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Xu J, Wang R, Zhang X, Zhuang W, Zhang Y, Lin J, Zhan P, Chen S, Lu H, Wang A, Liao C. Identification and expression profiling of GAPDH family genes involved in response to Sclerotinia sclerotiorum infection and phytohormones in Brassica napus. FRONTIERS IN PLANT SCIENCE 2024; 15:1360024. [PMID: 38745922 PMCID: PMC11091349 DOI: 10.3389/fpls.2024.1360024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a crucial enzyme in glycolysis, an essential metabolic pathway for carbohydrate metabolism across all living organisms. Recent research indicates that phosphorylating GAPDH exhibits various moonlighting functions, contributing to plant growth and development, autophagy, drought tolerance, salt tolerance, and bacterial/viral diseases resistance. However, in rapeseed (Brassica napus), the role of GAPDHs in plant immune responses to fungal pathogens remains unexplored. In this study, 28 genes encoding GAPDH proteins were revealed in B. napus and classified into three distinct subclasses based on their protein structural and phylogenetic relationships. Whole-genome duplication plays a major role in the evolution of BnaGAPDHs. Synteny analyses revealed orthologous relationships, identifying 23, 26, and 26 BnaGAPDH genes with counterparts in Arabidopsis, Brassica rapa, and Brassica oleracea, respectively. The promoter regions of 12 BnaGAPDHs uncovered a spectrum of responsive elements to biotic and abiotic stresses, indicating their crucial role in plant stress resistance. Transcriptome analysis characterized the expression profiles of different BnaGAPDH genes during Sclerotinia sclerotiorum infection and hormonal treatment. Notably, BnaGAPDH17, BnaGAPDH20, BnaGAPDH21, and BnaGAPDH22 exhibited sensitivity to S. sclerotiorum infection, oxalic acid, hormone signals. Intriguingly, under standard physiological conditions, BnaGAPDH17, BnaGAPDH20, and BnaGAPDH22 are primarily localized in the cytoplasm and plasma membrane, with BnaGAPDH21 also detectable in the nucleus. Furthermore, the nuclear translocation of BnaGAPDH20 was observed under H2O2 treatment and S. sclerotiorum infection. These findings might provide a theoretical foundation for elucidating the functions of phosphorylating GAPDH.
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Affiliation(s)
- Jing Xu
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xiong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Zhuang
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Yang Zhang
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Jianxin Lin
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Penglin Zhan
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Shanhu Chen
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Heding Lu
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Airong Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changjian Liao
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
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Brasileiro ACM, Gimenes MA, Pereira BM, Mota APZ, Aguiar MN, Martins ACQ, Passos MAS, Guimaraes PM. The Stilbene Synthase Family in Arachis: A Genome-Wide Study and Functional Characterization in Response to Stress. Genes (Basel) 2023; 14:2181. [PMID: 38137003 PMCID: PMC10742623 DOI: 10.3390/genes14122181] [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: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its health benefits, such as preventing and treating various human diseases and disorders. Chalcone (CHS) and Stilbene (STS) Synthases are plant-specific type III Polyketide Synthases (PKSs) that share the same substrates and are key branch enzymes in the biosynthesis of flavonoids and stilbenoids, respectively. Although resveratrol accumulation in response to external stimulus has been described in peanut, there are no comprehensive studies of the CHS and STS gene families in the genus Arachis. In the present study, we identified and characterized 6 CHS and 46 STS genes in the tetraploid peanut and an average of 4 CHS and 22 STS genes in three diploid wild species (Arachis duranensis, Arachis ipaënsis and Arachis stenosperma). The CHS and STS gene and protein structures, chromosomal distributions, phylogenetic relationships, conserved amino acid domains, and cis-acting elements in the promoter regions were described for all Arachis species studied. Based on gene expression patterns of wild A. stenosperma STS genes in response to different biotic and abiotic stresses, we selected the candidate AsSTS4 gene, which is strongly induced by ultraviolet (UV) light exposure, for further functional investigation. The AsSTS4 overexpression in peanut hairy roots significantly reduced (47%) root-knot nematode infection, confirming that stilbene synthesis activation in transgenic plants can increase resistance to pathogens. These findings contribute to understanding the role of resveratrol in stress responses in Arachis species and provide the basis for genetic engineering for improved production of valuable secondary metabolites in plants.
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Affiliation(s)
- Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Marcos Aparecido Gimenes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Bruna Medeiros Pereira
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Ana Paula Zotta Mota
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Matheus Nascimento Aguiar
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Andressa Cunha Quintana Martins
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Mario Alfredo Saraiva Passos
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
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Zhao Z, Wang Y, Peng Z, Luo Z, Zhao M, Wang J. Allelic expression of AhNSP2-B07 due to parent of origin affects peanut nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193465. [PMID: 37426991 PMCID: PMC10325728 DOI: 10.3389/fpls.2023.1193465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 07/11/2023]
Abstract
Legumes are well-known for establishing a symbiotic relationship with rhizobia in root nodules to fix nitrogen from the atmosphere. The nodulation signaling pathway 2 (NSP2) gene plays a critical role in the symbiotic signaling pathway. In cultivated peanut, an allotetraploid (2n = 4x = 40, AABB) legume crop, natural polymorphisms in a pair of NSP2 homoeologs (Na and Nb) located on chromosomes A08 and B07, respectively, can cause loss of nodulation. Interestingly, some heterozygous (NBnb) progeny produced nodules, while some others do not, suggesting non-Mendelian inheritance in the segregating population at the Nb locus. In this study, we investigated the non-Mendelian inheritance at the NB locus. Selfing populations were developed to validate the genotypical and phenotypical segregating ratios. Allelic expression was detected in roots, ovaries, and pollens of heterozygous plants. Bisulfite PCR and sequencing of the Nb gene in gametic tissue were performed to detect the DNA methylation variations of this gene in different gametic tissues. The results showed that only one allele at the Nb locus expressed in peanut roots during symbiosis. In the heterozygous (Nbnb) plants, if dominant allele expressed, the plants produced nodules, if recessive allele expressed, then no nodules were produced. qRT-PCR experiments revealed that the expression of Nb gene in the ovary was extremely low, about seven times lower than that in pollen, regardless of genotypes or phenotypes of the plants at this locus. The results indicated that Nb gene expression in peanut depends on the parent of origin and is imprinted in female gametes. However, no significant differences of DNA methylation level were detected between these two gametic tissues by bisulfite PCR and sequencing. The results suggested that the remarkable low expression of Nb in female gametes may not be caused by DNA methylation. This study provided a unique genetic basis of a key gene involved in peanut symbiosis, which could facilitate understanding the regulation of gene expression in symbiosis in polyploid legumes.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Yichun Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
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Li L, Cheng X, Kong X, Jia P, Wang X, Zhang L, Zhang X, Zhang Y, Zhang Z, Zhang B. Comparative Transcriptomic Analysis Reveals the Negative Response Mechanism of Peanut Root Morphology and Nitrate Assimilation to Nitrogen Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:732. [PMID: 36840080 PMCID: PMC9960604 DOI: 10.3390/plants12040732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Root architecture plays a fundamental role in crop yield, which is sensitive to nitrogen fertilizer. Although it is well studied that nitrogen fertilizer significantly promotes peanut (Arachis hypogaea L.) growth and yield, less information was available on how its root development responds to nitrogen deficiency. In this study, the growth and development of roots were inhibited, as indicated by the significantly decreased root dry weight and length and the lateral root number, especially under 10 days of nitrogen deficiency treatment. The activities and the expression of the genes related to nitrogen assimilation enzymes including nitrate reductase, glutamine synthetase, glutamate dehydrogenase, and glutamine oxoglutarate aminotransferase and the genes encoding the nitrate transporters were significantly decreased under 10 days of nitrogen deficiency treatment, which may lead to a decrease in nitrate content, as indicated by the significantly decreased nitrogen balance index. Transcriptome sequencing revealed a total of 293 (119 up- and 174 downregulated) and 2271 (1165 up- and 1106 downregulated) differentially expressed genes (DEGs) identified after five and ten days of nitrogen deficiency treatments, respectively. Bioinformatic analysis showed that these DEGs were mainly involved in nitrate transportation and assimilation, phytohormone signal transduction, and the lignin biosynthesis pathway. Furthermore, a putative schematic diagram of nitrogen deficiency inhibiting root growth was established, which gives us a better understanding of nitrogen metabolism in peanut roots and a theoretical basis for improving nitrogen use efficiency.
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Affiliation(s)
- Lijie Li
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiangguo Cheng
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiangjun Kong
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Peipei Jia
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaohui Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lei Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaotian Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yi Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Liu N, Wu B, Pandey MK, Huang L, Luo H, Chen Y, Zhou X, Chen W, Huai D, Yu B, Chen H, Guo J, Lei Y, Liao B, Varshney RK, Jiang H. Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut ( A. monticola). FRONTIERS IN PLANT SCIENCE 2022; 13:1065267. [PMID: 36589096 PMCID: PMC9802669 DOI: 10.3389/fpls.2022.1065267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The wild allotetraploid peanut Arachis monticola contains a higher oil content than the cultivated allotetraploid Arachis hypogaea. Besides the fact that increasing oil content is the most important peanut breeding objective, a proper understanding of its molecular mechanism controlling oil accumulation is still lacking. METHODS We investigated this aspect by performing comparative transcriptomics from developing seeds between three wild and five cultivated peanut varieties. RESULTS The analyses not only showed species-specific grouping transcriptional profiles but also detected two gene clusters with divergent expression patterns between two species enriched in lipid metabolism. Further analysis revealed that expression alteration of lipid metabolic genes with co-expressed transcription factors in wild peanut led to enhanced activity of oil biogenesis and retarded the rate of lipid degradation. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. CG and CHG context methylation was found to antagonistically correlate with gene expression during seed development. Differentially methylated region analysis and transgenic assay further illustrated that variations of DNA methylation between wild and cultivated peanuts could affect the oil content via altering the expression of peroxisomal acyl transporter protein (Araip.H6S1B). DISCUSSION From the results, we deduced that DNA methylation may negatively regulate lipid metabolic genes and transcription factors to subtly affect oil accumulation divergence between wild and cultivated peanuts. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.
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Affiliation(s)
- Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Guimaraes PM, Quintana AC, Mota APZ, Berbert PS, Ferreira DDS, de Aguiar MN, Pereira BM, de Araújo ACG, Brasileiro ACM. Engineering Resistance against Sclerotinia sclerotiorum Using a Truncated NLR (TNx) and a Defense-Priming Gene. PLANTS (BASEL, SWITZERLAND) 2022; 11:3483. [PMID: 36559595 PMCID: PMC9786959 DOI: 10.3390/plants11243483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The association of both cell-surface PRRs (Pattern Recognition Receptors) and intracellular receptor NLRs (Nucleotide-Binding Leucine-Rich Repeat) in engineered plants have the potential to activate strong defenses against a broad range of pathogens. Here, we describe the identification, characterization, and in planta functional analysis of a novel truncated NLR (TNx) gene from the wild species Arachis stenosperma (AsTIR19), with a protein structure lacking the C-terminal LRR (Leucine Rich Repeat) domain involved in pathogen perception. Overexpression of AsTIR19 in tobacco plants led to a significant reduction in infection caused by Sclerotinia sclerotiorum, with a further reduction in pyramid lines containing an expansin-like B gene (AdEXLB8) potentially involved in defense priming. Transcription analysis of tobacco transgenic lines revealed induction of hormone defense pathways (SA; JA-ET) and PRs (Pathogenesis-Related proteins) production. The strong upregulation of the respiratory burst oxidase homolog D (RbohD) gene in the pyramid lines suggests its central role in mediating immune responses in plants co-expressing the two transgenes, with reactive oxygen species (ROS) production enhanced by AdEXLB8 cues leading to stronger defense response. Here, we demonstrate that the association of potential priming elicitors and truncated NLRs can produce a synergistic effect on fungal resistance, constituting a promising strategy for improved, non-specific resistance to plant pathogens.
