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Chen L, Cai M, Liu J, Jiang X, Liu J, Zhenxing W, Wang Y, Li Y. Genome-wide identification and expression analyses of SWEET gene family reveal potential roles in plant development, fruit ripening and abiotic stress responses in cranberry ( Vaccinium macrocarpon Ait). PeerJ 2024; 12:e17974. [PMID: 39308825 PMCID: PMC11416763 DOI: 10.7717/peerj.17974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
The sugars will eventually be exported transporter (SWEET) family is a novel class of sugar transporters that play a crucial role in plant growth, development, and responses to stress. Cranberry (Vaccinium macrocarpon Ait.) is a nutritious berry with economic importance, but little is known about SWEET gene family functions in this small fruit. In this research, 13 VmSWEET genes belonging to four clades were identified in the cranberry genome for the first time. In the conserved domains, we observed seven phosphorylation sites and four amino acid residues that might be crucial for the binding function. The majority of VmSWEET genes in each clade shared similar gene structures and conserved motifs, showing that the VmSWEET genes were highly conserved during evolution. Chromosomal localization and duplication analyses showed that VmSWEET genes were unevenly distributed in eight chromosomes and two pairs of them displayed synteny. A total of 79 cis-acting elements were predicted in the promoter regions of VmSWEETs including elements responsive to plant hormones, light, growth and development and stress responses. qRT-PCR analysis showed that VmSWEET10.1 was highly expressed in flowers, VmSWEET16 was highly expressed in upright and runner stems, and VmSWEET3 was highly expressed in the leaves of both types of stems. In fruit, the expression of VmSWEET14 and VmSWEET16 was highest of all members during the young fruit stage and were downregulated as fruit matured. The expression of VmSWEET4 was higher during later developmental stages than earlier developmental stages. Furthermore, qRT-PCR results revealed a significant up-regulation of VmSWEET10.2, under osmotic, saline, salt-alkali, and aluminum stress conditions, suggesting it has a crucial role in mediating plant responses to various environmental stresses. Overall, these results provide new insights into the characteristics and evolution of VmSWEET genes. Moreover, the candidate VmSWEET genes involved in the growth, development and abiotic stress responses can be used for molecular breeding to improve cranberry fruit quality and abiotic stress resistance.
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Affiliation(s)
- Li Chen
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Mingyu Cai
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Jiaxin Liu
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Xuxin Jiang
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Jiayi Liu
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Wang Zhenxing
- Jilin Agricultural University, College of Horticulture, Changchun, China
| | - Yunpeng Wang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yadong Li
- Jilin Agricultural University, College of Horticulture, Changchun, China
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Cai Z, Ruan L, Wei W, He W, Yang H, Chen H, Liang Z, Huang Z, Lan X, Zhang X, Huang R, Zhao C, Li T, He L, Li H. Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development. BMC Genomics 2024; 25:699. [PMID: 39020298 PMCID: PMC11253480 DOI: 10.1186/s12864-024-10599-2] [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: 03/21/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated. RESULTS In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars. CONCLUSIONS Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.
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Affiliation(s)
- Zhaoqin Cai
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Lixia Ruan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wanling Wei
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wen He
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Haixia Yang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Huixian Chen
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenhua Liang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenling Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiu Lan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiufen Zhang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Ruolan Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Chunhui Zhao
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Tianyuan Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, PR China.
| | - Hengrui Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China.
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Mansoor S, Tripathi P, Ghimire A, Hamid S, Abd El-Moniem D, Chung YS, Kim Y. Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots. PLANT CELL REPORTS 2024; 43:169. [PMID: 38864921 PMCID: PMC11169057 DOI: 10.1007/s00299-024-03250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
KEY MESSAGE The study unveils Si's regulatory influence by regulating DEGs, TFs, and TRs. Further bHLH subfamily and auxin transporter pathway elucidates the mechanisms enhancing root development and nodulation. Soybean is a globally important crop serving as a primary source of vegetable protein for millions of individuals. The roots of these plants harbour essential nitrogen fixing structures called nodules. This study investigates the multifaceted impact of silicon (Si) application on soybean, with a focus on root development, and nodulation employing comprehensive transcriptomic analyses and gene regulatory network. RNA sequence analysis was utilised to examine the change in gene expression and identify the noteworthy differentially expressed genes (DEGs) linked to the enhancement of soybean root nodulation and root development. A set of 316 genes involved in diverse biological and molecular pathways are identified, with emphasis on transcription factors (TFs) and transcriptional regulators (TRs). The study uncovers TF and TR genes, categorized into 68 distinct families, highlighting the intricate regulatory landscape influenced by Si in soybeans. Upregulated most important bHLH subfamily and the involvement of the auxin transporter pathway underscore the molecular mechanisms contributing to enhanced root development and nodulation. The study bridges insights from other research, reinforcing Si's impact on stress-response pathways and phenylpropanoid biosynthesis crucial for nodulation. The study reveals significant alterations in gene expression patterns associated with cellular component functions, root development, and nodulation in response to Si.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea
| | - Pooja Tripathi
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, USA
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamia University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Diaa Abd El-Moniem
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea.
| | - Yoonha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Vasileva A, Durakova A, Kalaydzhiev H, Dimitrova-Dicheva M, Goranova Z, Vasilev V, Temelkova M. Nectarine powder of Bulgarian origin: Physicochemical composition, antioxidant activity, microbiological and sorption characteristics. Heliyon 2024; 10:e24059. [PMID: 38268587 PMCID: PMC10806340 DOI: 10.1016/j.heliyon.2024.e24059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
One way to improve the quality of food products is by conducting more thorough research on regional foods. This approach has several benefits, such as promoting human health, supporting the local economy, and preserving cultural food traditions. In this regard, our study investigated the potential of nectarine powder as a regional fruit product that could be developed into a global innovation. The present study examined: the physicochemical composition, antioxidant activity, microbiological load, and adsorption and desorption characteristics of the nectarine powder. The fruit powder was acquired through the use of a heat pump dryer, where drying took place at 42 °C for a duration of 8 h until achieving a moisture content ranging from 13.5 % to 14.5 %. The approximate physicochemical values are as follows: proteins, total carbohydrates, crude fiber, ash content and total lipids. Microbiological parameters, namely the total count of mesophilic aerobic and facultative anaerobic microorganisms, yeasts and molds, Escherichia coli, Salmonella spp., coagulase-positive staphylococci, and coliforms were checked and found to be within the acceptable limits as stipulated by the relevant state standards. Antioxidant activity was demonstrated through the utilization of various methods, including DPPH (33.19 ± 0.09mMTE/g extract), ABRS (2.55 ± 0.05mMTE/g extract), FRAP (1.43 ± 0.03mMTE/g extract) and CUPRAC (0.83 ± 0.01mMTE/g extract) methods. Investigation of the mass transfer sorption characteristics is performed using the gravimetric-static method. The conditions of the experiment were selected according to the usual conditions in which the food products are found in the commercial depot. The equilibrium and monolayer moisture data are investigated at 10 °C, 25 °C and 40 °C and relative air humidity in the wide range from 11 % to 87 %, achieved by the salts saturated solutions. To depict the adsorption and desorption isotherms, the modified models of Halsey, Chung-Pfost, Henderson, and Oswin were selected.
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Affiliation(s)
- Adelina Vasileva
- Department of Mechanical and Instrument Engineering, Technical University of Sofia, Branch Plovdiv, Tsanko Duistabanov Street 25, 4000 Plovdiv, Bulgaria
| | - Albena Durakova
- Department of Process Engineering, University of Food Technologies, Maritza Boulevard 26, 4002 Plovdiv, Bulgaria
| | - Hristo Kalaydzhiev
- Department of Analytical and Physical Chemistry, University of Food Technologies, Maritza Boulevard 26, 4002 Plovdiv, Bulgaria
| | - Milena Dimitrova-Dicheva
- Department of Milk and Dairy Products Technology, University of Food Technologies, Maritza Boulevard 26, 4002 Plovdiv, Bulgaria
| | - Zhivka Goranova
- Department of Food Technology, Institute of Food Preservation and Quality, Vasil Aprilov Boulevard 154, 4003 Plovdiv, Agricultural Academy, Bulgaria
| | - Vasko Vasilev
- Department of Economics and Finance, University of Agribusiness and Rural Development (UARD), Dunav Boulevard 78, BG-4003 Plovdiv, Bulgaria
| | - Milena Temelkova
- Department of Language Training Centre, University of Food Technologies - Plovdiv, Maritza Boulevard 26, BG-4002 Plovdiv, Bulgaria
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Wu B, Shi S, Zhang H, Lu B, Nan P, A Y. Anabolic metabolism of autotoxic substance coumarins in plants. PeerJ 2023; 11:e16508. [PMID: 38077428 PMCID: PMC10710134 DOI: 10.7717/peerj.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Background Autotoxicity is an intraspecific manifestation of allelopathy in plant species. The specialized metabolites and their derivatives that cause intraspecific allelopathic inhibition in the plant are known as autotoxic substances. Consequently, autotoxic substances production seriously affects the renewal and stability of ecological communities. Methods This article systematically summarizes the types of autotoxic substances present in different plants. They mainly include phenolic compounds, terpenoids, and nitrogenous organic compounds. Phenolic coumarins are the main autotoxic substances in many plants. Therefore, we also discuss differences in coumarin types and content among plant varieties, developmental stages, and tissue parts, as well as their mechanisms of autotoxicity. In addition, we review the metabolic pathways involved in coumarin biosynthesis, the key enzymes, genes, and transcription factors, as well as factors affecting coumarin biosynthesis. Results Coumarin biosynthesis involves three stages: (1) the formation of the coumarin nucleus; (2) acylation, hydroxylation, and cyclization; (3) structural modification. The key enzymes involved in the coumarin nuclear formation stage include PAL, C4H, 4CL, HCT, CAOMT, COSY, F6'H, and CCoAOMT1, and the key genes involved include BGA, CYP450 and MDR, among others. Ortho-hydroxylation is a key step in coumarin biosynthesis and PS, COSY and S8H are the key enzymes involved in this process. Finally, UGTs are responsible for the glycosylation modification of coumarins, and the MaUGT gene may therefore be involved in coumarin biosynthesis. Conclusion It is important to elucidate the autotoxicity and anabolic mechanisms of coumarins to create new germplasms that produce fewer autotoxic substances.
