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Saleem MS, Khan SH, Ahmad A, Rana IA, Naveed ZA, Khan AI. The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger. Front Genome Ed 2024; 6:1401088. [PMID: 39328243 PMCID: PMC11424549 DOI: 10.3389/fgeed.2024.1401088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.
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Affiliation(s)
- Muhammad Sulyman Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zunaira Afzal Naveed
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Azeem Iqbal Khan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
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Ma J, Yang L, Dang Y, Shahzad K, Song J, Jia B, Wang L, Feng J, Wang N, Pei W, Wu M, Zhang X, Zhang J, Wu J, Yu J. Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland cotton. J Adv Res 2024:S2090-1232(24)00324-2. [PMID: 39106927 DOI: 10.1016/j.jare.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/02/2024] [Accepted: 08/02/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Interspecific introgression between Gossypium hirsutum and G. barbadense allows breeding cotton with outstanding fiber length (FL). However, the dynamic gene regulatory network of FL-related genes has not been characterized, and the functional mechanism through which the hub gene GhTUB5 mediates fiber elongation has yet to be determined. METHODS Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. The function of GhTUB5 was determined by ectopic expression of two TUB5 alleles in Arabidopsis and knockout of GhTUB5 in upland cotton. Yeast two-hybrid, split-luciferase and pull-down assays were conducted to screen for interacting proteins, and upstream genes were identified by yeast one-hybrid, dual-LUC and electrophoretic mobility shift assays. RESULTS The 32,612, 30,837 and 30,277 genes expressed at 5, 10 and 15 days postanthesis (dpa) were grouped into 19 distinct coexpression modules, and 988 genes in the MEblack module were enriched in the cell wall process and exhibited significant associations with FL. A total of 20 FL-QTLs were identified, each explaining 3.34-16.04 % of the phenotypic variance in the FL. Furthermore, several FL-QTLs contained 15 genes that were differentially expressed in the MEblack module including the tubulin beta gene (TUB5). Compared with the wild type, the overexpression of GhTUB5 and GbTUB5 in Arabidopsis suppressed root cell length but promoted cellulose synthesis. Knockout of GhTUB5 resulted in longer fiber lines. Protein-based experiments revealed that GhTUB5 interacts with GhZFP6. Additionally, GhTUB5 was directly activated by GhHD-ZIP7, a homeobox-leucine zipper transcription factor, and its paralogous gene was previously reported to mediate fiber elongation. CONCLUSION This study opens a new avenue to dissect functional mechanism of cotton fiber elongation. Our findings provide some molecular details on how GhTUB5 mediates the FL phenotype in cotton.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuanyue Dang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Man Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jianyong Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China.
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He J, Zeng C, Li M. Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300203. [PMID: 38465224 PMCID: PMC10919289 DOI: 10.1002/ggn2.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Indexed: 03/12/2024]
Abstract
Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.
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Affiliation(s)
- Jianjie He
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Can Zeng
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
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Sun L, Alariqi M, Wang Y, Wang Q, Xu Z, Zafar MN, Yang G, Jia R, Hussain A, Chen Y, Ding X, Zhou J, Wang G, Wang F, Li J, Zou J, Zhu X, Yu L, Sun Y, Liang S, Hui F, Chen L, Guo W, Wang Y, Zhu H, Lindsey K, Nie X, Zhang X, Jin S. Construction of Host Plant Insect-Resistance Mutant Library by High-Throughput CRISPR/Cas9 System and Identification of A Broad-Spectrum Insect Resistance Gene. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306157. [PMID: 38032126 PMCID: PMC10811493 DOI: 10.1002/advs.202306157] [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: 08/29/2023] [Revised: 10/17/2023] [Indexed: 12/01/2023]
Abstract
Insects pose significant challenges in cotton-producing regions. Here, they describe a high-throughput CRISPR/Cas9-mediated large-scale mutagenesis library targeting endogenous insect-resistance-related genes in cotton. This library targeted 502 previously identified genes using 968 sgRNAs, generated ≈2000 T0 plants and achieved 97.29% genome editing with efficient heredity, reaching upto 84.78%. Several potential resistance-related mutants (10% of 200 lines) their identified that may contribute to cotton-insect molecular interaction. Among these, they selected 139 and 144 lines showing decreased resistance to pest infestation and targeting major latex-like protein 423 (GhMLP423) for in-depth study. Overexpression of GhMLP423 enhanced insect resistance by activating the plant systemic acquired resistance (SAR) of salicylic acid (SA) and pathogenesis-related (PR) genes. This activation is induced by an elevation of cytosolic calcium [Ca2+ ]cyt flux eliciting reactive oxygen species (ROS), which their demoted in GhMLP423 knockout (CR) plants. Protein-protein interaction assays revealed that GhMLP423 interacted with a human epidermal growth factor receptor substrate15 (EPS15) protein at the cell membrane. Together, they regulated the systemically propagating waves of Ca2+ and ROS, which in turn induced SAR. Collectively, this large-scale mutagenesis library provides an efficient strategy for functional genomics research of polyploid plant species and serves as a solid platform for genetic engineering of insect resistance.