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Affiliation(s)
- Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
| | | | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, CNRS, Université Côte d’Azur, 06903 Sophia Antipolis, France
| | | | | | | | | | | | - Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
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Alexander A, Singh VK, Mishra A. Introgression of a novel gene AhBINR differentially expressed during PGPR Brachybacterium saurashtrense-Arachis hypogaea interaction enhances plant performance under nitrogen starvation and salt stress in tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111429. [PMID: 36029896 DOI: 10.1016/j.plantsci.2022.111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Plant growth-promoting rhizobacteria provide endurance during environmental stress conditions. Previously, we have shown that the interaction of the halotolerant diazotrophic bacteria Brachybacterium saurashtrense JG06 induces physio-biochemical and molecular changes in Arachis hypogaea under nitrogen starvation conditions. Here we deciphered the role of a novel gene AhBINR that was differentially overexpressed in A. hypogaea after interaction with B. saurashtrense JG06 under nitrogen deficit conditions. Overexpression of the AhBINR gene in the model plant (tobacco) showed higher growth parameters (root length, shoot length, fresh weight, and dry weight) under nitrogen starvation and salt stress in comparison to the wild type and vector control. Transgenic plants were enabled with a higher photosynthesis rate, which provides the support for better performance under N2 starvation and salt stress. Results showed that the transgenic plants overexpressing the AhBINR gene had better physiological status and lower ROS accumulation under adverse conditions. Microarray transcriptome analysis showed that the transcription factors, biotic and abiotic stress, photosynthesis, and metabolism-related genes were differentially expressed (total 736 and 6530 genes were expressed under nitrogen deficit and salt stress conditions, respectively at a 5-fold change level) in comparison to wild type plants. Overall results showed the involvement of the AhBINR gene in the activation of the abiotic stress (nitrogen starvation and salt stress) related pathways, which can be overexpressed after legume-rhizobacterial interaction.
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Affiliation(s)
- Ankita Alexander
- Division of Applied Phycology and Biotechnology, CSIR, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Vijay K Singh
- Division of Applied Phycology and Biotechnology, CSIR, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India.
| | - Avinash Mishra
- Division of Applied Phycology and Biotechnology, CSIR, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Ribeiro IM, Vinson CC, Coca GC, Ferreira CDS, Franco AC, Williams TCR. Differences in the metabolic and functional mechanisms used to tolerate flooding in Guazuma ulmifolia (Lam.) from flood-prone Amazonian and dry Cerrado savanna populations. TREE PHYSIOLOGY 2022; 42:2116-2132. [PMID: 35640151 DOI: 10.1093/treephys/tpac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Flood tolerance is crucial to the survival of tree species subject to long periods of flooding, such as those present in the Amazonian várzea. Tolerance can be mediated by adjustments of metabolism, physiology and morphology, reinforcing the need to investigate the physiological and biochemical mechanisms used by tropical tree species to survive this stress. Moreover, such mechanisms may vary between populations that are subjected to differences in the frequency of flooding events. Here, we aimed to identify the mechanisms used by two populations of the tropical tree Guazuma ulmifolia (Lam.) to tolerate flooding: an Amazonian population frequently exposed to flooding and a Cerrado population, adapted to a dry environment. Young plants were subjected to a flooding of the roots and lower stem for 32 days, followed by 17 days of recovery. Amazonian plants exhibited greater increases in shoot length and higher maximum photosynthetic rate (Amax) compared with non-flooded plants from 7 days of flooding onwards, whereas increased Amax occurred later in flooded Cerrado plants and was not accompanied by increased shoot length. Lactate accumulated in roots of Cerrado plants after 24 h flooding, together with transcripts coding for lactate dehydrogenase in roots of both Cerrado and Amazonian plants. After 7 days of flooding, lactate decreased and alcohol dehydrogenase activity increased transiently, together with concentrations of alanine, γ-aminobutyric acid and succinate, indicating activation of metabolic processes associated with low oxygen availability. Other amino acids also increased in flooded Cerrado plants, revealing more extensive metabolic changes than in Amazonian plants. Wetland and dryland populations of G. ulmifolia revealed the great capacity to tolerate flooding stress through a suite of alterations in photosynthetic gas exchange and metabolism. However, the integrated physiological, biochemical and molecular analyses realized here indicated that wetland plants acclimatized more efficiently with increased shoot elongation and more rapid restoration of normal metabolism.
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Affiliation(s)
- Isadora M Ribeiro
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
| | - Christina C Vinson
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
| | - Guilherme C Coca
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
| | - Cristiane da S Ferreira
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
| | - Augusto C Franco
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
| | - Thomas C R Williams
- Department of Botany, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Asa Norte, Brasília DF 70910-900, Brazil
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9
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Zhang Y, Du P, Xiong F, Zhang X, Song H. WRKY Genes Improve Drought Tolerance in Arachis duranensis. FRONTIERS IN PLANT SCIENCE 2022; 13:910408. [PMID: 35720609 PMCID: PMC9199494 DOI: 10.3389/fpls.2022.910408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
WRKY transcription factor participates in plant growth and development and response to biotic and abiotic stresses. Arachis duranensis, a turfgrass, has high drought tolerance, yet little is known about AdWRKYs response to drought stress in A. duranensis. In this study, RNA-seq identified five AdWRKYs, including AdWRKY18, AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, which were upregulated under drought stress. Orthologous relationships between AdWRKYs and Arabidopsis WRKY were determined to predict the regulatory networks of the five AdWRKYs based on AtWRKYs. Additionally, protein-protein interactions were predicted using differentially expressed proteins from RNA-seq. The quantitative real-time PCR (qRT-PCR) results showed that AdWRKY40 was upregulated, while AdWRKY42, AdWRKY56, and AdWRKY64 were downregulated at different time-points under drought stress. The predicted regulatory networks showed that AdWRKY40 activates COR47, RD21, and RD29A expression under drought stress. Besides, AdWRKY56 regulated CesA8 under drought stress. Aradu.YIQ80 (NAC019) interacted with AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, while Aradu.Z5H58 (NAC055) interacted with AdWRKY42 and AdWRKY64 under drought stress. This study used Arabidopsis to assess AdWRKYs function and regulatory networks, providing a basis for understanding drought tolerance in A. duranensis.
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Affiliation(s)
- Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Pei Du
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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10
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Hong WJ, Lee SK, Kim SH, Kim YJ, Moon S, Kim EJ, Silva J, Jung KH. Comparative transcriptome analysis of pollen and anther wall reveals novel insights into the regulatory mechanisms underlying anther wall development and its dehiscence in rice. PLANT CELL REPORTS 2022; 41:1229-1242. [PMID: 35249124 DOI: 10.1007/s00299-022-02852-3] [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: 12/10/2021] [Accepted: 02/15/2022] [Indexed: 05/25/2023]
Abstract
To further understand the regulatory mechanism for anther dehiscence in rice, we carried out transcriptome analysis for the following two tissues: the anther wall and pollen at the anthesis stage. With the anatomical meta-expression data, in addition to these tissues, the differentially expressed genes (DEGs) between the two tissues were further refined to identify 1,717 pollen-preferred genes and 534 anther wall-preferred genes. A GUS transgenic line and RT-qPCR analysis for anther wall-preferred genes supported the fidelity of our gene candidates for further analysis. The refined DEGs were functionally classified through Gene Ontology (GO) enrichment and MapMan analyses. Through the analysis of cis-acting elements and alternative splicing variants, we also suggest the feature of regulatory sequences in promoter regions for anther wall-preferred expression and provide information of the unique splicing variants in anther wall. Subsequently, it was found that hormone signaling and the resulting transcriptional regulation pathways may play an important role in anther dehiscence and anther wall development. Our results could provide useful insights into future research to broaden the molecular mechanism of anther dehiscence or anther wall development in rice.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Su Kyoung Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Seok-Hui Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Eui-Jung Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Jeniffer Silva
- Department of Research and Development, The Bridge Biofoundry, Ciudad del Saber, Clayton, 0843-03081, Panama
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea.
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11
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Zhang T, Wang Z, Zhang Y, Yang G, Song H. Dissection of valine-glutamine genes and their responses to drought stress in Arachis hypogaea cv. Tifrunner. Funct Integr Genomics 2022; 22:491-501. [PMID: 35366145 DOI: 10.1007/s10142-022-00847-7] [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: 11/26/2021] [Revised: 03/04/2022] [Accepted: 03/16/2022] [Indexed: 11/04/2022]
Abstract
Valine-glutamine sequences (VQs) interact with WRKY transcription factors (TFs), forming VQ-WRKY protein complexes crucial for plant development and response to environmental changes. Cultivated peanut (Arachis hypogaea) is a tetraploid from A. duranensis and A. ipaensis cross. The Arachis spp. WRKY TFs have been identified, but Arachis VQs are largely unknown. This study identified VQs in A. duranensis, A. ipaensis, A. monticola, A. hypogaea cv. Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The study analyzed the homologous relationships between VQs in these Arachis spp. The VQ drought-tolerant genes were detected and VQ-WRKY interactions were determined in A. hypogaea cv. Tifrunner. The results showed that tetraploid Arachis spp. retained duplicated VQs, but lost ancestral VQs after allopolyploidization. The number of VQs in A. monticola, A. hypogaea cv. Fuhuasheng, and A. hypogaea cv. Shitouqi increased relative to their diploid ancestors. RNA-seq and quantitative real-time PCR experiments confirmed that three AhTVQs tolerate drought stress in A. hypogaea cv. Tifrunner. However, evidence of VQ-WRKY interaction for drought stress response is lacking in A. hypogaea cv. Tifrunner. Nevertheless, this study identified VQ-WRKY interactions, which possibly have multiple functions in A. hypogaea cv. Tifrunner. Altogether, this study dissected Arachis VQs, providing insights into Arachis VQ evolution and drought function.
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Affiliation(s)
- Tian Zhang
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zicheng Wang
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yongli Zhang
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China.