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Affiliation(s)
- Bei Wu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shangli Shi
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Huihui Zhang
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Baofu Lu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pan Nan
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yun A
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
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6
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Tang Y. Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression. Nucleus 2023; 14:2178201. [PMID: 36794966 PMCID: PMC9980628 DOI: 10.1080/19491034.2023.2178201] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.
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Affiliation(s)
- Yu Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
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7
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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8
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Lourkisti R, Antoine S, Pailly O, Luro F, Gibon Y, Oustric J, Santini J, Berti L. GABA shunt pathway is stimulated in response to early defoliation-induced carbohydrate limitation in Mandarin fruits. Heliyon 2023; 9:e15573. [PMID: 37128327 PMCID: PMC10148037 DOI: 10.1016/j.heliyon.2023.e15573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
The regulation of sugar and organic acid metabolism during fruit development has a major effect on high-quality fruit production. The reduction of leaf area is a common feature in plant growth, induced by abiotic and biotic stresses and disturbing source/sink ratio, thus impacting fruit quality. Here, we induced carbohydrate limitation by partial leaf defoliation at the beginning of the second stage of mandarin development (before the citrate peak). Resulting changes were monitored in the short-term (48 h and 1 week) and long-term (7 weeks) after the defoliation. Short-term response to early defoliation implied metabolic settings to re-feed TCA for sustaining respiration rate. These features involved (i) vacuolar sucrose degradation (high acid invertase activity and mRNA expression level) and enhanced glycolytic flux (high ATP-phosphofructokinase activity), (ii) malic and citric acid utilization (increased phosphoenolpyruvate kinase and NADP-Isocitrate dehydrogenase) associated with vacuolar citric acid release (high mRNA expression of the transporter CsCit1) and (iii) stimulation of GABA shunt pathway (low GABA content and increased mRNA expression of succinate semialdehyde dehydrogenase). A steady-state proline level was found in ED fruits although an increase in P5CS mRNA expression level. These results contribute to a better knowledge of the molecular basis of the relationship between defoliation and sugar and organic acid metabolism in mandarin fruit.
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Affiliation(s)
- Radia Lourkisti
- Unité mixte de recherche (UMR) 6134 Laboratoire Sciences pour l’Environnement (SPE) Centre national de la recherche scientifique (CNRS), Université de Corse, 20250, France
- Corresponding author.
| | - Sandrine Antoine
- Unité mixte de recherche (UMR) 6134 Laboratoire Sciences pour l’Environnement (SPE) Centre national de la recherche scientifique (CNRS), Université de Corse, 20250, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université Montpellier, 20230 San Giuliano, France
| | | | - François Luro
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université Montpellier, 20230 San Giuliano, France
| | - Yves Gibon
- UMR 1332 BFP, INRAE, Université de Bordeaux, 33883 Villenave d’Ornon, France
- MetaboHUB, Bordeaux Metabolome, INRAE, Université de Bordeaux, 33140 Villenave d’Ornon, France
| | - Julie Oustric
- Unité mixte de recherche (UMR) 6134 Laboratoire Sciences pour l’Environnement (SPE) Centre national de la recherche scientifique (CNRS), Université de Corse, 20250, France
| | - Jérémie Santini
- Unité mixte de recherche (UMR) 6134 Laboratoire Sciences pour l’Environnement (SPE) Centre national de la recherche scientifique (CNRS), Université de Corse, 20250, France
| | - Liliane Berti
- Unité mixte de recherche (UMR) 6134 Laboratoire Sciences pour l’Environnement (SPE) Centre national de la recherche scientifique (CNRS), Université de Corse, 20250, France
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Krishna TPA, Maharajan T, Ceasar SA. The Role of Membrane Transporters in the Biofortification of Zinc and Iron in Plants. Biol Trace Elem Res 2023; 201:464-478. [PMID: 35182385 DOI: 10.1007/s12011-022-03159-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/11/2022] [Indexed: 01/11/2023]
Abstract
Over three billion people suffer from various health issues due to the low supply of zinc (Zn) and iron (Fe) in their food. Low supply of micronutrients is the main cause of malnutrition and biofortification could help to solve this issue. Understanding the molecular mechanisms of biofortification is challenging. The membrane transporters are involved in the uptake, transport, storage, and redistribution of Zn and Fe in plants. These transporters are also involved in biofortification and help to load the Zn and Fe into the endosperm of the seeds. Very little knowledge is available on the role and functions of membrane transporters involved in seed biofortification. Understanding the mechanism and role of membrane transporters could be helpful to improve biofortification. In this review, we provide the details on membrane transporters involved in the uptake, transport, storage, and redistribution of Zn and Fe. We also discuss available information on transporters involved in seed biofortification. This review will help plant breeders and molecular biologists understand the importance and implications of membrane transporters for seed biofortification.
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Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India.
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Comprehensive Analysis of Betula platyphylla Suk. PIF Gene Family and Their Potential Functions in Growth and Development. Int J Mol Sci 2022; 23:ijms232315326. [PMID: 36499652 PMCID: PMC9738378 DOI: 10.3390/ijms232315326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 11/21/2022] [Indexed: 12/09/2022] Open
Abstract
Phytochrome-interacting factors (PIFs) are transcription factors with the basic helix-loop-helix (bHLH) domain. As integration factors between different signal pathways, members of the PIF protein family regulate many aspects of plant growth and development, such as seed germination, photomorphogenesis, thermomorphogenesis, rhythm regulation, flowering response, stomatal development, and stress responses. Our previous studies have shown that the BpSPL2 gene may regulate plants' adventitious root development through PIF genes. Within the Betula platyphylla genome, we identified eight PIF (BpPIFs) genes. We analysed and named them based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that transposition or segmental duplication events played a minor role in the expansion of BpPIFs. The comparative syntenic analysis combined with phylogenetic analysis provided a deep insight into the phylogenetic relationships of BpPIF genes, suggesting that BpPIF proteins are closer to PtPIF than to AtPIF. The analysis of cis-acting elements in promoter regions of BpPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. In addition, we found that these promoters have the transcription factor of B. platyphylla SPL2 (BpSPL2) binding motif GTAC. Expression analysis demonstrated that BpPIF genes, especially BpPIF4, BpPIF9b, and BpPIF10, might be the potential target genes of BpSPL2 in the process of adventitious root formation. Besides providing a comprehensive understanding of the BpPIF family, we propose a hypothetical gene network regulatory model for adventitious root formation.
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11
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Li Y, Liao B, Wang Y, Luo H, Wang S, Li C, Song W, Zhang K, Yang B, Lu S, Zhang B, Li Y. Transcriptome and metabolome analyses provide insights into the relevance of pericarp thickness variations in Camellia drupifera and Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2022; 13:1016475. [PMID: 36388553 PMCID: PMC9647060 DOI: 10.3389/fpls.2022.1016475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Camellia fruit is a woody edible oil source with a recalcitrant pericarp, which increases processing costs. However, the relevance of pericarp thickness variations in Camellia species remains unclear. Therefore, this study aimed to identify pericarp differences at the metabolic and transcription levels between thick-pericarp Camellia drupifera BG and thin-pericarp Camellia oleifera SG. Forty differentially accumulated metabolites were screened through non-targeted UHPLC-Q-TOF MS-based metabolite profiling. S-lignin was prominently upregulated in BG compared with SG, contributing to the thick pericarp of BG. KEGG enrichment and coexpression network analysis showed 29 differentially expressed genes associated with the lignin biosynthetic pathway, including 21 genes encoding catalysts and 8 encoding transcription factors. Nine upregulated genes encoding catalysts potentially led to S-lignin accumulation in BG pericarp, and transcription factors NAC and MYB were possibly involved in major transcriptional regulatory mechanisms. Conventional growth-related factors WRKYs and AP2/ERFs were positively associated while pathogenesis-related proteins MLP328 and NCS2 were negatively associated with S-lignin content. Thus, Camellia balances growth and defense possibly by altering lignin biosynthesis. The results of this study may guide the genetic modifications of C. drupifera to optimize its growth-defense balance and improve seed accessibility.
