression of LcPIN2 is related to root elongation, suggesting that they may play an important role in these processes. Experiment data indicates that LcPIN5 and LcPIN8 might play a key role in auxin transport in Liriodendron stems and leaves under abiotic stress. Analyzed the response of LcPIN genes to abiotic stress and as a basis for uncovering the biological role of LcPIN genes in development and adaption to adverse environments. This study provides a foundation for further genetic and functional analyses.
Collapse
Affiliation(s)
- Lingfeng Hu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Pengkai Wang
- College of Horticulture Technology, Suzhou Agricultural Vocational and Technical College, Suzhou, 215000, China
| | - Xiaofei Long
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiaji Zhang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yan Pan
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Tielong Cheng
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| |
Collapse
|
39
|
Pan L, Yu Q, Wang J, Han H, Mao L, Nyporko A, Maguza A, Fan L, Bai L, Powles S. An ABCC-type transporter endowing glyphosate resistance in plants. Proc Natl Acad Sci U S A 2021; 118:e2100136118. [PMID: 33846264 PMCID: PMC8072331 DOI: 10.1073/pnas.2100136118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glyphosate is the most widely used herbicide in world agriculture and for general vegetation control in a wide range of situations. Global and often intensive glyphosate selection of very large weedy plant populations has resulted in widespread glyphosate resistance evolution in populations of many weed species. Here, working with a glyphosate-resistant (GR) Echinochloa colona population that evolved in a Western Australia agricultural field, we identified an ATP-binding cassette (ABC) transporter (EcABCC8) that is consistently up-regulated in GR plants. When expressed in transgenic rice, this EcABCC8 transporter endowed glyphosate resistance. Equally, rice, maize, and soybean overexpressing the EcABCC8 ortholog genes were made resistant to glyphosate. Conversely, CRISPR/Cas9-mediated knockout of the EcABCC8 ortholog gene OsABCC8 increased rice susceptibility to glyphosate. Subcellular localization analysis and quantification of glyphosate cellular levels in treated ABCC8 transgenic rice plants and isolated leaf protoplasts as well as structural modeling support that EcABCC8 is likely a plasma membrane-localized transporter extruding cytoplasmic glyphosate to the apoplast, lowering the cellular glyphosate level. This is a report of a membrane transporter effluxing glyphosate in a GR plant species, and its function is likely conserved in crop plant species.
Collapse
Affiliation(s)
- Lang Pan
- Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
- College of Plant Protection, Hunan Agricultural University, 410128 Changsha, China
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, WA 6009, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, WA 6009, Australia;
| | - Junzhi Wang
- Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
| | - Heping Han
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, WA 6009, Australia
| | - Lingfeng Mao
- Institute of Crop Science, Zhejiang University-Xuan Gu Agricultural Joint Innovation Center, Zhejiang University, 310058 Hangzhou, China
| | - Alex Nyporko
- Department of Molecular Biotechnology and Bioinformatics, Taras Shevchenko National University of Kyiv, 01033 Kiev, Ukraine
| | - Anna Maguza
- Department of Molecular Biotechnology and Bioinformatics, Taras Shevchenko National University of Kyiv, 01033 Kiev, Ukraine
| | - Longjiang Fan
- Institute of Crop Science, Zhejiang University-Xuan Gu Agricultural Joint Innovation Center, Zhejiang University, 310058 Hangzhou, China
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, 410125 Changsha, China;
- College of Plant Protection, Hunan Agricultural University, 410128 Changsha, China
| | - Stephen Powles
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, WA 6009, Australia;
| |
Collapse
|
40
|
Weng X, Zhou X, Xie S, Gu J, Wang ZY. Identification of cassava alternative splicing-related genes and functional characterization of MeSCL30 involvement in drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:130-142. [PMID: 33486203 DOI: 10.1016/j.plaphy.2021.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/12/2021] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional regulation strategy that can increase the proteome diversity and regulate mRNA level in eukaryote. Multi-exon genes can be alternative spliced to generate two or more transcripts, thereby increasing the adaptation to the external stress conditions in planta. However, AS-related proteins were less explored in cassava which is an important staple crop in the tropical area. A total of 365 genes encoding AS-related proteins were identified and renamed in the cassava genome, and the transcriptional and splicing changes of 15 randomly selected genes were systematically investigated in the tissues under diverse abiotic stress conditions. 13 out of 15 genes undergo AS in the tissues and under diverse environmental stress condition. Importantly, the greatest changes of splicing patterns were found in the leaf or in response to temperature stress, indicating that AS-related proteins had their tissue-specific regulation patterns and might be participated in the plant adaptation to temperature stress. We then found that overexpression of MeSCL30 in Arabidopsis enhanced the tolerance to drought stress through maintaining reactive oxygen species (ROS) homeostasis and increasing the expression of drought-responsive genes. Therefore, these findings refined the AS-related protein-coding genes and provided novel insights for manipulation of AS-related genes in order to enhance the resistance to environmental stress in plant.