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12
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Martins ACQ, Mota APZ, Carvalho PASV, Passos MAS, Gimenes MA, Guimaraes PM, Brasileiro ACM. Transcriptome Responses of Wild Arachis to UV-C Exposure Reveal Genes Involved in General Plant Defense and Priming. PLANTS 2022; 11:plants11030408. [PMID: 35161389 PMCID: PMC8838480 DOI: 10.3390/plants11030408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022]
Abstract
Stress priming is an important strategy for enhancing plant defense capacity to deal with environmental challenges and involves reprogrammed transcriptional responses. Although ultraviolet (UV) light exposure is a widely adopted approach to elicit stress memory and tolerance in plants, the molecular mechanisms underlying UV-mediated plant priming tolerance are not fully understood. Here, we investigated the changes in the global transcriptome profile of wild Arachis stenosperma leaves in response to UV-C exposure. A total of 5751 differentially expressed genes (DEGs) were identified, with the majority associated with cell signaling, protein dynamics, hormonal and transcriptional regulation, and secondary metabolic pathways. The expression profiles of DEGs known as indicators of priming state, such as transcription factors, transcriptional regulators and protein kinases, were further characterized. A meta-analysis, followed by qRT-PCR validation, identified 18 metaDEGs as being commonly regulated in response to UV and other primary stresses. These genes are involved in secondary metabolism, basal immunity, cell wall structure and integrity, and may constitute important players in the general defense processes and establishment of a priming state in A. stenosperma. Our findings contribute to a better understanding of transcriptional dynamics involved in wild Arachis adaptation to stressful conditions of their natural habitats.
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Affiliation(s)
- Andressa Cunha Quintana Martins
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília 70770-917, DF, Brazil
| | - Ana Paula Zotta Mota
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília 70770-917, DF, Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Paula Andrea Sampaio Vasconcelos Carvalho
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- Instituto de Biociências, Department de Genética, Universidade Estadual Paulista (UNESP), Botucatu 70770-917, SP, Brazil
| | - Mario Alfredo Saraiva Passos
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília 70770-917, DF, Brazil
| | - Marcos Aparecido Gimenes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
| | - Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília 70770-917, DF, Brazil
| | - Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (A.C.Q.M.); (A.P.Z.M.); (P.A.S.V.C.); (M.A.S.P.); (M.A.G.); (P.M.G.)
- National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília 70770-917, DF, Brazil
- Correspondence:
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13
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Mota APZ, Brasileiro ACM, Vidigal B, Oliveira TN, da Cunha Quintana Martins A, Saraiva MADP, de Araújo ACG, Togawa RC, Grossi-de-Sá MF, Guimaraes PM. Defining the combined stress response in wild Arachis. Sci Rep 2021; 11:11097. [PMID: 34045561 PMCID: PMC8160017 DOI: 10.1038/s41598-021-90607-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
Nematodes and drought are major constraints in tropical agriculture and often occur simultaneously. Plant responses to these stresses are complex and require crosstalk between biotic and abiotic signaling pathways. In this study, we explored the transcriptome data of wild Arachis species subjected to drought (A-metaDEG) and the root-knot nematode Meloidogyne arenaria (B-metaDEG) via meta-analysis, to identify core-stress responsive genes to each individual and concurrent stresses in these species. Transcriptome analysis of a nematode/drought bioassay (cross-stress) showed that the set of stress responsive DEGs to concurrent stress is distinct from those resulting from overlapping A- and B-metaDEGs, indicating a specialized and unique response to combined stresses in wild Arachis. Whilst individual biotic and abiotic stresses elicit hormone-responsive genes, most notably in the jasmonic and abscisic acid pathways, combined stresses seem to trigger mainly the ethylene hormone pathway. The overexpression of a cross-stress tolerance candidate gene identified here, an endochitinase-encoding gene (AsECHI) from Arachis stenosperma, reduced up to 30% of M. incognita infection and increased post-drought recovery in Arabidopsis plants submitted to both stresses. The elucidation of the network of cross-stress responsive genes in Arachis contributes to better understanding the complex regulation of biotic and abiotic responses in plants facilitating more adequate crop breeding for combined stress tolerance.
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Affiliation(s)
- Ana Paula Zotta Mota
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.8532.c0000 0001 2200 7498Universidade Federal do Rio Grande do Sul, Porto Alegre, RS Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.8183.20000 0001 2153 9871Present Address: CIRAD, UMR AGAP, 34398 Montpellier, France ,grid.463758.b0000 0004 0445 8705Present Address: AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Ana Cristina Miranda Brasileiro
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Bruna Vidigal
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Thais Nicolini Oliveira
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Andressa da Cunha Quintana Martins
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Mario Alfredo de Passos Saraiva
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Ana Claudia Guerra de Araújo
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Roberto C. Togawa
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Maria Fatima Grossi-de-Sá
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.411952.a0000 0001 1882 0945Universidade Católica de Brasília (UCB)-Genomic Sciences and Biotechnology, Brasilia, DF Brazil
| | - Patricia Messenberg Guimaraes
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
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14
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Zhang L, Zhang H, Yang S. Cytosolic TaGAPC2 Enhances Tolerance to Drought Stress in Transgenic Arabidopsis Plants. Int J Mol Sci 2020; 21:ijms21207499. [PMID: 33053684 PMCID: PMC7590034 DOI: 10.3390/ijms21207499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 11/16/2022] Open
Abstract
Drought is a major natural disaster that seriously affects agricultural production, especially for winter wheat in boreal China. As functional proteins, the functions and mechanisms of glyceraldehyde-3-phosphate dehydrogenase in cytoplasm (GAPCs) have remained little investigated in wheat subjected to adverse environmental conditions. In this study, we cloned and characterized a GAPC isoform TaGAPC2 in wheat. Over-expression of TaGApC2-6D in Arabidopsis led to enhanced root length, reduced reactive oxygen species (ROS) production, and elevated drought tolerance. In addition, the dual-luciferase assays showed that TaWRKY28/33/40/47 could positively regulate the expression of TaGApC2-6A and TaGApC2-6D. Further results of the yeast two-hybrid system and bimolecular fluorescence complementation assay (BiFC) demonstrate that TaPLDδ, an enzyme producing phosphatidic acid (PA), could interact with TaGAPC2-6D in plants. These results demonstrate that TaGAPC2 regulated by TaWRKY28/33/40/47 plays a crucial role in drought tolerance, which may influence the drought stress conditions via interaction with TaPLDδ. In conclusion, our results establish a new positive regulation mechanism of TaGAPC2 that helps wheat fine-tune its drought response.
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15
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Vinson CC, Mota APZ, Porto BN, Oliveira TN, Sampaio I, Lacerda AL, Danchin EGJ, Guimaraes PM, Williams TCR, Brasileiro ACM. Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses. Sci Rep 2020; 10:15258. [PMID: 32943670 PMCID: PMC7498584 DOI: 10.1038/s41598-020-72191-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022] Open
Abstract
Raffinose family oligosaccharides (RFOs) are implicated in plant regulatory mechanisms of abiotic stresses tolerance and, despite their antinutritional proprieties in grain legumes, little information is available about the enzymes involved in RFO metabolism in Fabaceae species. In the present study, the systematic survey of legume proteins belonging to five key enzymes involved in the metabolism of RFOs (galactinol synthase, raffinose synthase, stachyose synthase, alpha-galactosidase, and beta-fructofuranosidase) identified 28 coding-genes in Arachis duranensis and 31 in A. ipaënsis. Their phylogenetic relationships, gene structures, protein domains, and chromosome distribution patterns were also determined. Based on the expression profiling of these genes under water deficit treatments, a galactinol synthase candidate gene (AdGolS3) was identified in A. duranensis. Transgenic Arabidopsis plants overexpressing AdGolS3 exhibited increased levels of raffinose and reduced stress symptoms under drought, osmotic, and salt stresses. Metabolite and expression profiling suggested that AdGolS3 overexpression was associated with fewer metabolic perturbations under drought stress, together with better protection against oxidative damage. Overall, this study enabled the identification of a promising GolS candidate gene for metabolic engineering of sugars to improve abiotic stress tolerance in crops, whilst also contributing to the understanding of RFO metabolism in legume species.
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Affiliation(s)
- Christina C Vinson
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Departamento de Botânica, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Ana P Z Mota
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Brenda N Porto
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Thais N Oliveira
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Iracyara Sampaio
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Departamento de Botânica, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Ana L Lacerda
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | | | - Patricia M Guimaraes
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Thomas C R Williams
- Departamento de Botânica, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Ana C M Brasileiro
- EMBRAPA Recursos Genéticos e Biotecnologia. Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil.
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16
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Carvalho PASDV, de Carvalho Moretzsohn M, Brasileiro ACM, Guimarães PM, da Silveira Agostini-Costa T, da Silva JP, Gimenes MA. Presence of resveratrol in wild Arachis species adds new value to this overlooked genetic resource. Sci Rep 2020; 10:12787. [PMID: 32733034 PMCID: PMC7393359 DOI: 10.1038/s41598-020-68648-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 05/25/2020] [Indexed: 12/05/2022] Open
Abstract
Genus Arachis comprises 82 species distributed into nine taxonomic sections. Most Arachis species are wild and those from Arachis section have been evaluated for many traits, since they can be used in peanut breeding. Most of the remaining species have been neglected and understudied. Recently, resveratrol content and expression of a resveratrol synthase gene were analyzed in wild Arachis species. Our aim was to expand the knowledge about resveratrol in Arachis, analyzing species from five sections and evaluating the expression of a resveratrol synthase (RS) gene responsive to ultraviolet light (UV) along the time. In a first experiment, the resveratrol content after UV induction was analyzed on detached leaves of 12 species from five sections. Variation was observed among species and accessions of the same species. The highest contents were found in A. lignosa (843.9 μg/g) and A. triseminata (745.4 μg/g). In a second experiment, RS expression and resveratrol content in four species and one synthetic amphidiploid were analyzed at 0, 7, 15 and 24 h pos induction (hpi) with UV. In most genotypes, the highest RS expression level was at 0 hpi, whereas the highest resveratrol content was at 15 hpi. Our results suggested that resveratrol is ubiquitously present in the genus Arachis with different capacities of synthesis among species and accessions in response to ultraviolet treatment. Presence of resveratrol in wild Arachis species adds new value to these genetic resources.
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Affiliation(s)
| | | | | | | | | | - Joseane Padilha da Silva
- Embrapa Recursos Genéticos E Biotecnologia, Parque Estação Biológica, Brasília, DF, 70770-917, Brazil
| | - Marcos A Gimenes
- Embrapa Recursos Genéticos E Biotecnologia, Parque Estação Biológica, Brasília, DF, 70770-917, Brazil.
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17
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Furlan AL, Bianucci E, Giordano W, Castro S, Becker DF. Proline metabolic dynamics and implications in drought tolerance of peanut plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:566-578. [PMID: 32320942 DOI: 10.1016/j.plaphy.2020.04.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 05/25/2023]
Abstract
Proline accumulation and metabolism are associated with mechanisms of abiotic stress avoidance in plants. Proline accumulation generally improves osmotic stress tolerance whereas proline metabolism can have varying effects from ATP generation to the formation of reactive oxygen species. To further understand the roles of proline in stress protection, two peanut cultivars with contrasting tolerance to drought were examined by transcriptional and biochemical analyses during water stress. Plants exposed to polyethylene glycol had diminished relative water content and increased proline content; while, only the drought sensitive plants, cultivar Granoleico, showed lipid oxidative damage (measured as thiobarbituric acid reactive substances). The expression of proline biosynthesis genes (P5CS1, P5CS2a, P5CS2b, P5CR) was increased in both cultivars upon exposure to water stress. However, the relative expression of proline catabolism genes (ProDH1, ProDH2) was increased only in the sensitive cultivar during stress. Exogenous addition of proline and the proline analogue thiazolidine-4-carboxylic acid (T4C), both substrates of proline dehydrogenase, was also used to exacerbate and identify plant responses. Pretreatment of plants with T4C induced unique changes in the drought tolerant EC-98 cultivar such as higher mRNA levels of proline biosynthetic and catabolic ProDH genes, even in the absence of water stress. The increased levels of ProDH gene expression, potentially associated with higher T4C conversion to cysteine, may contribute to the tolerant phenotype.