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Affiliation(s)
- Yongjuan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Boyong Liao
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huihua Luo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Shimin Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Caiqin Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wenpei Song
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kunchang Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Boqun Yang
- State-owned Xiaokeng Forest Farm in Qujiang District of Shaoguan City, Shaoguan, China
| | - Shaoqiang Lu
- State-owned Xiaokeng Forest Farm in Qujiang District of Shaoguan City, Shaoguan, China
| | - Bipei Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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12
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Soltani N, Firouzabadi FN, Shafeinia A, Shirali M, Sadr AS. De Novo transcriptome assembly and differential expression analysis of catharanthus roseus in response to salicylic acid. Sci Rep 2022; 12:17803. [PMID: 36280677 PMCID: PMC9592577 DOI: 10.1038/s41598-022-20314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023] Open
Abstract
The anti-cancer vinblastine and vincristine alkaloids can only be naturally found in periwinkle (Catharanthus roseus). Both of these alkaloids' accumulations are known to be influenced by salicylic acid (SA). The transcriptome data to reveal the induction effect (s) of SA, however, seem restricted at this time. In this study, the de novo approach of transcriptome assembly was performed on the RNA-Sequencing (RNA-Seq) data in C. roseus. The outcome demonstrated that SA treatment boosted the expression of all the genes in the Terpenoid Indole Alkaloids (TIAs) pathway that produces the vinblastine and vincristine alkaloids. These outcomes supported the time-course measurements of vincristine alkaloid, the end product of the TIAs pathway, and demonstrated that SA spray had a positive impact on transcription and alkaloid synthesis. Additionally, the abundance of transcription factor families including bHLH, C3H, C2H2, MYB, MYB-related, AP2/ ERF, NAC, bZIP, and WRKY suggests a role for a variety of transcription families in response to the SA stimuli. Di-nucleotide and tri-nucleotide SSRs were the most prevalent SSR markers in microsatellite analyses, making up 39% and 34% of all SSR markers, respectively, out of the 77,192 total SSRs discovered.
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Affiliation(s)
- Narges Soltani
- Production Engineering and Plant Genetics Department, Faculty of Agriculture and Natural Resources, Lorestan University, P.O. Box 465, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture and Natural Resources, Lorestan University, P.O. Box 465, Khorramabad, Iran.
| | - Alireza Shafeinia
- Department of Plant Production & Genetics, Faculty of Agriculture, Agricultural Sciences & Natural Resources, University of Khuzestan, Mollasani, Iran
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Hillsborough, BT26 6DR, UK
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5AJ, UK
| | - Ayeh Sadat Sadr
- South of Iran Aquaculture Research Institute (SIARI), Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), Ahvaz, Iran.
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13
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Ahmadzadeh M, Keshtkar AH, Moslemkhany K, Ahmadzadeh M. Effect of the plant probiotic bacteria on terpenoid indole alkaloid biosynthesis pathway gene expression profiling, vinblastine and vincristine content in the root of Catharanthus roseus. Mol Biol Rep 2022; 49:10357-10365. [PMID: 36097118 DOI: 10.1007/s11033-022-07841-z] [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: 08/30/2021] [Revised: 07/30/2022] [Accepted: 08/04/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Catharanthus roseus is the sole resource of vinblastine and vincristine, two TIAs of great interest for their powerful anticancer activities. Increasing the concentration of these alkaloids in various organs of the plant is one of the important goals in C. roseus breeding programs. Plant probiotic bacteria (PBB) act as biotic elicitors and can induce the synthesis of secondary products in plants. The purpose of this research is to study the effects of PBB on expression of the TIA biosynthetic pathway genes and the content of alkaloids in C. roseus. METHODS AND RESULTS The individual and combined effects of P. fluorescens strains 169 and A. brasilense strains Ab-101 was studied for expression of the TIA biosynthetic pathway genes (G10H, DAT, T16H and CrPRX) using qRT-PCR and the content of vinblastine and vincristine using HPLC method in roots of C. roseus. P. fluorescens. This drastically increased the content of vinblastine and vincristine alkaloids, compared to the control in the roots, to 174 and 589 (µg/g), respectively. Molecular analysis showed bacterium significantly increased the expression of more genes in the TIA biosynthetic pathway compared to the control. P. fluorescens increased the expression of the final gene of the biosynthetic pathway (CrPRX) 47.9 times compared to the control. Our findings indicate the correlation between transcriptional and metabolic outcomes. The same was true for A. brasilense. CONCLUSIONS It can be concluded that seed treatments and seedling root treatments composed of naturally occurring probiotic bacteria are likely to be widely applicable for inducing enhanced alkaloid contents in medicinal plants.
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Affiliation(s)
- M Ahmadzadeh
- Faculty of Agriculture, Buali Sina University, Hamedan, Iran
| | - A H Keshtkar
- Faculty of Agriculture, Buali Sina University, Hamedan, Iran.
| | - K Moslemkhany
- Seed and Plant Certification and Registration Institute, Agricultural Research, Education and Extension Organisation (AREEO), Tehran, Iran
| | - M Ahmadzadeh
- College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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14
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Wang J, Yang C, Zhao W, Wang Y, Qiao L, Wu B, Zhao J, Zheng X, Wang J, Zheng J. Genome-wide association study of grain hardness and novel Puroindoline alleles in common wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:40. [PMID: 37313507 PMCID: PMC10248618 DOI: 10.1007/s11032-022-01303-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Grain hardness (HI) is a key trait for wheat milling and end-use quality. Puroindoline genes (PINs) are the major genes responsible for grain hardness, but other QTLs also contribute to the trait. Therefore, it is essential to identify loci associated with the HI and allelic variations of PINs in wheat. In the present study, 287 accessions from Shanxi province representing 70 years of wheat breeding were grown in one rainfed and two irrigated conditions to study grain hardness. Genome-wide association analysis (GWAS) was performed using the 15 K array, and the variability of PIN alleles was investigated. Among the accessions, hard wheat was most common. The broad-sense heritability (H2) among the three environments was 99.5%, suggesting HI was mainly affected by heredity. GWAS identified nine significant marker-trait associations (MTAs), including that PINs, which explained 7.03% to 17.70% of phenotypic variation. Four MTAs on chromosome 2A, 2B, 5A, and 7A were novel loci. As for diversity of PINs, a total of 11 PINs haplotypes were detected, composed of 12 allelic variations of the PIN gene. The most frequent haplotypes were Pina-D1a/Pinb-D1b (43.9%) and Pina-Dla/Pinb-D1p (18.8%), and both the frequency of Pina-D1a/Pinb-D1b and the HI value increased with breeding years were related to local dietary habits probably. A novel double deletion allele of the PINs haplotype was found in Donghei1206. These results will be useful not only in understanding of the genetics of the HI but also in breeding for improved grain texture. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01303-x.
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Affiliation(s)
- Junyou Wang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801 China
| | - Chenkang Yang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Wenjia Zhao
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801 China
| | - Ying Wang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Ling Qiao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Bangbang Wu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Juanling Wang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
| | - Jun Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, 041000 China
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15
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Mahmoud LM, Kaur P, Stanton D, Grosser JW, Dutt M. A cationic lipid mediated CRISPR/Cas9 technique for the production of stable genome edited citrus plants. PLANT METHODS 2022; 18:33. [PMID: 35303912 PMCID: PMC8932238 DOI: 10.1186/s13007-022-00870-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/05/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND The genetic engineering of crops has enhanced productivity in the face of climate change and a growing global population by conferring desirable genetic traits, including the enhancement of biotic and abiotic stress tolerance, to improve agriculture. The clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system has been found to be a promising technology for genomic editing. Protoplasts are often utilized for the development of genetically modified plants through in vitro integration of a recombinant DNA fragment into the plant genome. We targeted the citrus Nonexpressor of Pathogenesis-Related 3 (CsNPR3) gene, a negative regulator of systemic acquired resistance (SAR) that governs the proteasome-mediated degradation of NPR1 and developed a genome editing technique targeting citrus protoplast DNA to produce stable genome-edited citrus plants. RESULTS Here, we determined the best cationic lipid nanoparticles to deliver donor DNA and described a protocol using Lipofectamine™ LTX Reagent with PLUS Reagent to mediate DNA delivery into citrus protoplasts. A Cas9 construct containing a gRNA targeting the CsNPR3 gene was transfected into citrus protoplasts using the cationic lipid transfection agent Lipofectamine with or without polyethylene glycol (PEG, MW 6000). The optimal transfection efficiency for the encapsulation was 30% in Lipofectamine, 51% in Lipofectamine with PEG, and 2% with PEG only. Additionally, plasmid encapsulation in Lipofectamine resulted in the highest cell viability percentage (45%) compared with PEG. Nine edited plants were obtained and identified based on the T7EI assay and Sanger sequencing. The developed edited lines exhibited downregulation of CsNPR3 expression and upregulation of CsPR1. CONCLUSIONS Our results demonstrate that utilization of the cationic lipid-based transfection agent Lipofectamine is a viable option for the successful delivery of donor DNA and subsequent successful genome editing in citrus.
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Affiliation(s)
- Lamiaa M Mahmoud
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
- Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Prabhjot Kaur
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel Stanton
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA.
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16
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Potential of engineering the myo-inositol oxidation pathway to increase stress resilience in plants. Mol Biol Rep 2022; 49:8025-8035. [PMID: 35294703 DOI: 10.1007/s11033-022-07333-0] [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: 10/28/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
Myo-inositol is one of the most abundant form of inositol. The myo-inositol (MI) serves as substrate to diverse biosynthesis pathways and hence it is conserved across life forms. The biosynthesis of MI is well studied in animals. Beyond biosynthesis pathway, implications of MI pathway and enzymes hold potential implications in plant physiology and crop improvement. Myo-inositol oxygenase (MIOX) enzyme catabolize MI into D-glucuronic acid (D-GlcUA). The MIOX enzyme family is well studied across few plants. More recently, the MI associated pathway's crosstalk with other important biosynthesis and stress responsive pathways in plants has drawn attention. The overall outcome from different plant species studied so far are very suggestive that MI derivatives and associated pathways could open new directions to explore stress responsive novel metabolic networks. There are evidences for upregulation of MI metabolic pathway genes, specially MIOX under different stress condition. We also found MIOX genes getting differentially expressed according to developmental and stress signals in Arabidopsis and wheat. In this review we try to highlight the missing links and put forward a tailored view over myo-inositol oxidation pathway and MIOX proteins.
