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Arisha MH, Ahmad MQ, Tang W, Liu Y, Yan H, Kou M, Wang X, Zhang Y, Li Q. RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato. Sci Rep 2020; 10:12573. [PMID: 32724138 PMCID: PMC7387466 DOI: 10.1038/s41598-020-69232-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/02/2020] [Indexed: 11/09/2022] Open
Abstract
Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stress-responsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato.
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Affiliation(s)
- Mohamed Hamed Arisha
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China. .,Department of Horticulture, Faculty of Agriculture, Zagazig University, Sharkia, 44511, Egypt.
| | - Muhammad Qadir Ahmad
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China.,Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Hui Yan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Qiang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China.
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Zhang Y, Held MA, Showalter AM. Elucidating the roles of three β-glucuronosyltransferases (GLCATs) acting on arabinogalactan-proteins using a CRISPR-Cas9 multiplexing approach in Arabidopsis. BMC PLANT BIOLOGY 2020; 20:221. [PMID: 32423474 PMCID: PMC7236193 DOI: 10.1186/s12870-020-02420-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/29/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Arabinogalactan-proteins (AGPs) are one of the most complex protein families in the plant kingdom and are present in the cell walls of all land plants. AGPs are implicated in diverse biological processes such as plant growth, development, reproduction, and stress responses. AGPs are extensively glycosylated by the addition of type II arabinogalactan (AG) polysaccharides to hydroxyproline residues in their protein cores. Glucuronic acid (GlcA) is the only negatively charged sugar added to AGPs and the functions of GlcA residues on AGPs remain to be elucidated. RESULTS Three members of the CAZy GT14 family (GLCAT14A-At5g39990, GLCAT14B-At5g15050, and GLCAT14C-At2g37585), which are responsible for transferring glucuronic acid (GlcA) to AGPs, were functionally characterized using a CRISPR/Cas9 gene editing approach in Arabidopsis. RNA seq and qRT-PCR data showed all three GLCAT genes were broadly expressed in different plant tissues, with GLCAT14A and GLCAT14B showing particularly high expression in the micropylar endosperm. Biochemical analysis of the AGPs from knock-out mutants of various glcat single, double, and triple mutants revealed that double and triple mutants generally had small increases of Ara and Gal and concomitant reductions of GlcA, particularly in the glcat14a glcat14b and glcat14a glcat14b glcat14c mutants. Moreover, AGPs isolated from all the glcat mutants displayed significant reductions in calcium binding compared to WT. Further phenotypic analyses found that the glcat14a glcat14b and glcat14a glcat14b glcat14c mutants exhibited significant delays in seed germination, reductions in root hair length, reductions in trichome branching, and accumulation of defective pollen grains. Additionally, both glcat14b glcat14c and glcat14a glcat14b glcat14c displayed significantly shorter siliques and reduced seed set. Finally, all higher-order mutants exhibited significant reductions in adherent seed coat mucilage. CONCLUSIONS This research provides genetic evidence that GLCAT14A-C function in the transfer of GlcA to AGPs, which in turn play a role in a variety of biochemical and physiological phenotypes including calcium binding by AGPs, seed germination, root hair growth, trichome branching, pollen development, silique development, seed set, and adherent seed coat mucilage accumulation.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Environmental & Plant Biology, Ohio University, Athens, OH 45701–2979 USA
| | - Michael A. Held
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH 45701–2979 USA
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Environmental & Plant Biology, Ohio University, Athens, OH 45701–2979 USA
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Thakur V, Bains S, Pathania S, Sharma S, Kaur R, Singh K. Comparative transcriptomics reveals candidate transcription factors involved in costunolide biosynthesis in medicinal plant-Saussurea lappa. Int J Biol Macromol 2020; 150:52-67. [DOI: 10.1016/j.ijbiomac.2020.01.312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023]
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Saikia B, Singh S, Debbarma J, Velmurugan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C. Multigene CRISPR/Cas9 genome editing of hybrid proline rich proteins (HyPRPs) for sustainable multi-stress tolerance in crops: the review of a promising approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:857-869. [PMID: 32377037 PMCID: PMC7196567 DOI: 10.1007/s12298-020-00782-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 02/21/2020] [Indexed: 05/05/2023]
Abstract
The recent global climate change has directly impacted major biotic and abiotic stress factors affecting crop productivity worldwide. Therefore, the need of the hour is to develop sustainable multiple stress tolerant crops through modern biotechnological approaches to cope with climate change. Hybrid proline rich proteins (HyPRPs) are the cell-wall structural proteins, which contain an N-terminal repetitive proline-rich domain and a C-terminal conserved eight-cysteine motif domain. HyPRPs are known to regulate multiple abiotic and biotic stress responses in plants. Recently, a few HyPRPs have been characterized as negative regulators of abiotic and biotic stress responses in different plants. Disruption of such negative regulators for desirable positive phenotypic traits has been made possible through the advent of advanced genome engineering tools. In the past few years, CRISPR/Cas9 has emerged as a novel breakthrough technology for crop improvement by target specific editing of known negative regulatory host genes. Here, we have described the mechanism of action and the role of known HyPRPs in regulating different biotic and abiotic stress responses in major crop plants. We have also discussed the importance of the CRISPR/Cas9 based genome editing system in targeting known negative regulatory HyPRPs for multi-stress crop tolerance using the tomato crop model. Application of genome editing to manipulate the HyPRPs of major crop plants holds promise in developing newer stress management methods in this rapidly changing climate and would lead in the future to sustain crop productivity.
