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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024; 23:607-623. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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Cai K, Zhu S, Jiang Z, Xu K, Sun X, Li X. Biological macromolecules mediated by environmental signals affect flowering regulation in plants: A comprehensive review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108931. [PMID: 39003975 DOI: 10.1016/j.plaphy.2024.108931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
Flowering time is a crucial developmental stage in the life cycle of plants, as it determines the reproductive success and overall fitness of the organism. The precise regulation of flowering time is influenced by various internal and external factors, including genetic, environmental, and hormonal cues. This review provided a comprehensive overview of the molecular mechanisms and regulatory pathways of biological macromolecules (e.g. proteins and phytohormone) and environmental factors (e.g. light and temperature) involved in the control of flowering time in plants. We discussed the key proteins and signaling pathways that govern the transition from vegetative growth to reproductive development, highlighting the intricate interplay between genetic networks, environmental cues, and phytohormone signaling. Additionally, we explored the impact of flowering time regulation on plant adaptation, crop productivity, and agricultural practices. Moreover, we summarized the similarities and differences of flowering mechanisms between annual and perennial plants. Understanding the mechanisms underlying flowering time control is not only essential for fundamental plant biology research but also holds great potential for crop improvement and sustainable agriculture.
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Affiliation(s)
- Kefan Cai
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Siting Zhu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zeyu Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Singh D, Chaudhary P, Taunk J, Singh CK, Chinnusamy V, Sevanthi AM, Singh VJ, Pal M. Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding. Crit Rev Biotechnol 2024; 44:817-836. [PMID: 37455414 DOI: 10.1080/07388551.2023.2231630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Raabe K, Sun L, Schindfessel C, Honys D, Geelen D. A word of caution: T-DNA-associated mutagenesis in plant reproduction research. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3248-3258. [PMID: 38477707 DOI: 10.1093/jxb/erae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
T-DNA transformation is prevalent in Arabidopsis research and has expanded to a broad range of crops and model plants. While major progress has been made in optimizing the Agrobacterium-mediated transformation process for various species, a variety of pitfalls associated with the T-DNA insertion may lead to the misinterpretation of T-DNA mutant analysis. Indeed, secondary mutagenesis either on the integration site or elsewhere in the genome, together with epigenetic interactions between T-DNA inserts or frequent genomic rearrangements, can be tricky to differentiate from the effect of the knockout of the gene of interest. These are mainly the case for genomic rearrangements that become balanced in filial generations without consequential phenotypical defects, which may be confusing particularly for studies that aim to investigate fertility and gametogenesis. As a cautionary note to the plant research community studying gametogenesis, we here report an overview of the consequences of T-DNA-induced secondary mutagenesis with emphasis on the genomic imbalance on gametogenesis. Additionally, we present a simple guideline to evaluate the T-DNA-mutagenized transgenic lines to decrease the risk of faulty analysis with minimal experimental effort.
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Affiliation(s)
- Karel Raabe
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Limin Sun
- Horticell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Cédric Schindfessel
- Horticell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Danny Geelen
- Horticell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Khassanova G, Oshergina I, Ten E, Jatayev S, Zhanbyrshina N, Gabdola A, Gupta NK, Schramm C, Pupulin A, Philp-Dutton L, Anderson P, Sweetman C, Jenkins CL, Soole KL, Shavrukov Y. Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1354413. [PMID: 38766473 PMCID: PMC11099236 DOI: 10.3389/fpls.2024.1354413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.
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Affiliation(s)
- Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Irina Oshergina
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Nursaule Zhanbyrshina
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Ademi Gabdola
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Narendra K. Gupta
- Department of Plant Physiology, Sri Karan Narendra (SNK) Agricultural University, Jobster, Rajastan, India
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Antonio Pupulin
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Lauren Philp-Dutton
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Colin L.D. Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Kajla A, Schoen A, Paulson C, Yadav IS, Neelam K, Riera-Lizarazu O, Leonard J, Gill BS, Venglat P, Datla R, Poland J, Coleman G, Rawat N, Tiwari V. Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:159. [PMID: 37344686 DOI: 10.1007/s00122-023-04403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Abstract
KEY MESSAGE This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0 Mb (231.0-242 Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.
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Affiliation(s)
- Anmol Kajla
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Adam Schoen
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Carl Paulson
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Inderjit Singh Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | | | | | - Jeff Leonard
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Raju Datla
- Global Institute of Food Security, Saskatoon, SK, Canada
| | - Jesse Poland
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Gary Coleman
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Vijay Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA.
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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John M, Grimm D, Korte A. Predicting Gene Regulatory Interactions Using Natural Genetic Variation. Methods Mol Biol 2023; 2698:301-322. [PMID: 37682482 DOI: 10.1007/978-1-0716-3354-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.
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Affiliation(s)
- Maura John
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Dominik Grimm
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany.
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Tao CN, Buswell W, Zhang P, Walker H, Johnson I, Field K, Schwarzenbacher R, Ton J. A single amino acid transporter controls the uptake of priming-inducing beta-amino acids and the associated tradeoff between induced resistance and plant growth. THE PLANT CELL 2022; 34:4840-4856. [PMID: 36040205 PMCID: PMC9709968 DOI: 10.1093/plcell/koac271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Selected β-amino acids, such as β-aminobutyric acid (BABA) and R-β-homoserine (RBH), can prime plants for resistance against a broad spectrum of diseases. Here, we describe a genome-wide screen of fully annotated Arabidopsis thaliana T-DNA insertion lines for impaired in RBH-induced immunity (iri) mutants against the downy mildew pathogen Hyaloperonospora arabidopsidis, yielding 104 lines that were partially affected and four lines that were completely impaired in RBH-induced resistance (IR). We confirmed the iri1-1 mutant phenotype with an independent T-DNA insertion line in the same gene, encoding the high-affinity amino acid transporter LYSINE HISTIDINE TRANSPORTER 1 (LHT1). Uptake experiments with yeast cells expressing LHT1 and mass spectrometry-based quantification of RBH and BABA in leaves of lht1 mutant and LHT1 overexpression lines revealed that LHT1 acts as the main transporter for cellular uptake and systemic distribution of RBH and BABA. Subsequent characterization of lht1 mutant and LHT1 overexpression lines for IR and growth responses revealed that the levels of LHT1-mediated uptake determine the tradeoff between IR and plant growth by RBH and BABA.