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17
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Daryani P, Darzi Ramandi H, Dezhsetan S, Mirdar Mansuri R, Hosseini Salekdeh G, Shobbar ZS. Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:81-106. [PMID: 34623472 DOI: 10.1007/s00122-021-03953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
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Affiliation(s)
- Parisa Daryani
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Dezhsetan
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran.
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18
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Volf M, Volfová T, Seifert CL, Ludwig A, Engelmann RA, Jorge LR, Richter R, Schedl A, Weinhold A, Wirth C, van Dam NM. A mosaic of induced and non-induced branches promotes variation in leaf traits, predation and insect herbivore assemblages in canopy trees. Ecol Lett 2021; 25:729-739. [PMID: 34958165 DOI: 10.1111/ele.13943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022]
Abstract
Forest canopies are complex and highly diverse environments. Their diversity is affected by pronounced gradients in abiotic and biotic conditions, including variation in leaf chemistry. We hypothesised that branch-localised defence induction and vertical stratification in mature oaks constitute sources of chemical variation that extend across trophic levels. To test this, we combined manipulation of plant defences, predation monitoring, food-choice trials with herbivores and sampling of herbivore assemblages. Both induction and vertical stratification affected branch chemistry, but the effect of induction was stronger. Induction increased predation in the canopy and reduced herbivory in bioassays. The effects of increased predation affected herbivore assemblages by decreasing their abundance, and indirectly, their richness. In turn, we show that there are multiple factors contributing to variation across canopies. Branch-localised induction, variation between tree individuals and predation may be the ones with particularly strong effects on diverse assemblages of insects in temperate forests.
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Affiliation(s)
- Martin Volf
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tereza Volfová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Carlo L Seifert
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Faculty of Forest Sciences and Forest Ecology, Department of Forest Nature Conservation, Georg-August-University, Göttingen, Germany
| | - Antonia Ludwig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, University of Leipzig, Leipzig, Germany
| | - Rolf A Engelmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, University of Leipzig, Leipzig, Germany
| | - Leonardo Ré Jorge
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Ronny Richter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, University of Leipzig, Leipzig, Germany.,Geoinformatics and Remote Sensing, Institute for Geography, University of Leipzig, Leipzig, Germany
| | - Andreas Schedl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, University of Leipzig, Leipzig, Germany.,Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
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19
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Li X, Cheng Y, Wang M, Cui S, Guan J. Weighted gene coexpression correlation network analysis reveals a potential molecular regulatory mechanism of anthocyanin accumulation under different storage temperatures in 'Friar' plum. BMC PLANT BIOLOGY 2021; 21:576. [PMID: 34872513 PMCID: PMC8647467 DOI: 10.1186/s12870-021-03354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Flesh is prone to accumulate more anthocyanin in postharvest 'Friar' plum (Prunus salicina Lindl.) fruit stored at an intermediate temperature. However, little is known about the molecular mechanism of anthocyanin accumulation regulated by storage temperature in postharvest plum fruit. RESULTS To reveal the potential molecular regulation mechanism of anthocyanin accumulation in postharvest 'Friar' plum fruit stored at different temperatures (0 °C, 10 °C and 25 °C), the fruit quality, metabolite profile and transcriptome of its flesh were investigated. Compared to the plum fruit stored at 0 °C and 25 °C, the fruit stored at 10 °C showed lower fruit firmness after 14 days and reduced the soluble solids content after 21 days of storage. The metabolite analysis indicated that the fruit stored at 10 °C had higher contents of anthocyanins (pelargonidin-3-O-glucoside, cyanidin-3-O-glucoside, cyanidin-3-O-rutinoside and quercetin-3-O-rutinose), quercetin and sucrose in the flesh. According to the results of weighted gene coexpression correlation network analysis (WGCNA), the turquoise module was positively correlated with the content of anthocyanin components, and flavanone 3-hydroxylase (F3H) and chalcone synthase (CHS) were considered hub genes. Moreover, MYB family transcription factor APL (APL), MYB10 transcription factor (MYB10), ethylene-responsive transcription factor WIN1 (WIN1), basic leucine zipper 43-like (bZIP43) and transcription factor bHLH111-like isoform X2 (bHLH111) were closely related to these hub genes. Further qRT-PCR analysis verified that these transcription factors were specifically more highly expressed in plum flesh stored at 10 °C, and their expression profiles were significantly positively correlated with the structural genes of anthocyanin synthesis as well as the content of anthocyanin components. In addition, the sucrose biosynthesis-associated gene sucrose synthase (SS) was upregulated at 10 °C, which was also closely related to the anthocyanin content of plum fruit stored at 10 °C. CONCLUSIONS The present results suggest that the transcription factors APL, MYB10, WIN1, bZIP43 and bHLH111 may participate in the accumulation of anthocyanin in 'Friar' plum flesh during intermediate storage temperatures by regulating the expression of anthocyanin biosynthetic structural genes. In addition, the SS gene may play a role in anthocyanin accumulation in plum flesh by regulating sucrose biosynthesis.
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Affiliation(s)
- Xueling Li
- College of Life Science, Hebei Normal University, Shijiazhuang, Hebei Province, 050024, People's Republic of China
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei Province, 050051, People's Republic of China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, Hebei Province, 050051, People's Republic of China
| | - Yudou Cheng
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei Province, 050051, People's Republic of China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, Hebei Province, 050051, People's Republic of China
| | - Meng Wang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China
| | - Sujuan Cui
- College of Life Science, Hebei Normal University, Shijiazhuang, Hebei Province, 050024, People's Republic of China
| | - Junfeng Guan
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei Province, 050051, People's Republic of China.
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, Hebei Province, 050051, People's Republic of China.
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20
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Zhao C, Ma G, Zhou L, Zhang S, Su L, Sun X, Borrás-Hidalgo O, Li K, Yue Q, Zhao L. Effects of nitrogen levels on gene expression and amino acid metabolism in Welsh onion. BMC Genomics 2021; 22:803. [PMID: 34743697 PMCID: PMC8573885 DOI: 10.1186/s12864-021-08130-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
Background Welsh onion constitutes an important crop due to its benefits in traditional medicine. Nitrogen is an important nutrient for plant growth and yield; however, little is known about its influence on the mechanisms of Welsh onion regulation genes. In this study, we introduced a gene expression and amino acid analysis of Welsh onion treated with different concentrations of nitrogen (N0, N1, and N2 at 0 kg/ha, 130 kg/ha, and 260 kg/ha, respectively). Results Approximately 1,665 genes were differentially regulated with different concentrations of nitrogen. Gene ontology enrichment analysis revealed that the genes involved in metabolic processes, protein biosynthesis, and transportation of amino acids were highly represented. KEGG analysis indicated that the pathways were related to amino acid metabolism, cysteine, beta-alanine, arginine, proline, and glutathione. Differential gene expression in response to varying nitrogen concentrations resulted in different amino acid content. A close relationship between gene expression and the content of amino acids was observed. Conclusions This work examined the effects of nitrogen on gene expression and amino acid synthesis and provides important evidence on the efficient use of nitrogen in Welsh onion.
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Affiliation(s)
- Chen Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,Shandong Provincial Key Laboratory of Food and Fermentation Engineering, Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Guanchu Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Lin Zhou
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Song Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Le Su
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xin Sun
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Orlando Borrás-Hidalgo
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Kunlun Li
- Jinan Hangchen Biotechnology Co., Ltd, Jinan, China
| | - Qiulin Yue
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.
| | - Lin Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab. of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.
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Liu Y, Patra B, Singh SK, Paul P, Zhou Y, Li Y, Wang Y, Pattanaik S, Yuan L. Terpenoid indole alkaloid biosynthesis in Catharanthus roseus: effects and prospects of environmental factors in metabolic engineering. Biotechnol Lett 2021; 43:2085-2103. [PMID: 34564757 PMCID: PMC8510960 DOI: 10.1007/s10529-021-03179-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022]
Abstract
Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis. PURPOSE OF WORK: Catharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.
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Affiliation(s)
- Yongliang Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yan Zhou
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yongqing Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Ling Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
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Wu H, Ren Z, Zheng L, Guo M, Yang J, Hou L, Qanmber G, Li F, Yang Z. The bHLH transcription factor GhPAS1 mediates BR signaling to regulate plant development and architecture in cotton. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.cj.2020.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Kallow S, Panis B, Vu DT, Vu TD, Paofa J, Mertens A, Swennen R, Janssens SB. Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives. BMC PLANT BIOLOGY 2021; 21:415. [PMID: 34503446 PMCID: PMC8431884 DOI: 10.1186/s12870-021-03142-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/06/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population. RESULTS Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. CONCLUSIONS We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.