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Affiliation(s)
- Lin Sun
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
- Institute of Industrial CropsShandong Academy of Agricultural SciencesJinanShandong250100China
| | - Muna Alariqi
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
- Department of Agronomy and Pastures, Faculty of AgricultureSana’a UniversitySana’aYemen
| | - Yaxin Wang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Qiongqiong Wang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Zhongping Xu
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Muhammad Naeem Zafar
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Guangqin Yang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ruoyu Jia
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Amjad Hussain
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Yilin Chen
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Xiao Ding
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Jiawei Zhou
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Guanying Wang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Fuqiu Wang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Jianying Li
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Jiawei Zou
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Xiangqian Zhu
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Lu Yu
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Yiwen Sun
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Sijia Liang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Fengjiao Hui
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Luo Chen
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Weifeng Guo
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim BasinTarim UniversityAlaerXinjiang843300China
| | - Yanqin Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim BasinTarim UniversityAlaerXinjiang843300China
| | - Huaguo Zhu
- College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggangHubei438000China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversityDurhamDH1 3LEUK
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiangChina
| | - Xianlong Zhang
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Shuangxia Jin
- Hubei Hongshan LaboratoryNational Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Farinati S, Draga S, Betto A, Palumbo F, Vannozzi A, Lucchin M, Barcaccia G. Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1223861. [PMID: 37521915 PMCID: PMC10382145 DOI: 10.3389/fpls.2023.1223861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.
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Khan AH, Min L, Ma Y, Zeeshan M, Jin S, Zhang X. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:680-697. [PMID: 36221230 PMCID: PMC10037161 DOI: 10.1111/pbi.13946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 05/16/2023]
Abstract
Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Muhammad Zeeshan
- Guangxi Key Laboratory for Agro‐Environment and Agro‐Product Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, College of AgricultureGuanxi UniversityNanningChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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8
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Hu Y, Patra P, Pisanty O, Shafir A, Belew ZM, Binenbaum J, Ben Yaakov S, Shi B, Charrier L, Hyams G, Zhang Y, Trabulsky M, Caldararu O, Weiss D, Crocoll C, Avni A, Vernoux T, Geisler M, Nour-Eldin HH, Mayrose I, Shani E. Multi-Knock-a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants. NATURE PLANTS 2023; 9:572-587. [PMID: 36973414 PMCID: PMC7615256 DOI: 10.1038/s41477-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Plant genomes are characterized by large and complex gene families that often result in similar and partially overlapping functions. This genetic redundancy severely hampers current efforts to uncover novel phenotypes, delaying basic genetic research and breeding programmes. Here we describe the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in Arabidopsis by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. We computationally designed 59,129 optimal single-guide RNAs that each target two to ten genes within a family at once. Furthermore, partitioning the library into ten sublibraries directed towards a different functional group allows flexible and targeted genetic screens. From the 5,635 single-guide RNAs targeting the plant transportome, we generated over 3,500 independent Arabidopsis lines that allowed us to identify and characterize the first known cytokinin tonoplast-localized transporters in plants. With the ability to overcome functional redundancy in plants at the genome-scale level, the developed strategy can be readily deployed by scientists and breeders for basic research and to expedite breeding efforts.