Collapse
Affiliation(s)
- Xun Weng
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Xiaoxia Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Jinbao Gu
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
| |
Collapse
|
41
|
Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions. PLANTS 2021; 10:plants10010148. [PMID: 33450896 PMCID: PMC7828368 DOI: 10.3390/plants10010148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of Eucalyptus cladocalyx, a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as GEM-related 5 and prohibitin-3, were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.
Collapse
|
42
|
Campobenedetto C, Mannino G, Beekwilder J, Contartese V, Karlova R, Bertea CM. The application of a biostimulant based on tannins affects root architecture and improves tolerance to salinity in tomato plants. Sci Rep 2021; 11:354. [PMID: 33432010 PMCID: PMC7801735 DOI: 10.1038/s41598-020-79770-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023] Open
Abstract
Roots have important roles for plants to withstand adverse environmental conditions, including salt stress. Biostimulant application was shown to enhance plant resilience towards abiotic stresses. Here, we studied the effect of a tannin-based biostimulant on tomato (Solanum lycopersicum L.) grown under salt stress conditions. We investigated the related changes at both root architecture (via imaging and biometric analysis) and gene expression (RNA-Seq/qPCR) levels. Moreover, in order to identify the main compounds potentially involved in the observed effects, the chemical composition of the biostimulant was evaluated by UV/Vis and HPLC-ESI-Orbitrap analysis. Sixteen compounds, known to be involved in root development and having a potential antioxidant properties were identified. Significant increase of root weight (+ 24%) and length (+ 23%) was observed when the plants were grown under salt stress and treated with the biostimulant. Moreover, transcriptome analysis revealed that the application of the biostimulant upregulated 285 genes, most of which correlated to root development and salt stress tolerance. The 171 downregulated genes were mainly involved in nutrient uptake. These data demonstrated that the biostimulant is able not only to restore root growth in salty soils, but also to provide the adequate plant nourishment by regulating the expression of essential transcription factors and stress responsive genes.
Collapse
Affiliation(s)
- Cristina Campobenedetto
- grid.7605.40000 0001 2336 6580Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy ,Green Has Italia S.P.A, Canale, CN Italy ,grid.4818.50000 0001 0791 5666Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708 PB 9 Wageningen, The Netherlands
| | - Giuseppe Mannino
- grid.7605.40000 0001 2336 6580Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Jules Beekwilder
- grid.4818.50000 0001 0791 5666Wageningen University and Research Centre, Bioscience, Wageningen, The Netherlands
| | | | - Rumyana Karlova
- grid.4818.50000 0001 0791 5666Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708 PB 9 Wageningen, The Netherlands
| | - Cinzia M. Bertea
- grid.7605.40000 0001 2336 6580Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| |
Collapse
|
43
|
Xie Q, Essemine J, Pang X, Chen H, Jin J, Cai W. Abscisic Acid Regulates the Root Growth Trajectory by Reducing Auxin Transporter PIN2 Protein Levels in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:632676. [PMID: 33763094 PMCID: PMC7982918 DOI: 10.3389/fpls.2021.632676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/15/2021] [Indexed: 05/03/2023]
Abstract
The root is in direct contact with soil. Modulation of root growth in response to alterations in soil conditions is pivotal for plant adaptation. Extensive research has been conducted concerning the adjustment of root elongation and architecture in response to environmental factors. However, little is known about the modulation of the root growth trajectory, as well as its hormonal mechanism. Here we report that abscisic acid (ABA) participated in controlling root growth trajectory. The roots upon ABA treatment or from ABA-accumulation double mutant cyp707a1,3 exhibit agravitropism-like growth pattern (wavy growth trajectory). The agravitropism-like phenotype is mainly ascribed to the compromised shootward transportation of auxin since we detected a reduced fluorescence intensity of auxin reporter DR5:VENUS in the root epidermis upon exogenous ABA application or in the endogenous ABA-accumulation double mutant cyp707a1,3. We then tried to decipher the mechanism by which ABA suppressed shootward auxin transport. The membrane abundance of PIN2, a facilitator of shootward auxin transport, was significantly reduced following ABA treatment and in cyp707a1,3. Finally, we revealed that ABA reduced the membrane PIN2 intensity through suppressing the PIN2 expression rather than accelerating PIN2 degradation. Ultimately, our results suggest a pivotal role for ABA in the root growth trajectory and the hormonal interactions orchestrating this process.