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Affiliation(s)
- Simon Kallow
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Royal Botanic Gardens Kew, Millennium Seed Bank, Wakehurst, Ardingly, Sussex, RH17 6TN, UK.
| | - Bart Panis
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Bioversity International, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Dang Toan Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Tuong Dang Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Janet Paofa
- National Agricultural Research Institute, Laloki, Port Moresby, 121, Papua New Guinea
| | - Arne Mertens
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Rony Swennen
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15B Naguru East Road, Upper Naguru, 7878, Kampala, Uganda
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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Gallego AM, Rojas LF, Valencia WG, Atehortúa L, Urrea AI, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N. Transcriptomic analyses of cacao flavonoids produced in photobioreactors. BMC Genomics 2021; 22:551. [PMID: 34281511 PMCID: PMC8287782 DOI: 10.1186/s12864-021-07871-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Theobroma cacao is a major source of flavonoids such as catechins and their monomers proanthocyanidins (PAs), widely studied for their potential benefits in cardiovascular diseases. Light has been shown to promote plant secondary metabolite production in vitro. In this study, cacao cells cultured in 7.5 L stirred tank photobioreactors (STPs) were exposed to a change of white to blue LED lights for 28 days (d). RESULTS Transcriptomic analyses were performed in three time points comparing changing expression patterns, after cell exposure to white light (d0-VS-d14), after a shift from white to blue light (d14-VS-d15), and after an extended period of blue light for the following 15 days (d15-VS-d28). Under white light, there was enrichment in metabolic pathways associated with cell growth (carbon, glycolysis, and amino acid biosynthesis) accompanied by a significant increase in the PAs content. In the shift to blue light, further increase in PAs content was observed concomitantly with the significant expression of TWO-COMPONENT RESPONSE REGULATOR genes involved in the early stress responses via circadian clock and hormone pathways. Under blue light exposure, we observed a depletion of PAs content associated with ROS-mediated stress pathways. CONCLUSIONS Light effects on large-scale cell cultures in photobioreactors are complex and pleiotropic; however, we have been able to identify key regulatory players upstream cacao flavonoid biosynthesis in STPs, including TWO-COMPONENT SYSTEM and ROS-signaling genes. The crosstalk between flavonoid biosynthesis and regulatory networks led to understand the dynamics of flavonoid production and degradation in response to light-driven ROS signals. This can be used to optimize the time, and the yield of in vitro targeted metabolites in large-scale culture systems.
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Affiliation(s)
- Adriana M Gallego
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Luisa F Rojas
- Grupo de Biotransformación, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Wilmar G Valencia
- Centro de Investigación, Desarrollo y Calidad CIDCA, Compañía Nacional de Chocolates S.A.S, Km 2 Vía Belén autopista, Medellín-Bogotá, Colombia
| | - Lucía Atehortúa
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Aura I Urrea
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Andrew S Fister
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
- Present address: Pairwise Plants, 110 TW Alexander Dr, Durham, NC, USA
| | - Mark J Guiltinan
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Siela N Maximova
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Natalia Pabón-Mora
- Grupo Evo-Devo en Plantas, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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McCoy RM, Julian R, Kumar SRV, Ranjan R, Varala K, Li Y. A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020364. [PMID: 33668664 PMCID: PMC7918732 DOI: 10.3390/plants10020364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 05/05/2023]
Abstract
Upon sensing developmental or environmental cues, epigenetic regulators transform the chromatin landscape of a network of genes to modulate their expression and dictate adequate cellular and organismal responses. Knowledge of the specific biological processes and genomic loci controlled by each epigenetic regulator will greatly advance our understanding of epigenetic regulation in plants. To facilitate hypothesis generation and testing in this domain, we present EpiNet, an extensive gene regulatory network (GRN) featuring epigenetic regulators. EpiNet was enabled by (i) curated knowledge of epigenetic regulators involved in DNA methylation, histone modification, chromatin remodeling, and siRNA pathways; and (ii) a machine-learning network inference approach powered by a wealth of public transcriptome datasets. We applied GENIE3, a machine-learning network inference approach, to mine public Arabidopsis transcriptomes and construct tissue-specific GRNs with both epigenetic regulators and transcription factors as predictors. The resultant GRNs, named EpiNet, can now be intersected with individual transcriptomic studies on biological processes of interest to identify the most influential epigenetic regulators, as well as predicted gene targets of the epigenetic regulators. We demonstrate the validity of this approach using case studies of shoot and root apical meristem development.
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Affiliation(s)
- Rachel M. McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Russell Julian
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Shoban R. V. Kumar
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Rajeev Ranjan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kranthi Varala
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-765-494-0104
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Chen Z, Zhao J, Song J, Han S, Du Y, Qiao Y, Liu Z, Qiao J, Li W, Li J, Wang H, Xing B, Pan Q. Influence of graphene on the multiple metabolic pathways of Zea mays roots based on transcriptome analysis. PLoS One 2021; 16:e0244856. [PMID: 33395448 PMCID: PMC7781479 DOI: 10.1371/journal.pone.0244856] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
Graphene reportedly exerts positive effects on plant root growth and development, although the corresponding molecular response mechanism remains to be elucidated. Maize seeds were randomly divided into a control and experimental group, and the roots of Zea mays L. seedlings were watered with different concentrations (0-100 mg/L) of graphene to explore the effects and molecular mechanism of graphene on the growth and development of Z. mays L. Upon evaluating root growth indices, 50 mg/L graphene remarkably increased total root length, root volume, and the number of root tips and forks of maize seedlings compared to those of the control group. We observed that the contents of nitrogen and potassium in rhizosphere soil increased following the 50 mg/L graphene treatment. Thereafter, we compared the transcriptome changes in Z. mays roots in response to the 50 mg/L graphene treatment. Transcriptional factor regulation, plant hormone signal transduction, nitrogen and potassium metabolism, as well as secondary metabolism in maize roots subjected to graphene treatment, exhibited significantly upregulated expression, all of which could be related to mechanisms underlying the response to graphene. Based on qPCR validations, we proposed several candidate genes that might have been affected with the graphene treatment of maize roots. The transcriptional profiles presented here provide a foundation for deciphering the mechanism underlying graphene and maize root interaction.
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Affiliation(s)
- Zhiwen Chen
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
- * E-mail: (ZC); (JZ)
| | - Jianguo Zhao
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
- * E-mail: (ZC); (JZ)
| | - Jie Song
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
| | - Shenghua Han
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
| | - Yaqin Du
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
| | - Yuying Qiao
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
| | - Zehui Liu
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
| | - Jun Qiao
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
| | - Weijia Li
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
| | - Jingwei Li
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
| | - Haiyan Wang
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, P.R. China
| | - Baoyan Xing
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
| | - Qiliang Pan
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Institute of Carbon Materials Science, Shanxi Datong University, Datong, P.R. China
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Fungal Endophytes from Orchidaceae: Diversity and Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Brenya E, Chen ZH, Tissue D, Papanicolaou A, Cazzonelli CI. Prior exposure of Arabidopsis seedlings to mechanical stress heightens jasmonic acid-mediated defense against necrotrophic pathogens. BMC PLANT BIOLOGY 2020; 20:548. [PMID: 33287718 PMCID: PMC7720613 DOI: 10.1186/s12870-020-02759-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/26/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Prolonged mechanical stress (MS) causes thigmomorphogenesis, a stress acclimation response associated with increased disease resistance. What remains unclear is if; 1) plants pre-exposed to a short period of repetitive MS can prime defence responses upon subsequent challenge with necrotrophic pathogens, 2) MS mediates plant immunity via jasmonic acid (JA) signalling, and 3) a short period of repetitive MS can cause long-term changes in gene expression resembling a stress-induced memory. To address these points, 10-days old juvenile Arabidopsis seedlings were mechanically stressed for 7-days using a soft brush and subsequently challenged with the necrotrophic pathogens, Alternaria brassicicola, and Botrytis cinerea. Here we assessed how MS impacted structural cell wall appositions, disease symptoms and altered gene expression in response to infection. RESULTS The MS-treated plants exhibited enhanced cell wall appositions and jasmonic acid (JA) accumulation that correlated with a reduction in disease progression compared to unstressed plants. The expression of genes involved in JA signalling, callose deposition, peroxidase and phytoalexin biosynthesis and reactive oxygen species detoxification were hyper-induced 4-days post-infection in MS-treated plants. The loss-of-function in JA signalling mediated by the JA-insensitive coronatine-insensitive 1 (coi1) mutant impaired the hyper-induction of defense gene expression and promoted pathogen proliferation in MS-treated plants subject to infection. The basal expression level of PATHOGENESIS-RELATED GENE 1 and PLANT DEFENSIN 1.2 defense marker genes were constitutively upregulated in rosette leaves for 5-days post-MS, as well as in naïve cauline leaves that differentiated from the inflorescence meristem well after ceasing MS. CONCLUSION This study reveals that exposure of juvenile Arabidopsis plants to a short repetitive period of MS can alter gene expression and prime plant resistance upon subsequent challenge with necrotrophic pathogens via the JA-mediated COI1 signalling pathway. MS may facilitate a stress-induced memory to modulate the plant's response to future stress encounters. These data advance our understanding of how MS primes plant immunity against necrotrophic pathogens and how that could be utilised in sustainable agricultural practices.
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Affiliation(s)
- Eric Brenya
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- Present address: Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Hesler Biology Building. 1441 Circle Drive, Knoxville, TN, 37996, USA
| | - Zhong-Hua Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
| | - David Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Christopher Ian Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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Zheng C, Shen F, Wang Y, Wu T, Xu X, Zhang X, Han Z. Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics 2020; 21:852. [PMID: 33261554 PMCID: PMC7709433 DOI: 10.1186/s12864-020-07257-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Results Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°. Conclusions Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.
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Affiliation(s)
- Caixia Zheng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Shen C, Yuan J. Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata). BMC PLANT BIOLOGY 2020; 20:471. [PMID: 33054710 PMCID: PMC7557022 DOI: 10.1186/s12870-020-02683-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. RESULTS In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. CONCLUSIONS The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China.