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Affiliation(s)
- Ana Laura Furlan
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800, Río Cuarto, Córdoba, Argentina; Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Eliana Bianucci
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Walter Giordano
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Stella Castro
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Martins AC, Mehta A, Murad AM, Mota AP, Saraiva MA, Araújo AC, Miller RN, Brasileiro AC, Guimarães PM. Proteomics unravels new candidate genes for Meloidogyne resistance in wild Arachis. J Proteomics 2020; 217:103690. [DOI: 10.1016/j.jprot.2020.103690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/29/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
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Mota APZ, Oliveira TN, Vinson CC, Williams TCR, Costa MMDC, Araujo ACG, Danchin EGJ, Grossi-de-Sá MF, Guimaraes PM, Brasileiro ACM. Contrasting Effects of Wild Arachis Dehydrin Under Abiotic and Biotic Stresses. FRONTIERS IN PLANT SCIENCE 2019; 10:497. [PMID: 31057593 PMCID: PMC6482428 DOI: 10.3389/fpls.2019.00497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/01/2019] [Indexed: 05/22/2023]
Abstract
Plant dehydrins (DNHs) belong to the LEA (Late Embryogenesis Abundant) protein family and are involved in responses to multiple abiotic stresses. DHNs are classified into five subclasses according to the organization of three conserved motifs (K-; Y-; and S-segments). In the present study, the DHN protein family was characterized by molecular phylogeny, exon/intron organization, protein structure, and tissue-specificity expression in eight Fabaceae species. We identified 20 DHN genes, encompassing three (YnSKn, SKn, and Kn) subclasses sharing similar gene organization and protein structure. Two additional low conserved DHN Φ-segments specific to the legume SKn-type of proteins were also found. The in silico expression patterns of DHN genes in four legume species (Arachis duranensis, A. ipaënsis, Glycine max, and Medicago truncatula) revealed that their tissue-specific regulation is associated with the presence or absence of the Y-segment. Indeed, DHN genes containing a Y-segment are mainly expressed in seeds, whereas those without the Y-segment are ubiquitously expressed. Further qRT-PCR analysis revealed that, amongst stress responsive dehydrins, a SKn-type DHN gene from A. duranensis (AdDHN1) showed opposite response to biotic and abiotic stress with a positive regulation under water deficit and negative regulation upon nematode infection. Furthermore, transgenic Arabidopsis lines overexpressing (OE) AdDHN1 displayed improved tolerance to multiple abiotic stresses (freezing and drought) but increased susceptibility to the biotrophic root-knot nematode (RKN) Meloidogyne incognita. This contradictory role of AdDHN1 in responses to abiotic and biotic stresses was further investigated by qRT-PCR analysis of transgenic plants using a set of stress-responsive genes involved in the abscisic acid (ABA) and jasmonic acid (JA) signaling pathways and suggested an involvement of DHN overexpression in these stress-signaling pathways.
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Affiliation(s)
- Ana Paula Zotta Mota
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thais Nicolini Oliveira
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Botânica, Universidade de Brasília, Brasília, Brazil
| | - Christina Cleo Vinson
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Botânica, Universidade de Brasília, Brasília, Brazil
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20
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Karmakar K, Kundu A, Rizvi AZ, Dubois E, Severac D, Czernic P, Cartieaux F, DasGupta M. Transcriptomic Analysis With the Progress of Symbiosis in 'Crack-Entry' Legume Arachis hypogaea Highlights Its Contrast With 'Infection Thread' Adapted Legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:271-285. [PMID: 30109978 DOI: 10.1094/mpmi-06-18-0174-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In root-nodule symbiosis, rhizobial invasion and nodule organogenesis is host controlled. In most legumes, rhizobia enter through infection threads and nodule primordium in the cortex is induced from a distance. But in dalbergoid legumes like Arachis hypogaea, rhizobia directly invade cortical cells through epidermal cracks to generate the primordia. Herein, we report the transcriptional dynamics with the progress of symbiosis in A. hypogaea at 1 day postinfection (dpi) (invasion), 4 dpi (nodule primordia), 8 dpi (spread of infection in nodule-like structure), 12 dpi (immature nodules containing rod-shaped rhizobia), and 21 dpi (mature nodules with spherical symbiosomes). Expression of putative ortholog of symbiotic genes in 'crack entry' legume A. hypogaea was compared with infection thread-adapted model legumes. The contrasting features were i) higher expression of receptors like LYR3 and EPR3 as compared with canonical Nod factor receptors, ii) late induction of transcription factors like NIN and NSP2 and constitutive high expression of ERF1, EIN2, bHLH476, and iii) induction of divergent pathogenesis-responsive PR-1 genes. Additionally, symbiotic orthologs of SymCRK, ROP6, RR9, SEN1, and DNF2 were not detectable and microsynteny analysis indicated the absence of a RPG homolog in diploid parental genomes of A. hypogaea. The implications are discussed and a molecular framework that guides crack-entry symbiosis in A. hypogaea is proposed.
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Affiliation(s)
- Kanchan Karmakar
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Anindya Kundu
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Ahsan Z Rizvi
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Emeric Dubois
- 3 Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 05, France
| | - Dany Severac
- 3 Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 05, France
| | - Pierre Czernic
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Fabienne Cartieaux
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Maitrayee DasGupta
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
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21
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Comparative proteomics and gene expression analysis in Arachis duranensis reveal stress response proteins associated to drought tolerance. J Proteomics 2019; 192:299-310. [DOI: 10.1016/j.jprot.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/10/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022]
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Mota APZ, Vidigal B, Danchin EGJ, Togawa RC, Leal-Bertioli SCM, Bertioli DJ, Araujo ACG, Brasileiro ACM, Guimaraes PM. Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. BMC PLANT BIOLOGY 2018; 18:159. [PMID: 30081841 PMCID: PMC6080386 DOI: 10.1186/s12870-018-1373-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/26/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Root-Knot Nematode (RKN), Meloidogyne arenaria, significantly reduces peanut grain quality and yield worldwide. Whilst the cultivated species has low levels of resistance to RKN and other pests and diseases, peanut wild relatives (Arachis spp.) show rich genetic diversity and harbor high levels of resistance to many pathogens and environmental constraints. Comparative transcriptome analysis can be applied to identify candidate resistance genes. RESULTS Transcriptome analysis during the early stages of RKN infection of two peanut wild relatives, the highly RKN resistant Arachis stenosperma and the moderately susceptible A. duranensis, revealed genes related to plant immunity with contrasting expression profiles. These included genes involved in hormone signaling and secondary metabolites production and also members of the NBS-LRR class of plant disease resistance (R) genes. From 345 NBS-LRRs identified in A.duranensis reference genome, 52 were differentially expressed between inoculated and control samples, with the majority occurring in physical clusters unevenly distributed on eight chromosomes with preferential tandem duplication. The majority of these NBS-LRR genes showed contrasting expression behaviour between A. duranensis and A. stenosperma, particularly at 6 days after nematode inoculation, coinciding with the onset of the Hypersensitive Response in the resistant species. The physical clustering of some of these NBS-LRR genes correlated with their expression patterns in the contrasting genotypes. Four NBS-LRR genes exclusively expressed in A. stenosperma are located within clusters on chromosome Aradu. A09, which harbors a QTL for RKN resistance, suggesting a functional role for their physical arrangement and their potential involvement in this defense response. CONCLUSION The identification of functional novel R genes in wild Arachis species responsible for triggering effective defense cascades can contribute to the crop genetic improvement and enhance peanut resilience to RKN.
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Affiliation(s)
- Ana Paula Zotta Mota
- EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS Brazil
| | - Bruna Vidigal
- EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF Brazil
| | | | | | | | - David John Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Vinson CC, Mota APZ, Oliveira TN, Guimaraes LA, Leal-Bertioli SCM, Williams TCR, Nepomuceno AL, Saraiva MAP, Araujo ACG, Guimaraes PM, Brasileiro ACM. Early responses to dehydration in contrasting wild Arachis species. PLoS One 2018; 13:e0198191. [PMID: 29847587 PMCID: PMC5976199 DOI: 10.1371/journal.pone.0198191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/14/2018] [Indexed: 12/04/2022] Open
Abstract
Wild peanut relatives (Arachis spp.) are genetically diverse and were selected throughout evolution to a range of environments constituting, therefore, an important source of allelic diversity for abiotic stress tolerance. In particular, A. duranensis and A. stenosperma, the parents of the reference Arachis A-genome genetic map, show contrasting transpiration behavior under limited water conditions. This study aimed to build a comprehensive gene expression profile of these two wild species under dehydration stress caused by the withdrawal of hydroponic nutrient solution. For this purpose, roots of both genotypes were collected at seven time-points during the early stages of dehydration and used to construct cDNA paired-end libraries. Physiological analyses indicated initial differences in gas exchange parameters between the drought-tolerant genotype of A. duranensis and the drought-sensitive genotype of A. stenosperma. High-quality Illumina reads were mapped against the A. duranensis reference genome and resulted in the identification of 1,235 and 799 Differentially Expressed Genes (DEGs) that responded to the stress treatment in roots of A. duranensis and A. stenosperma, respectively. Further analysis, including functional annotation and identification of biological pathways represented by these DEGs confirmed the distinct gene expression behavior of the two contrasting Arachis species genotypes under dehydration stress. Some species-exclusive and common DEGs were then selected for qRT-PCR analysis, which corroborated the in silico expression profiling. These included genes coding for regulators and effectors involved in drought tolerance responses, such as activation of osmosensing molecular cascades, control of hormone and osmolyte content, and protection of macromolecules. This dataset of transcripts induced during the dehydration process in two wild Arachis genotypes constitute new tools for the understanding of the distinct gene regulation processes in these closely related species but with contrasting drought responsiveness. In addition, our findings provide insights into the nature of drought tolerance in wild germoplasm, which might be explored as novel sources of diversity and useful wild alleles to develop climate-resilient crop varieties.