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Affiliation(s)
- Chia-Nan Tao
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Will Buswell
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Peijun Zhang
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Heather Walker
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
- Department of Animal and Plant Sciences, biOMICS Facility, University of Sheffield, Sheffield, S10 2TN, UK
| | - Irene Johnson
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Katie Field
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Roland Schwarzenbacher
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, S10 2TN, UK
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Niazian M, Belzile F, Torkamaneh D. CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1044. [PMID: 35448772 PMCID: PMC9027312 DOI: 10.3390/plants11081044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022]
Abstract
Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective "in root" functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.
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Affiliation(s)
- Mohsen Niazian
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
- Field and Horticultural Crops Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj 6616936311, Iran
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
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13
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Oh Y, Kim SG. RPS5A Promoter-Driven Cas9 Produces Heritable Virus-Induced Genome Editing in Nicotiana attenuata. Mol Cells 2021; 44:911-919. [PMID: 34963106 PMCID: PMC8718363 DOI: 10.14348/molcells.2021.0237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/27/2022] Open
Abstract
The virus-induced genome editing (VIGE) system aims to induce targeted mutations in seeds without requiring any tissue culture. Here, we show that tobacco rattle virus (TRV) harboring guide RNA (gRNA) edits germ cells in a wild tobacco, Nicotiana attenuata, that expresses Streptococcus pyogenes Cas9 (SpCas9). We first generated N. attenuata transgenic plants expressing SpCas9 under the control of 35S promoter and infected rosette leaves with TRV carrying gRNA. Gene-edited seeds were not found in the progeny of the infected N. attenuata. Next, the N. attenuata ribosomal protein S5 A (RPS5A) promoter fused to SpCas9 was employed to induce the heritable gene editing with TRV. The RPS5A promoter-driven SpCas9 successfully produced monoallelic mutations at three target genes in N. attenuata seeds with TRV-delivered guide RNA. These monoallelic mutations were found in 2%-6% seeds among M1 progenies. This editing method provides an alternative way to increase the heritable editing efficacy of VIGE.
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Affiliation(s)
- Youngbin Oh
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon 34141, Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon 34141, Korea
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14
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Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A. A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nat Genet 2021; 53:638-649. [PMID: 33859415 PMCID: PMC8763319 DOI: 10.1038/s41588-021-00840-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023]
Abstract
A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This atlas recapitulates diverse pathways and protein complexes, and predicts the functions of 108 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, a key enzyme for plasmalogen synthesis. We also show that C15orf57 encodes a protein that binds the AP2 complex, localizes to clathrin-coated pits and enables efficient transferrin uptake. Finally, we provide an interactive webtool for the community to explore our results, which establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of new gene functions.
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Affiliation(s)
- Michael Wainberg
- Department of Genetics, Stanford University, Stanford, CA, USA,Department of Computer Science, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Roarke A. Kamber
- Department of Genetics, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Akshay Balsubramani
- Department of Genetics, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Robin M. Meyers
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Daniel Hornburg
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joanne Chan
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mingxin Gu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA, USA,Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA,Correspondence and requests for materials should be addressed to M.C.B. or A.K. ;
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA,Department of Computer Science, Stanford University, Stanford, CA, USA,Correspondence and requests for materials should be addressed to M.C.B. or A.K. ;
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15
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Cui Y, Zeng X, Xiong Q, Wei D, Liao J, Xu Y, Chen G, Zhou Y, Dong H, Wan H, Liu Z, Li J, Guo L, Jung C, He Y, Qian W. Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1649-1660. [PMID: 33249500 DOI: 10.1093/jxb/eraa563] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
In crops there are quantitative trait loci (QTLs) in which some of the causal quantitative trait genes (QTGs) have not been functionally characterized even in the model plant Arabidopsis. We propose an approach to delineate QTGs in rapeseed by coordinating expression of genes located within QTLs and known orthologs related to traits from Arabidopsis. Using this method in developing siliques 15 d after pollination in 71 lines of rapeseed, we established an acyl-lipid metabolism co-expression network with 21 modules composed of 270 known acyl-lipid genes and 3503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein processes, seed maturation, and phytohormone metabolism. Moreover, the core module closely associated with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analysed using Arabidopsis knockout and overexpression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 overexpression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping, this study provides new insights into the detection of QTGs and into acyl-lipid metabolism in rapeseed.