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Affiliation(s)
- Yangjie Hu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Priyanka Patra
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Odelia Pisanty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Zeinu Mussa Belew
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Shir Ben Yaakov
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Bihai Shi
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Laurence Charrier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gal Hyams
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yuqin Zhang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Maor Trabulsky
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Omer Caldararu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniela Weiss
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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9
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Alariqi M, Ramadan M, Wang Q, Yang Z, Hui X, Nie X, Ahmed A, Chen Q, Wang Y, Zhu L, Zhang X, Jin S. Cotton 4-coumarate-CoA ligase 3 enhanced plant resistance to Verticillium dahliae by promoting jasmonic acid signaling-mediated vascular lignification and metabolic flux. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36994650 DOI: 10.1111/tpj.16223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/13/2023] [Accepted: 03/25/2023] [Indexed: 05/17/2023]
Abstract
Lignins and their antimicrobial-related polymers cooperatively enhance plant resistance to pathogens. Several isoforms of 4-coumarate-coenzyme A ligases (4CLs) have been identified as indispensable enzymes involved in lignin and flavonoid biosynthetic pathways. However, their roles in plant-pathogen interaction are still poorly understood. This study uncovers the role of Gh4CL3 in cotton resistance to the vascular pathogen Verticillium dahliae. The cotton 4CL3-CRISPR/Cas9 mutant (CR4cl) exhibited high susceptibility to V. dahliae. This susceptibility was most probably due to the reduction in the total lignin content and the biosynthesis of several phenolic metabolites, e.g., rutin, catechin, scopoletin glucoside, and chlorogenic acid, along with jasmonic acid (JA) attenuation. These changes were coupled with a significant reduction in 4CL activity toward p-coumaric acid substrate, and it is likely that recombinant Gh4CL3 could specifically catalyze p-coumaric acid to form p-coumaroyl-coenzyme A. Thus, overexpression of Gh4CL3 (OE4CL) showed increasing 4CL activity that augmented phenolic precursors, cinnamic, p-coumaric, and sinapic acids, channeling into lignin and flavonoid biosyntheses and enhanced resistance to V. dahliae. Besides, Gh4CL3 overexpression activated JA signaling that instantly stimulated lignin deposition and metabolic flux in response to pathogen, which all established an efficient plant defense response system, and inhibited V. dahliae mycelium growth. Our results propose that Gh4CL3 acts as a positive regulator for cotton resistance against V. dahliae by promoting JA signaling-mediated enhanced cell wall rigidity and metabolic flux.
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Affiliation(s)
- Muna Alariqi
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Agronomy and Pastures, Faculty of Agriculture, Sana'a University, Sana'a, Yemen
| | - Mohamed Ramadan
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiongqiong Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Xi Hui
- Shihezi University, Shihezi, Xinjiang, China
| | - Xinhui Nie
- Shihezi University, Shihezi, Xinjiang, China
| | - Amani Ahmed
- College of Food Science, Huazhong Agricultural University, Wuhan, China
| | - Qiansi Chen
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Yanyin Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer, Xinjiang, 843300, China
| | - Longfu Zhu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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10
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Qin A, Aluko OO, Liu Z, Yang J, Hu M, Guan L, Sun X. Improved cotton yield: Can we achieve this goal by regulating the coordination of source and sink? FRONTIERS IN PLANT SCIENCE 2023; 14:1136636. [PMID: 37063185 PMCID: PMC10090392 DOI: 10.3389/fpls.2023.1136636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Cotton is one of the major cash crops globally. It is characterized by determinate growth and multiple fruiting, which makes the source-sink contradiction more obvious. Coordination between source and sink is crucial for normal growth, yield, and quality of cotton. Numerous studies reported how the assimilate transport and distribution under varying environmental cues affected crop yields. However, less is known about the functional mechanism underlying the assimilate transport between source and sink, and how their distribution impacts cotton growth. Here, we provided an overview of the assimilate transport and distribution mechanisms , and discussed the regulatory mechanisms involved in source-sink balance in relation to cotton yield. Therefore, this review enriched our knowledge of the regulatory mechanism involved in source-sink relationship for improved cotton yield.
