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Ndreca B, Huttly A, Bibi S, Bayon C, Lund G, Ham J, Alarcón-Reverte R, Addy J, Tarkowská D, Pearce S, Hedden P, Thomas SG, Phillips AL. Stacked mutations in wheat homologues of rice SEMI-DWARF1 confer a novel semi-dwarf phenotype. BMC PLANT BIOLOGY 2024; 24:384. [PMID: 38724935 PMCID: PMC11080193 DOI: 10.1186/s12870-024-05098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Semi-dwarfing alleles are used widely in cereals to confer improved lodging resistance and assimilate partitioning. The most widely deployed semi-dwarfing alleles in rice and barley encode the gibberellin (GA)-biosynthetic enzyme GA 20-OXIDASE2 (GA20OX2). The hexaploid wheat genome carries three homoeologous copies of GA20OX2, and because of functional redundancy, loss-of-function alleles of a single homoeologue would not be selected in wheat breeding programmes. Instead, approximately 70% of wheat cultivars carry gain-of-function mutations in REDUCED HEIGHT 1 (RHT1) genes that encode negative growth regulators and are degraded in response to GA. Semi-dwarf Rht-B1b or Rht-D1b alleles encode proteins that are insensitive to GA-mediated degradation. However, because RHT1 is expressed ubiquitously these alleles have pleiotropic effects that confer undesirable traits in some environments. RESULTS We have applied reverse genetics to combine loss-of-function alleles in all three homoeologues of wheat GA20OX2 and its paralogue GA20OX1 and evaluated their performance in three years of field trials. ga20ox1 mutants exhibited a mild height reduction (approximately 3%) suggesting GA20OX1 plays a minor role in stem elongation in wheat. ga20ox2 mutants have reduced GA1 content and are 12-32% shorter than their wild-type segregants, comparable to the effect of the Rht-D1b 'Green Revolution' allele. The ga20ox2 mutants showed no significant negative effects on yield components in the spring wheat variety 'Cadenza'. CONCLUSIONS Our study demonstrates that chemical mutagenesis can expand genetic variation in polyploid crops to uncover novel alleles despite the difficulty in identifying appropriate mutations for some target genes and the negative effects of background mutations. Field experiments demonstrate that mutations in GA20OX2 reduce height in wheat, but it will be necessary to evaluate the effect of these alleles in different genetic backgrounds and environments to determine their value in wheat breeding as alternative semi-dwarfing alleles.
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Affiliation(s)
- Barbora Ndreca
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Alison Huttly
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Sajida Bibi
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Nuclear Institute for Agriculture and Biology, Faisalabad, Punjab, Pakistan
| | - Carlos Bayon
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - George Lund
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Joshua Ham
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | - John Addy
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
| | - Stephen Pearce
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Peter Hedden
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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Osman K, Desjardins SD, Simmonds J, Burridge AJ, Kanyuka K, Henderson IR, Edwards KJ, Uauy C, Franklin FCH, Higgins JD, Sanchez-Moran E. FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis. THE NEW PHYTOLOGIST 2024. [PMID: 38584326 DOI: 10.1111/nph.19716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1-3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position. We analysed figl1 mutants and virus-induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid. FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1-fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals. Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding.
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Affiliation(s)
- Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
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Zhou X, Zhao Y, Ni P, Ni Z, Sun Q, Zong Y. CRISPR-mediated acceleration of wheat improvement: advances and perspectives. J Genet Genomics 2023; 50:815-834. [PMID: 37741566 DOI: 10.1016/j.jgg.2023.09.007] [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: 08/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.
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Affiliation(s)
- Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Pei Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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Dracatos PM, Lu J, Sánchez‐Martín J, Wulff BB. Resistance that stacks up: engineering rust and mildew disease control in the cereal crops wheat and barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1938-1951. [PMID: 37494504 PMCID: PMC10502761 DOI: 10.1111/pbi.14106] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023]
Abstract
Staying ahead of the arms race against rust and mildew diseases in cereal crops is essential to maintain and preserve food security. The methodological challenges associated with conventional resistance breeding are major bottlenecks for deploying resistance (R) genes in high-yielding crop varieties. Advancements in our knowledge of plant genomes, structural mechanisms, innovations in bioinformatics, and improved plant transformation techniques have alleviated this bottleneck by permitting rapid gene isolation, functional studies, directed engineering of synthetic resistance and precise genome manipulation in elite crop cultivars. Most cloned cereal R genes encode canonical immune receptors which, on their own, are prone to being overcome through selection for resistance-evading pathogenic strains. However, the increasingly large repertoire of cloned R genes permits multi-gene stacking that, in principle, should provide longer-lasting resistance. This review discusses how these genomics-enabled developments are leading to new breeding and biotechnological opportunities to achieve durable rust and powdery mildew control in cereals.
