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Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024; 56:1225-1234. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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Sharma N, Raman H, Wheeler D, Kalenahalli Y, Sharma R. Data-driven approaches to improve water-use efficiency and drought resistance in crop plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111852. [PMID: 37659733 DOI: 10.1016/j.plantsci.2023.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.
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Affiliation(s)
- Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia.
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
| | - Yogendra Kalenahalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India
| | - Rita Sharma
- Department of Biological Sciences, BITS Pilani, Pilani Campus, Rajasthan 333031, India
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Zhang Q, Ye Z, Wang Y, Zhang X, Kong W. Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis. Genes (Basel) 2023; 14:1417. [PMID: 37510320 PMCID: PMC10379978 DOI: 10.3390/genes14071417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.
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Affiliation(s)
- Qing Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ziqi Ye
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yinghao Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Gao J, Zhang Y, Xu C, Wang X, Wang P, Huang S. Abscisic acid collaborates with lignin and flavonoid to improve pre-silking drought tolerance by tuning stem elongation and ear development in maize (Zea mays L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:437-454. [PMID: 36786687 DOI: 10.1111/tpj.16147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/08/2023] [Indexed: 05/10/2023]
Abstract
Drought is a major abiotic stress reducing maize (Zea mays) yield worldwide especially before and during silking. The mechanism underlying drought tolerance in maize and the roles of different organs have not been elucidated. Hence, we conducted field trials under pre-silking drought conditions using two maize genotypes: FM985 (drought-tolerant) and ZD958 (drought-sensitive). The two genotypes did not differ in plant height, grain number, and yield under control conditions. However, the grain number per ear and the yield of FM985 were 38.1 and 35.1% higher and plants were 17.6% shorter than ZD958 under drought conditions. More 13 C photosynthates were transported to the ear in FM985 than in ZD958, which increased floret fertility and grain number. The number of differentially expressed genes was much higher in stem than in other organs. Stem-ear interactions are key determinants of drought tolerance, in which expression of genes related to abscisic acid, lignin, and flavonoid biosynthesis and carbon metabolism in the stem was induced by drought, which inhibited stem elongation and promoted assimilate allocation to the ear in FM985. In comparison with ZD958, the activities of trehalose 6-phosphate phosphatase and sucrose non-fermentation-associated kinase 1 were higher in the stem and lower in the kernel of FM985, which facilitated kernel formation. These results reveal that, beyond the ear response, stem elongation is involved in the whole process of drought tolerance before silking. Abscisic acid together with trehalose 6-phosphate, lignin, and flavonoid suppresses stem elongation and allocates assimilates into the ear, providing a novel and systematic regulatory pathway for drought tolerance in maize.
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Affiliation(s)
- Jia Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Yingjun Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chenchen Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Pu Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shoubing Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Scientific Observation and Experimental Station of Crop High Efficient Use of Water in Wuqiao, Ministry of Agriculture and Rural Affairs, Wuqiao, 061802, China
- Innovation Center of Agricultural Technology for Lowland Plain of Hebei, Wuqiao, 061802, China
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Oltehua-López O, Arteaga-Vázquez MA, Sosa V. Stem transcriptome screen for selection in wild and cultivated pitahaya ( Selenicereus undatus): an epiphytic cactus with edible fruit. PeerJ 2023; 11:e14581. [PMID: 36632141 PMCID: PMC9828283 DOI: 10.7717/peerj.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
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Affiliation(s)
| | | | - Victoria Sosa
- Biologia Evolutiva, Instituto de Ecologia AC, Xalapa, Veracruz, Mexico
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Subramani M, Urrea CA, Habib R, Bhide K, Thimmapuram J, Kalavacharla V. Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean ( Phaseolus vulgaris L.) in Response to Terminal Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010210. [PMID: 36616341 PMCID: PMC9824821 DOI: 10.3390/plants12010210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 06/10/2023]
Abstract
We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Carlos A. Urrea
- Panhandle Research and Extension Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA
| | - Rasheed Habib
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Ketaki Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907, USA
| | | | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Cobo-Simón I, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Maloof JN, Méndez-Cea B, Seco JI, Linares JC, Gallego FJ. De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar ( Cedrus atlantica). FRONTIERS IN PLANT SCIENCE 2023; 14:1116863. [PMID: 37152146 PMCID: PMC10155838 DOI: 10.3389/fpls.2023.1116863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Introduction Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge about the molecular and eco-physiological mechanisms that control drought resilience is thus key, since water shortage appears as one of the main abiotic factors threatening forests ecosystems. However, our current background is scarce, especially in conifers, due to their huge and complex genomes. Methods Here we investigated the eco-physiological and transcriptomic basis of drought response of the climate change-threatened conifer Cedrus atlantica. We studied C. atlantica seedlings from two locations with contrasting drought conditions to investigate a local adaptation. Seedlings were subjected to experimental drought conditions, and were monitored at immediate (24 hours) and extended (20 days) times. In addition, post-drought recovery was investigated, depicting two contrasting responses in both locations (drought resilient and non-resilient). Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of drought resilience and investigate a rapid local adaptation of C. atlantica. Results De novo transcriptome assembly was performed for the first time in this species, providing differences in gene expression between the immediate and extended treatments, as well as among the post-drought recovery phenotypes. Weighted gene co-expression network analysis showed a regulation of stomatal closing and photosynthetic activity during the immediate drought, consistent with an isohydric dynamic. During the extended drought, growth and flavonoid biosynthesis inhibition mechanisms prevailed, probably to increase root-to-shoot ratio and to limit the energy-intensive biosynthesis of secondary metabolites. Drought sensitive individuals failed in metabolism and photosynthesis regulation under drought stress, and in limiting secondary metabolite production. Moreover, genomic differences (SNPs) were found between drought resilient and sensitive seedlings, and between the two studied locations, which were mostly related to transposable elements. Discussion This work provides novel insights into the transcriptomic basis of drought response of C. atlantica, a set of candidate genes mechanistically involved in its drought sensitivity and evidence of a rapid local adaptation. Our results may help guide conservation programs for this threatened conifer, contribute to advance drought-resilience research and shed light on trees' adaptive potential to current climate change.
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Affiliation(s)
- Irene Cobo-Simón
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Irene Cobo-Simón,
| | - Jèssica Gómez-Garrido
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Esteve-Codina
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Dabad
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tyler Alioto
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Julin N. Maloof
- Department of Plant Biology, University of California at Davis, Davis, CA, United States
| | - Belén Méndez-Cea
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - José Ignacio Seco
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
| | - Juan Carlos Linares
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
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9
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An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea. Commun Biol 2022; 5:1106. [PMID: 36261617 PMCID: PMC9581958 DOI: 10.1038/s42003-022-04083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Large-scale transcriptome analysis can provide a systems-level understanding of biological processes. To accelerate functional genomic studies in chickpea, we perform a comprehensive transcriptome analysis to generate full-length transcriptome and expression atlas of protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) from 32 different tissues/organs via deep sequencing. The high-depth RNA-seq dataset reveal expression dynamics and tissue-specificity along with associated biological functions of PCGs and lncRNAs during development. The coexpression network analysis reveal modules associated with a particular tissue or a set of related tissues. The components of transcriptional regulatory networks (TRNs), including transcription factors, their cognate cis-regulatory motifs, and target PCGs/lncRNAs that determine developmental programs of different tissues/organs, are identified. Several candidate tissue-specific and abiotic stress-responsive transcripts associated with quantitative trait loci that determine important agronomic traits are also identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions. A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.
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10
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Jiao P, Ma R, Wang C, Chen N, Liu S, Qu J, Guan S, Ma Y. Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:932667. [PMID: 36247625 PMCID: PMC9557922 DOI: 10.3389/fpls.2022.932667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/02/2022] [Indexed: 05/24/2023]
Abstract
Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA-mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety "M8186" at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA-mRNA analysis, 16 miRNA-target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, "plant hormone signal transduction", "phenylpropane biosynthesis", "glutathione metabolism", and "starch and sucrose metabolism", were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.