Collapse
Affiliation(s)
- Qijun Xie
- Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- Qijun Xie,
| | - Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaochen Pang
- Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Haiying Chen
- Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jing Jin
- Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weiming Cai
- Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Weiming Cai, ;
| |
Collapse
|
44
|
Bélanger S, Baldrich P, Lemay M, Marchand S, Esteves P, Meyers BC, Belzile F. The commitment of barley microspores into embryogenesis correlates with miRNA-directed regulation of members of the SPL, GRF and HD-ZIPIII transcription factor families. PLANT DIRECT 2020; 4:e00289. [PMID: 36406053 PMCID: PMC9671080 DOI: 10.1002/pld3.289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/26/2020] [Accepted: 10/19/2020] [Indexed: 05/19/2023]
Abstract
Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs and the degradome of barley microspores collected prior to (day 0) and after (days 2 and 5) the application of a stress treatment known to induce embryogenesis. Microspores isolated at these timepoints were uniform in both appearance and in their complements of sRNAs. We detected 68 miRNAs in microspores. The abundance of 51 of these miRNAs differed significantly during microspore development. One group of miRNAs was induced when the stress treatment was applied, prior to being repressed when microspores transitioned to embryogenesis. Another group of miRNAs were up-regulated in day-2 microspores and their abundance remained stable or increased in day-5 microspores, a timepoint at which the first clear indications of the transition toward embryogenesis were visible. Collectively, these miRNAs might play a role in the modulation of the stress response, the repression of gametic development, and/or the gain of embryogenic potential. A degradome analysis allowed us to validate the role of miRNAs in regulating 41 specific transcripts. We showed that the transition of microspores toward the embryogenesis pathway involves miRNA-directed regulation of members of the ARF, SPL, GRF, and HD-ZIPIII transcription factor families. We noted that 41.5% of these targets were shared between day-2 and day-5 microspores while 26.8% were unique to day-5 microspores. The former set may act to disrupt transcripts involved in pollen development while the latter set may drive the commitment to embryogenesis.
Collapse
Affiliation(s)
- Sébastien Bélanger
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | - Marc‐André Lemay
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Suzanne Marchand
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Patricio Esteves
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - François Belzile
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| |
Collapse
|
45
|
Isayenkov S, Hilo A, Rizzo P, Tandron Moya YA, Rolletschek H, Borisjuk L, Radchuk V. Adaptation Strategies of Halophytic Barley Hordeum marinum ssp. marinum to High Salinity and Osmotic Stress. Int J Mol Sci 2020; 21:ijms21239019. [PMID: 33260985 PMCID: PMC7730945 DOI: 10.3390/ijms21239019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
The adaptation strategies of halophytic seaside barley Hordeum marinum to high salinity and osmotic stress were investigated by nuclear magnetic resonance imaging, as well as ionomic, metabolomic, and transcriptomic approaches. When compared with cultivated barley, seaside barley exhibited a better plant growth rate, higher relative plant water content, lower osmotic pressure, and sustained photosynthetic activity under high salinity, but not under osmotic stress. As seaside barley is capable of controlling Na+ and Cl− concentrations in leaves at high salinity, the roots appear to play the central role in salinity adaptation, ensured by the development of thinner and likely lignified roots, as well as fine-tuning of membrane transport for effective management of restriction of ion entry and sequestration, accumulation of osmolytes, and minimization of energy costs. By contrast, more resources and energy are required to overcome the consequences of osmotic stress, particularly the severity of reactive oxygen species production and nutritional disbalance which affect plant growth. Our results have identified specific mechanisms for adaptation to salinity in seaside barley which differ from those activated in response to osmotic stress. Increased knowledge around salt tolerance in halophytic wild relatives will provide a basis for improved breeding of salt-tolerant crops.
Collapse
Affiliation(s)
- Stanislav Isayenkov
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
- Institute of Food Biotechnology and Genomics NAS of Ukraine, Osipovskogo Street, 2a, 04123 Kyiv, Ukraine
- Correspondence: (S.I.); (V.R.)
| | - Alexander Hilo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
| | - Paride Rizzo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
| | - Yudelsy Antonia Tandron Moya
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
| | - Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; (A.H.); (P.R.); (Y.A.T.M.); (H.R.); (L.B.)