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Zhao Q, Fan Z, Qiu L, Che Q, Wang T, Li Y, Wang Y. MdbHLH130, an Apple bHLH Transcription Factor, Confers Water Stress Resistance by Regulating Stomatal Closure and ROS Homeostasis in Transgenic Tobacco. FRONTIERS IN PLANT SCIENCE 2020; 11:543696. [PMID: 33163009 PMCID: PMC7581937 DOI: 10.3389/fpls.2020.543696] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/31/2020] [Indexed: 05/06/2023]
Abstract
Drought is a major environmental factor that significantly limits crop yield and quality worldwide. Basic helix-loop-helix (bHLH) transcription factors have been reported to participate in the regulation of various abiotic stresses. In this study, a bHLH transcription factor in apple, MdbHLH130, which contains a highly conserved bHLH domain, was isolated and characterized. qRT-PCR and PMdbHLH130::GUS analyses showed that MdbHLH130 was notably induced in response to dehydration stress. Compared with the wild-type (WT), transgenic apple calli overexpressing MdbHLH130 displayed greater resistance to PEG6000 treatment. In contrast, the MdbHLH130-Anti lines were more sensitive to PEG6000 treatment than WT. Moreover, ectopic expression of MdbHLH130 in tobacco improved tolerance to water deficit stress, and plants exhibited higher germination rates and survival rates, longer roots, and lower ABA-induced stomatal closure and leaf water loss than the WT control. Furthermore, overexpression of MdbHLH130 in tobacco also led to lower electrolyte leakage, malondialdehyde contents, and reactive oxygen species (ROS) accumulation and upregulation of the expression of some ROS-scavenging and stress-responsive genes under water deficit stress. In addition, MdbHLH130 transgenic tobacco plants exhibited improved tolerance to oxidative stress compared with WT. In conclusion, these results indicate that MdbHLH130 acts as a positive regulator of water stress responses through modulating stomatal closure and ROS-scavenging in tobacco.
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Affiliation(s)
- Qiang Zhao
- Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Zihao Fan
- Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Lina Qiu
- Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Qinqin Che
- Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Ting Wang
- Editorial Office of YanTai Fruits, Yantai Academy of Agricultural Sciences, Yantai, China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, China
| | - Yongzhang Wang
- Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Lu J, Fu Y, Li M, Wang S, Wang J, Yang Q, Ye J, Zhang X, Ma H, Chang F. Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis. Int J Mol Sci 2020; 21:ijms21176116. [PMID: 32854314 PMCID: PMC7503369 DOI: 10.3390/ijms21176116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.
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Affiliation(s)
- Jianan Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Ying Fu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Mengyu Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Shuangshuang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Jingya Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Qi Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
| | - Fang Chang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
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Xie Y, Ying J, Xu L, Wang Y, Dong J, Chen Y, Tang M, Li C, M'mbone Muleke E, Liu L. Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.). BMC PLANT BIOLOGY 2020; 20:373. [PMID: 32770962 PMCID: PMC7414755 DOI: 10.1186/s12870-020-02585-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size. RESULTS A total of 2606 differentially expressed genes (DEGs) were shared between 'NAU-DY' (large acicular) and 'NAU-YB' (medium obovate), which were significantly enriched in 'phenylpropanoid biosynthesis', 'glucosinolate biosynthesis', and 'starch and sucrose metabolism' pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between 'NAU-DY' and 'NAU-YH' (small circular), whereas 12 miRNAs exhibited specific differential expression in 'NAU-DY'. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis. CONCLUSION This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.
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Affiliation(s)
- Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Cui Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Everlyne M'mbone Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Wang W, Wang Y, Zhang S, Xie K, Zhang C, Xi Y, Sun F. Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass. Mol Biol Rep 2020; 47:4439-4454. [PMID: 32476099 DOI: 10.1007/s11033-020-05561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/27/2020] [Indexed: 11/27/2022]
Abstract
The large basic leucine zipper (bZIP) transcription factor family is conserved in plants. These proteins regulate growth, development, and stress response. Here, we conducted a genome-wide analysis to identify the bZIP genes associated with stress resistance in switchgrass (Panicum virgatum L.). We identified 178 PvbZIPs unevenly distributed on 18 switchgrass chromosomes. An evolutionary analysis segregated them into 10 subfamilies. Gene structure and conserved motif analyses indicated that the same subfamily members shared similar intron-exon modes and motif compositions. This finding corroborated the proposed PvbZIP family grouping. A promoter analysis showed that PvbZIP genes participate in various stress responses. Phylogenetic and synteny analyses characterized 111 switchgrass bZIPs as orthologs of 70 rice bZIPs. A protein interaction network analysis revealed that 22 proteins are involved in salt and drought tolerance. An expression atlas disclosed that the expression patterns of several PvbZIPs differ among various tissues and developmental stages. Online data demonstrated that 16 PvbZIPs were significantly downregulated and five were significantly upregulated in response to heat stress. Other PvbZIPs participated in responses to abiotic stress such as salt, drought, cold, and heat. Our genome-wide analysis and identification of the switchgrass bZIP family characterized multiple candidate PvbZIPs that regulate growth and stress response. This study lays theoretical and empirical foundations for future functional investigations into other transcription factors.
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Affiliation(s)
- Weiwei Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yongfeng Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shumeng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kunliang Xie
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fengli Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Shangguan L, Fang X, Jia H, Chen M, Zhang K, Fang J. Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. 'Fujiminori'). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:617-637. [PMID: 32255927 PMCID: PMC7113366 DOI: 10.1007/s12298-020-00759-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/21/2019] [Accepted: 01/03/2020] [Indexed: 05/04/2023]
Abstract
The fruit is the most important economical organ in the grape; accordingly, to investigate the grapevine genomic methylation landscape and examine its functional significance during fruit development, we generated whole genome DNA methylation maps for various developmental stages in the fruit of grapevine. In this study, thirteen DNA methylation-related genes and their expression profiles were identified and analyzed. The methylation levels for mC, mCG, mCHG, and mCHH contexts in 65 days after flowering (65DAF) fruit (véraison stage) were higher than those in 40DAF (green stage) and 90DAF (mature stage) fruits. Relative to methylation in the mC context, methylation levels in the mCHH context were higher than those of mCG and mCHG. The DNA methylation level in the ncRNA regions was significantly higher than that in exon, gene, intron, and mRNA regions. The differentially methylated regions (DMRs) and differentially methylated promoters (DMPs) in 65DAF_vs_40DAF were both higher than those in 90DAF_vs_65DAF and 90DAF_vs_40DAF. Most DMRs (or DMPs) were involved in metabolic processes and cell processes, binding, and catalytic activity. These results indicated that DNA methylation represses gene expression during grape fruit development, and it broadens our understanding of the landscape and function of DNA methylation in grapevine genomes.
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Affiliation(s)
- Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Xiang Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
| | - Haifeng Jia
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Mengxia Chen
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Kekun Zhang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
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Ke YZ, Wu YW, Zhou HJ, Chen P, Wang MM, Liu MM, Li PF, Yang J, Li JN, Du H. Genome-wide survey of the bHLH super gene family in Brassica napus. BMC PLANT BIOLOGY 2020; 20:115. [PMID: 32171243 PMCID: PMC7071649 DOI: 10.1186/s12870-020-2315-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. RESULTS We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. CONCLUSION The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.
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Affiliation(s)
- Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Hong-Jun Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ping Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
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Wairich A, de Oliveira BHN, Arend EB, Duarte GL, Ponte LR, Sperotto RA, Ricachenevsky FK, Fett JP. The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa). Sci Rep 2019; 9:16144. [PMID: 31695138 PMCID: PMC6834603 DOI: 10.1038/s41598-019-52502-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/14/2019] [Indexed: 01/12/2023] Open
Abstract
Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in O. sativa and its wild progenitor O. rufipogon. We identified 622 and 2,017 differentially expressed genes in O. sativa and O. rufipogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identified the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profile in response to low Fe condition. Our results indicate that the Combined Strategy is not specific to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversified. Therefore, adaptation to Fe2+ acquisition via IRT1 in flooded soils precedes O. sativa domestication.
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Affiliation(s)
- Andriele Wairich
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ben Hur Neves de Oliveira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ezequiel Barth Arend
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Leitão Duarte
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Roani Ponte
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Janette Palma Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Madhusudhan P, Sinha P, Rajput LS, Bhattacharya M, Sharma T, Bhuvaneshwari V, Gaikwad K, Krishnan SG, Singh AK. Effect of temperature on Pi54-mediated leaf blast resistance in rice. World J Microbiol Biotechnol 2019; 35:148. [PMID: 31549233 DOI: 10.1007/s11274-019-2724-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022]
Abstract
Assessment of temperature effect on plant resistance against diseases has become essential under climate change scenario as temperature rise is anticipated to modify host resistance. To determine temperature influence on resistance gene, a pair of near-isogenic rice lines differing for the Pi54 resistance gene was assessed against leaf blast. Blast resistance was determined as the extent of infection efficiency (IE) and sporulation (SP) at suboptimal (22 °C and 32 °C) and optimal temperature (27 °C) of pathogen aggressiveness. Relative resistance for IE and SP was higher at suboptimal temperature as compared to that of optimal temperature. Maximum level of resistance was at 22 °C where higher levels of expression of Pi54 and defence-regulatory transcription factor WRKY45 were also noted. At 32 °C, although some level of resistance noted, but level of Pi54 and WRKY45 expression was too low, suggesting that resistance recorded at higher temperature was due to reduced pathogen aggressiveness. At the optimal temperature for pathogen aggressiveness, comparatively lower levels of Pi54 and WRKY45 expression suggest possible temperature-induced interruption of the defence processes. The variation in resistance patterns modulated by temperature is appeared to be due to pathogen's sensitivity to temperature that leads to varying levels of Pi54 gene activation. Quick and violent activity of the pathogen at optimal temperature came into sight for the interruption of defence process activated by Pi54 gene. Evaluation of blast resistance genes under variable temperature conditions together with weather data could be applied in screening rice genotypes for selection of resistance having resilience to temperature rise.