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Affiliation(s)
- Peter M. Dracatos
- La Trobe Institute for Sustainable Agriculture & Food (LISAF)Department of Animal, Plant and Soil SciencesLa Trobe UniversityVIC 3086Australia
| | - Jing Lu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
- College of Life SciencesSichuan UniversityChengduChina
- Chengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Javier Sánchez‐Martín
- Department of Microbiology and Genetics, Spanish‐Portuguese Agricultural Research Center (CIALE)University of SalamancaSalamancaSpain
| | - Brande B.H. Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
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6
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Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proc Natl Acad Sci U S A 2023; 120:e2306494120. [PMID: 37703281 PMCID: PMC10515147 DOI: 10.1073/pnas.2306494120] [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: 04/24/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
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Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Hongchun Xiong
- Department of Plant Sciences, University of California, Davis, CA95616
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Germán F. Burguener
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Hans Vasquez-Gross
- Department of Plant Sciences, University of California, Davis, CA95616
- Nevada Bioinformatics Center, University of Nevada, Reno, NV89557
| | - Qiujie Liu
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Kimberly Garland-Campbell
- United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA99164
| | - Shahryar F. Kianian
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN55108-6086
| | - Gina Brown-Guedira
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Unit, Raleigh, NC27695
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, SaskatoonS7N 5A8, Canada
| | - Justin D. Faris
- United States Department of Agriculture - Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND58102
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
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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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Chen J, Watson-Lazowski A, Kamble NU, Vickers M, Seung D. Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis. BMC PLANT BIOLOGY 2023; 23:363. [PMID: 37460981 DOI: 10.1186/s12870-023-04369-7] [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: 10/31/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains. RESULTS To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example. CONCLUSION We provide a valuable resource for studying endosperm development in this increasingly important crop species.
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Affiliation(s)
- Jiawen Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alexander Watson-Lazowski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | | | - Martin Vickers
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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9
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Ni P, Zhao Y, Zhou X, Liu Z, Huang Z, Ni Z, Sun Q, Zong Y. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol 2023; 24:156. [PMID: 37386475 PMCID: PMC10308706 DOI: 10.1186/s13059-023-02990-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in the ePPEmax* architecture. ePPEplus enhances the efficiency by an average 33.0-fold and 6.4-fold compared to the original PPE and ePPE, respectively. Importantly, a robust multiplex prime editing platform is established for simultaneous editing of four to ten genes in protoplasts and up to eight genes in regenerated wheat plants at frequencies up to 74.5%, thus expanding the applicability of prime editors for stacking of multiple agronomic traits.
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Affiliation(s)
- Pei Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zehua Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengwei Huang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Zhang H, Liu Y, Zhang X, Ji W, Kang Z. A necessary considering factor for breeding: growth-defense tradeoff in plants. STRESS BIOLOGY 2023; 3:6. [PMID: 37676557 PMCID: PMC10441926 DOI: 10.1007/s44154-023-00086-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/27/2023] [Indexed: 09/08/2023]
Abstract
Crop diseases cause enormous yield losses and threaten global food security. Deployment of resistant cultivars can effectively control the disease and to minimize crop losses. However, high level of genetic immunity to disease was often accompanied by an undesired reduction in crop growth and yield. Recently, literatures have been rapidly emerged in understanding the mechanism of disease resistance and development genes in crop plants. To determine how and why the costs and the likely benefit of resistance genes caused in crop varieties, we re-summarized the present knowledge about the crosstalk between plant development and disease resistance caused by those genes that function as plasma membrane residents, MAPK cassette, nuclear envelope (NE) channels components and pleiotropic regulators. Considering the growth-defense tradeoffs on the basis of current advances, finally, we try to understand and suggest that a reasonable balancing strategies based on the interplay between immunity with growth should be considered to enhance immunity capacity without yield penalty in future crop breeding.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Yuanming Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiangyu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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11
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Wang D, Li Y, Wang H, Xu Y, Yang Y, Zhou Y, Chen Z, Zhou Y, Gui L, Guo Y, Zhou C, Tang W, Zheng S, Wang L, Guo X, Zhang Y, Cui F, Lin X, Jiao Y, He Y, Li J, He F, Liu X, Xiao J. Boosting wheat functional genomics via an indexed EMS mutant library of KN9204. PLANT COMMUNICATIONS 2023:100593. [PMID: 36945776 PMCID: PMC10363553 DOI: 10.1016/j.xplc.2023.100593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/02/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation. However, the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding. In this study, we created a library for KN9204, a popular wheat variety in northern China, with a reference genome, transcriptome, and epigenome of different tissues, using ethyl methyl sulfonate (EMS) mutagenesis. This library contains a vast developmental diversity of critical tissues and transition stages. Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79% of coding genes had mutations, and each line had an average of 1383 EMS-type SNPs. We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1, Q, TaTB1, and WFZP. We tested 100 lines with severe mutations in 80 NAC transcription factors (TFs) under drought and salinity stress and identified 13 lines with altered sensitivity. Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress, including SNAC1, DREB2B, CML16, and ZFP182, factors known to respond to abiotic stress. Thus, we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.