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Affiliation(s)
- Christina Cleo Vinson
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF–Brazil
| | - Ana Paula Zotta Mota
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS—Brazil
| | - Thais Nicolini Oliveira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS—Brazil
| | - Larissa Arrais Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
| | | | | | | | | | - Ana Claudia Guerra Araujo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
| | | | - Ana C. M. Brasileiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
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Amorim LLB, Ferreira-Neto JRC, Bezerra-Neto JP, Pandolfi V, de Araújo FT, da Silva Matos MK, Santos MG, Kido EA, Benko-Iseppon AM. Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR. PLANT METHODS 2018; 14:88. [PMID: 30337949 PMCID: PMC6182843 DOI: 10.1186/s13007-018-0354-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM). In addition, the regulation of four target transcripts, under the same referred conditions was also scrutinized. RESULTS geNorm, NormFinder, BestKeeper, and ΔCt method results indicated a set of three statistically validated RGs for each stress condition: (I) root dehydration (actin, ubiquitin-conjugating enzyme E2 variant 1D, and a Phaseolus vulgaris unknown gene-UNK), and (II) salt (ubiquitin-conjugating enzyme E2 variant 1D, F-box protein, and UNK). The expression profile of the target transcripts suggests that flavonoids are important players in the cowpea response to the abiotic stresses analyzed, since chalcone isomerase and chalcone synthase were up-regulated in the tolerant and sensitive accessions. A lipid transfer protein also participates in the cowpea tolerance mechanisms to root dehydration and salt stress. The referred transcript was up-regulated in the two tolerant accessions and presented no differential expression in the sensitive counterparts. Chitinase B, in turn, generally related to plant defense, was an important target transcript under salt stress, being up-regulated at the tolerant, and down-regulated in the sensitive accession. CONCLUSIONS Reference genes suitable for qPCR analyses in cowpea under root dehydration and salt stress were identified. This action will lead to a more accurate and reliable analysis of gene expression on this species. Additionally, the results obtained in this study may guide future research on gene expression in cowpea under other abiotic stress types that impose osmotic imbalance. The target genes analyzed, in turn, deserve functional evaluation due to their transcriptional regulation under stresses and biotechnological potential.
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Affiliation(s)
- Lidiane Lindinalva Barbosa Amorim
- Instituto Federal de Educação, Ciência e Tecnologia do Piauí, Oeiras, Piauí Brazil
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | | | | | - Valesca Pandolfi
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | | | | | - Mauro Guida Santos
- Botany Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | - Ederson Akio Kido
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
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Xie XG, Fu WQ, Zhang FM, Shi XM, Zeng YT, Li H, Zhang W, Dai CC. The Endophytic Fungus Phomopsis liquidambari Increases Nodulation and N 2 Fixation in Arachis hypogaea by Enhancing Hydrogen Peroxide and Nitric Oxide Signalling. MICROBIAL ECOLOGY 2017; 74:427-440. [PMID: 28168354 DOI: 10.1007/s00248-017-0944-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/22/2017] [Indexed: 05/16/2023]
Abstract
The continuous cropping obstacles in monoculture fields are a major production constraint for peanuts. Application of the endophytic fungus Phomopsis liquidambari has increased peanut yields, and nodulation and N2 fixation increases have been considered as important factors for P. liquidambari infection-improved peanut yield. However, the mechanisms involved in this process remain unknown. This work showed that compared with only Bradyrhizobium inoculation, co-inoculation with P. liquidambari significantly elevated endogenous H2O2 and NO levels in peanut roots. Pre-treatment of seedlings with specific scavengers of H2O2 (CAT) and NO (cPTIO) blocked P. liquidambari-induced nodulation and N2 fixation. CAT not only suppressed the P. liquidambari-induced nodulation and N2 fixation, but also suppressed the enhanced H2O2 and NO generation. Nevertheless, the cPTIO did not significantly inhibit the induced H2O2 biosynthesis, implying that H2O2 acted upstream of NO production. These results were confirmed by observations that exogenous H2O2 and sodium nitroprusside (SNP) reversed the inhibition of P. liquidambari-increased nodulation and N2 fixation by the specific scavengers. The transcriptional activities of the symbiosis-related genes SymRK and CCaMK of peanut-Bradyrhizobium interactions also increased significantly in response to P. liquidambari, H2O2 and SNP treatments. The pot experiment further confirmed that the P. liquidambari infection-enhanced H2O2 and NO signalling pathways were significantly related to the increase in peanut nodulation and N2 fixation. This is the first report that endophytic fungus P. liquidambari can increase peanut-Bradyrhizobium interactions via enhanced H2O2/NO-dependent signalling crosstalk, which is conducive to the alleviation of continuous cropping obstacles via an increase in nodulation and N2 fixation.
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Affiliation(s)
- Xing-Guang Xie
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Wan-Qiu Fu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Feng-Min Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Xiao-Min Shi
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Ying-Ting Zeng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Hui Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Qixia District, Nanjing, Jiangsu Province, 210023, China.
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He M, Cui S, Yang X, Mu G, Chen H, Liu L. Selection of suitable reference genes for abiotic stress-responsive gene expression studies in peanut by real-time quantitative PCR. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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27
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Guimaraes LA, Mota APZ, Araujo ACG, de Alencar Figueiredo LF, Pereira BM, de Passos Saraiva MA, Silva RB, Danchin EGJ, Guimaraes PM, Brasileiro ACM. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene. PLANT MOLECULAR BIOLOGY 2017; 94:79-96. [PMID: 28243841 PMCID: PMC5437183 DOI: 10.1007/s11103-017-0594-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/13/2017] [Indexed: 05/08/2023]
Abstract
Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.
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Affiliation(s)
- Larissa Arrais Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Ana Paula Zotta Mota
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Claudia Guerra Araujo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | | | - Bruna Medeiros Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | - Raquel Bispo Silva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRA, University of Nice Sophia Antipolis, CNRS, 06900, Sophia Antipolis, France
| | - Patricia Messenberg Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
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Guimaraes LA, Pereira BM, Araujo ACG, Guimaraes PM, Brasileiro ACM. Ex vitro hairy root induction in detached peanut leaves for plant-nematode interaction studies. PLANT METHODS 2017; 13:25. [PMID: 28400855 PMCID: PMC5387216 DOI: 10.1186/s13007-017-0176-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/02/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Peanut (Arachis hypogaea) production is largely affected by a variety of abiotic and biotic stresses, including the root-knot nematode (RKN) Meloidogyne arenaria that causes yield losses worldwide. Transcriptome studies of wild Arachis species, which harbor resistance to a number of pests and diseases, disclosed several candidate genes for M. arenaria resistance. Peanut is recalcitrant to genetic transformation, so the use of Agrobacterium rhizogenes-derived hairy roots emerged as an alternative for in-root functional characterization of these candidate genes. RESULTS The present report describes an ex vitro methodology for hairy root induction in detached leaves based on the well-known ability of peanut to produce roots spontaneously from its petiole, which can be maintained for extended periods under high-humidity conditions. Thirty days after infection with the A. rhizogenes 'K599' strain, 90% of the detached leaves developed transgenic hairy roots with 5 cm of length in average, which were then inoculated with M. arenaria. For improved results, plant transformation, and nematode inoculation parameters were adjusted, such as bacterial cell density and growth stage; moist chamber conditions and nematode inoculum concentration. Using this methodology, a candidate gene for nematode resistance, AdEXLB8, was successfully overexpressed in hairy roots of the nematode-susceptible peanut cultivar 'Runner', resulting in 98% reduction in the number of galls and egg masses compared to the control, 60 days after M. arenaria infection. CONCLUSIONS This methodology proved to be more practical and cost-effective for functional validation of peanut candidate genes than in vitro and composite plant approaches, as it requires less space, reduces analysis costs and displays high transformation efficiency. The reduction in the number of RKN galls and egg masses in peanut hairy roots overexpressing AdEXLB8 corroborated the use of this strategy for functional characterization of root expressing candidate genes. This approach could be applicable not only for peanut-nematode interaction studies but also to other peanut root diseases, such as those caused by fungi and bacteria, being also potentially extended to other crop species displaying similar petiole-rooting competence.
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Affiliation(s)
- Larissa Arrais Guimaraes
- Parque Estação Biológica, Embrapa Recursos Genéticos e Biotecnologia, CP 02372, Final W5 Norte, Brasília, DF Brazil
| | - Bruna Medeiros Pereira
- Parque Estação Biológica, Embrapa Recursos Genéticos e Biotecnologia, CP 02372, Final W5 Norte, Brasília, DF Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF Brazil
| | - Ana Claudia Guerra Araujo
- Parque Estação Biológica, Embrapa Recursos Genéticos e Biotecnologia, CP 02372, Final W5 Norte, Brasília, DF Brazil
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Peng Z, Liu F, Wang L, Zhou H, Paudel D, Tan L, Maku J, Gallo M, Wang J. Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation. Sci Rep 2017; 7:40066. [PMID: 28059169 PMCID: PMC5216375 DOI: 10.1038/srep40066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/30/2016] [Indexed: 11/17/2022] Open
Abstract
The molecular mechanisms of symbiosis in cultivated peanut with a ‘crack entry’ infection process are largely understudied. In this study, we investigated the root transcriptional profiles of two pairs of non-nodulating (nod−) and nodulating (nod+) sister inbred peanut lines, E4/E5 and E7/E6, and their nod+ parents, F487A and PI262090 during rhizobial infection and nodule initiation by using RNA-seq technology. A total of 143, 101, 123, 215, 182, and 289 differentially expressed genes (DEGs) were identified in nod− E4, E7 and nod+ E5, E6, F487A, and PI262090 after inoculation with Bradyrhizobium sp. Different deficiencies at upstream of symbiotic signaling pathway were revealed in the two nod− genotypes. DEGs specific in nod+ genotypes included orthologs to some known symbiotic signaling pathway genes, such as NFR5, NSP2, NIN, ERN1, and many other novel and/or functionally unknown genes. Gene ontology (GO) enrichment analysis of nod+ specific DEGs revealed 54 significantly enriched GO terms, including oxidation-reduction process, metabolic process, and catalytic activity. Genes related with plant defense systems, hormone biosynthesis and response were particularly enriched. To our knowledge, this is the first report revealing symbiosis-related genes in a genome-wide manner in peanut representative of the ‘crack entry’ species.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Fengxia Liu
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.,State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), China Agricultural University, Beijing 100193, China
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Hai Zhou
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Lubin Tan
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.,State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), China Agricultural University, Beijing 100193, China
| | - James Maku
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.,Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
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30
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Moazzam Jazi M, Ghadirzadeh Khorzoghi E, Botanga C, Seyedi SM. Identification of Reference Genes for Quantitative Gene Expression Studies in a Non-Model Tree Pistachio (Pistacia vera L.). PLoS One 2016; 11:e0157467. [PMID: 27308855 PMCID: PMC4911069 DOI: 10.1371/journal.pone.0157467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/30/2016] [Indexed: 01/01/2023] Open
Abstract
The tree species, Pistacia vera (P. vera) is an important commercial product that is salt-tolerant and long-lived, with a possible lifespan of over one thousand years. Gene expression analysis is an efficient method to explore the possible regulatory mechanisms underlying these characteristics. Therefore, having the most suitable set of reference genes is required for transcript level normalization under different conditions in P. vera. In the present study, we selected eight widely used reference genes, ACT, EF1α, α-TUB, β-TUB, GAPDH, CYP2, UBQ10, and 18S rRNA. Using qRT-PCR their expression was assessed in 54 different samples of three cultivars of P. vera. The samples were collected from different organs under various abiotic treatments (cold, drought, and salt) across three time points. Several statistical programs (geNorm, NormFinder, and BestKeeper) were applied to estimate the expression stability of candidate reference genes. Results obtained from the statistical analysis were then exposed to Rank aggregation package to generate a consensus gene rank. Based on our results, EF1α was found to be the superior reference gene in all samples under all abiotic treatments. In addition to EF1α, ACT and β-TUB were the second best reference genes for gene expression analysis in leaf and root. We recommended β-TUB as the second most stable gene for samples under the cold and drought treatments, while ACT holds the same position in samples analyzed under salt treatment. This report will benefit future research on the expression profiling of P. vera and other members of the Anacardiaceae family.
