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Li B, Jia Y, Xu L, Zhang S, Long Z, Wang R, Guo Y, Zhang W, Jiao C, Li C, Xu Y. Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1282-1298. [PMID: 38124464 PMCID: PMC11022822 DOI: 10.1111/pbi.14264] [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: 05/04/2023] [Revised: 11/09/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.
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Affiliation(s)
- Bo Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Zhoukai Long
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Rong Wang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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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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4
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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [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: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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5
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Shen L, Liu Y, Zhang L, Sun Z, Wang Z, Jiao Y, Shen K, Guo Z. A transcriptional atlas identifies key regulators and networks for the development of spike tissues in barley. Cell Rep 2023; 42:113441. [PMID: 37971941 DOI: 10.1016/j.celrep.2023.113441] [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: 01/10/2022] [Revised: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Grain number and size determine grain yield in crops and are closely associated with spikelet fertility and grain filling in barley (Hordeum vulgare). Abortion of spikelet primordia within individual barley spikes causes a 30%-50% loss in the potential number of grains during development from the awn primordium stage to the tipping stage, after that grain filling is the primary factor regulating grain size. To identify transcriptional signatures associated with spike development, we use a six-rowed barley cultivar (Morex) to develop a spatiotemporal transcriptome atlas containing 255 samples covering 17 stages and 5 positions along the spike. We identify several fundamental regulatory networks, in addition to key regulators of spike development and morphology. Specifically, we show HvGELP96, encoding a GDSL domain-containing protein, as a regulator of spikelet fertility and grain number. Our transcriptional atlas offers a powerful resource to answer fundamental questions in spikelet development and degeneration in barley.
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Affiliation(s)
- Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China.
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6
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Huang L, Gao G, Jiang C, Guo G, He Q, Zong Y, Liu C, Yang P. Generating homozygous mutant populations of barley microspores by ethyl methanesulfonate treatment. ABIOTECH 2023; 4:202-212. [PMID: 37970468 PMCID: PMC10638298 DOI: 10.1007/s42994-023-00108-6] [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: 01/12/2023] [Accepted: 05/31/2023] [Indexed: 11/17/2023]
Abstract
Induced mutations are important for genetic research and breeding. Mutations induced by physical or chemical mutagenesis are usually heterozygous during the early generations. However, mutations must be fixed prior to phenotyping or field trials, which requires additional rounds of self-pollination. Microspore culture is an effective method to produce double-haploid (DH) plants that are fixed homozygotes. In this study, we conducted ethyl methanesulfonate (EMS)-induced mutagenesis of microspore cultures of barley (Hordeum vulgare) cultivar 'Hua30' and landrace 'HTX'. The EMS concentrations were negatively correlated with the efficiency of callus induction and the frequency of mutant plant regeneration. The two genotypes showed different regeneration efficiencies. The phenotypic variation of the regenerated M1 plants and the presence of genome-wide nucleotide mutations, revealed by whole-genome sequencing, highlight the utility of EMS-induced mutagenesis of isolated microspore cultures for developing DH mutants. Genome-wide analysis of the mutation frequency in the regenerated plants revealed that a considerable proportion of mutations resulted from microspore culture (somaclonal variation) rather than EMS-induced mutagenesis. In addition to producing a population of 1972 homozygous mutant lines that are available for future field trials, this study lays the foundation for optimizing the regeneration efficiency of DH plants and the richness of mutations (mainly by fine-tuning the mutagen dosage).
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Affiliation(s)
- Linli Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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7
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Szurman-Zubrzycka M, Kurowska M, Till BJ, Szarejko I. Is it the end of TILLING era in plant science? FRONTIERS IN PLANT SCIENCE 2023; 14:1160695. [PMID: 37674734 PMCID: PMC10477672 DOI: 10.3389/fpls.2023.1160695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING is based on chemical or physical mutagenesis followed by the rapid identification of mutations within genes of interest. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs. Nevertheless, classical mutagenesis is a random process, giving rise to mutations all over the genome. Therefore TILLING mutants carry background mutations, some of which may affect the phenotype and should be eliminated, which is often time-consuming. Recently, new strategies of targeted genome editing, including CRISPR/Cas9-based methods, have been developed and optimized for many plant species. These methods precisely target only genes of interest and produce very few off-targets. Thus, the question arises: is it the end of TILLING era in plant studies? In this review, we recap the basics of the TILLING strategy, summarize the current status of plant TILLING research and present recent TILLING achievements. Based on these reports, we conclude that TILLING still plays an important role in plant research as a valuable tool for generating genetic variation for genomics and breeding projects.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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He J, Zhang K, Yan S, Tang M, Zhou W, Yin Y, Chen K, Zhang C, Li M. Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library. Genome Res 2023; 33:798-809. [PMID: 37290935 PMCID: PMC10317123 DOI: 10.1101/gr.277650.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/19/2023] [Indexed: 06/10/2023]
Abstract
The recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the genome complexity, it is a big challenge to accomplish large-scale targeted mutagenesis in polyploid plants. Here, we demonstrate the feasibility of using a pooled CRISPR library to achieve genome-scale targeted editing in an allotetraploid crop of Brassica napus A total of 18,414 sgRNAs were designed to target 10,480 genes of interest, and afterward, 1104 regenerated transgenic plants harboring 1088 sgRNAs were obtained. Editing interrogation results revealed that 93 of the 178 genes were identified as mutated, thus representing an editing efficiency of 52.2%. Furthermore, we have discovered that Cas9-mediated DNA cleavages tend to occur at all the target sites guided by the same individual sgRNA, a novel finding in polyploid plants. Finally, we show the strong capability of reverse genetic screening for various traits with the postgenotyped plants. Several genes, which might dominate the fatty acid profile and seed oil content and have yet to be reported, were unveiled from the forward genetic studies. Our research provides valuable resources for functional genomics, elite crop breeding, and a good reference for high-throughput targeted mutagenesis in other polyploid plants.
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Affiliation(s)
- Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Mi Tang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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9
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Sakuma S, Koppolu R. Form follows function in Triticeae inflorescences. BREEDING SCIENCE 2023; 73:46-56. [PMID: 37168815 PMCID: PMC10165339 DOI: 10.1270/jsbbs.22085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/21/2022] [Indexed: 05/13/2023]
Abstract
Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
- Corresponding authors (e-mail: and )
| | - Ravi Koppolu
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Corresponding authors (e-mail: and )
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10
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Yu K, Wei L, Yuan H, Zhang W, Zeng X, Wang B, Wang Y. Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley). FRONTIERS IN PLANT SCIENCE 2022; 13:1076000. [PMID: 36561451 PMCID: PMC9763626 DOI: 10.3389/fpls.2022.1076000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.
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Affiliation(s)
- Kuohai Yu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Lingling Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B. FIND-IT: Accelerated trait development for a green evolution. SCIENCE ADVANCES 2022; 8:eabq2266. [PMID: 36001660 PMCID: PMC9401622 DOI: 10.1126/sciadv.abq2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.
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Affiliation(s)
- Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Magnus Rasmussen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Emiko Murozuka
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sandip M. Kale
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sabrina Bodevin
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lise Tang Petersen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jeppe Opstrup Husum
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mikkel K. Jensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lillian Ambus Møller
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Zoran Gojkovic
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Klaus Lengeler
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ross T. Fennessy
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Rosa Garcia Sanchez
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jochen Förster
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ole Olsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Centre for Synthetic Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Geoffrey B. Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
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