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Affiliation(s)
- Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China; Center for Agricultural Resources Research, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Haojie Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Xu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxin Zhou
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni, Inc, Chengdu 610000, China
| | - Yuqing Zhou
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixuan Gui
- Department of Life Science, Tcuni, Inc, Chengdu 610000, China
| | - Yi Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Chunjiang Zhou
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Lei Wang
- Center for Agricultural Resources Research, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiulin Guo
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yingjun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang 050035, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai 264025, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Yuehui He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China; Center for Agricultural Resources Research, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Fei He
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing 100101, China.
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing 100101, China.
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12
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Transcriptional signatures of wheat inflorescence development. Sci Rep 2022; 12:17224. [PMID: 36241895 PMCID: PMC9568521 DOI: 10.1038/s41598-022-21571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.
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13
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Klymiuk V, Chawla HS, Wiebe K, Ens J, Fatiukha A, Govta L, Fahima T, Pozniak CJ. Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing. Commun Biol 2022; 5:826. [PMID: 35978056 PMCID: PMC9386016 DOI: 10.1038/s42003-022-03773-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/26/2022] [Indexed: 01/06/2023] Open
Abstract
Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to characterize new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single, incompletely dominant gene designated as Yr84. Through bulked segregant analysis sequencing (BSA-Seq) we identified a 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used to design genetic markers for recombinant screening, further refining the interval of Yr84 to a 2.3-3.3 Mb in tetraploid wheat genomes. This interval contains 34 candidate genes encoding for protein domains involved in disease resistance responses. Furthermore, KASP markers closely-linked to Yr84 were developed to facilitate marker-assisted selection for rust resistance breeding.
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Affiliation(s)
- Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Harmeet Singh Chawla
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Krystalee Wiebe
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Jennifer Ens
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Andrii Fatiukha
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Liubov Govta
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
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14
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Jiang C, Lei M, Guo Y, Gao G, Shi L, Jin Y, Cai Y, Himmelbach A, Zhou S, He Q, Yao X, Kan J, Haberer G, Duan F, Li L, Liu J, Zhang J, Spannagl M, Liu C, Stein N, Feng Z, Mascher M, Yang P. A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley. PLANT COMMUNICATIONS 2022; 3:100317. [PMID: 35605197 PMCID: PMC9284286 DOI: 10.1016/j.xplc.2022.100317] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 05/26/2023]
Abstract
Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M3 lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaomiao Lei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuefeng Yao
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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15
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Awan MJA, Pervaiz K, Rasheed A, Amin I, Saeed NA, Dhugga KS, Mansoor S. Genome edited wheat- current advances for the second green revolution. Biotechnol Adv 2022; 60:108006. [PMID: 35732256 DOI: 10.1016/j.biotechadv.2022.108006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/21/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022]
Abstract
Common wheat is a major source of nutrition around the globe, but unlike maize and rice hybrids, no breakthrough has been made to enhance wheat yield since Green Revolution. With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. Wheat has a huge hexaploidy genome of approximately 17 GB with 85% repetition, and it is a daunting task to induce any mutation across three homeologues that can be helpful for the enhancement of agronomic traits. The CRISPR-Cas9 system provides a promising platform for genome editing in a site-specific manner. In wheat, CRISPR-Cas9 is being used in the improvement of yield, grain quality, biofortification, resistance against diseases, and tolerance against abiotic factors. The promising outcomes of the CRISPR-based multiplexing approach circumvent the constraint of targeting merely one gene at a time. Deployment