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Affiliation(s)
- Maryam Moazzam Jazi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | | | - Christopher Botanga
- Department of Biological Sciences, Chicago State University, Chicago, Illinois, United States of America
| | - Seyed Mahdi Seyedi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
- * E-mail:
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31
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de Lima JC, de Costa F, Füller TN, Rodrigues-Corrêa KCDS, Kerber MR, Lima MS, Fett JP, Fett-Neto AG. Reference Genes for qPCR Analysis in Resin-Tapped Adult Slash Pine As a Tool to Address the Molecular Basis of Commercial Resinosis. FRONTIERS IN PLANT SCIENCE 2016; 7:849. [PMID: 27379135 PMCID: PMC4909774 DOI: 10.3389/fpls.2016.00849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/30/2016] [Indexed: 05/30/2023]
Abstract
Pine oleoresin is a major source of terpenes, consisting of turpentine (mono- and sesquiterpenes) and rosin (diterpenes) fractions. Higher oleoresin yields are of economic interest, since oleoresin derivatives make up a valuable source of materials for chemical industries. Oleoresin can be extracted from living trees, often by the bark streak method, in which bark removal is done periodically, followed by application of stimulant paste containing sulfuric acid and other chemicals on the freshly wounded exposed surface. To better understand the molecular basis of chemically-stimulated and wound induced oleoresin production, we evaluated the stability of 11 putative reference genes for the purpose of normalization in studying Pinus elliottii gene expression during oleoresinosis. Samples for RNA extraction were collected from field-grown adult trees under tapping operations using stimulant pastes with different compositions and at various time points after paste application. Statistical methods established by geNorm, NormFinder, and BestKeeper softwares were consistent in pointing as adequate reference genes HISTO3 and UBI. To confirm expression stability of the candidate reference genes, expression profiles of putative P. elliottii orthologs of resin biosynthesis-related genes encoding Pinus contorta β-pinene synthase [PcTPS-(-)β-pin1], P. contorta levopimaradiene/abietadiene synthase (PcLAS1), Pinus taeda α-pinene synthase [PtTPS-(+)αpin], and P. taeda α-farnesene synthase (PtαFS) were examined following stimulant paste application. Increased oleoresin yields observed in stimulated treatments using phytohormone-based pastes were consistent with higher expression of pinene synthases. Overall, the expression of all genes examined matched the expected profiles of oleoresin-related transcript changes reported for previously examined conifers.
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Affiliation(s)
- Júlio C. de Lima
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Fernanda de Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Thanise N. Füller
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | | | - Magnus R. Kerber
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Mariano S. Lima
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Janette P. Fett
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Arthur G. Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
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Kumar D, Rampuria S, Singh NK, Kirti PB. A novel zinc-binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco. FEBS Open Bio 2016; 6:200-10. [PMID: 27047748 PMCID: PMC4794784 DOI: 10.1002/2211-5463.12040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/11/2015] [Accepted: 01/08/2016] [Indexed: 12/26/2022] Open
Abstract
A novel zinc-binding alcohol dehydrogenase 2 (AdZADH2) was significantly upregulated in a wild peanut, Arachis diogoi treated with conidia of late leaf spot (LLS) pathogen, Phaeoisariopsis personata. This upregulation was not observed in a comparative analysis of cultivated peanut, which is highly susceptible to LLS. This zinc-binding alcohol dehydrogenase possessed a Rossmann fold containing NADB domain in addition to the MDR domain present in all previously characterized plant ADH genes/proteins. Transient over-expression of AdZADH2 under an estradiol inducible promoter (XVE) resulted in hypersensitive response (HR)-like cell death in tobacco leaf. However, the same level of cell death was not observed when the domains were transiently expressed individually. Cell death observed in tobacco was associated with overexpression of cell death related proteins, antioxidative enzymes such as SOD, CAT and APX and pathogenesis-related (PR) proteins. In A. diogoi, AdZADH2 expression was significantly upregulated in response to the plant signaling hormones salicylic acid, methyl jasmonate, and sodium nitroprusside.
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Affiliation(s)
- Dilip Kumar
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Sakshi Rampuria
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Naveen Kumar Singh
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Pulugurtha B Kirti
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
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Ma R, Xu S, Zhao Y, Xia B, Wang R. Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Analysis of Gene Expression in Lycoris aurea. FRONTIERS IN PLANT SCIENCE 2016; 7:536. [PMID: 27200013 PMCID: PMC4843812 DOI: 10.3389/fpls.2016.00536] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/05/2016] [Indexed: 05/18/2023]
Abstract
Lycoris aurea (L' Hér.) Herb, a perennial grass species, produces a unique variety of pharmacologically active Amaryllidaceae alkaloids. However, the key enzymes and their expression pattern involved in the biosynthesis of Amaryllidaceae alkaloids (especially for galanthamine) are far from being fully understood. Quantitative real-time polymerase chain reaction (qRT-PCR), a commonly used method for quantifying gene expression, requires stable reference genes to normalize its data. In this study, to choose the appropriate reference genes under different experimental conditions, 14 genes including YLS8 (mitosis protein YLS8), CYP2 (Cyclophilin 2), CYP 1 (Cyclophilin 1), TIP41 (TIP41-like protein), EXP2 (Expressed protein 2), PTBP1 (Polypyrimidine tract-binding protein 1), EXP1 (Expressed protein 1), PP2A (Serine/threonine-protein phosphatase 2A), β-TUB (β-tubulin), α-TUB (α-tubulin), EF1-α (Elongation factor 1-α), UBC (Ubiquitin-conjugating enzyme), ACT (Actin) and GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) were selected from the transcriptome datasets of L. aurea. And then, expressions of these genes were assessed by qRT-PCR in various tissues and the roots under different treatments. The expression stability of the 14 candidates was analyzed by three commonly used software programs (geNorm, NormFinder, and BestKeeper), and their results were further integrated into a comprehensive ranking based on the geometric mean. The results show the relatively stable genes for each subset as follows: (1) EXP1 and TIP41 for all samples; (2) UBC and EXP1 for NaCl stress; (3) PTBP1 and EXP1 for heat stress, polyethylene glycol (PEG) stress and ABA treatment; (4) UBC and CYP2 for cold stress; (5) PTBP1 and PP2A for sodium nitroprusside (SNP) treatment; (6) CYP1 and TIP41 for methyl jasmonate (MeJA) treatment; and (7) EXP1 and TIP41 for various tissues. The reliability of these results was further enhanced through comparison between part qRT-PCR result and RNA sequencing (RNA-seq) data. In summary, our results identified appropriate reference genes for qRT-PCR in L. aurea, and will facilitate gene expression studies under these conditions.
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Affiliation(s)
- Rui Ma
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| | - Yucheng Zhao
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical UniversityNanjing, China
| | - Bing Xia
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
- *Correspondence: Ren Wang
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Guimaraes PM, Guimaraes LA, Morgante CV, Silva OB, Araujo ACG, Martins ACQ, Saraiva MAP, Oliveira TN, Togawa RC, Leal-Bertioli SCM, Bertioli DJ, Brasileiro ACM. Root Transcriptome Analysis of Wild Peanut Reveals Candidate Genes for Nematode Resistance. PLoS One 2015; 10:e0140937. [PMID: 26488731 PMCID: PMC4619257 DOI: 10.1371/journal.pone.0140937] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022] Open
Abstract
Wild peanut relatives (Arachis spp.) are genetically diverse and were adapted to a range of environments during the evolution course, constituting an important source of allele diversity for resistance to biotic and abiotic stresses. The wild diploid A. stenosperma harbors high levels of resistance to a variety of pathogens, including the root-knot nematode (RKN) Meloidogyne arenaria, through the onset of the Hypersensitive Response (HR). In order to identify genes and regulators triggering this defense response, a comprehensive root transcriptome analysis during the first stages of this incompatible interaction was conducted using Illumina Hi-Seq. Overall, eight cDNA libraries were produced generating 28.2 GB, which were de novo assembled into 44,132 contigs and 37,882 loci. Differentially expressed genes (DEGs) were identified and clustered according to their expression profile, with the majority being downregulated at 6 DAI, which coincides with the onset of the HR. Amongst these DEGs, 27 were selected for further qRT-PCR validation allowing the identification of nematode-responsive candidate genes that are putatively related to the resistance response. Those candidates are engaged in the salycilic (NBS-LRR, lipocalins, resveratrol synthase) and jasmonic (patatin, allene oxidase cyclase) acids pathways, and also related to hormonal balance (auxin responsive protein, GH3) and cellular plasticity and signaling (tetraspanin, integrin, expansin), with some of them showing contrasting expression behavior between Arachis RKN-resistant and susceptible genotypes. As these candidate genes activate different defensive signaling systems, the genetic (HR) and the induced resistance (IR), their pyramidding in one genotype via molecular breeding or transgenic strategy might contribute to a more durable resistance, thus improving the long-term control of RKN in peanut.
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Affiliation(s)
| | | | | | - Orzenil B. Silva
- EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF, Brazil
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Lacerda ALM, Fonseca LN, Blawid R, Boiteux LS, Ribeiro SG, Brasileiro ACM. Reference Gene Selection for qPCR Analysis in Tomato-Bipartite Begomovirus Interaction and Validation in Additional Tomato-Virus Pathosystems. PLoS One 2015; 10:e0136820. [PMID: 26317870 PMCID: PMC4552598 DOI: 10.1371/journal.pone.0136820] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/09/2015] [Indexed: 12/15/2022] Open
Abstract
Quantitative Polymerase Chain Reaction (qPCR) is currently the most sensitive technique used for absolute and relative quantification of a target gene transcript, requiring the use of appropriated reference genes for data normalization. To accurately estimate the relative expression of target tomato (Solanum lycopersicum L.) genes responsive to several virus species in reverse transcription qPCR analysis, the identification of reliable reference genes is mandatory. In the present study, ten reference genes were analyzed across a set of eight samples: two tomato contrasting genotypes ('Santa Clara', susceptible, and its near-isogenic line 'LAM 157', resistant); subjected to two treatments (inoculation with Tomato chlorotic mottle virus (ToCMoV) and its mock-inoculated control) and in two distinct times after inoculation (early and late). Reference genes stability was estimated by three statistical programs (geNorm, NormFinder and BestKeeper). To validate the results over broader experimental conditions, a set of ten samples, corresponding to additional three tomato-virus pathosystems that included tospovirus, crinivirus and tymovirus + tobamovirus, was analyzed together with the tomato-ToCMoV pathosystem dataset, using the same algorithms. Taking into account the combined analyses of the ranking order outputs from the three algorithms, TIP41 and EF1 were identified as the most stable genes for tomato-ToCMoV pathosystem, and TIP41 and EXP for the four pathosystems together, and selected to be used as reference in the forthcoming expression qPCR analysis of target genes in experimental conditions involving the aforementioned tomato-virus pathosystems.
