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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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2
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Zhou Y, Liu J, Guo J, Wang Y, Ji H, Chu X, Xiao K, Qi X, Hu L, Li H, Hu M, Tang W, Yan J, Yan H, Bai X, Ge L, Lyu M, Chen J, Xu Z, Chen M, Ma Y. GmTDN1 improves wheat yields by inducing dual tolerance to both drought and low-N stress. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1606-1621. [PMID: 35514029 PMCID: PMC9342622 DOI: 10.1111/pbi.13836] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/12/2023]
Abstract
Genetically enhancing drought tolerance and nutrient use efficacy enables sustainable and stable wheat production in drought-prone areas exposed to water shortages and low soil fertility, due to global warming and declining natural resources. In this study, wheat plants, exhibiting improved drought tolerance and N-use efficacy, were developed by introducing GmTDN1, a gene encoding a DREB-like transcription factor, into two modern winter wheat varieties, cv Shi4185 and Jimai22. Overexpressing GmTDN1 in wheat resulted in significantly improved drought and low-N tolerance under drought and N-deficient conditions in the greenhouse. Field trials conducted at three different locations over a period of 2-3 consecutive years showed that both Shi4185 and Jimai22 GmTDN1 transgenic lines were agronomically superior to wild-type plants, and produced significantly higher yields under both drought and N-deficient conditions. No yield penalties were observed in these transgenic lines under normal well irrigation conditions. Overexpressing GmTDN1 enhanced photosynthetic and osmotic adjustment capacity, antioxidant metabolism, and root mass of wheat plants, compared to those of wild-type plants, by orchestrating the expression of a set of drought stress-related genes as well as the nitrate transporter, NRT2.5. Furthermore, transgenic wheat with overexpressed NRT2.5 can improve drought tolerance and nitrogen (N) absorption, suggesting that improving N absorption in GmTDN1 transgenic wheat may contribute to drought tolerance. These findings may lead to the development of new methodologies with the capacity to simultaneously improve drought tolerance and N-use efficacy in cereal crops to ensure sustainable agriculture and global food security.
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Affiliation(s)
- Yongbin Zhou
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Jun Liu
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Jinkao Guo
- Shijiazhuang Academy of Agricultural and Forestry SciencesResearch Center of Wheat Engineering Technology of HebeiShijiazhuangChina
| | - Yanxia Wang
- Shijiazhuang Academy of Agricultural and Forestry SciencesResearch Center of Wheat Engineering Technology of HebeiShijiazhuangChina
| | - Hutai Ji
- Institute of Wheat ResearchShanxi Academy of Agricultural SciencesLinfenChina
| | - Xiusheng Chu
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
| | - Kai Xiao
- College of AgronomyAgricultural University of Hebei ProvinceBaodingChina
| | - Xueli Qi
- Wheat Research InstituteHenan Academy of Agricultural SciencesZhengzhouChina
| | - Lin Hu
- Wheat Research InstituteHenan Academy of Agricultural SciencesZhengzhouChina
| | - Hui Li
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Mengyun Hu
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Wensi Tang
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Jiji Yan
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Huishu Yan
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Xinxuan Bai
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Linhao Ge
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Mingjie Lyu
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Jun Chen
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Zhaoshi Xu
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Ming Chen
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
| | - Youzhi Ma
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijingChina
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3
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Liang Y, Wei G, Ning K, Zhang G, Liu Y, Dong L, Chen S. Contents of lobetyolin, syringin, and atractylolide III in Codonopsis pilosula are related to dynamic changes of endophytes under drought stress. Chin Med 2021; 16:122. [PMID: 34809641 PMCID: PMC8607676 DOI: 10.1186/s13020-021-00533-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023] Open
Abstract
Background Codonopsis pilosula, an important medicinal plant, can accumulate certain metabolites under moderate drought stress. Endophytes are involved in the metabolite accumulations within medicinal plants. It is still unknown that the endophytes of C. pilosula are associated with the accumulations of metabolites. This study aims to investigate the promoting effect of endophytes on the accumulations of active substances in C. pilosula under drought stress. Methods High–performance liquid chromatography and high–throughput sequencing technology were performed to investigate changes in the contents of secondary metabolite and endophyte abundances of C. pilosula under drought stress, respectively. Spearman’s correlation analysis was further conducted to identify the endophytic biomarkers related to accumulations of pharmacodynamic compounds. Culture-dependent experiments were performed to confirm the functions of endophytes in metabolite accumulations. Results The distribution of pharmacological components and diversity and composition of endophytes showed tissue specificity within C. pilosula. The contents of lobetyolin, syringin, and atractylolide III in C. pilosula under drought stress were increased by 8.47%‒86.47%, 28.78%‒230.98%, and 32.17%‒177.86%, respectively, in comparison with those in untreated groups. The Chao 1 and Shannon indices in different parts of drought–stressed C. pilosula increased compared with those in untreated parts. The composition of endophytic communities in drought treatment parts of C. pilosula was different from that in control parts. A total of 226 microbial taxa were identified as potential biomarkers, of which the abundances of 42 taxa were significantly and positively correlated to the pharmacodynamic contents. Culture-dependent experiments confirmed that the contents of lobetyolin and atractylolide III were increased by the application of Epicoccum thailandicum, Filobasidium magnum, and Paraphoma rhaphiolepidis at the rates of 11.12%‒46.02%, and that the content of syringin was increased by Pseudomonas nitroreducens at the rates of 118.61%‒119.36%. Conclusions Certain endophytes participated in the accumulations of bioactive metabolites, which provided a scientific evidence for the development and application of microorganisms to improve the quality of traditional Chinese medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00533-z.