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Affiliation(s)
- Peng Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ruiqi Ma
- College of Plant Science, Jilin University, Changchun, China
| | - Chunlai Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nannan Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Siyan Liu
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jing Qu
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yiyong Ma
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China
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11
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de Camargo AC, Speisky H, Bridi R, Núñez Pizarro P, Larena A, Pinaffi-Langley ACDC, Shahidi F, Schwember AR. Chickpeas from a Chilean Region Affected by a Climate-Related Catastrophe: Effects of Water Stress on Grain Yield and Flavonoid Composition. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030691. [PMID: 35163956 PMCID: PMC8840598 DOI: 10.3390/molecules27030691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
The Valparaiso region in Chile was decreed a zone affected by catastrophe in 2019 as a consequence of one of the driest seasons of the last 50 years. In this study, three varieties (‘Alfa-INIA’, ‘California-INIA’, and one landrace, ‘Local Navidad’) of kabuli-type chickpea seeds produced in 2018 (control) and 2019 (climate-related catastrophe, hereafter named water stress) were evaluated for their grain yield. Furthermore, the flavonoid profile of both free and esterified phenolic extracts was determined using liquid chromatography-mass spectrometry, and the concentration of the main flavonoid, biochanin A, was determined using liquid chromatography with diode array detection. The grain yield was decreased by up to 25 times in 2019. The concentration of biochanin A was up to 3.2 times higher in samples from the second season (water stress). This study demonstrates that water stress induces biosynthesis of biochanin A. However, positive changes in the biochanin A concentration are overshadowed by negative changes in the grain yield. Therefore, water stress, which may be worsened by climate change in the upcoming years, may jeopardize both the production of chickpeas and the supply of biochanin A, a bioactive compound that can be used to produce dietary supplements and/or nutraceuticals.
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Affiliation(s)
- Adriano Costa de Camargo
- Laboratory of Antioxidants, Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile;
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
- Correspondence: (A.C.d.C.); (A.R.S.)
| | - Hernán Speisky
- Laboratory of Antioxidants, Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile;
| | - Raquel Bridi
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380000, Chile;
| | - Paula Núñez Pizarro
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Arturo Larena
- Departamento de Farmacia, Facultad de Química, Pontificia Universidad Católica de Chile, Avda Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Ana Clara da C. Pinaffi-Langley
- Department of Nutritional Sciences, College of Allied Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5ST, Canada;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
- Correspondence: (A.C.d.C.); (A.R.S.)
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Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress. Int J Mol Sci 2022; 23:ijms23010569. [PMID: 35008994 PMCID: PMC8745624 DOI: 10.3390/ijms23010569] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 02/01/2023] Open
Abstract
Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.