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Affiliation(s)
- Ana L. M. Lacerda
- Embrapa Recursos Genéticos e Biotecnologia, Embrapa, Brasília, DF, Brazil
| | | | - Rosana Blawid
- Embrapa Recursos Genéticos e Biotecnologia, Embrapa, Brasília, DF, Brazil
| | | | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Embrapa, Brasília, DF, Brazil
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Biochemical traits and proteomic changes in postharvest flowers of medicinal chrysanthemum exposed to enhanced UV-B radiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 149:272-9. [PMID: 26114222 DOI: 10.1016/j.jphotobiol.2015.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/27/2015] [Accepted: 06/18/2015] [Indexed: 11/23/2022]
Abstract
The article studied UV-B effects on biochemical traits and proteomic changes in postharvest flowers of medicinal chrysanthemum. The experiment about UV-B effects on biochemical traits in flowers included six levels of UV-B treatments (0 (UV0), 50 (UV50), 200 (UV200), 400 (UV400), 600 (UV600) and 800 (UV800) μWcm(-2)). UV400, UV600 and UV800 treatments significantly increased the contents of hydrogen peroxide, malondialdehyde and UV-B absorbing compounds, and the activity of phenylalanine ammonia lyase enzyme over the control. The contents of chlorogenic acid and flavone in flowers were significantly increased by UV-B treatments (except for UV50 and UV800). Two-dimensional gel electrophoresis was utilized to analyze proteomic changes in flowers with or without UV-B radiation. Results indicated that 43 protein spots (>1.5-fold difference in volume) were detected, including 19 spots with a decreasing trend and 24 spots with an increasing trend, and 19 differentially expressed protein spots were successfully indentified by MALDI-TOF MS. The indentified proteins were classified based on functions, the most of which were involved in photosynthesis, respiration, protein biosynthesis and degradation and defence. An overall assessment using biochemical and differential proteomic data revealed that UV-B radiation could affect biochemical reaction and promote secondary metabolism processes in postharvest flowers.
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37
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Kumar D, Rampuria S, Singh NK, Shukla P, Kirti PB. Characterization of a vacuolar processing enzyme expressed in Arachis diogoi in resistance responses against late leaf spot pathogen, Phaeoisariopsis personata. PLANT MOLECULAR BIOLOGY 2015; 88:177-91. [PMID: 25893777 DOI: 10.1007/s11103-015-0318-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
Vacuolar processing enzymes are cysteine proteases responsible for maturation of vacuolar proteins. They have been shown to possess caspase-1-like activity, mediate cell death and display increased activity during pathogen infections. A transcript derived fragment corresponding to VPE was found to be up-regulated in a cDNA-AFLP analysis of host responses of a wild peanut, Arachis diogoi upon challenge from the late leaf spot pathogen Phaeoisariopsis personata, which was subsequently validated by q-PCR in a time course analysis, where susceptible peanut did not show its upregulation. In transient conditional and constitutive expression studies in tobacco leaves using agroinfiltration, we have observed that expression of AdVPE was associated with hypersensitive response (HR) like cell death. AdVPE expression was found to be high at 24 h post estradiol application and this was associated with the enhanced co-expression of molecular markers of HR cell death genes and genes for pathogenesis related proteins indicating that AdVPE positively regulates defense responses and its estradiol induced expression is sufficient for HR-like cell death in tobacco. We found that AdVPE expression was very strongly induced in response to sodium nitroprusside, which indicates its involvement in stress signaling. Induced expression of AdVPE in response to jasmonic acid and ethylene also indicates its involvement in an interconnected network of signaling. Transgenic tobacco plants ectopically expressing AdVPE exhibited enhanced resistance against Phytophthora parasitica var. nicotianae, Alternaria alternata var. nicotianae and Rhizoctonia solani. To our knowledge, this is the first report on the heterologous expression of a pathogen induced VPE enhancing resistance to fungal pathogens with cell death phenomenon under transient expression.
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Affiliation(s)
- Dilip Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India,
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Brasileiro ACM, Morgante CV, Araujo ACG, Leal-Bertioli SCM, Silva AK, Martins ACQ, Vinson CC, Santos CMR, Bonfim O, Togawa RC, Saraiva MAP, Bertioli DJ, Guimaraes PM. Transcriptome Profiling of Wild Arachis from Water-Limited Environments Uncovers Drought Tolerance Candidate Genes. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:1876-1892. [PMID: 26752807 PMCID: PMC4695501 DOI: 10.1007/s11105-015-0882-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important legume cultivated mostly in drought-prone areas where its productivity can be limited by water scarcity. The development of more drought-tolerant varieties is, therefore, a priority for peanut breeding programs worldwide. In contrast to cultivated peanut, wild relatives have a broader genetic diversity and constitute a rich source of resistance/tolerance alleles to biotic and abiotic stresses. The present study takes advantage of this diversity to identify drought-responsive genes by analyzing the expression profile of two wild species, Arachis duranensis and Arachis magna (AA and BB genomes, respectively), in response to progressive water deficit in soil. Data analysis from leaves and roots of A. duranensis (454 sequencing) and A. magna (suppression subtractive hybridization (SSH)) stressed and control complementary DNA (cDNA) libraries revealed several differentially expressed genes in silico, and 44 of them were selected for further validation by quantitative RT-PCR (qRT-PCR). This allowed the identification of drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress imposition in both species. This is the first report on identification of differentially expressed genes under drought stress and recovery in wild Arachis species. The generated transcriptome data, besides being a valuable resource for gene discovery, will allow the characterization of new alleles and development of molecular markers associated with drought responses in peanut. These together constitute important tools for the peanut breeding program and also contribute to a better comprehension of gene modulation in response to water deficit and rehydration.
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Affiliation(s)
- Ana C. M. Brasileiro
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Carolina V. Morgante
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
- />Embrapa Semiárido, Petrolina, PE Brazil
| | - Ana C. G. Araujo
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Soraya C. M. Leal-Bertioli
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Amanda K. Silva
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Andressa C. Q. Martins
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Christina C. Vinson
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Candice M. R. Santos
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
- />CONAB, Brasília, DF Brazil
| | - Orzenil Bonfim
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Roberto C. Togawa
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Mario A. P. Saraiva
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | | | - Patricia M. Guimaraes
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
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Chu Y, Guimarães LA, Wu CL, Timper P, Holbrook CC, Ozias-Akins P. A Technique to Study Meloidogyne arenaria Resistance in Agrobacterium rhizogenes-Transformed Peanut. PLANT DISEASE 2014; 98:1292-1299. [PMID: 30703931 DOI: 10.1094/pdis-12-13-1241-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A reliable peanut root transformation system would be useful to study the functions of genes involved in root biology and disease resistance. The objective of this study was to establish an effective protocol to produce composite plants mediated by Agrobacterium rhizogenes transformation. In total, 75% of transformed peanut seedlings produced an average of 2.83 transgenic roots per plant. Peanut seed had the highest germination rate after treatment in a chlorine gas chamber for 8 h compared with 16 h in chlorine gas or Clorox and mercuric chloride immersion treatments. High transformation efficiency was achieved when the wound site for A. rhizogenes inoculation was covered with vermiculite instead of enclosing the whole plant in a high humidity chamber. On average, 2.5 galls from Meloidogyne arenaria infection were formed per transgenic root from susceptible genotype TifGP-2. These data indicate that A. rhizogenes-transformed roots can be used to phenotype the host response to nematode challenge. Transformation of RLP-2, a candidate resistance gene for M. arenaria integrated into a silencing construct, did not alter the resistance response of Tifguard, even though downregulation of endogenous RLP-2 expression was detected in transformed roots. It is likely that RLP-2 is not the gene conditioning M. arenaria resistance in peanut.
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Affiliation(s)
- Y Chu
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton 31793-5766
| | - L A Guimarães
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton 31793-5766
| | - C L Wu
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton 31793-5766
| | - P Timper
- United States Department of Agriculture-Agricultural Research Service, Tifton, GA 31793; and
| | - C C Holbrook
- United States Department of Agriculture-Agricultural Research Service, Tifton, GA 31793; and
| | - P Ozias-Akins
- Department of Horticulture, The University of Georgia Tifton Campus
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Furlan AL, Bianucci E, Tordable MADC, Castro S, Dietz KJ. Antioxidant enzyme activities and gene expression patterns in peanut nodules during a drought and rehydration cycle. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:704-713. [PMID: 32481025 DOI: 10.1071/fp13311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/29/2014] [Indexed: 05/21/2023]
Abstract
Drought stress is one of the most important environmental factors that affect plant growth and limit biomass production. Most studies focus on drought stress development but the reversibility of the effects receives less attention. Therefore, the present work aims to explore the biological nitrogen fixation (BNF) of the symbiotic association between peanut (Arachis hypogaea L.) and Bradyrhizobium sp. during a drought-recovery cycle with a focus on the response of enzyme activity and gene expression of the antioxidant system. Peanuts exposed to drought stress had impaired BNF, as indicated by lower nitrogenase activity, and decreased leghaemoglobin content; the latter was reversed to control values upon rehydration. Previous results demonstrated that reactive oxygen species (O2·- and H2O2) were accumulated as a consequence of drought stress, suggesting that nodules experience oxidative stress. In addition, marker transcripts responsive to drought, abscisic acid and H2O2 were upregulated. Increased transcript levels of glutathione reductase were associated with an increased enzyme activity but superoxide dismutase and glutathione S-transferase activities were unchanged, despite upregulated gene transcription. In contrast, increased activity of ascorbate peroxidase (APX) was unrelated with changes in cytosolic APX transcript levels suggesting isogene specificity. In conclusion, the work exemplarily demonstrates the efficient and dynamic regulation of antioxidant enzymes and marker compounds during drought cycling, which is likely to be a prerequisite for functional optimisation of nodule metabolism.
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Affiliation(s)
- Ana Laura Furlan
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto. Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Eliana Bianucci
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto. Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Mar A Del Carmen Tordable
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto. Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Stella Castro
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto. Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, D-33501 Bielefeld, Germany
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Brulle F, Bernard F, Vandenbulcke F, Cuny D, Dumez S. Identification of suitable qPCR reference genes in leaves of Brassica oleracea under abiotic stresses. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:459-71. [PMID: 24566730 DOI: 10.1007/s10646-014-1209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/08/2014] [Indexed: 05/20/2023]
Abstract
Real-time quantitative PCR is nowadays a standard method to study gene expression variations in various samples and experimental conditions. However, to interpret results accurately, data normalization with appropriate reference genes appears to be crucial. The present study describes the identification and the validation of suitable reference genes in Brassica oleracea leaves. Expression stability of eight candidates was tested following drought and cold abiotic stresses by using three different softwares (BestKeeper, NormFinder and geNorm). Four genes (BolC.TUB6, BolC.SAND1, BolC.UBQ2 and BolC.TBP1) emerged as the most stable across the tested conditions. Further gene expression analysis of a drought- and a cold-responsive gene (BolC.DREB2A and BolC.ELIP, respectively), confirmed the stability and the reliability of the identified reference genes when used for normalization in the leaves of B. oleracea. These four genes were finally tested upon a benzene exposure and all appeared to be useful reference genes along this toxicological condition. These results provide a good starting point for future studies involving gene expression measurement on leaves of B. oleracea exposed to environmental modifications.