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Affiliation(s)
- Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiao Zeng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jinghang Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Yonghong Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr., Kiel, Germany
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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16
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Miki D, Zinta G, Zhang W, Peng F, Feng Z, Zhu JK. CRISPR/Cas9-Based Genome Editing Toolbox for Arabidopsis thaliana. Methods Mol Biol 2021; 2200:121-146. [PMID: 33175375 DOI: 10.1007/978-1-0716-0880-7_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CRISPR/Cas9 system has emerged as a powerful genome engineering tool to study gene function and improve plant traits. Genome editing is achieved at a specific genome sequence by Cas9 endonuclease to generate double standard breaks (DSBs) directed by short guide RNAs (sgRNAs). The DSB is repaired by error-prone nonhomologous end joining (NHEJ) or error-free homology-directed repair (HDR) pathways, resulting in gene mutation or sequence replacement, respectively. These cellular DSB repair pathways can be exploited to knock out or replace genes. Also, cytidine or adenine base editors (CBEs or ABEs) fused to catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) are used to perform precise base editing without generating DSBs. In this chapter, we describe a detailed procedure to carry out single/multiple gene mutations and precise base editing in the Arabidopsis genome by using CRISPR/Cas9-based system. Specifically, the steps of target gene selection, sgRNA design, vector construction, transformation, and analysis of transgenic lines are described. The protocol is potentially adaptable to perform genome editing in other plant species such as rice.
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Affiliation(s)
- Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fangnan Peng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
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17
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Zhu Y, Ji C, Cao W, Shen J, Zhao Q, Jiang L. Identification and characterization of unconventional membrane protein trafficking regulators in Arabidopsis: A genetic approach. JOURNAL OF PLANT PHYSIOLOGY 2020; 252:153229. [PMID: 32750645 DOI: 10.1016/j.jplph.2020.153229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Proper trafficking and subcellular localization of membrane proteins are essential for plant growth and development. The plant endomembrane system contains several membrane-bound organelles with distinct functions including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosome, prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. Multiple approaches have been successfully used to identify and study the regulators and components important for signal transduction, growth and development, as well as membrane trafficking in the endomembrane system in plants. These include the homologous characterization of the counterparts in mammals or yeast employing both reverse genetic as well as the forward genetic screen approaches. However, the deletion or mutation of membrane trafficking related proteins usually leads to seedling lethality due to their essential roles in plant development and organelle biogenesis. To overcome the limitation of lethal phenotype of the target proteins, we used DEX-inducible RNAi knock-down lines to study their function in plants. More recently, we developed and used both RNAi knock-down and T-DNA insertional lines as starting materials to screen for mutations that could suppress and rescue the lethal phenotype, or a suppressor screening. Further characterization of the newly identified suppressor mutants has resulted in the identification of novel negative regulators in mediating membrane trafficking and organelle biogenesis in plants. In this review, we summarize the current approaches in studying protein trafficking in the endomembrane system. We then describe three examples of suppressor screening with distinct starting materials (i.e. FREE1, MON1, and SH3P2 that are regulators of MVB, vacuole, and autophagosomes, respectively) to discuss the rationale, procedures, advantages and disadvantages, and possible outcomes of such a suppressor screening. We finally propose that these novel screening approaches will lead to the identification of new unconventional players in regulating protein trafficking and organelle biogenesis in plants and discuss their impact on plant cell biology research.
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Affiliation(s)
- Ying Zhu
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Changyang Ji
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenhan Cao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Qiong Zhao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, Shenzhen, China.
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18
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Jiang N, Lee YS, Mukundi E, Gomez-Cano F, Rivero L, Grotewold E. Diversity of genetic lesions characterizes new Arabidopsis flavonoid pigment mutant alleles from T-DNA collections. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110335. [PMID: 31928687 DOI: 10.1016/j.plantsci.2019.110335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 05/22/2023]
Abstract
The visual phenotypes afforded by flavonoid pigments have provided invaluable tools for modern genetics. Many Arabidopsis transparent testa (tt) mutants lacking the characteristic proanthocyanidin (PA) seed coat pigmentation and often failing to accumulate anthocyanins in vegetative tissues have been characterized. These mutants have significantly contributed to our understanding of flavonoid biosynthesis, regulation, and transport. A comprehensive screening for tt mutants in available large T-DNA collection lines resulted in the identification of 16 independent lines lacking PAs and anthocyanins, or with seed coat pigmentation clearly distinct from wild type. Segregation analyses and the characterization of second alleles in the genes disrupted by the indexed T-DNA insertions demonstrated that all the lines contained at least one additional mutation responsible for the tt phenotypes. Using a combination of RNA-Seq and whole genome re-sequencing and confirmed through complementation, we show here that these mutations correspond to novel alleles of ttg1 (two alleles), tt3 (two alleles), tt5 (two alleles), ban (two alleles), tt1 (two alleles), and tt8 (six alleles), which harbored additional T-DNA insertions, indels, missense mutations, and large genomic deletion. Several of the identified alleles offer interesting perspectives on flavonoid biosynthesis and regulation.
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Affiliation(s)
- Nan Jiang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Luz Rivero
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA.
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19
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Tang RJ, Luan M, Wang C, Lhamo D, Yang Y, Zhao FG, Lan WZ, Fu AG, Luan S. Plant Membrane Transport Research in the Post-genomic Era. PLANT COMMUNICATIONS 2020; 1:100013. [PMID: 33404541 PMCID: PMC7747983 DOI: 10.1016/j.xplc.2019.100013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 05/17/2023]
Abstract
Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.
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Affiliation(s)
- Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Mingda Luan
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dhondup Lhamo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yang Yang
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Fu-Geng Zhao
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Wen-Zhi Lan
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ai-Gen Fu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Corresponding author
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20
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Schroeder MM, Lai Y, Shirai M, Alsalek N, Tsuchiya T, Roberts P, Eulgem T. A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina. Sci Rep 2019; 9:20083. [PMID: 31882671 PMCID: PMC6934584 DOI: 10.1038/s41598-019-56401-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022] Open
Abstract
Dubbed as a "global destroyer of crops", the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.