of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 endonuclease (CRISPR-Cas9) and Cas9 variant systems such as cytidine base editing, adenosine base editing, and prime editing in wheat has been used to induce point mutations more precisely. Scientists have acquired major events such as induction of male sterility, fertility restoration, and alteration of seed dormancy through Cas9 in wheat that can facilitate breeding programs for elite variety development. Furthermore, a recent discovery in tissue culturing enables scientists to significantly enhance regeneration efficiency in wheat by transforming the GRF4-GIF1 cassette. Rapid generation advancement by speed breeding technology provides the opportunity for the generation advancement of the desired plants to segregate out unwanted transgenes and allows rapid integration of gene-edited wheat into the breeding pipeline. The combination of these novel technologies addresses some of the most important limiting factors for sustainable and climate-smart wheat that should lead to the second "Green Revolution" for global food security.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Komal Pervaiz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguanccun South Street, Beijing 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Kanwarpal S Dhugga
- Corteva Agriscience, Johnston, IA, USA; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
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16
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Dixon LE, Pasquariello M, Badgami R, Levin KA, Poschet G, Ng PQ, Orford S, Chayut N, Adamski NM, Brinton J, Simmonds J, Steuernagel B, Searle IR, Uauy C, Boden SA. MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat. SCIENCE ADVANCES 2022; 8:eabn5907. [PMID: 35544571 PMCID: PMC9094671 DOI: 10.1126/sciadv.abn5907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/25/2022] [Indexed: 05/26/2023]
Abstract
Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
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Affiliation(s)
- Laura E. Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Roshani Badgami
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Kara A. Levin
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Gernot Poschet
- Centre of Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany
| | - Pei Qin Ng
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Simon Orford
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Noam Chayut
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nikolai M. Adamski
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jemima Brinton
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Burkhard Steuernagel
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain R. Searle
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott A. Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
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17
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Reynolds MP, Slafer GA, Foulkes JM, Griffiths S, Murchie EH, Carmo-Silva E, Asseng S, Chapman SC, Sawkins M, Gwyn J, Flavell RB. A wiring diagram to integrate physiological traits of wheat yield potential. NATURE FOOD 2022; 3:318-324. [PMID: 37117579 DOI: 10.1038/s43016-022-00512-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 04/30/2023]
Abstract
As crop yields are pushed closer to biophysical limits, achieving yield gains becomes increasingly challenging and will require more insight into deterministic pathways to yields. Here, we propose a wiring diagram as a platform to illustrate the interrelationships of the physiological traits that impact wheat yield potential and to serve as a decision support tool for crop scientists. The wiring diagram is based on the premise that crop yield is a function of photosynthesis (source), the investment of assimilates into reproductive organs (sinks) and the underlying processes that enable expression of both. By illustrating these linkages as coded wires, the wiring diagram can show connections among traits that may not have been apparent, and can inform new research hypotheses and guide crosses designed to accumulate beneficial traits and alleles in breeding. The wiring diagram can also serve to create an ever-richer common point of reference for refining crop models in the future.
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Affiliation(s)
| | - Gustavo Ariel Slafer
- Catalonian Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Center for Research in Agrotechnology (AGROTECNIO), Lleida, Spain.
- University of Lleida, Lleida, Spain.
| | | | | | | | | | | | | | - Mark Sawkins
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
- Texas A&M AgriLife Research, Weslaco, TX, USA
| | - Jeff Gwyn
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
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18
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Avni R, Lux T, Minz‐Dub A, Millet E, Sela H, Distelfeld A, Deek J, Yu G, Steuernagel B, Pozniak C, Ens J, Gundlach H, Mayer KFX, Himmelbach A, Stein N, Mascher M, Spannagl M, Wulff BBH, Sharon A. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:179-192. [PMID: 34997796 PMCID: PMC10138734 DOI: 10.1111/tpj.15664] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 05/20/2023]
Abstract
Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.