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Affiliation(s)
- Franck Brulle
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Lille Nord de France, EA 4483, Lille 2, B.P. 83, 59006, Lille Cedex, France
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42
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Morgante CV, Brasileiro ACM, Roberts PA, Guimaraes LA, Araujo ACG, Fonseca LN, Leal-Bertioli SCM, Bertioli DJ, Guimaraes PM. A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1298-1309. [PMID: 32481196 DOI: 10.1071/fp13096] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/11/2013] [Indexed: 06/11/2023]
Abstract
Root-knot nematodes constitute a constraint for important crops, including peanut (Arachis hypogaea L.). Resistance to Meloidogyne arenaria has been identified in the peanut wild relative Arachis stenosperma Krapov. & W. C. Greg., in which the induction of feeding sites by the nematode was inhibited by an early hypersensitive response (HR). Here, the transcription expression profiles of 19 genes selected from Arachis species were analysed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), during the early phases of an A. stenosperma-M. arenaria interaction. Sixteen genes were significantly differentially expressed in infected and non-infected roots, in at least one of the time points analysed: 3, 6, and 9 days after inoculation. These genes are involved in the HR and production of secondary metabolites related to pathogen defence. Seven genes encoding a resistance protein MG13, a helix-loop helix protein, an ubiquitin protein ligase, a patatin-like protein, a catalase, a DUF538 protein, and a resveratrol synthase, were differentially expressed in all time points analysed. Transcripts of two genes had their spatial and temporal distributions analysed by in situ hybridisation that validated qRT-PCR data. The identification of candidate resistance genes involved in wild peanut resistance to Meloidogyne can provide additional resources for peanut breeding and transgenic approaches.
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Affiliation(s)
| | - Ana C M Brasileiro
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Philip A Roberts
- University of California, Nematology Department, 2251 Spieth Hall Riverside, CA 92521, USA
| | - Larissa A Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Ana C G Araujo
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Leonardo N Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - David J Bertioli
- Universidade de Brasília, Departamento de Genética e Morfologia, Campus Universitario Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Patricia M Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
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Reddy DS, Bhatnagar-Mathur P, Cindhuri KS, Sharma KK. Evaluation and validation of reference genes for normalization of quantitative real-time PCR based gene expression studies in peanut. PLoS One 2013; 8:e78555. [PMID: 24167633 PMCID: PMC3805511 DOI: 10.1371/journal.pone.0078555] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
The quantitative real-time PCR (qPCR) based techniques have become essential for gene expression studies and high-throughput molecular characterization of transgenic events. Normalizing to reference gene in relative quantification make results from qPCR more reliable when compared to absolute quantification, but requires robust reference genes. Since, ideal reference gene should be species specific, no single internal control gene is universal for use as a reference gene across various plant developmental stages and diverse growth conditions. Here, we present validation studies of multiple stably expressed reference genes in cultivated peanut with minimal variations in temporal and spatial expression when subjected to various biotic and abiotic stresses. Stability in the expression of eight candidate reference genes including ADH3, ACT11, ATPsyn, CYP2, ELF1B, G6PD, LEC and UBC1 was compared in diverse peanut plant samples. The samples were categorized into distinct experimental sets to check the suitability of candidate genes for accurate and reliable normalization of gene expression using qPCR. Stability in expression of the references genes in eight sets of samples was determined by geNorm and NormFinder methods. While three candidate reference genes including ADH3, G6PD and ELF1B were identified to be stably expressed across experiments, LEC was observed to be the least stable, and hence must be avoided for gene expression studies in peanut. Inclusion of the former two genes gave sufficiently reliable results; nonetheless, the addition of the third reference gene ELF1B may be potentially better in a diverse set of tissue samples of peanut.
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Affiliation(s)
- Dumbala Srinivas Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
- * E-mail:
| | - Katamreddy Sri Cindhuri
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Kiran K. Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
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Kundu A, Patel A, Pal A. Defining reference genes for qPCR normalization to study biotic and abiotic stress responses in Vigna mungo. PLANT CELL REPORTS 2013; 32:1647-58. [PMID: 23868569 DOI: 10.1007/s00299-013-1478-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 05/20/2023]
Abstract
Expression of ACT, EF1A; H2A, EF1A, ACT and 18S, TUB showed stability under MYMIV, salinity and drought stress, respectively; these are recommended as reference genes for qPCR normalization in Vigna mungo. Accurate gene expression profiling through qPCR depends on selection of appropriate reference gene(s) for normalization. Due to lack of unanimous internal standard, suitable constitutively expressed reference genes are selected that exhibit stable expression under diverse experimental conditions. In this communication, a comparative evaluation of stability among seven V. mungo genes encoding actin (ACT), histone H2A (H2A), elongation factor 1-alpha (EF1A), 18S rRNA (18S), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), cyclophilin (CYP) and tubulin (TUB) under biotic (MYMIV) and abiotic (drought and salinity) stress conditions has been attempted. Specificity and amplification efficiency for each primer pair were verified; however, cumulative assessment of their accumulated transcripts revealed no uniformity. Therefore, individual stability and suitability of these seven candidates have been assessed in silico, by two widely used algorithms, geNorm and Normfinder. Based on the computed results, high stability was obtained for ACT and EF1A during MYMIV stress, while H2A, EFIA and ACT were found to be most suitable in salinity stress experiments and TUB and 18S during drought treatments. Combinations of ACT/TUB or ACT/EFIA were recommended for their use in the pooled analysis, while expression of 18S and CYP showed greater variations and therefore considered unsuitable as reference genes. Additionally, precise quantification of the target gene VmPRX under these stresses was shown to be a function of reference genes' stability, which tends to get affected when normalized with the least stable genes. Hence, use of these normalizers will facilitate accurate and reliable analyses of gene expression in V. mungo.
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Affiliation(s)
- Anirban Kundu
- Division of Plant Biology, Bose Institute, Kolkata, 700054, West Bengal, India
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45
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Bhardwaj J, Chauhan R, Swarnkar MK, Chahota RK, Singh AK, Shankar R, Yadav SK. Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC Genomics 2013; 14:647. [PMID: 24059455 PMCID: PMC3853109 DOI: 10.1186/1471-2164-14-647] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup. RESULTS Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress. CONCLUSIONS De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.
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Affiliation(s)
- Jyoti Bhardwaj
- Plant Metabolic Engineering Laboratory, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur 176061, HP, India.
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Warzybok A, Migocka M. Reliable reference genes for normalization of gene expression in cucumber grown under different nitrogen nutrition. PLoS One 2013; 8:e72887. [PMID: 24058446 PMCID: PMC3772881 DOI: 10.1371/journal.pone.0072887] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/20/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, nitrogen is the most important nutritional factor limiting the yield of cultivated crops. Since nitrogen is essential for synthesis of nucleotides, amino acids and proteins, studies on gene expression in plants cultivated under different nitrogen availability require particularly careful selection of suitable reference genes which are not affected by nitrogen limitation. Therefore, the objective of this study was to select the most reliable reference genes for qPCR analysis of target cucumber genes under varying nitrogen source and availability. Among twelve candidate cucumber genes used in this study, five are highly homologous to the commonly used internal controls, whereas seven novel candidates were previously identified through the query of the cucumber genome. The expression of putative reference genes and the target CsNRT1.1 gene was analyzed in roots, stems and leaves of cucumbers grown under nitrogen deprivation, varying nitrate availability or different sources of nitrogen (glutamate, glutamine or NH3). The stability of candidate genes expression significantly varied depending on the tissue type and nitrogen supply. However, in most of the outputs genes encoding CACS, TIP41, F-box protein and EFα proved to be the most suitable for normalization of CsNRT1.1 expression. In addition, our results suggest the inclusion of 3 or 4 references to obtain highly reliable results of target genes expression in all cucumber organs under nitrogen-related stress.
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Affiliation(s)
- Anna Warzybok
- Wrocław University, Institute of Experimental Biology, Department of Plant Molecular Physiology, Wroclaw, Poland
- * E-mail:
| | - Magdalena Migocka
- Wrocław University, Institute of Experimental Biology, Department of Plant Molecular Physiology, Wroclaw, Poland
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Štajner N, Cregeen S, Javornik B. Evaluation of reference genes for RT-qPCR expression studies in hop (Humulus lupulus L.) during infection with vascular pathogen verticillium albo-atrum. PLoS One 2013; 8:e68228. [PMID: 23874551 PMCID: PMC3709999 DOI: 10.1371/journal.pone.0068228] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/28/2013] [Indexed: 11/18/2022] Open
Abstract
Hop plant (Humulus lupulus L.), cultivated primarily for its use in the brewing industry, is faced with a variety of diseases, including severe vascular diseases, such as Verticillium wilt, against which no effective protection is available. The understanding of disease resistance with tools such as differentially expressed gene studies is an important objective of plant defense mechanisms. In this study, we evaluated twenty-three reference genes for RT-qPCR expression studies on hop under biotic stress conditions. The candidate genes were validated on susceptible and resistant hop cultivars sampled at three different time points after infection with Verticillium albo-atrum. The stability of expression and the number of genes required for accurate normalization were assessed by three different Excel-based approaches (geNorm v.3.5 software, NormFinder, and RefFinder). High consistency was found among them, identifying the same six best reference genes (YLS8, DRH1, TIP41, CAC, POAC and SAND) and five least stably expressed genes (CYCL, UBQ11, POACT, GAPDH and NADH). The candidate genes in different experimental subsets/conditions resulted in different rankings. A combination of the two best reference genes, YLS8 and DRH1, was used for normalization of RT-qPCR data of the gene of interest (PR-1) implicated in biotic stress of hop. We outlined the differences between normalized and non-normalized values and the importance of RT-qPCR data normalization. The high correlation obtained among data standardized with different sets of reference genes confirms the suitability of the reference genes selected for normalization. Lower correlations between normalized and non-normalized data may reflect different quantity and/or quality of RNA samples used in RT-qPCR analyses.
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Affiliation(s)
- Nataša Štajner
- Biotechnical Faculty, Agronomy Department, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Cregeen
- Biotechnical Faculty, Agronomy Department, University of Ljubljana, Ljubljana, Slovenia
| | - Branka Javornik
- Biotechnical Faculty, Agronomy Department, University of Ljubljana, Ljubljana, Slovenia
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Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC, Bertioli DJ. Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 2012; 13:387. [PMID: 22888963 PMCID: PMC3496627 DOI: 10.1186/1471-2164-13-387] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/05/2012] [Indexed: 11/25/2022] Open
Abstract
Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development. Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR. Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
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Affiliation(s)
- Patricia M Guimarães
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372 Final W5 Norte, Brasília, DF, Brazil.
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