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11
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Zhang J, Wu P, Li N, Xu X, Wang S, Chang S, Zhang Y, Wang X, Liu W, Ma Y, Manghwar H, Zhang X, Min L, Guo X. A male-sterile mutant with necrosis-like dark spots on anthers was generated in cotton. FRONTIERS IN PLANT SCIENCE 2023; 13:1102196. [PMID: 36699851 PMCID: PMC9868585 DOI: 10.3389/fpls.2022.1102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Although conventional hybrid breeding has paved the way for improving cotton production and other properties, it is undoubtedly time and labor consuming, while the cultivation of male sterile line can fix the problem. Here, we induced male sterile mutants by simultaneously editing three cotton EXCESS MICROSPOROCYTES1 (GhEMS1) genes by CRISPR/Cas9. Notably, the GhEMS1 genes are homologous to AtEMS1 genes, which inhibit the production of middle layer and tapetum cells as well, leading to male sterility in cotton. Interestingly, there are necrosis-like dark spots on the surface of the anthers of GhEMS1s mutants, which is different from AtEMS1 mutant whose anther surface is clean and smooth, suggesting that the function of EMS1 gene has not been uncovered yet. Moreover, we have detected mutations in GhEMS1 genes from T0 to T3 mutant plants, which had necrosis-like dark spots as well, indicating that the mutation of the three GhEMS1 genes could be stably inherited. Dynamic transcriptomes showed plant hormone pathway and anther development genetic network were differential expression in mutant and wild-type anthers. And the lower level of IAA content in the mutant anthers than that in the wild type at four anther developmental stages may be the reason for the male sterility. This study not only facilitates the exploration of the basic research of cotton male sterile lines, but also provides germplasms for accelerating the hybrid breeding in cotton.
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Affiliation(s)
- Jun Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Peng Wu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ning Li
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaolan Xu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Songxin Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Siyuan Chang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuping Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xingxing Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wangshu Liu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xianlong Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaoping Guo
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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12
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Lorenzo CD, Debray K, Herwegh D, Develtere W, Impens L, Schaumont D, Vandeputte W, Aesaert S, Coussens G, De Boe Y, Demuynck K, Van Hautegem T, Pauwels L, Jacobs TB, Ruttink T, Nelissen H, Inzé D. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize. THE PLANT CELL 2023; 35:218-238. [PMID: 36066192 PMCID: PMC9806654 DOI: 10.1093/plcell/koac243] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/30/2022] [Indexed: 05/04/2023]
Abstract
Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. Although new technologies are being applied to tackle this problem, we are approaching a plateau in crop improvement using conventional breeding. Recent advances in CRISPR/Cas9-mediated gene engineering have paved the way to accelerate plant breeding to meet this increasing demand. However, many traits are governed by multiple small-effect genes operating in complex interactive networks. Here, we present the gene discovery pipeline BREEDIT, which combines multiplex genome editing of whole gene families with crossing schemes to improve complex traits such as yield and drought tolerance. We induced gene knockouts in 48 growth-related genes into maize (Zea mays) using CRISPR/Cas9 and generated a collection of over 1,000 gene-edited plants. The edited populations displayed (on average) 5%-10% increases in leaf length and up to 20% increases in leaf width compared with the controls. For each gene family, edits in subsets of genes could be associated with enhanced traits, allowing us to reduce the gene space to be considered for trait improvement. BREEDIT could be rapidly applied to generate a diverse collection of mutants to identify promising gene modifications for later use in breeding programs.