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Rajkumar MS, Garg R, Jain M. Genome-wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress. PHYSIOLOGIA PLANTARUM 2022; 174:e13611. [PMID: 34957568 DOI: 10.1111/ppl.13611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Drought stress limits plant growth, resulting in a significant yield loss in chickpea. The diversification in genome sequence and selective sweep of allele(s) in different genotypes of a crop plant may play an important role in the determination of agronomic traits, including drought stress response. We investigated, via whole genome resequencing, the DNA polymorphisms between two sets of chickpea genotypes with contrasting drought stress responses (3 drought-sensitive vs. 6 drought-tolerant). In total, 36,406 single nucleotide polymorphisms (SNPs) and 3407 insertions or deletions (InDels) differentiating drought-sensitive and drought-tolerant chickpea genotypes were identified. Interestingly, most (91%) of these DNA polymorphisms were located in chromosomes 1 and 4. The genes harboring DNA polymorphisms in their promoter and/or coding regions and exhibiting differential expression under control and/or drought stress conditions between/within the drought-sensitive and tolerant genotypes were found implicated in the stress response. Furthermore, we identified DNA polymorphisms within the cis-regulatory motifs in the promoter region of abiotic stress-related and QTL-associated genes, which might contribute to the differential expression of the candidate drought-responsive genes. In addition, we revealed the effect of nonsynonymous SNPs on mutational sensitivity and stability of the encoded proteins. Taken together, we identified DNA polymorphisms having relevance in drought stress response and revealed candidate genes to engineer drought tolerance in chickpea.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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14
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Shin MG, Nuzhdin SV. Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models. Front Genet 2021; 12:684882. [PMID: 34552613 PMCID: PMC8450460 DOI: 10.3389/fgene.2021.684882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Due to increasing demand for new advanced crops, considerable efforts have been made to explore the improvement of stress and disease resistance cultivar traits through the study of wild crops. When both wild and interspecific hybrid materials are available, a common approach has been to study two types of materials separately and simply compare the quantitative trait locus (QTL) regions. However, combining the two types of materials can potentially create a more efficient method of finding predictive QTLs. In this simulation study, we focused on scenarios involving causal marker expression suppressed by trans-regulatory mechanisms, where the otherwise easily lost associated signals benefit the most from combining the two types of data. A probabilistic sampling approach was used to prioritize consistent genotypic phenotypic patterns across both types of data sets. We chose random forest and gradient boosting to apply the prioritization scheme and found that both facilitated the investigation of predictive causal markers in most of the biological scenarios simulated.
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Affiliation(s)
- Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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15
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Li Q, Qiao X, Jia L, Zhang Y, Zhang S. Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties. Int J Mol Sci 2021; 22:ijms22179622. [PMID: 34502530 PMCID: PMC8456318 DOI: 10.3390/ijms22179622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.
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16
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Li P, Zheng T, Zhang Z, Liu W, Qiu L, Wang J, Cheng T, Zhang Q. Integrative Identification of Crucial Genes Associated With Plant Hormone-Mediated Bud Dormancy in Prunus mume. Front Genet 2021; 12:698598. [PMID: 34295354 PMCID: PMC8290171 DOI: 10.3389/fgene.2021.698598] [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: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Prunus mume is an important ornamental woody plant with winter-flowering property, which is closely related to bud dormancy. Despite recent scientific headway in deciphering the mechanism of bud dormancy in P. mume, the overall picture of gene co-expression regulating P. mume bud dormancy is still unclear. Here a total of 23 modules were screened by weighted gene co-expression network analysis (WGCNA), of which 12 modules were significantly associated with heteroauxin, abscisic acid (ABA), and gibberellin (GA), including GA1, GA3, and GA4. The yellow module, which was positively correlated with the content of ABA and negatively correlated with the content of GA, was composed of 1,426 genes, among which 156 transcription factors (TFs) were annotated with transcriptional regulation function. An enrichment analysis revealed that these genes are related to the dormancy process and plant hormone signal transduction. Interestingly, the expression trends of PmABF2 and PmABF4 genes, the core members of ABA signal transduction, were positively correlated with P. mume bud dormancy. Additionally, the PmSVP gene had attracted lots of attention because of its co-expression, function enrichment, and expression level. PmABF2, PmABF4, and PmSVP were the genes with a high degree of expression in the co-expression network, which was upregulated by ABA treatment. Our results provide insights into the underlying molecular mechanism of plant hormone-regulated dormancy and screen the hub genes involved in bud dormancy in P. mume.