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Affiliation(s)
- Raz Avni
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Anna Minz‐Dub
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Eitan Millet
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Hanan Sela
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Assaf Distelfeld
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Jasline Deek
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
| | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | | | - Curtis Pozniak
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Jennifer Ens
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
- Faculty of Life SciencesTechnical University MunichWeihenstephanMunichD‐80333Germany
| | - Axel Himmelbach
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Nils Stein
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Martin Mascher
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigPuschstrasse 4LeipzigD‐04103Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Amir Sharon
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
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Zi Y, Cheng D, Li H, Guo J, Ju W, Wang C, Humphreys DG, Liu A, Cao X, Liu C, Liu J, Zhao Z, Song J. Effects of the different waxy proteins on starch biosynthesis, starch physicochemical properties and Chinese noodle quality in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:23. [PMID: 37309456 PMCID: PMC10248619 DOI: 10.1007/s11032-022-01292-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Noodles are an important food in Asia. Wheat starch is the most important component in Chinese noodles. Loss of the waxy genes leads to lower activity of starch synthesis enzymes and decreased amylose content that further affects starch properties and noodle quality. To study the effects of different waxy (Wx) protein subunits on starch biosynthesis and processing quality, the high-yielding wheat cultivar Jimai 22 was treated with the mutagen ethyl methane sulfonate (EMS) to produce a population of Wx lines and chosen 7 Wx protein combinations. The amylose content increased but swelling power decreased as the number of Wx proteins increased. Both GBSS activity and gene expression were the lowest for the waxy mutant, followed by the mutants with 1 Wx protein. The combinations of these mutant alleles lead to reductions in both RNA expression and protein levels. Noodles made from materials with 2 Wx protein subunits had the highest score, which agreed with peak viscosity. The influence of the Wx-B1 protein on amylose synthesis and noodle quality was the highest, whereas the influence of Wx-A1 protein was the lowest. Mutants with lower amylose content caused by the absence of 1 subunit, especially the Wx-B1 subunit, had superior noodle quality. Additionally, the identified mutant lines can be used as intermediate materials to improve wheat quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01292-x.
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Affiliation(s)
- Yan Zi
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Dungong Cheng
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Haosheng Li
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jun Guo
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Wei Ju
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Canguo Wang
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - D. G. Humphreys
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, K.W. Neatby Building, 960 Carling Avenue, Ottawa, K1A 06C ON UK
| | - Aifeng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Xinyou Cao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Cheng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianjun Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Zhendong Zhao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianmin Song
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
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Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. Nat Commun 2022; 13:1607. [PMID: 35338132 PMCID: PMC8956640 DOI: 10.1038/s41467-022-29132-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance. Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
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21
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Awan MJA, Rasheed A, Saeed NA, Mansoor S. Aegilops tauschii presents a genetic roadmap for hexaploid wheat improvement. Trends Genet 2022; 38:307-309. [DOI: 10.1016/j.tig.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
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22
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Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat Biotechnol 2022; 40:422-431. [PMID: 34725503 PMCID: PMC8926922 DOI: 10.1038/s41587-021-01058-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 08/16/2021] [Indexed: 01/02/2023]
Abstract
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.
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23
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Esposito S, D'Agostino N, Taranto F, Sonnante G, Sestili F, Lafiandra D, De Vita P. Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis. Front Genet 2022; 13:1058471. [PMID: 36482886 PMCID: PMC9723387 DOI: 10.3389/fgene.2022.1058471] [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: 10/04/2022] [Accepted: 11/07/2022] [Indexed: 03/22/2023] Open
Abstract
Although wheat (Triticum aestivum L.) is the main staple crop in the world and a major source of carbohydrates and proteins, functional genomics and allele mining are still big challenges. Given the advances in next-generation sequencing (NGS) technologies, the identification of causal variants associated with a target phenotype has become feasible. For these reasons, here, by combining sequence capture and target-enrichment methods with high-throughput NGS re-sequencing, we were able to scan at exome-wide level 46 randomly selected bread wheat individuals from a recombinant inbred line population and to identify and classify a large number of single nucleotide polymorphisms (SNPs). For technical validation of results, eight randomly selected SNPs were converted into Kompetitive Allele-Specific PCR (KASP) markers. This resource was established as an accessible and reusable molecular toolkit for allele data mining. The dataset we are making available could be exploited for novel studies on bread wheat genetics and as a foundation for starting breeding programs aimed at improving different key agronomic traits.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | | | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
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24
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Jung C, Till B. Mutagenesis and genome editing in crop improvement: perspectives for the global regulatory landscape. TRENDS IN PLANT SCIENCE 2021; 26:1258-1269. [PMID: 34465535 DOI: 10.1016/j.tplants.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 05/21/2023]
Abstract
Plant breeding depends on broad genetic variation. New allelic variation can be produced by targeted or random mutagenesis. Seemingly, random mutagenesis is outdated because clustered regularly interspaced short palindromic repeats (CRISPR)-Cas technology is much more precise and potentially faster. Unfortunately, genome editing is not accessible to breeders in many countries due to legal constraints. Therefore, random mutagenesis remains a vital method to create new allelic variation. Mutant offspring, however, suffer from a heavy mutation load, and application in polyploid crops is limited because multiple mutations are typically required. Exploiting random mutations became more efficient due to recent technological advancements, such as sequence-based mutant screening and genomic background selection. In this review, random and targeted mutagenesis will be compared, highlighting the legal situation.