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Affiliation(s)
- Yichuan Liang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Youping Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China.
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4
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Liang Y, Wei G, Ning K, Li M, Zhang G, Luo L, Zhao G, Wei J, Liu Y, Dong L, Chen S. Increase in carbohydrate content and variation in microbiome are related to the drought tolerance of Codonopsis pilosula. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:19-35. [PMID: 34034158 DOI: 10.1016/j.plaphy.2021.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Drought stress is one of the main limiting factors in geographical distribution and production of Codonopsis pilosula. Understanding the biochemical and genetic information of the response of C. pilosula to drought stress is urgently needed for breeding tolerant varieties. Here, carbohydrates, namely trehalose, raffinose, maltotetraose, sucrose, and melezitose, significantly accumulated in C. pilosula roots under drought stress and thus served as biomarkers for drought stress response. Compared with those in the control group, the expression levels of key genes such as adenosine diphosphate glucose pyrophosphorylase, starch branching enzyme, granule-bound starch synthase, soluble starch synthase, galacturonate transferase, cellulose synthase A catalytic subunit, cellulase Korrigan in the carbohydrate biosynthesis pathway were markedly up-regulated in C. pilosula roots in the drought treatment group, some of them even exceeded 70%. Notably, and that of key genes including trehalose-6-phosphatase, trehalose-6-phosphate phosphatase, galactinol synthase, and raffinose synthase in the trehalose and raffinose biosynthesis pathways was improved by 12.6%-462.2% in C. pilosula roots treated by drought stress. The accumulation of carbohydrates in C. pilosula root or rhizosphere soil was correlated with microbiome variations. Analysis of exogenous trehalose and raffinose confirmed that increased carbohydrate content improved the drought tolerance of C. pilosula in a dose-dependent manner. This study provided solid foundation for breeding drought-tolerant C. pilosula varieties and developing drought-resistant microbial fertilizers.
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Affiliation(s)
- Yichuan Liang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Mengzhi Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lu Luo
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guanghui Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, 570311, China.
| | - Youping Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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5
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Leitão ST, Bicho MC, Pereira P, Paulo MJ, Malosetti M, Araújo SDS, van Eeuwijk F, Vaz Patto MC. Common bean SNP alleles and candidate genes affecting photosynthesis under contrasting water regimes. HORTICULTURE RESEARCH 2021; 8:4. [PMID: 33384448 PMCID: PMC7775448 DOI: 10.1038/s41438-020-00434-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 06/01/2023]
Abstract
Water deficit is a major worldwide constraint to common bean (Phaseolus vulgaris L.) production, being photosynthesis one of the most affected physiological processes. To gain insights into the genetic basis of the photosynthetic response of common bean under water-limited conditions, a collection of 158 Portuguese accessions was grown under both well-watered and water-deficit regimes. Leaf gas-exchange parameters were measured and photosynthetic pigments quantified. The same collection was genotyped using SNP arrays, and SNP-trait associations tested considering a linear mixed model accounting for the genetic relatedness among accessions. A total of 133 SNP-trait associations were identified for net CO2 assimilation rate, transpiration rate, stomatal conductance, and chlorophylls a and b, carotenes, and xanthophyll contents. Ninety of these associations were detected under water-deficit and 43 under well-watered conditions, with only two associations common to both treatments. Identified candidate genes revealed that stomatal regulation, protein translocation across membranes, redox mechanisms, hormone, and osmotic stress signaling were the most relevant processes involved in common bean response to water-limited conditions. These candidates are now preferential targets for common bean water-deficit-tolerance breeding. Additionally, new sources of water-deficit tolerance of Andean, Mesoamerican, and admixed origin were detected as accessions valuable for breeding, and not yet explored.