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Affiliation(s)
- Mercedes M Schroeder
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, United States of America
| | - Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Miwa Shirai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, United States of America
| | - Natalie Alsalek
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, United States of America
- School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Philip Roberts
- Institute of Integrative Genome Biology, Department of Nematology, University of California, Riverside, Riverside, California, United States of America
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, United States of America.
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21
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Frank U, Kublik S, Mayer D, Engel M, Schloter M, Durner J, Gaupels F. A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing. BMC PLANT BIOLOGY 2019; 19:539. [PMID: 31801481 PMCID: PMC6894221 DOI: 10.1186/s12870-019-2162-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. RESULTS Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation. CONCLUSIONS The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
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Affiliation(s)
- Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dörte Mayer
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
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22
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Improvement of multiplex semi-nested PCR system for screening of rare mutations by high-throughput sequencing. Biotechniques 2019; 67:294-298. [PMID: 31621390 DOI: 10.2144/btn-2019-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The CRISPR/Cas9 system is an efficient gene-editing method, but it is difficult to obtain mutants for some specific species and special genome structures. A previously reported multiplexed, semi-nested PCR target-enrichment approach, which does not rely on transgenic technology, has been shown to be an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced rice population. However, this strategy has the potential for further optimization. Here, we describe an improved multiplex semi-nested PCR target-enrichment strategy with simplified processing procedures, reduced false-positive rates and increased mutation detection frequency (1 mutation/73 Kb).
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23
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Rutter MT, Murren CJ, Callahan HS, Bisner AM, Leebens-Mack J, Wolyniak MJ, Strand AE. Distributed phenomics with the unPAK project reveals the effects of mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:199-211. [PMID: 31155775 DOI: 10.1111/tpj.14427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.
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Affiliation(s)
- Matthew T Rutter
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Hilary S Callahan
- Department of Biology, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - April M Bisner
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, 120 Carlton St, Athens, GA, 30602, USA
| | | | - Allan E Strand
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
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24
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Analysis of Drought Tolerance and Associated Traits in Upland Cotton at the Seedling Stage. Int J Mol Sci 2019; 20:ijms20163888. [PMID: 31404956 PMCID: PMC6720584 DOI: 10.3390/ijms20163888] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton.
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25
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Hussain B, Lucas SJ, Budak H. CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement. Brief Funct Genomics 2019; 17:319-328. [PMID: 29912293 DOI: 10.1093/bfgp/ely016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system uses single-guide RNAs for genome editing, making it a simple, robust, powerful tool for targeted gene mutagenesis, knockout and knock-in/replacement, as well as transcriptional regulation. Here, we review the working principles, components and potential modifications of CRISPR/Cas9 for efficient single and multiplex gene editing in plants. We also describe recent work that has used CRISPR/Cas9 to improve economically important traits in crop plants. Although the apparent ease of CRISPR/Cas9-mediated editing may make it appear as though scientists are merely playing with plant genomes, the combined power of CRISPR/Cas9 has enabled vital research to be completed in the battle toward optimization and adaptation of crop species, permitting crucial advances to be achieved in crop improvement.
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Affiliation(s)
- Babar Hussain
- Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Stuart James Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Turkey
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, MT, USA
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26
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Jyoti A, Kaushik S, Srivastava VK, Datta M, Kumar S, Yugandhar P, Kothari SL, Rai V, Jain A. The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants. Semin Cell Dev Biol 2019; 96:77-90. [PMID: 30951893 DOI: 10.1016/j.semcdb.2019.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/26/2022]
Abstract
Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.
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Affiliation(s)
- Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Shailesh Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Shanker L Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
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27
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Hu N, Xian Z, Li N, Liu Y, Huang W, Yan F, Su D, Chen J, Li Z. Rapid and user-friendly open-source CRISPR/Cas9 system for single- or multi-site editing of tomato genome. HORTICULTURE RESEARCH 2019; 6:7. [PMID: 30603093 PMCID: PMC6312546 DOI: 10.1038/s41438-018-0082-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 05/19/2023]
Abstract
CRISPR/Cas9-induced genome editing is a powerful tool for studying gene function in a variety of organisms, including plants. Using multi-sgRNAs to target one or more genes is helpful to improve the efficacy of gene editing and facilitate multi-gene editing. Here, we describe a CRISPR/Cas9 system which can be conveniently developed as a CRISPR kit. SgRNA expression cassettes can be rapidly generated by one-step PCR using our CRISPR kit. In our kit, there are two binary vectors pHNCas9 and pHNCas9HT. The binary vector pHNCas9 was constructed to allow to assemble up to eight sgRNA expression cassettes by one-step Golden Gate cloning. Another binary vector pHNCas9HT can be used to generate a large number of single target constructs by directly transforming ligation reactions products into A. tumefaciens without several procedures, such as PCR and plasmid extraction. The two binary vectors are designed according to the principles of standard BioBrick assembly to be used as an open-source tool. For example, we used BioBrick as a visual T-DNA tag. We also developed a primer design aid to complement the system. With this primer design aid, researchers can rapidly obtain primers and GC content, and sgRNA sequence of target site. Our CRISPR/Cas9 system can perform single- and multi-site editing and multiple gene editing to produce various types of mutations in tomato. This rapid and user-friendly CRISPR/Cas9 system for tomato can be potentially used for mutagenesis of important crop species for genetic improvement and is suitable for research into the function of genes.