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Affiliation(s)
- Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Sanjay Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
| | - Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Natarajan Velmurugan
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
- Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Naharlagun, Arunachal Pradesh 791110 India
| | - Hariprasanna Dekaboruah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat, Assam 785700 India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
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Sun S, Wang X, Wang K, Cui X. Dissection of complex traits of tomato in the post-genome era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1763-1776. [PMID: 31745578 DOI: 10.1007/s00122-019-03478-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.
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Affiliation(s)
- Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Applications of Sesquiterpene Lactones: A Review of Some Potential Success Cases. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10093001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sesquiterpene lactones, a vast range of terpenoids isolated from Asteraceae species, exhibit a broad spectrum of biological effects and several of them are already commercially available, such as artemisinin. Here the most recent and impactful results of in vivo, preclinical and clinical studies involving a selection of ten sesquiterpene lactones (alantolactone, arglabin, costunolide, cynaropicrin, helenalin, inuviscolide, lactucin, parthenolide, thapsigargin and tomentosin) are presented and discussed, along with some of their derivatives. In the authors’ opinion, these compounds have been neglected compared to others, although they could be of great use in developing important new pharmaceutical products. The selected sesquiterpenes show promising anticancer and anti-inflammatory effects, acting on various targets. Moreover, they exhibit antifungal, anxiolytic, analgesic, and antitrypanosomal activities. Several studies discussed here clearly show the potential that some of them have in combination therapy, as sensitizing agents to facilitate and enhance the action of drugs in clinical use. The derivatives show greater pharmacological value since they have better pharmacokinetics, stability, potency, and/or selectivity. All these natural terpenoids and their derivatives exhibit properties that invite further research by the scientific community.
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Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive ( Cichorium endivia L.). Genes (Basel) 2020; 11:genes11040462. [PMID: 32340299 PMCID: PMC7231076 DOI: 10.3390/genes11040462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/18/2022] Open
Abstract
The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.
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Li Q, Sapkota M, van der Knaap E. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. HORTICULTURE RESEARCH 2020; 7:36. [PMID: 32194972 PMCID: PMC7072075 DOI: 10.1038/s41438-020-0258-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 05/14/2023]
Abstract
Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
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Affiliation(s)
- Qiang Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
- Department of Horticulture, University of Georgia, Athens, GA USA
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Li C, Wu J, Hu KD, Wei SW, Sun HY, Hu LY, Han Z, Yao GF, Zhang H. PyWRKY26 and PybHLH3 cotargeted the PyMYB114 promoter to regulate anthocyanin biosynthesis and transport in red-skinned pears. HORTICULTURE RESEARCH 2020; 7:37. [PMID: 32194973 PMCID: PMC7072072 DOI: 10.1038/s41438-020-0254-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/30/2019] [Accepted: 01/15/2020] [Indexed: 05/19/2023]
Abstract
Red pear is favored because of its bright appearance and abundant anthocyanins. Anthocyanin biosynthesis is controlled by transcription factors (TFs) forming regulatory complexes. In red-skinned pears, the WRKY TFs have a significant relationship with anthocyanin biosynthesis, but the molecular mechanism of the WRKY TFs involved in regulating color formation in red-skinned pear is unclear. In this study, the TFs PyWRKY31 and PyWRKY26 were screened as candidate genes for controlling anthocyanin biosynthesis by transcriptome data and bioinformatics analysis. The effect of anthocyanin accumulations after cotransformation of PyWRKY31 or PyWRKY26 with its partners PyMYB10, PyMYB114, and PybHLH3 was verified in tobacco leaves and strawberry receptacles by a transient expression system. RT-qPCR analysis and a dual-luciferase reporter system further confirmed that this cotransformation activated the expression of PyDFR, PyANS, and PyUFGT in anthocyanin biosynthesis and PyGST in anthocyanin transport instead of the PyABC transporter and PyAVP. Furthermore, the cotransformed PyWRKY26 and PybHLH3 could bind to the PyMYB114 promoter, and PyWRKY26 directly activated the transcription of PyMYB114. In addition, the TF PyWRKY26 could interact with PybHLH3, as confirmed by firefly luciferase complementation and yeast two-hybrid (Y2H) assays. These results showed that the interaction of PyWRKY26 and PybHLH3 could cotarget the PyMYB114 promoter, which resulted in anthocyanin accumulation in red-skinned pear. This study further strengthened the understanding of the regulatory mechanism of anthocyanin accumulation and contributed to improving the appearance of red-skinned pears.