- Correspondence: (S.I.); (V.R.)
| |
Collapse
|
46
|
Zhang S, Tajima H, Nambara E, Blumwald E, Bassil E. Auxin Homeostasis and Distribution of the Auxin Efflux Carrier PIN2 Require Vacuolar NHX-Type Cation/H + Antiporter Activity. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1311. [PMID: 33023035 PMCID: PMC7601841 DOI: 10.3390/plants9101311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/17/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022]
Abstract
The Arabidopsis vacuolar Na+/H+ transporters (NHXs) are important regulators of intracellular pH, Na+ and K+ homeostasis and necessary for normal plant growth, development, and stress acclimation. Arabidopsis contains four vacuolar NHX isoforms known as AtNHX1 to AtNHX4. The quadruple knockout nhx1nhx2nhx3nhx4, lacking any vacuolar NHX-type antiporter activity, displayed auxin-related phenotypes including loss of apical dominance, reduced root growth, impaired gravitropism and less sensitivity to exogenous IAA and NAA, but not to 2,4-D. In nhx1nhx2nhx3nhx4, the abundance of the auxin efflux carrier PIN2, but not PIN1, was drastically reduced at the plasma membrane and was concomitant with an increase in PIN2 labeled intracellular vesicles. Intracellular trafficking to the vacuole was also delayed in the mutant. Measurements of free IAA content and imaging of the auxin sensor DII-Venus, suggest that auxin accumulates in root tips of nhx1nhx2nhx3nhx4. Collectively, our results indicate that vacuolar NHX dependent cation/H+ antiport activity is needed for proper auxin homeostasis, likely by affecting intracellular trafficking and distribution of the PIN2 efflux carrier.
Collapse
Affiliation(s)
- Shiqi Zhang
- Boyce Thompson Institute, Ithaca, NY 14850, USA;
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (H.T.); (E.B.)
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (H.T.); (E.B.)
| | - Elias Bassil
- Horticultural Sciences Department, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA
| |
Collapse
|
47
|
Rajagopal D, Mathew MK. Role of Arabidopsis RAB5 GEF vps9a in maintaining potassium levels under sodium chloride stress. PLANT DIRECT 2020; 4:e00273. [PMID: 33103044 PMCID: PMC7576885 DOI: 10.1002/pld3.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 05/07/2023]
Abstract
Salt stress is one of the major factors impacting crop productivity worldwide. Through a variety of effector and signaling pathways, plants achieve survival under salinity stress by maintaining high cytosolic potassium/sodium ion (K+/Na+) ratios, preventing Na+ cytotoxicity, and retaining osmotic balance. Ras-related protein 5 (Rab5) members are involved in the trafficking of endosomes to the vacuole or plasma membrane (PM). The vacuolar protein sorting- associated protein 9 (vps9a) encodes the single guanine nucleotide exchange factor (GEF) that activates all three known Rab5 proteins in Arabidopsis thaliana. Previous work from our group has reported the critical function of vps9a for the operation of salt-induced endocytic pathway, as well as the expansion of endomembrane compartments under saline stress conditions. Here we show an additional role of vps9a in plant response to salt stress via maintenance of K+ status of the cell rather than Na+ homeostasis. Our results show that roots from vps9a-2 mutant, subjected to 100 mM NaCl, display alterations in transcript levels of genes involved in the K+ homeostasis pathway. Concurrent with the observed sensitivity of vps9a-2 mutant under NaCl stress, exposure to low K+ environments resulted in growth retardation, and reduced rate of endocytosis. Furthermore, vps9a-2 mutant displays reduced expression of auxin reporter, Direct Repeat-5 (DR5), and alterations in polarity and abundance of auxin efflux carrier PIN- FORMED2 (PIN2). Imposition of NaCl stress was found to be restrictive to the elongation capacity of cells in the root elongation zone of vps9a-2 mutant. Together our results indicate that alterations in K+ homeostasis and associated cellular changes causing increased cell wall pH, contribute to diminished root growth and compromised survival of vps9a-2 mutant under salt stress conditions.