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Affiliation(s)
- Nan Hu
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Zhiqiang Xian
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Ning Li
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Yudong Liu
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Wei Huang
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Fang Yan
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Deding Su
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Jingxuan Chen
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 405200 People’s Republic of China
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28
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A Highly Efficient Cell Division-Specific CRISPR/Cas9 System Generates Homozygous Mutants for Multiple Genes in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123925. [PMID: 30544514 PMCID: PMC6321140 DOI: 10.3390/ijms19123925] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
The CRISPR/Cas9 system has been widely used for targeted genome editing in numerous plant species. In Arabidopsis, constitutive promoters usually result in a low efficiency of heritable mutation in the T1 generation. In this work, CRISPR/Cas9 gene editing efficiencies using different promoters to drive Cas9 expression were evaluated. Expression of Cas9 under the constitutive CaMV 35S promoter resulted in a 2.3% mutation rate in T1 plants and failed to produce homozygous mutations in the T1 and T2 generations. In contrast, expression of Cas9 under two cell division-specific promoters, YAO and CDC45, produced mutation rates of 80.9% to 100% in the T1 generation with nonchimeric mutations in the T1 (4.4–10%) and T2 (32.5–46.1%) generations. The pCDC45 promoter was used to modify a previously reported multiplex CRISPR/Cas9 system, replacing the original constitutive ubiquitin promoter. The multi-pCDC45-Cas9 system produced higher mutation efficiencies than the multi-pUBQ-Cas9 system in the T1 generation (60.17% vs. 43.71%) as well as higher efficiency of heritable mutations (11.30% vs. 4.31%). Sextuple T2 homozygous mutants were identified from a construct targeting seven individual loci. Our results demonstrate the advantage of using cell division promoters for CRISPR/Cas9 gene editing applications in Arabidopsis, especially in multiplex applications.
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29
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Tyagi S, Mazumdar PA, Mayee P, Shivaraj SM, Anand S, Singh A, Madhurantakam C, Sharma P, Das S, Kumar A, Singh A. Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:251-266. [PMID: 30466591 DOI: 10.1016/j.plantsci.2018.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.
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Affiliation(s)
- Shikha Tyagi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | | | - Pratiksha Mayee
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Department of Research, Ankur Seeds Pvt. Ltd., 27, Nagpur, Maharashtra, 440018, India
| | - S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Departement de Phytologie, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Saurabh Anand
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Anupama Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Chaithanya Madhurantakam
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Prateek Sharma
- Department of Energy and Environment, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Sandip Das
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Arun Kumar
- National Phytotron Facility, IARI, New Delhi, 110012, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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30
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Genetic Analysis of Chloroplast Biogenesis, and Function and Mutant Collections. Methods Mol Biol 2018. [PMID: 29987733 DOI: 10.1007/978-1-4939-8654-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Since the time DNA was discovered as the code of life, genetic analysis has greatly advanced our understanding of the relation between genotype and phenotype and associated molecular mechanisms in various organisms including plants and algae. Forward genetics from phenotype to genotype has identified causal genes of interesting phenotypes induced by chemical, ionizing-radiation, or DNA insertional mutagenesis. Meanwhile, reverse genetics from genotype to phenotype has revealed physiological and molecular roles of known gene sequences. During the past dozen years, many molecular genetic tools have been developed to investigate gene functions quickly and efficiently. In this chapter, we introduce several approaches of forward and reverse genetics, including random chemical and DNA insertional mutagenesis, activation tagging, RNA interference, and gene overexpression and induction systems, with some examples of genetic studies of chloroplast biology mainly in Arabidopsis thaliana. We also briefly describe methods for chemical and DNA insertion mutagenesis and how to obtain sequence-tagged mutants from public collections. With greatly improved DNA sequencing and genome-editing technologies, model organisms as well as diverse species can be used for molecular biology. Genetic analysis can play an increasingly important role in elucidating chloroplast biogenesis and functions.
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31
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Singh PK, Nag A, Arya P, Kapoor R, Singh A, Jaswal R, Sharma TR. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice. Int J Mol Sci 2018; 19:E1141. [PMID: 29642631 PMCID: PMC5979409 DOI: 10.3390/ijms19041141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.
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Affiliation(s)
- Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Nag
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
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32
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Nuccio ML, Potter L, Stiegelmeyer SM, Curley J, Cohn J, Wittich PE, Tan X, Davis J, Ni J, Trullinger J, Hall R, Bate NJ. Strategies and tools to improve crop productivity by targeting photosynthesis. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0377. [PMID: 28808096 DOI: 10.1098/rstb.2016.0377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/15/2022] Open
Abstract
Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Michael L Nuccio
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Laura Potter
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Suzy M Stiegelmeyer
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Joseph Curley
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jonathan Cohn
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Peter E Wittich
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Xiaoping Tan
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jimena Davis
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Junjian Ni
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jon Trullinger
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Rick Hall
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Nicholas J Bate
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
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33
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Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum. G3-GENES GENOMES GENETICS 2018; 8:1079-1094. [PMID: 29378822 PMCID: PMC5844295 DOI: 10.1534/g3.117.300301] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS)-treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive-induced variants in next-generation sequencing (NGS) data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7×) from 586 independently mutagenized individuals and detected 5,399,493 homozygous single nucleotide polymorphisms (SNPs). Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ability of short stretches of homology to generate these error-prone positions suggests that incompletely assembled or poorly mapped repeated sequences are one driver of these error-prone positions. Removal of these false positives left 1,275,872 homozygous and 477,531 heterozygous EMS-induced SNPs, which, congruent with the mutagenic mechanism of EMS, were >98% G:C to A:T transitions. Through this analysis, we generated a collection of sequence indexed mutants of sorghum. This collection contains 4035 high-impact homozygous mutations in 3637 genes and 56,514 homozygous missense mutations in 23,227 genes. Each line contains, on average, 2177 annotated homozygous SNPs per genome, including seven likely gene knockouts and 96 missense mutations. The number of mutations in a transcript was linearly correlated with the transcript length and also the G+C count, but not with the GC/AT ratio. Analysis of the detected mutagenized positions identified CG-rich patches, and flanking sequences strongly influenced EMS-induced mutation rates. This method for detecting false positive-induced mutations is generally applicable to any organism, is independent of the choice of in silico variant-calling algorithm, and is most valuable when the true mutation rate is likely to be low, such as in laboratory-induced mutations or somatic mutation detection in medicine.