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Affiliation(s)
| | | | - Denia Herwegh
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ward Develtere
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Lennert Impens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dries Schaumont
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Wout Vandeputte
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Stijn Aesaert
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Griet Coussens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Yara De Boe
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kirin Demuynck
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Van Hautegem
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Thomas B Jacobs
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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13
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Li B, Fu C, Zhou J, Hui F, Wang Q, Wang F, Wang G, Xu Z, Che L, Yuan D, Wang Y, Zhang X, Jin S. Highly Efficient Genome Editing Using Geminivirus-Based CRISPR/Cas9 System in Cotton Plant. Cells 2022; 11:cells11182902. [PMID: 36139477 PMCID: PMC9496795 DOI: 10.3390/cells11182902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Upland cotton (Gossypium hirsutum), an allotetraploid, contains At- and Dt- subgenome and most genes have multiple homologous copies, which pose a huge challenge to investigate genes’ function due to the functional redundancy. Therefore, it is of great significance to establish effective techniques for the functional genomics in cotton. In this study, we tested two novel genome editing vectors and compared them with the CRISPR/Cas9 system (pRGEB32-GhU6.7) developed in our laboratory previously. In the first new vector, the sgRNA transcription unite was constructed into the replicon (LIR-Donor-SIR-Rep-LIR) of the bean yellow dwarf virus (BeYDV) and named as pBeYDV-Cas9-KO and in the second vector, the ubiquitin promoter that drives Cas9 protein was replaced with a constitutive CaMV 35S promoter and defined as pRGEB32-35S. The results from transgenic cotton calli/plants revealed that pBeYDV-Cas9-KO vector showed the highest editing efficiency of GhCLA1 in At and Dt subgenomes edited simultaneously up to 73.3% compared to the 44.6% of pRGEB32-GhU6.7 and 51.2% of pRGEB32-35S. The editing efficiency of GhCLA1 in At and Dt subgenome by pBeYDV-Cas9-KO was 85.7% and 97.2%, respectively, whereas the efficiency by pRGEB32-GhU6.7 and pRGEB32-35S vectors was 67.7%, 86.5%, 84%, and 87.2%, respectively. The editing profile of pBeYDV-Cas9-KO was mainly composed of fragment deletion, accounting for 84.0% and ranging 1–10 bp in length. The main editing sites are located at positions 11–17 upstream of PAM site. The off-target effects were not detected in all potential off-target sites. Taken together, the pBeYDV-Cas9-KO system has high editing efficiency and specificity with wide editing range than the traditional CRISPR/Cas9 system, which provides a powerful tool for cotton functional genomics research and molecular breeding.
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Affiliation(s)
- Bo Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Crop Biotechnology, Urumqi 830091, China
| | - Chunyang Fu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Zhou
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengjiao Hui
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiongqiong Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fuqiu Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianlian Che
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojun Yuan
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanqin Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer 843300, China
- Correspondence: (Y.W.); (S.J.)
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Y.W.); (S.J.)
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14
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Jiang M, Li X, Dong X, Zu Y, Zhan Z, Piao Z, Lang H. Research Advances and Prospects of Orphan Genes in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:947129. [PMID: 35874010 PMCID: PMC9305701 DOI: 10.3389/fpls.2022.947129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Ye Zu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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15
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Zhu Q, Jin S, Yuan Y, Liu Q, Zhang X, Wilson I. CRISPR/Cas9‐mediated saturated mutagenesis of the cotton
MIR482
family for dissecting the functionality of individual members in disease response. PLANT DIRECT 2022; 6:e410. [PMID: 35685042 PMCID: PMC9170593 DOI: 10.1002/pld3.410] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/20/2022] [Accepted: 05/11/2022] [Indexed: 05/31/2023]
Affiliation(s)
- Qian‐Hao Zhu
- CSIRO Agriculture and Food Canberra ACT Australia
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan Hubei China
| | - Yuman Yuan
- CSIRO Agriculture and Food Canberra ACT Australia
| | - Qing Liu
- CSIRO Agriculture and Food Canberra ACT Australia
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan Hubei China
| | - Iain Wilson
- CSIRO Agriculture and Food Canberra ACT Australia
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16
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Tan Z, Shi J, Lv R, Li Q, Yang J, Ma Y, Li Y, Wu Y, Zhang R, Ma H, Li Y, Zhu L, Zhu L, Zhang X, Kong J, Yang W, Min L. Fast anther dehiscence status recognition system established by deep learning to screen heat tolerant cotton. PLANT METHODS 2022; 18:53. [PMID: 35449108 PMCID: PMC9026675 DOI: 10.1186/s13007-022-00884-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND From an economic perspective, cotton is one of the most important crops in the world. The fertility of male reproductive organs is a key determinant of cotton yield. Anther dehiscence or indehiscence directly determines the probability of fertilization in cotton. Thus, rapid and accurate identification of cotton anther dehiscence status is important for judging anther growth status and promoting genetic breeding research. The development of computer vision technology and the advent of big data have prompted the application of deep learning techniques to agricultural phenotype research. Therefore, two deep learning models (Faster R-CNN and YOLOv5) were proposed to detect the number and dehiscence status of anthers. RESULT The single-stage model based on YOLOv5 has higher recognition speed and the ability to deploy to the mobile end. Breeding researchers can apply this model to terminals to achieve a more intuitive understanding of cotton anther dehiscence status. Moreover, three improvement strategies are proposed for the Faster R-CNN model, where the improved model has higher detection accuracy than the YOLOv5 model. We have made three improvements to the Faster R-CNN model and after the ensemble of the three models and original Faster R-CNN model, R2 of "open" reaches to 0.8765, R2 of "close" reaches to 0.8539, R2 of "all" reaches to 0.8481, higher than the prediction results of either model alone, which are completely able to replace the manual counting results. We can use this model to quickly extract the dehiscence rate of cotton anthers under high temperature (HT) conditions. In addition, the percentage of dehiscent anthers of 30 randomly selected cotton varieties were observed from the cotton population under normal conditions and HT conditions through the ensemble of the Faster R-CNN model and manual counting. The results show that HT decreased the percentage of dehiscent anthers in different cotton lines, consistent with the manual method. CONCLUSIONS Deep learning technology have been applied to cotton anther dehiscence status recognition instead of manual methods for the first time to quickly screen HT-tolerant cotton varieties. Deep learning can help to explore the key genetic improvement genes in the future, promoting cotton breeding and improvement.