Collapse
Affiliation(s)
- Divya Rajagopal
- National Centre for Biological SciencesTIFRBangaloreKarnatakaIndia
| | - M. K. Mathew
- National Centre for Biological SciencesTIFRBangaloreKarnatakaIndia
| |
Collapse
|
48
|
Two Alternative Splicing Variants of AtERF73/HRE1, HRE1α and HRE1β, Have Differential Transactivation Activities in Arabidopsis. Int J Mol Sci 2020; 21:ijms21196984. [PMID: 32977426 PMCID: PMC7582492 DOI: 10.3390/ijms21196984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
AtERF73/HRE1 is an AP2/ERF transcription factor in Arabidopsis and has two distinct alternative splicing variants, HRE1α and HRE1β. In this study, we examined the differences between the molecular functions of HRE1α and HRE1β. We found that HRE1α and HRE1β are both involved in hypoxia response and root development and have transactivation activity. Two conserved motifs in the C-terminal region of HRE1α and HRE1β, EELL and LWSY-like, contributed to their transactivation activity, specifically the four E residues in the EELL motif and the MGLWS amino acid sequence at the end of the LWSY-like motif. The N-terminal region of HRE1β also showed transactivation activity, mediated by the VDDG motif, whereas that of HRE1α did not. The transactivation activity of HRE1β was stronger than that of HRE1α in Arabidopsis protoplasts. Both transcription factors transactivated downstream genes via the GCC box. RNA-sequencing analysis further supported that both HRE1α and HRE1β might regulate gene expression associated with the hypoxia stress response, although they may transactivate different subsets of genes in downstream pathways. Our results, together with previous studies, suggested that HRE1α and HRE1β differentially transactivate downstream genes in hypoxia response and root development in Arabidopsis.
Collapse
|
49
|
Yang T, Feng H, Zhang S, Xiao H, Hu Q, Chen G, Xuan W, Moran N, Murphy A, Yu L, Xu G. The Potassium Transporter OsHAK5 Alters Rice Architecture via ATP-Dependent Transmembrane Auxin Fluxes. PLANT COMMUNICATIONS 2020; 1:100052. [PMID: 33367257 PMCID: PMC7747981 DOI: 10.1016/j.xplc.2020.100052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/29/2019] [Accepted: 04/27/2020] [Indexed: 05/24/2023]
Abstract
Plant HAK/KUP/KT family members function as plasma membrane (PM) H+/K+ symporters and may modulate chemiosmotically-driven polar auxin transport (PAT). Here, we show that inactivation of OsHAK5, a rice K+ transporter gene, decreased rootward and shootward PAT, tiller number, and the length of both lateral roots and root hairs, while OsHAK5 overexpression increased PAT, tiller number, and root hair length, irrespective of the K+ supply. Inhibitors of ATP-binding-cassette type-B transporters, NPA and BUM, abolished the OsHAK5-overexpression effect on PAT. The mechanistic basis of these changes included the OsHAK5-mediated decrease of transmembrane potential (depolarization), increase of extracellular pH, and increase of PM-ATPase activity. These findings highlight the dual roles of OsHAK5 in altering cellular chemiosmotic gradients (generated continuously by PM H+-ATPase) and regulating ATP-dependent auxin transport. Both functions may underlie the prominent effect of OsHAK5 on rice architecture, which may be exploited in the future to increase crop yield via genetic manipulations.
Collapse
Affiliation(s)
- Tianyuan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Huimin Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Song Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Huojun Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingdi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Guang Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Nava Moran
- The R.H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Angus Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ling Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
50
|
Ren Z, Zhang D, Cao L, Zhang W, Zheng H, Liu Z, Han S, Dong Y, Zhu F, Liu H, Su H, Chen Y, Wu L, Zhu Y, Ku L. Functions and regulatory framework of ZmNST3 in maize under lodging and drought stress. PLANT, CELL & ENVIRONMENT 2020; 43:2272-2286. [PMID: 32562291 DOI: 10.1111/pce.13829] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 05/23/2023]
Abstract
The growth and development of maize are negatively affected by various abiotic stresses including drought, high salinity, extreme temperature, and strong wind. Therefore, it is important to understand the molecular mechanisms underlying abiotic stress resistance in maize. In the present work, we identified that a novel NAC transcriptional factor, ZmNST3, enhances maize lodging resistance and drought stress tolerance. ChIP-Seq and expression of target genes analysis showed that ZmNST3 could directly regulate the expression of genes related to cell wall biosynthesis which could subsequently enhance lodging resistance. Furthermore, we also demonstrated that ZmNST3 affected the expression of genes related to the synthesis of antioxidant enzyme secondary metabolites that could enhance drought resistance. More importantly, we are the first to report that ZmNST3 directly binds to the promoters of CESA5 and Dynamin-Related Proteins2A (DRP2A) and activates the expression of genes related to secondary cell wall cellulose biosynthesis. Additionally, we revealed that ZmNST3 directly binds to the promoters of GST/GlnRS and activates genes which could enhance the production of antioxidant enzymes in vivo. Overall, our work contributes to a comprehensive understanding of the regulatory network of ZmNST3 in regulating maize lodging and drought stress resistance.
Collapse
Affiliation(s)
- Zhenzhen Ren
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Dongling Zhang
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Liru Cao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Weiqiang Zhang
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhixue Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shengbo Han
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yahui Dong
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Fangfang Zhu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Huafeng Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Liancheng Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|