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Affiliation(s)
- Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany.
| | - Bradley Till
- Veterinary Genetics Laboratory, University of California, Davis, Old Davis Road, Davis, CA 95616, USA.
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25
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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding. ABIOTECH 2021; 2:375-385. [PMID: 36304421 PMCID: PMC9590522 DOI: 10.1007/s42994-021-00042-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022]
Abstract
Common wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.
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26
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van Voorthuizen MJ, Song J, Novák O, Jameson PE. Plant Growth Regulators INCYDE and TD-K Underperform in Cereal Field Trials. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112309. [PMID: 34834672 PMCID: PMC8618831 DOI: 10.3390/plants10112309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Using plant growth regulators to alter cytokinin homeostasis with the aim of enhancing endogenous cytokinin levels has been proposed as a strategy to increase yields in wheat and barley. The plant growth regulators INCYDE and CPPU inhibit the cytokinin degrading enzyme cytokinin oxidase/dehydrogenase (CKX), while TD-K inhibits the process of senescence. We report that the application of these plant growth regulators in wheat and barley field trials failed to enhance yields, or change the components of yields. Analyses of the endogenous cytokinin content showed a high concentration of trans-zeatin (tZ) in both wheat and barley grains at four days after anthesis, and statistically significant, but probably biologically insignificant, increases in cisZ-O-glucoside, along with small decreases in cZ riboside (cZR), dihydro Z (DHZ), and DHZR and DHZOG cytokinins, following INCYDE application to barley at anthesis. We discuss possible reasons for the lack of efficacy of the three plant growth regulators under field conditions and comment on future approaches to manipulating yield in the light of the strong homeostatic mechanisms controlling endogenous cytokinin levels.
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Affiliation(s)
- Matthew J. van Voorthuizen
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; (M.J.v.V.); (J.S.)
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; (M.J.v.V.); (J.S.)
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Faculty of Science of Palacký University, CZ-783 71 Olomouc, Czech Republic;
| | - Paula E. Jameson
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; (M.J.v.V.); (J.S.)
- School of Life Sciences, Yantai University, Yantai 264005, China
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27
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Lyra DH, Griffiths CA, Watson A, Joynson R, Molero G, Igna AA, Hassani-Pak K, Reynolds MP, Hall A, Paul MJ. Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel. Food Energy Secur 2021; 10:e292. [PMID: 34594548 PMCID: PMC8459250 DOI: 10.1002/fes3.292] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Trehalose 6‐phosphate (T6P) signalling regulates carbon use and allocation and is a target to improve crop yields. However, the specific contributions of trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) genes to source‐ and sink‐related traits remain largely unknown. We used enrichment capture sequencing on TPS and TPP genes to estimate and partition the genetic variation of yield‐related traits in a spring wheat (Triticum aestivum) breeding panel specifically built to capture the diversity across the 75,000 CIMMYT wheat cultivar collection. Twelve phenotypes were correlated to variation in TPS and TPP genes including plant height and biomass (source), spikelets per spike, spike growth and grain filling traits (sink) which showed indications of both positive and negative gene selection. Individual genes explained proportions of heritability for biomass and grain‐related traits. Three TPS1 homologues were particularly significant for trait variation. Epistatic interactions were found within and between the TPS and TPP gene families for both plant height and grain‐related traits. Gene‐based prediction improved predictive ability for grain weight when gene effects were combined with the whole‐genome markers. Our study has generated a wealth of information on natural variation of TPS and TPP genes related to yield potential which confirms the role for T6P in resource allocation and in affecting traits such as grain number and size confirming other studies which now opens up the possibility of harnessing natural genetic variation more widely to better understand the contribution of native genes to yield traits for incorporation into breeding programmes.