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34
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Atanasov KE, Liu C, Tiburcio AF, Alcázar R. Generation of EMS-Mutagenized Populations of Arabidopsis thaliana for Polyamine Genetics. Methods Mol Biol 2018; 1694:343-346. [PMID: 29080179 DOI: 10.1007/978-1-4939-7398-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the recent years, genetic engineering of polyamine biosynthetic genes has provided evidence for their involvement in plant stress responses and different aspects of plant development. Such approaches are being complemented with the use of reverse genetics, in which mutants affected on a particular trait, tightly associated with polyamines, are isolated and the causal genes mapped. Reverse genetics enables the identification of novel genes in the polyamine pathway, which may be involved in downstream signaling, transport, homeostasis, or perception. Here, we describe a basic protocol for the generation of ethyl methanesulfonate (EMS) mutagenized populations of Arabidopsis thaliana for its use in reverse genetics applied to polyamines.
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Affiliation(s)
- Kostadin E Atanasov
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Barcelona, Spain
| | - Changxin Liu
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Barcelona, Spain
| | - Antonio F Tiburcio
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Barcelona, Spain
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Barcelona, Spain.
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Xu P, Su H, Chen W, Lu P. The Application of a Meiocyte-Specific CRISPR/Cas9 (MSC) System and a Suicide-MSC System in Generating Inheritable and Stable Mutations in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1007. [PMID: 30061908 PMCID: PMC6055057 DOI: 10.3389/fpls.2018.01007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/20/2018] [Indexed: 05/02/2023]
Abstract
The CRISPR/Cas9 system has been widely used for generating targeted mutations in various species. In Arabidopsis, it largely relies on the edited cells where the Cas9 protein performs its activity to obtain heritable and stable mutated lines. Here, we designed an improved CRISPR/Cas9 system, named as the MSC (meiocyte-specific CRISPR/Cas9) system, in which the Cas9 expression is driven by an experimentally approved meiocyte-specific promoter (AtDMC1 promoter). Two endogenous genes, including vegetative gene AtDET2 and reproductive gene AtDMC1, were targeted. We obtained heterozygous T1 plants for targeted genes with high efficiency (64%). In the T2 generation, the homozygous plants were abundant with high efficiency (37%). Analysis of Sanger sequencing results of T2 generation revealed that heritable gene mutations were high (52%). Moreover, we showed that the MSC system could sufficiently delete a middle size DNA fragment (∼500 bp) between two cleavage sites with a high rate (64.15%) in the T1 plants, providing direct evidence for making complete knock-out or certain domain-depletion mutations. In addition, we further made a suicide-MSC system, which can edit the targeted endogenous gene and the exogenous Cas9 gene simultaneously, not only successfully avoiding the further destroy of alleles brought in by molecular complementary or genic allelic test, but also maintaining the stable mutated alleles for functional studies. In short, the two systems provide new approaches to generate mutations for gene functional studies.
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Wang D, Wang S, Chao J, Wu X, Sun Y, Li F, Lv J, Gao X, Liu G, Wang Y. Morphological phenotyping and genetic analyses of a new chemical-mutagenized population of tobacco (Nicotiana tabacum L.). PLANTA 2017; 246:149-163. [PMID: 28401357 DOI: 10.1007/s00425-017-2690-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
MAIN CONCLUSION A novel tobacco mutant library was constructed, screened, and characterized as a crucial genetic resource for functional genomics and applied research. A comprehensive mutant library is a fundamental resource for investigating gene functions, especially after the completion of genome sequencing. A new tobacco mutant population induced by ethyl methane sulfonate mutagenesis was developed for functional genomics applications. We isolated 1607 mutant lines and 8610 mutant plants with altered morphological phenotypes from 5513 independent M2 families that consisted of 69,531 M2 plants. The 2196 mutations of abnormal phenotypes in the M2 putative mutants were classified into four groups with 17 major categories and 51 subcategories. More than 60% of the abnormal phenotypes observed fell within the five major categories including plant height, leaf shape, leaf surface, leaf color, and flowering time. The 465 M2 mutants exhibited multiple phenotypes, and 1054 of the 2196 mutations were pleiotropic. Verification of the phenotypes in advanced generations indicated that 70.63% of the M3 lines, 84.87% of the M4 lines, and 95.75% of the M5 lines could transmit original mutant phenotypes of the corresponding M2, M3, and M4 mutant plants. Along with the increased generation of mutants, the ratios of lines inheriting OMPs increased and lines with emerging novel mutant phenotypes decreased. Genetic analyses of 18 stably heritable mutants showed that two mutants were double recessive, five were monogenic recessive, eight presented monogenic dominant inheritance, and three presented semi-dominant inheritance. The pleiotropy pattern, saturability evaluation, research prospects of genome, and phenome of the mutant populations were also discussed. Simultaneously, this novel mutant library provided a fundamental resource for investigating gene functions in tobacco.