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Affiliation(s)
- Ping Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Zhiyong Zhang
- Department of Hematology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Weichao Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Like Qiu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture; Beijing Laboratory of Urban and Rural Ecological Environment; Engineering Research Center of Landscape Environment of Ministry of Education; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,School of Landscape Architecture, Beijing Forestry University, Beijing, China
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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18
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Vargas-Ortiz E, Ramírez-Tobias HM, González-Escobar JL, Gutiérrez-García AK, Bojórquez-Velázquez E, Espitia-Rangel E, Barba de la Rosa AP. Biomass, chlorophyll fluorescence, and osmoregulation traits let differentiation of wild and cultivated Amaranthus under water stress. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 220:112210. [PMID: 34000487 DOI: 10.1016/j.jphotobiol.2021.112210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Amaranths are recognized by their high nutritive value and their natural tolerance to environmental stresses. In this study, physiological differences in response to water stress were compared between A. hybridus, a wild species considered as weed, and A. hypochondriacus, the most cultivated species for grain production, under the hypothesis that wild species have better adaptation to stress. In both species, photosynthetic parameters, pigments, and gene expression of selected genes were assessed. Biomass, effective quantum efficiency (ΦPSII), photochemical quenching (qP), and electron transport rate (ETR) values were reduced only in A. hybridus due to water deficit. Drought stress promoted proline accumulation by twice in A. hybridus but until three times in A. hypochondriacus. In both species, drought stress reduced net assimilation rate (A), transpiration rate (E), stomatal conductance (gs), and the expression of phosphoenol pyruvate carboxylase (PEPC). While, maximum quantum efficiency (Fv/Fm), chlorophyll, betacyanins, and the expression of ribulose1-5, bisphosphate carboxylase/oxygenase large subunit (LSU) did not change when plants were subjected to water stress. Likewise, both species accumulated total phenolic compounds and Oxalyl-CoA gene was up-regulated in response to drought. Our results have shown that A. hypochondriacus, the cultivated species, exhibited better tolerance to drought than A. hybridus, the wild species, probably due to an unconsciously selected trait during the domestication process.
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Affiliation(s)
- Erandi Vargas-Ortiz
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C Camino a La Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, SLP 78216, Mexico.
| | | | - Jorge Luis González-Escobar
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C Camino a La Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, SLP 78216, Mexico.
| | - Ana K Gutiérrez-García
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C Camino a La Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, SLP 78216, Mexico.
| | - Esaú Bojórquez-Velázquez
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C Camino a La Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, SLP 78216, Mexico.
| | - Eduardo Espitia-Rangel
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, 56250 Texcoco, Estado de México, Mexico.
| | - Ana Paulina Barba de la Rosa
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C Camino a La Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, SLP 78216, Mexico.
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Badhan S, Ball AS, Mantri N. First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts. Int J Mol Sci 2021; 22:E396. [PMID: 33401455 PMCID: PMC7795094 DOI: 10.3390/ijms22010396] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
The current genome editing system Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR/Cas9) has already confirmed its proficiency, adaptability, and simplicity in several plant-based applications. Together with the availability of a vast amount of genome data and transcriptome data, CRISPR/Cas9 presents a massive opportunity for plant breeders and researchers. The successful delivery of ribonucleoproteins (RNPs), which are composed of Cas9 enzyme and a synthetically designed single guide RNA (sgRNA) and are used in combination with various transformation methods or lately available novel nanoparticle-based delivery approaches, allows targeted mutagenesis in plants species. Even though this editing technique is limitless, it has still not been employed in many plant species to date. Chickpea is the second most crucial winter grain crop cultivated worldwide; there are currently no reports on CRISPR/Cas9 gene editing in chickpea. Here, we selected the 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes, both associated with drought tolerance for CRISPR/Cas9 editing in chickpea protoplast. The 4CL represents a key enzyme involved in phenylpropanoid metabolism in the lignin biosynthesis pathway. It regulates the accumulation of lignin under stress conditions in several plants. The RVE7 is a MYB transcription factor which is part of regulating circadian rhythm in plants. The knockout of these selected genes in the chickpea protoplast using DNA-free CRISPR/Cas9 editing represents a novel approach for achieving targeted mutagenesis in chickpea. Results showed high-efficiency editing was achieved for RVE7 gene in vivo compared to the 4CL gene. This study will help unravel the role of these genes under drought stress and understand the complex drought stress mechanism pathways. This is the first study in chickpea protoplast utilizing CRISPR/Cas9 DNA free gene editing of drought tolerance associated genes.
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Affiliation(s)
| | | | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne 3000, Australia; (S.B.); (A.S.B.)
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