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Affiliation(s)
- Danilo H Lyra
- Computational & Analytical Sciences Rothamsted Research Harpenden UK
| | | | - Amy Watson
- Plant Sciences Rothamsted Research Harpenden UK
| | | | - Gemma Molero
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT) Texcoco Mexico
| | | | | | - Matthew P Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT) Texcoco Mexico
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28
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Ji G, Xu Z, Fan X, Zhou Q, Yu Q, Liu X, Liao S, Feng B, Wang T. Identification of a major and stable QTL on chromosome 5A confers spike length in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:56. [PMID: 37309397 PMCID: PMC10236030 DOI: 10.1007/s11032-021-01249-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/29/2021] [Indexed: 06/14/2023]
Abstract
Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a cross between 13F10 and Chuanmai 42 (CM42) were evaluated for spike length in six environments. Sixty RILs consisting of 30 high and 30 low SLs were genotyped using the bulked segregant analysis exome sequencing (BSE-Seq) analysis for preliminary quantitative trait locus (QTL) mapping. A 6.69 Mb (518.43-525.12 Mb) region on chromosome 5AL was found to have a significant effect on the SL trait. Fifteen competitive allele-specific PCR (KASP) markers were successfully converted from the single nucleotide polymorphisms (SNPs) in the SL target region. Combined with four novel simple sequence repeat (SSR) markers, a genetic linkage map spanning 21.159 cM was constructed. The mapping result confirmed the identity of a major and stable QTL named QSl.cib-5A in the targeted region that explained 7.88-26.60% of the phenotypic variation in SL. QSl.cib-5A was narrowed to a region of 4.84 cM interval corresponding to a 4.67 Mb (516.60-521.27 Mb) physical region in the Chinese Spring RefSeq v2.0 containing 17 high-confidence genes with 25 transcripts. In addition, this QTL exhibited pleiotropic effects on spikelet density (SD), with the phenotypic variances proportion ranging from 11.34 to 19.92%. This study provides a foundational step for cloning the QSl.cib-5A, which is involved in the regulation of spike morphology in common wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01249-6.
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Affiliation(s)
- Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
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29
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Hafeez AN, Arora S, Ghosh S, Gilbert D, Bowden RL, Wulff BBH. Creation and judicious application of a wheat resistance gene atlas. MOLECULAR PLANT 2021; 14:1053-1070. [PMID: 33991673 DOI: 10.1016/j.molp.2021.05.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 05/18/2023]
Abstract
Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.
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Affiliation(s)
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - David Gilbert
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert L Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
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Xie Y, Ravet K, Pearce S. Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.). BMC Genomics 2021; 22:218. [PMID: 33765923 PMCID: PMC7995804 DOI: 10.1186/s12864-021-07475-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bowman-Birk inhibitors (BBI) are a family of serine-type protease inhibitors that modulate endogenous plant proteolytic activities during different phases of development. They also inhibit exogenous proteases as a component of plant defense mechanisms, and their overexpression can confer resistance to phytophagous herbivores and multiple fungal and bacterial pathogens. Dicot BBIs are multifunctional, with a "double-headed" structure containing two separate inhibitory loops that can bind and inhibit trypsin and chymotrypsin proteases simultaneously. By contrast, monocot BBIs have a non-functional chymotrypsin inhibitory loop, although they have undergone internal duplication events giving rise to proteins with multiple BBI domains. RESULTS We used a Hidden Markov Model (HMM) profile-based search to identify 57 BBI genes in the common wheat (Triticum aestivum L.) genome. The BBI genes are unevenly distributed, with large gene clusters in the telomeric regions of homoeologous group 1 and 3 chromosomes that likely arose through a series of tandem gene duplication events. The genomes of wheat progenitors also contain contiguous clusters of BBI genes, suggesting this family underwent expansion before the domestication of common wheat. However, the BBI gene family varied in size among different cultivars, showing this family remains dynamic. Because of these expansions, the BBI gene family is larger in wheat than other monocots such as maize, rice and Brachypodium. We found BBI proteins in common wheat with intragenic homologous duplications of cysteine-rich functional domains, including one protein with four functional BBI domains. This diversification may expand the spectrum of target substrates. Expression profiling suggests that some wheat BBI proteins may be involved in regulating endogenous proteases during grain development, while others were induced in response to biotic and abiotic stresses, suggesting a role in plant defense. CONCLUSIONS Genome-wide characterization reveals that the BBI gene family in wheat is subject to a high rate of homologous tandem duplication and deletion events, giving rise to a diverse set of encoded proteins. This information will facilitate the functional characterization of individual wheat BBI genes to determine their role in wheat development and stress responses, and their potential application in breeding.