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Affiliation(s)
- Dawei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Shaomei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xinru Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Yuhe Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Fengxia Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Jing Lv
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xiaoming Gao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
| | - Yuanying Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
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Abstract
Strigolactones (SLs) are a collection of related small molecules that act as hormones in plant growth and development. Intriguingly, SLs also act as ecological communicators between plants and mycorrhizal fungi and between host plants and a collection of parasitic plant species. In the case of mycorrhizal fungi, SLs exude into the soil from host roots to attract fungal hyphae for a beneficial interaction. In the case of parasitic plants, however, root-exuded SLs cause dormant parasitic plant seeds to germinate, thereby allowing the resulting seedling to infect the host and withdraw nutrients. Because a laboratory-friendly model does not exist for parasitic plants, researchers are currently using information gleaned from model plants like
Arabidopsis in combination with the chemical probes developed through chemical genetics to understand SL perception of parasitic plants. This work first shows that understanding SL signaling is useful in developing chemical probes that perturb SL perception. Second, it indicates that the chemical space available to probe SL signaling in both model and parasitic plants is sizeable. Because these parasitic pests represent a major concern for food insecurity in the developing world, there is great need for chemical approaches to uncover novel lead compounds that perturb parasitic plant infections.
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Affiliation(s)
- Shelley Lumba
- Cell and Systems Biology, University of Toronto, and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Michael Bunsick
- Cell and Systems Biology, University of Toronto, and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Peter McCourt
- Cell and Systems Biology, University of Toronto, and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Abstract
The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking. We discuss different strategies for uncovering the modes of action of such compounds and their use in unraveling membrane trafficking regulators. We also discuss how the bioactive chemicals that are currently used as probes to interrogate endomembrane trafficking were discovered and analyze the results regarding membrane trafficking and pathway crosstalk. The integration of different expertises and the rational implementation of chemical genetic strategies will improve the identification of molecular mechanisms that drive intracellular trafficking and our understanding of how trafficking interfaces with plant physiology and development.
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Affiliation(s)
- Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
| | - Ricardo Tejos
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, 111093 Iquique, Chile
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Ben-Amar A, Daldoul S, Reustle GM, Krczal G, Mliki A. Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics. Curr Genomics 2016; 17:460-475. [PMID: 28217003 PMCID: PMC5282599 DOI: 10.2174/1389202917666160520102827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 11/22/2022] Open
Abstract
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Samia Daldoul
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
| | - Götz M. Reustle
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Gabriele Krczal
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
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Tadele Z. Mutagenesis and TILLING to Dissect Gene Function in Plants. Curr Genomics 2016; 17:499-508. [PMID: 28217006 PMCID: PMC5282601 DOI: 10.2174/1389202917666160520104158] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/01/2015] [Accepted: 12/05/2015] [Indexed: 11/22/2022] Open
Abstract
Mutagenesis can be random or targeted and occur by nature or artificially by humans. However, the bulk of mutagenesis employed in plants are random and caused by physical agents such as x-ray and gamma-ray or chemicals such as ethyl-methane sulfonate (EMS). Researchers are interested in first identifying these mutations and/or polymorphisms in the genome followed by investigating their effects in the plant function as well as their application in crop improvement. The high-throughput technique called TILLING (Targeting Induced Local Lesion IN Genomes) has been already established and become popular for identifying candidate mutant individuals harboring mutations in the gene of interest. TILLING is a non-transgenic and reverse genetics method of identifying a single nucleotide changes. The procedure of TILLING comprises traditional mutagenesis using optimum type and concentration of mutagen, development of a non-chimeric population, DNA extraction and pooling, mutation detection as well as validation of results. In general, TILLING has proved to be robust in identifying useful mutant lines in diverse economically important crops of the world. The main goal of the current mini-review is to show the significance role played by mutagenesis and TILLING in the discovery of DNA lesions which are to be used in the improvement of crops for the trait of interest.
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Affiliation(s)
- Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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41
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Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit. Genetica 2016; 144:651-664. [PMID: 27722804 DOI: 10.1007/s10709-016-9932-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.
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Stefanowicz K, Lannoo N, Zhao Y, Eggermont L, Van Hove J, Al Atalah B, Van Damme EJM. Glycan-binding F-box protein from Arabidopsis thaliana protects plants from Pseudomonas syringae infection. BMC PLANT BIOLOGY 2016; 16:213. [PMID: 27716048 PMCID: PMC5050601 DOI: 10.1186/s12870-016-0905-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 09/26/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND A small group of F-box proteins consisting of a conserved F-box domain linked to a domain homologous to the glycan-binding protein has been identified within the genome of Arabidopsis thaliana. Previously, the so-called F-box-Nictaba protein, encoded by the gene At2g02360, was shown to be a functional lectin which binds N-acetyllactosamine structures. Here, we present a detailed qRT-PCR expression analysis of F-box-Nictaba in Arabidopsis plants upon different stresses and hormone treatments. RESULTS Expression of the F-box-Nictaba gene was enhanced after plant treatment with salicylic acid and after plant infection with the virulent Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000). β-glucuronidase histochemical staining of transgenic Arabidopsis plants displayed preferential activity of the At2g02360 promoter in trichomes present on young rosette leaves. qRT-PCR analyses confirmed high expression of F-box-Nictaba in leaf trichomes. A. thaliana plants overexpressing the gene showed less disease symptoms after Pst DC3000 infection with reduced bacterial colonization compared to infected wild type and F-box-Nictaba knock-out plants. CONCLUSIONS Our data show that the Arabidopsis F-box-Nictaba gene is a stress-inducible gene responsive to SA, bacterial infection and heat stress, and is involved in salicylic acid related plant defense responses. This knowledge enriched our understanding of the physiological importance of F-box-Nictaba, and can be used to create plants with better performance in changing environmental conditions.