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Affiliation(s)
- Zhihao Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiawei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rongjie Lv
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qingyuan Li
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430075, China
| | - Jing Yang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Huanhuan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yawei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China.
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Li JW, Zeng T, Xu ZZ, Li JJ, Hu H, Yu Q, Zhou L, Zheng RR, Luo J, Wang CY. Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter. PLANT METHODS 2022; 18:32. [PMID: 35292048 PMCID: PMC8925089 DOI: 10.1186/s13007-022-00863-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/24/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Traditional CRISPR/Cas9 systems that rely on U6 or U3 snRNA promoters (RNA polymerase III-dependent promoters) can only achieve constitutive gene editing in plants, hampering the functional analysis of specifically expressed genes. Ribozyme-mediated CRISPR/Cas9 systems increase the types of promoters which can be used to transcribe sgRNA. Therefore, such systems allow specific gene editing; for example, transcription of the artificial gene Ribozyme-sgRNA-Ribozyme (RGR) is initiated by an RNA polymerase II-dependent promoter. Genetic transformation is indispensable for editing plant genes. In certain plant species, including pyrethrum, genetic transformation remains challenging to do, limiting the functional verification of novel CRISPR/Cas9 systems. Thus, this study's aim was to develop a simple Agrobacterium rhizogenes-mediated hairy root transformation system to analyze the function of a ribozyme-mediated CRISPR/Cas9 system in pyrethrum. RESULTS A hairy root transformation system for pyrethrum is described, with a mean transformation frequency of 7%. Transgenic hairy roots transformed with the pBI121 vector exhibited significantly increased beta-glucuronidase staining as a visual marker of transgene expression. Further, a ribozyme-based CRISPR/Cas9 vector was constructed to edit the TcEbFS gene, which catalyzes synthesis of the defense-related compound (E)-β-farnesene in pyrethrum. The vector was transferred into the hairy roots of pyrethrum and two stably transformed hairy root transgenic lines obtained. Editing of the TcEbFS gene in the hairy roots was evaluated by gene sequencing, demonstrating that both hairy root transgenic lines had DNA base loss at the editing target site. Gas chromatography-mass spectrometry showed that the (E)-β-farnesene content was significantly decreased in both hairy root transgenic lines compared with the empty vector control group. Altogether, these results show that RGR can be driven by the CaMV35S promoter to realize TcEbFS gene editing in pyrethrum hairy roots. CONCLUSION An A. rhizogenes-mediated hairy root transformation and ribozyme-mediated CRISPR/Cas9 gene editing system in pyrethrum was established, thereby facilitating gene editing in specific organs or at a particular developmental stage in future pyrethrum research.
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Affiliation(s)
- Jia-Wen Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tuo Zeng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Zhi-Zhuo Xu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Jin Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Hu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Yu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhou
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ri-Ru Zheng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Luo
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Cai-Yun Wang
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Han S, Jiang S, Xiong R, Shafique K, Zahid KR, Wang Y. Response and tolerance mechanism of food crops under high temperature stress: a review. BRAZ J BIOL 2022; 82:e253898. [PMID: 35107484 DOI: 10.1590/1519-6984.253898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/23/2021] [Indexed: 01/15/2023] Open
Abstract
High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.