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Affiliation(s)
- Susana Trindade Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Maria Catarina Bicho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Priscila Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Marcos Malosetti
- Wageningen University & Research, Wageningen, The Netherlands
- Nunhems Vegetable Seeds, Nunhem, The Netherlands
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3-Technology and Innovation Campus, Centre Bio R&D Unit, Oliveira do Hospital, Lisboa, Portugal
| | | | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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6
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Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists. Curr Genet 2017; 64:365-387. [DOI: 10.1007/s00294-017-0761-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/22/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022]
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7
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Chiquito-Almanza E, Acosta-Gallegos JA, García-Álvarez NC, Garrido-Ramírez ER, Montero-Tavera V, Guevara-Olvera L, Anaya-López JL. Simultaneous Detection of Both RNA and DNA Viruses Infecting Dry Bean and Occurrence of Mixed Infections by BGYMV, BCMV and BCMNV in the Central-West Region of Mexico. Viruses 2017; 9:E63. [PMID: 28358318 PMCID: PMC5408669 DOI: 10.3390/v9040063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/17/2022] Open
Abstract
A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed to simultaneously detect bean common mosaic virus (BCMV), bean common mosaic necrotic virus (BCMNV), and bean golden yellow mosaic virus (BGYMV) from common bean leaves dried with silica gel using a single total nucleic acid extraction cetyl trimethyl ammonium bromide (CTAB) method. A mixture of five specific primers was used to amplify three distinct fragments corresponding to 272 bp from the AC1 gene of BGYMV as well as 469 bp and 746 bp from the CP gene of BCMV and BCMNV, respectively. The three viruses were detected in a single plant or in a bulk of five plants. The multiplex RT-PCR was successfully applied to detect these three viruses from 187 field samples collected from 23 municipalities from the states of Guanajuato, Nayarit and Jalisco, Mexico. Rates of single infections were 14/187 (7.5%), 41/187 (21.9%), and 35/187 (18.7%), for BGYMV, BCMV, and BCMNV, respectively; 29/187 (15.5%) samples were co-infected with two of these viruses and 10/187 (5.3%) with the three viruses. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting these viruses in the common bean and can be used for routine molecular diagnosis and epidemiological studies.
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Affiliation(s)
- Elizabeth Chiquito-Almanza
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
| | | | - Nadia C García-Álvarez
- INIFAP-Campo Experimental Santiago Ixcuintla, Santiago Ixcuintla, Nayarit, CP 63300, Mexico.
| | | | | | - Lorenzo Guevara-Olvera
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
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Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:581-601. [PMID: 26484978 DOI: 10.1089/omi.2015.0106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes.
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Affiliation(s)
| | - Rajesh Kumar Pathak
- 2 Department of Biotechnology, G. B. Pant Engineering College , Pauri Garhwal-246194, Uttarakhand, India
| | - Sanjay Mohan Gupta
- 3 Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research , DRDO, Haldwani, Uttarakhand, India
| | - Vikram Singh Gaur
- 4 College of Agriculture , Waraseoni, Balaghat, Madhya Pradesh, India
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9
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Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW. Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae). Genome Biol Evol 2016; 8:345-63. [PMID: 26739167 PMCID: PMC4779604 DOI: 10.1093/gbe/evv256] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 11/14/2022] Open
Abstract
Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.
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Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Joshua P Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Department of Biological Science, California State University Fullerton
| | - Eric K Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Samuel S Jones
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
| | - Sarah T Wagner
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Loren A Honaas
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Paula E Ralph
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | | | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Claude W dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
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Fan Y, Wang Q, Kang L, Liu W, Xu Q, Xing S, Tao C, Song Z, Zhu C, Lin C, Yan J, Li J, Sang T. Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6415-29. [PMID: 26175351 PMCID: PMC4588889 DOI: 10.1093/jxb/erv353] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the genetic basis of water use efficiency (WUE) and its roles in plant adaptation to a drought environment is essential for the production of second-generation energy crops in water-deficit marginal land. In this study, RNA-Seq and WUE measurements were performed for 78 individuals of Miscanthus lutarioriparius grown in two common gardens, one located in warm and wet Central China near the native habitats of the species and the other located in the semiarid Loess Plateau, the domestication site of the energy crop. The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location. A matrix correlation analysis was conducted between gene expression levels and WUE to identify candidate genes involved in the improvement of WUE from the native to the domestication site. A total of 48 candidate genes were identified and assigned to functional categories, including photosynthesis, stomatal regulation, protein metabolism, and abiotic stress responses. Of these genes, nearly 73% were up-regulated in the semiarid site. It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation. The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes.
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Affiliation(s)
- Yangyang Fan
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qin Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Tao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihong Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiyun Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Lin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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