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Affiliation(s)
- P Madhusudhan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Agricultural Research Station, Acharya N G Ranga Agricultural University, Nellore, Andhra Pradesh, 524003, India
| | - P Sinha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - L S Rajput
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Protection, ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, 452001, India
| | - M Bhattacharya
- Department of Agronomy, IOWA State University, Ames, IA, 5001-1051, USA
| | - Taru Sharma
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - V Bhuvaneshwari
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University, Maruteru, Andhra Pradesh, 534122, India
| | - Kishore Gaikwad
- National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Engelsdorf T, Kjaer L, Gigli-Bisceglia N, Vaahtera L, Bauer S, Miedes E, Wormit A, James L, Chairam I, Molina A, Hamann T. Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment. BMC PLANT BIOLOGY 2019; 19:320. [PMID: 31319813 PMCID: PMC6637594 DOI: 10.1186/s12870-019-1934-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/10/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Plant cell walls participate in all plant-environment interactions. Maintaining cell wall integrity (CWI) during these interactions is essential. This realization led to increased interest in CWI and resulted in knowledge regarding early perception and signalling mechanisms active during CWI maintenance. By contrast, knowledge regarding processes mediating changes in cell wall metabolism upon CWI impairment is very limited. RESULTS To identify genes involved and to investigate their contributions to the processes we selected 23 genes with altered expression in response to CWI impairment and characterized the impact of T-DNA insertions in these genes on cell wall composition using Fourier-Transform Infrared Spectroscopy (FTIR) in Arabidopsis thaliana seedlings. Insertions in 14 genes led to cell wall phenotypes detectable by FTIR. A detailed analysis of four genes found that their altered expression upon CWI impairment is dependent on THE1 activity, a key component of CWI maintenance. Phenotypic characterizations of insertion lines suggest that the four genes are required for particular aspects of CWI maintenance, cell wall composition or resistance to Plectosphaerella cucumerina infection in adult plants. CONCLUSION Taken together, the results implicate the genes in responses to CWI impairment, cell wall metabolism and/or pathogen defence, thus identifying new molecular components and processes relevant for CWI maintenance.
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Affiliation(s)
- Timo Engelsdorf
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491 Trondheim, Norway
- Present address: Division of Plant Physiology, Department of Biology, Philipps University of Marburg, 35043 Marburg, Germany
| | - Lars Kjaer
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW72AZ UK
- Present address: Sjælland erhvervsakademi, Breddahlsgade 1b, 4200 Slagelse, Zealand Denmark
| | - Nora Gigli-Bisceglia
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491 Trondheim, Norway
- Present address: Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Lauri Vaahtera
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491 Trondheim, Norway
| | - Stefan Bauer
- Energy Biosciences Institute, University of California, 120A Energy Biosciences Building, 2151 Berkeley Way, MC 5230, Berkeley, CA 94720-5230 USA
- Present address: Zymergen, Inc, 5980 Horton St, Suite 105, Emeryville, CA 94608 USA
| | - Eva Miedes
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo- UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Alexandra Wormit
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW72AZ UK
- Present address: RWTH Aachen, Institute for Biology I, Worringerweg 3, D-52056 Aachen, Germany
| | - Lucinda James
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW72AZ UK
- Present address: ADAS, Battlegate Road, Boxworth, Cambridge, CB23 4NN UK
| | - Issariya Chairam
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW72AZ UK
- Present address: ADAS, Battlegate Road, Boxworth, Cambridge, CB23 4NN UK
- Present address: Department of Nuclear Safety and Security, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo- UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Thorsten Hamann
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491 Trondheim, Norway
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW72AZ UK
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Reyes-Olalde JI, de Folter S. Control of stem cell activity in the carpel margin meristem (CMM) in Arabidopsis. PLANT REPRODUCTION 2019; 32:123-136. [PMID: 30671644 DOI: 10.1007/s00497-018-00359-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/24/2018] [Indexed: 05/29/2023]
Abstract
Overview of the current understanding of the molecular mechanisms that regulate meristem activity in the CMM compared to the SAM. Meristems are undifferentiated cells responsible for post-embryonic plant development. The meristems are able to form new organs continuously by carefully balancing between stem cell proliferation and cell differentiation. The plant stem cell niche in each meristem harbors the stem cells that are important to maintain each meristem. The shoot apical meristem (SAM) produces all above-parts of a plant and the molecular mechanisms active in the SAM are actively studied since many years, and models are available. During the reproductive phase of the plant, the inflorescence meristem gives rise to floral meristems, which give rise to the flowers. During floral development, the gynoecium forms that contains a new meristem inside, called the carpel margin meristem (CMM). In Arabidopsis, the gynoecium consists out of two fused carpels, where the CMM forms along the fused carpel margins. In this review, we focus on the molecular mechanisms taking place in the CMM, and we discuss similarities and differences found in the SAM.
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Affiliation(s)
- J Irepan Reyes-Olalde
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), CP 36824, Irapuato, Guanajuato, Mexico
- Universidad Politécnica del Valle de Toluca, CP 50904, Almoloya de Juárez, Estado de México, Mexico
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, CP 50180, Toluca, Estado de Mexico, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), CP 36824, Irapuato, Guanajuato, Mexico.
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Li GH, Chen HC, Liu JL, Luo WL, Xie DS, Luo SB, Wu TQ, Akram W, Zhong YJ. A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). BMC Genomics 2019; 20:343. [PMID: 31064320 PMCID: PMC6503552 DOI: 10.1186/s12864-019-5693-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. RESULTS We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines "Xianghongtai 01" and "Yinong 50D" with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69-61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. CONCLUSION Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa.
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Affiliation(s)
- Gui-Hua Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Han-Cai Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jia-Li Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Wen-Long Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Da-Sen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Shao-Bo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Ting-Quan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Waheed Akram
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Yu-Juan Zhong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China. .,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China.
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Osthoff A, Donà Dalle Rose P, Baldauf JA, Piepho HP, Hochholdinger F. Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress. BMC Genomics 2019; 20:325. [PMID: 31035922 PMCID: PMC6489292 DOI: 10.1186/s12864-019-5634-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Background Water deficit and soil salinity substantially influence plant growth and productivity. When occurring individually, plants often exhibit reduced growth resulting in yield losses. The simultaneous occurrence of these stresses enhances their negative effects. Unraveling the molecular mechanisms of combined abiotic stress responses is essential to secure crop productivity under unfavorable environmental conditions. Results This study examines the effects of water deficit, salinity and a combination of both on growth and transcriptome plasticity of barley seminal roots by RNA-Seq. Exposure to water deficit and combined stress for more than 4 days significantly reduced total seminal root length. Transcriptome sequencing demonstrated that 60 to 80% of stress type-specific gene expression responses observed 6 h after treatment were also present after 24 h of stress application. However, after 24 h of stress application, hundreds of additional genes were stress-regulated compared to the short 6 h treatment. Combined salt and water deficit stress application results in a unique transcriptomic response that cannot be predicted from individual stress responses. Enrichment analyses of gene ontology terms revealed stress type-specific adjustments of gene expression. Further, global reprogramming mediated by transcription factors and consistent over-representation of basic helix-loop-helix (bHLH) transcription factors, heat shock factors (HSF) and ethylene response factors (ERF) was observed. Conclusion This study reveals the complex transcriptomic responses regulating the perception and signaling of multiple abiotic stresses in barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5634-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alina Osthoff
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Petra Donà Dalle Rose
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599, Stuttgart, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany.
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Yang X, Pan Y, Singh PK, He X, Ren Y, Zhao L, Zhang N, Cheng S, Chen F. Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat. BMC PLANT BIOLOGY 2019; 19:153. [PMID: 31014249 PMCID: PMC6480828 DOI: 10.1186/s12870-019-1758-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/04/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fusarium crown rot (FCR) is a severe and chronic disease in common wheat and is able to cause serious yield loss and health problems to human and livestock. RESULTS Here, 234 Chinese wheat cultivars were evaluated in four greenhouse experiments for FCR resistance and genome-wide association studies (GWAS) were performed using the wheat 660 K genotyping assay. The results indicated that most cultivars evaluated showed FCR disease index (DI) of 40-60, while some cultivars showed stably good FCR resistance (DI < 30). GWAS identified 286 SNPs to be significantly associated with FCR resistance, of which 266, 6 and 8 were distributed on chromosomes 6A, 6B and 6D, respectively. The significant SNPs on 6A were located in a 7.0-Mb region containing 51 annotated genes. On the other hand, QTL mapping using a bi-parental population derived from UC1110 and PI610750 detected three QTLs on chromosomes 6A (explaining 7.77-10.17% of phenotypic variation), 2D (7.15-9.29%) and 2A (5.24-6.92%). The 6A QTL in the UC1110/PI610750 population falls into the same chromosomal region as those detected from GWAS, demonstrating its importance in Chinese materials for FCR resistance. CONCLUSION This study could provide useful information for utilization of FCR-resistant wheat germplasm and further understanding of molecular and genetics basis of FCR resistance in common wheat.