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Affiliation(s)
- Chuang Li
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kang-Di Hu
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Shu-Wei Wei
- Shandong Institute of Pomology, 271000 Taian, China
| | - Hong-Ye Sun
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Lan-Ying Hu
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
- Anhui Province Key Laboratory of Functional Compound Seasoning, Anhui Qiangwang Seasoning Food Co., Ltd., 236500 Jieshou, China
| | - Zhuo Han
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Gai-Fang Yao
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
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Guo W, Chen J, Li J, Huang J, Wang Z, Lim KJ. Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. HORTICULTURE RESEARCH 2020; 7:35. [PMID: 32194971 PMCID: PMC7072074 DOI: 10.1038/s41438-020-0256-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 05/22/2023]
Abstract
Juglandaceae species are plants of great economic value and have been cultivated, domesticated, and utilized by human society for a long time. Their edible, nutrient-rich nuts and tough, durable wood have attracted the attention of botanists and breeders. With the advent of the genomics era, genome sequencing of the Juglandaceae family has been greatly accelerated, and a large amount of data has been generated. In this paper, we introduce the Portal of Juglandaceae (PJU), a tool to bring all these data together. The PJU contains genomes, gene-coding sequences, protein sequences, various types of annotation information, expression data, and miRNA data, which are configured with BLAST, JBrowse, and our self-developed synteny analysis tool. The PJU has a user-friendly and straightforward interface that performs a variety of query tasks with a few simple operations. In the future, we hope that the PJU will serve as a hub for the study of the Juglandaceae family.
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Affiliation(s)
- Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jian Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
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Hui WK, Zhao FY, Wang JY, Chen XY, Li JW, Zhong Y, Li HY, Zheng JX, Zhang LZ, Que QM, Wu AM, Gong W. De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism. BMC Genomics 2020; 21:81. [PMID: 31992199 PMCID: PMC6986037 DOI: 10.1186/s12864-020-6521-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fei-Yan Zhao
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Yang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jue-Wei Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong-Yun Li
- Agricultural Technology Extension Center in Yantan District, Zigong, 643030, China
| | - Jun-Xing Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang-Zhen Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing-Min Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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Testone G, Baldoni E, Iannelli MA, Nicolodi C, Di Giacomo E, Pietrini F, Mele G, Giannino D, Frugis G. Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship Between Photosynthesis and Leaf Development. PLANTS (BASEL, SWITZERLAND) 2019; 8:E531. [PMID: 31766484 PMCID: PMC6963412 DOI: 10.3390/plants8120531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/18/2022]
Abstract
Cichorium endivia is a leafy crop closely related to Lactuca sativa that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. latifolium with broad leaves (escarole) and var. crispum with narrow crisp curly leaves (endive). To investigate the relationship between leaf morphology and photosynthetic activity, escaroles and endives were used as a crop model due to the striking morphological diversity of their leaves. We constructed a leaf database for transcription factors (TFs) and photosynthesis-related genes from a refined C. endivia transcriptome and used RNA-seq transcriptomic data from leaves of four commercial endive and escarole cultivars to explore transcription factor regulatory networks. Cluster and gene co-expression network (GCN) analyses identified two main anticorrelated modules that control photosynthesis. Analysis of the GCN network topological properties identified known and novel hub genes controlling photosynthesis, and candidate developmental genes at the boundaries between shape and function. Differential expression analysis between broad and curly leaves suggested three novel TFs putatively involved in leaf shape diversity. Physiological analysis of the photosynthesis properties and gene expression studies on broad and curly leaves provided new insights into the relationship between leaf shape and function.
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Affiliation(s)
- Giulio Testone
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Elena Baldoni
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche (CNR), Via Bassini 15, 20133 Milano, Italy
| | - Maria Adelaide Iannelli
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Chiara Nicolodi
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Elisabetta Di Giacomo
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Fabrizio Pietrini
- Istituto di Ricerca sugli Ecosistemi Terrestri (IRET), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Giovanni Mele
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Donato Giannino
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy; (G.T.); (E.B.); (M.A.I.); (C.N.); (E.D.G.); (G.M.); (D.G.)
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