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Affiliation(s)
- Karolina Stefanowicz
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nausicaä Lannoo
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Yafei Zhao
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lore Eggermont
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jonas Van Hove
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bassam Al Atalah
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Els J. M. Van Damme
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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43
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Onda Y, Mochida K. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics 2016; 17:358-67. [PMID: 27499684 PMCID: PMC4955029 DOI: 10.2174/1389202917666160331202742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
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44
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Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK. A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. PLANT CELL REPORTS 2016; 35:1519-33. [PMID: 26661595 PMCID: PMC5512712 DOI: 10.1007/s00299-015-1900-z] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/30/2015] [Accepted: 11/14/2015] [Indexed: 05/18/2023]
Abstract
The recently developed CRISPR/Cas9 system is a promising technology for targeted genome editing in a variety of species including plants. However, the first generation systems were designed to target one or two gene loci at a time. We designed a new multiplex CRISPR/Cas9 system that allows the co-expression of six sgRNA modules in one binary vector using a simple (three steps) cloning strategy in Arabidopsis. The transcription of the sgRNA modules is under the control of three different RNA Polymerase III-dependent promoters. We tested the efficiency of the new multiplex system by targeting six of the fourteen PYL families of ABA receptor genes in a single transformation experiment. One line with mutations in all six targeted PYLs was identified from 15 T1 plants. The mutagenesis frequency for the six individual PYL targets in the T1 lines ranged from 13 to 93 %. In the presence of ABA, the transgenic line identified as containing mutations in all six PYL genes produced the highest germination rate in the T2 progeny (37 %). Among these germinated seedlings, half of the analyzed plants (15/30) were homozygous mutants for at least four targeted genes and two plants (6.7 %) contained homozygous mutations in five of the targeted PYLs and the other targeted PYL had biallelic mutations. Homozygous sextuple mutants were identified in the T3 progeny and characterized together with previously described triple and sextuple PYL mutants. We anticipate that the application of this multiplex CRISPR/Cas9 system will strongly facilitate functional analysis of genes pathways and families.
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Affiliation(s)
- Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences (CAS), Shanghai, 200032, People's Republic of China
| | - Yanfei Mao
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Si Ha
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences (CAS), Shanghai, 200032, People's Republic of China
| | - Wenshan Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Sciences, Chongqing University, Chongqing, 400044, China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. THE NEW PHYTOLOGIST 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Mao Y, Zhang Z, Feng Z, Wei P, Zhang H, Botella JR, Zhu JK. Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:519-32. [PMID: 26360626 PMCID: PMC5515382 DOI: 10.1111/pbi.12468] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 05/18/2023]
Abstract
The Streptococcus-derived CRISPR/Cas9 system is being widely used to perform targeted gene modifications in plants. This customized endonuclease system has two components, the single-guide RNA (sgRNA) for target DNA recognition and the CRISPR-associated protein 9 (Cas9) for DNA cleavage. Ubiquitously expressed CRISPR/Cas9 systems (UC) generate targeted gene modifications with high efficiency but only those produced in reproductive cells are transmitted to the next generation. We report the design and characterization of a germ-line-specific Cas9 system (GSC) for Arabidopsis gene modification in male gametocytes, constructed using a SPOROCYTELESS (SPL) genomic expression cassette. Four loci in two endogenous genes were targeted by both systems for comparative analysis. Mutations generated by the GSC system were rare in T1 plants but were abundant (30%) in the T2 generation. The vast majority (70%) of the T2 mutant population generated using the UC system were chimeras while the newly developed GSC system produced only 29% chimeras, with 70% of the T2 mutants being heterozygous. Analysis of two loci in the T2 population showed that the abundance of heritable gene mutations was 37% higher in the GSC system compared to the UC system and the level of polymorphism of the mutations was also dramatically increased with the GSC system. Two additional systems based on germ-line-specific promoters (pDD45-GT and pLAT52-GT) were also tested, and one of them was capable of generating heritable homozygous T1 mutant plants. Our results suggest that future application of the described GSC system will facilitate the screening for targeted gene modifications, especially lethal mutations in the T2 population.
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Affiliation(s)
- Yanfei Mao
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pengliang Wei
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - José Ramón Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
- Correspondence: (Tel 1-765-496-7601; fax 1-765-494-0391,
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Abstract
Genetic screens have proven to be a useful tool in the dissection of biological processes in plants. Specifically, suppressor screens have been widely used to study signal transduction pathways. Here we provide a detailed protocol for ethyl methanesulfonate (EMS) mutagenesis used in our suppressor screens in Arabidopsis and discuss the basic principles behind suppressor screen design and downstream analyses.
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Affiliation(s)
- Xin Li
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, Room #3529, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4.
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Rothan C, Bres C, Garcia V, Just D. Tomato Resources for Functional Genomics. COMPENDIUM OF PLANT GENOMES 2016. [DOI: 10.1007/978-3-662-53389-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Strategies for altering plant traits using virus-induced gene silencing technologies. Methods Mol Biol 2015; 1287:25-41. [PMID: 25740354 DOI: 10.1007/978-1-4939-2453-0_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The rapid progress in genome sequencing and transcriptome analysis in model and crop plants has made possible the identification of a vast number of genes potentially associated with economically important complex traits. The ultimate goal is to assign functions to these genes by using forward and reverse genetic screens. Plant viruses have been developed for virus-induced gene silencing (VIGS) to generate rapid gene knockdown phenotypes in numerous plant species. To fulfill its potential for high-throughput phenomics, it is of prime importance to ensure that parameters conditioning the VIGS response, i.e., plant-virus interactions and associated loss-of-function screens, are "fit for purpose" and optimized to unequivocally conclude the role of a gene of interest in relation to a given trait. This chapter will review and discuss the different strategies used for the development of VIGS-based phenomics in model and crop species.
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