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Affiliation(s)
- S Han
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - S Jiang
- Zhengzhou Normal University, Bioengineering Research Center, Zhengzhou, Henan, P.R. China
| | - R Xiong
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - K Shafique
- Government Sadiq College Women University, Department of Botany, Bahawalpur, Pakistan
| | - K R Zahid
- Shenzhen University, Carson International Cancer Center, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen, Guangdong, China
| | - Y Wang
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
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Singh M, Nara U, Kumar A, Choudhary A, Singh H, Thapa S. Salinity tolerance mechanisms and their breeding implications. J Genet Eng Biotechnol 2021; 19:173. [PMID: 34751850 PMCID: PMC8578521 DOI: 10.1186/s43141-021-00274-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND The era of first green revolution brought about by the application of chemical fertilizers surely led to the explosion of food grains, but left behind the notable problem of salinity. Continuous application of these fertilizers coupled with fertilizer-responsive crops make the country self-reliant, but continuous deposition of these led to altered the water potential and thus negatively affecting the proper plant functioning from germination to seed setting. MAIN BODY Increased concentration of anion and cations and their accumulation and distribution cause cellular toxicity and ionic imbalance. Plants respond to salinity stress by any one of two mechanisms, viz., escape or tolerate, by either limiting their entry via root system or controlling their distribution and storage. However, the understanding of tolerance mechanism at the physiological, biochemical, and molecular levels will provide an insight for the identification of related genes and their introgression to make the crop more resilient against salinity stress. SHORT CONCLUSION Novel emerging approaches of plant breeding and biotechnologies such as genome-wide association studies, mutational breeding, marker-assisted breeding, double haploid production, hyperspectral imaging, and CRISPR/Cas serve as engineering tools for dissecting the in-depth physiological mechanisms. These techniques have well-established implications to understand plants' adaptions to develop more tolerant varieties and lower the energy expenditure in response to stress and, constitutively fulfill the void that would have led to growth resistance and yield penalty.
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Affiliation(s)
- Mandeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Usha Nara
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Antul Kumar
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anuj Choudhary
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Hardeep Singh
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Sittal Thapa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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Dalla Costa L, Vinciguerra D, Giacomelli L, Salvagnin U, Piazza S, Spinella K, Malnoy M, Moser C, Marchesi U. Integrated approach for the molecular characterization of edited plants obtained via Agrobacterium tumefaciens-mediated gene transfer. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03881-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractAgrobacterium tumefaciens-mediated gene transfer—actually the most used method to engineer plants—may lead to integration of multiple copies of T-DNA in the plant genome, as well as to chimeric tissues composed of modified cells and wild type cells. A molecular characterization of the transformed lines is thus a good practice to select the best ones for further investigation. Nowadays, several quantitative and semi-quantitative techniques are available to estimate the copy number (CN) of the T-DNA in genetically modified plants. In this study, we compared three methods based on (1) real-time polymerase chain reaction (qPCR), (2) droplet digital PCR (ddPCR), and (3) next generation sequencing (NGS), to carry out a molecular characterization of grapevine edited lines. These lines contain a knock-out mutation, obtained via CRISPR/Cas9 technology, in genes involved in plant susceptibility to two important mildew diseases of grapevine. According to our results, qPCR and ddPCR outputs are largely in agreement in terms of accuracy, especially for low CN values, while ddPCR resulted more precise than qPCR. With regard to the NGS analysis, the CNs detected with this method were often not consistent with those calculated by qPCR and ddPCR, and NGS was not able to discriminate the integration points in three out of ten lines. Nevertheless, the NGS method can positively identify T-DNA truncations or the presence of tandem/inverted repeats, providing distinct and relevant information about the transgene integration asset. Moreover, the expression analysis of Cas9 and single guide RNA (sgRNA), and the sequencing of the target site added new information to be related to CN data. This work, by reporting a practical case-study on grapevine edited lines, explores pros and cons of the most advanced diagnostic techniques available for the precocious selection of the proper transgenic material. The results may be of interest both to scientists developing new transgenic lines, and to laboratories in charge of GMO control.
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