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Affiliation(s)
- Xia Yang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Yubo Pan
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Mexico DF, Mexico
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Mexico DF, Mexico
| | - Yan Ren
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Lei Zhao
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Ning Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Shunhe Cheng
- Lixiahe Institute of Agricultural and Sciences, Yangzhou, 225007 Jiangsu China
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
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Pullen N, Zhang N, Dobon Alonso A, Penfield S. Growth rate regulation is associated with developmental modification of source efficiency. NATURE PLANTS 2019; 5:148-152. [PMID: 30718925 DOI: 10.1038/s41477-018-0357-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/21/2018] [Indexed: 05/19/2023]
Abstract
Plants modulate their growth rate according to seasonal and environmental cues using a suite of growth repressors known to interact directly with cellular machinery controlling cell division and growth. Mutants lacking growth repressors show increased growth rates1,2, but the mechanism by which these plants ensure source availability for faster growth is unclear. Here, we undertake a comprehensive analysis of the fast-growth phenotype of a quintuple growth-repressor mutant, using a combination of theoretical and experimental approaches to understand the physiological basis of source-sink coordination. Our results show that, in addition to the control of tissue growth rates, growth repressors also affect tissue composition and leaf thickness, modulating the efficiency of production of new photosynthetic capacity. Modelling suggests that increases in growth efficiency underlie growth-rate differences between the wild type and spatula della growth-repressor mutant, with spatula della requiring less carbon to synthesize a comparable photosynthetic capability to the wild type, and fixing more carbon per unit mass. We conclude that through control of leaf development, growth repressors regulate both source availability and sink strength to achieve growth-rate variation without risking a carbon deficit.
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Affiliation(s)
- Nick Pullen
- Crop Genetics, John Innes Centre, Norwich, UK
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Chen K, Yu Y, Sun K, Xiong H, Yu C, Chen P, Chen J, Gao G, Zhu A. The miRNAome of ramie (Boehmeria nivea L.): identification, expression, and potential roles of novel microRNAs in regulation of cadmium stress response. BMC PLANT BIOLOGY 2018; 18:369. [PMID: 30577815 PMCID: PMC6303851 DOI: 10.1186/s12870-018-1561-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/22/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) regulate numerous crucial abiotic stress processes in plants. However, information is limited on their involvement in cadmium (Cd) stress response and tolerance mechanisms in plants, including ramie (Boehmeria nivea L.) that produces a number of economic valuable as an important natural fibre crop and an ideal crop for Cd pollution remediation. RESULTS Four small RNA libraries of Cd-stressed and non-stressed leaves and roots of ramie were constructed. Using small RNA-sequencing, 73 novel miRNAs were identified. Genome-wide expression analysis revealed that a set of miRNAs was differentially regulated in response to Cd stress. In silico target prediction identified 426 potential miRNA targets that include several uptake or transport factors for heavy metal ions. The reliability of small RNA sequencing and the relationship between the expression levels of miRNAs and their target genes were confirmed by quantitative PCR (q-PCR). We showed that the expression patterns of miRNAs obtained by q-PCR were consistent with those obtained from small RNA sequencing. Moreover, we demonstrated that the expression of six randomly selected target genes was inversely related to that of their corresponding miRNAs, indicating that the miRNAs regulate Cd stress response in ramie. CONCLUSIONS This study enriches the number of Cd-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in ramie during Cd stress.
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Affiliation(s)
- Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yongting Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Kai Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Heping Xiong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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47
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Radanielson A, Gaydon D, Li T, Angeles O, Roth C. Modeling salinity effect on rice growth and grain yield with ORYZA v3 and APSIM-Oryza. EUROPEAN JOURNAL OF AGRONOMY : THE JOURNAL OF THE EUROPEAN SOCIETY FOR AGRONOMY 2018; 100:44-55. [PMID: 33343194 PMCID: PMC7729823 DOI: 10.1016/j.eja.2018.01.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
Development and testing of reliable tools for simulating rice production in salt-affected areas are presented in this paper. New functions were implemented in existing crop models ORYZA v3 and the cropping systems modelling framework APSIM. Field experiments covering two years, two different sites, and three varieties were used to validate both improved models. We used the salt balance module in the systems model APSIM to simulate the observed daily soil salinity with acceptable accuracy (RMSEn <35%), whereas ORYZA v3 used measured soil salinity at a given interval of days as a model input. Both models presented similarly good accuracy in simulating aboveground biomass, leaf area index, and grain yield for IR64 over a gradient of salinity conditions. The model index of agreement ranged from 0.86 to 0.99. Variability of yield under stressed and non-stressed conditions was simulated with a RMSE, of 191 kg ha-1 and 222 kg ha-1 , respectively, for ORYZA v3 and APSIM-Oryza, corresponding to an RMSEn of 14.8% and 17.3%. These values are within the bounds of experimental error, therefore indicating acceptable model performance. The model test simulating genotypic variability of rice crop responses resulted in similar levels of acceptable model performance with RMSEn ranging from 11.3 to 39.9% for observed total above ground biomass for IR64 and panicle biomass for IR29, respectively. With the improved models, more reliable tools are now available for use in risk assessment and evaluation of suitable management options for rice production in salt-affected areas. The approach presented may also be applied in improving other non-rice crop models to integrate a response to soil salinity - particularly in process-based models which capture stage-related stress tolerance variability and resource use efficiency.
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Affiliation(s)
- A.M. Radanielson
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Corresponding author.
| | - D.S. Gaydon
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Australia
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
| | - T. Li
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - O. Angeles
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - C.H. Roth
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Australia
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48
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Gallego AM, Rojas LF, Parra O, Rodriguez HA, Mazo Rivas JC, Urrea AI, Atehortúa L, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N. Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. Sci Rep 2018; 8:13575. [PMID: 30206304 PMCID: PMC6134037 DOI: 10.1038/s41598-018-31965-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022] Open
Abstract
Catechins, including catechin (C) and epicatechin (E), are the main type of flavonoids in cacao seeds. They play important roles in plant defense and have been associated with human health benefits. Although flavonoid biosynthesis has been extensively studied using in vitro and in vivo models, the regulatory mechanisms controlling their accumulation under light/dark conditions remain poorly understood. To identify differences in flavonoid biosynthesis (particularly catechins) under different light treatments, we used cacao cell suspensions exposed to white-blue light and darkness during 14 days. RNA-Seq was applied to evaluate differential gene expression. Our results indicate that light can effectively regulate flavonoid profiles, inducing a faster accumulation of phenolic compounds and shifting E/C ratios, in particular as a response to switching from white to blue light. The results demonstrated that HY5, MYB12, ANR and LAR were differentially regulated under light/dark conditions and could be targeted by overexpression aiming to improve catechin synthesis in cell cultures. In conclusion, our RNA-Seq analysis of cacao cells cultured under different light conditions provides a platform to dissect key aspects into the genetic regulatory network of flavonoids. These light-responsive candidate genes can be used further to modulate the flavonoid production in in vitro systems with value-added characteristics.
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Affiliation(s)
- Adriana M Gallego
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Luisa F Rojas
- Universidad de Antioquia, Grupo de Biotecnología-Escuela de Microbiología, Medellín, Colombia
| | - Oriana Parra
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Héctor A Rodriguez
- Corporación para Investigaciones Biológicas and Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, UNALMED-CIB, Medellín, Colombia
| | | | - Aura Inés Urrea
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Lucía Atehortúa
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Andrew S Fister
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Mark J Guiltinan
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Siela N Maximova
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States.
| | - Natalia Pabón-Mora
- Universidad de Antioquia, Instituto de Biología, Grupo Evo-Devo en Plantas, Medellín, Colombia.
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49
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Mushtaq S, Amjad M, Ziaf K, Afzal I. Gibberellins application timing modulates growth, physiology, and quality characteristics of two onion (Allium cepa L.) cultivars. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:25155-25161. [PMID: 29943247 DOI: 10.1007/s11356-018-2542-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Lack of scientific literature exists regarding the effects of gibberellic acid (GA3) application timings on various phenological and physiological aspects of seed crop of locally available onion cultivars. Therefore, current study was planned in Vegetable Research Area, University of Agriculture, Faisalabad to optimize the growth stage for GA3 application on seed production in two local onion cultivars (Phulkara and Dark Red) during 2013 and 2014. Application timings of gibberellins at 100 mg/L of H2O were as (G1) control (no spray), (G2) foliar application at 2-3 leaf stage, (G3) foliar application at 6-7 leaf stage, and (G4) foliar application at the time of flowering. Data on average of both years showed that tallest plants (66.15 cm) and maximum number of leaves per plant (84.56) were noted in cv. Phulkara when GA3 was applied at 2-3 leaf stage. Minimum number of days to initiate flowering (47.92) and maximum number of umbels per plant (15.45) were noted with GA3 application at 6-7 leaf stage in Phulkara and Dark Red, respectively. The highest seed yield per umbel (2.94 g) was recorded in cv. Dark Red when GA3 sprayed at 6-7 leaf stage, while GA3 application at the time of flowering in the cv. Phulkara produced seeds with highest seedling vigor index (586.79). Overall, it appears that seed yield and quality characters were promoted by the application of GA3 at different growth stages and could be valuable for seed production of onion.
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Affiliation(s)
- Salman Mushtaq
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Amjad
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Khurram Ziaf
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Irfan Afzal
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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50
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Neupane S, Ma Q, Mathew FM, Varenhorst AJ, Andersen EJ, Nepal MP. Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Biochem Genet 2018; 56:397-422. [PMID: 29500532 DOI: 10.1007/s10528-018-9851-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Qin Ma
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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