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Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BB. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:273-284. [PMID: 32744350 PMCID: PMC7868974 DOI: 10.1111/pbi.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/17/2020] [Indexed: 05/16/2023]
Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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Affiliation(s)
- M. Asyraf Md Hatta
- John Innes CentreNorwich Research ParkNorwichUK
- Department of Agriculture TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
| | - Sanu Arora
- John Innes CentreNorwich Research ParkNorwichUK
| | - Sreya Ghosh
- John Innes CentreNorwich Research ParkNorwichUK
| | - Oadi Matny
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
| | | | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichUK
| | - Soma Chakraborty
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Matthew N. Rouse
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
- USDA‐ARS Cereal Disease LaboratorySt. PaulMNUSA
| | | | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Brian J. Steffenson
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
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32
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Wu L, Han L, Li Q, Wang G, Zhang H, Li L. Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding. MOLECULAR PLANT 2021; 14:77-94. [PMID: 33340690 DOI: 10.1016/j.molp.2020.12.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 05/27/2023]
Abstract
The functional genes underlying phenotypic variation and their interactions represent "genetic mysteries". Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences. Due to advances in high-throughput multi-omics technologies, we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research. In this article, we provide a brief overview of current strategies to explore genetic mysteries. We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources. Next, we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries. We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning, which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits, and also provide a detailed procedure for systematic dissection of genetic mysteries,. Finally, we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.
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Affiliation(s)
- Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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33
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Li Y, Xiong H, Zhang J, Guo H, Zhou C, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Fang Z, Liu L. Genome-Wide and Exome-Capturing Sequencing of a Gamma-Ray-Induced Mutant Reveals Biased Variations in Common Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:793496. [PMID: 35095966 PMCID: PMC8790116 DOI: 10.3389/fpls.2021.793496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 05/13/2023]
Abstract
Induced mutagenesis is a powerful approach for the creation of novel germplasm and the improvement of agronomic traits. The evaluation of mutagenic effects and functional variations in crops is needed for breeding mutant strains. To investigate the mutagenic effects of gamma-ray irradiation in wheat, this study characterized genomic variations of wheat early heading mutant (eh1) as compared to wild-type (WT) Zhongyuan 9 (ZY9). Whole-genome resequencing of eh1 and ZY9 produced 737.7 Gb sequencing data and identified a total of 23,537,117 homozygous single nucleotide polymorphism (SNP) and 1,608,468 Indel. Analysis of SNP distribution across the chromosome suggests that mutation hotspots existed in certain chromosomal regions. Among the three subgenomes, the variation frequency in subgenome D was significantly lower than in subgenomes A and B. A total of 27.8 Gb data were obtained by exome-capturing sequencing, while 217,948 SNP and 13,554 Indel were identified. Variation annotation in the gene-coding sequences demonstrated that 5.0% of the SNP and 5.3% of the Indel were functionally important. Characterization of exomic variations in 12 additional gamma-ray-induced mutant lines further provided additional insights into the mutagenic effects of this approach. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis suggested that genes with functional variations were enriched in several metabolic pathways, including plant-pathogen interactions and ADP binding. Kompetitive allele-specific PCR (KASP) genotyping with selected SNP within functional genes indicated that 85.7% of the SNPs were polymorphic between the eh1 and wild type. This study provides a basic understanding of the mechanism behind gamma-ray irradiation in hexaploid wheat.
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Affiliation(s)
- Yuting Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiazi Zhang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengwu Fang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- Zhengwu Fang,
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Luxiang Liu,
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Jameson PE, Song J. Will cytokinins underpin the second 'Green Revolution'? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6872-6875. [PMID: 33382897 PMCID: PMC8202814 DOI: 10.1093/jxb/eraa447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This article comments on: Schwarz I, Scheirlinck MT, Otto E, Bartrina I, Schmidt RC, Schmülling T. 2020. Cytokinin regulates the activity of the inflorescence meristem and components of seed yield in oilseed rape. Journal of Experimental Botany 71, 7146–7159.
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Affiliation(s)
- Paula E Jameson
- School of Life Sciences, Yantai University,
Yantai, China
- School of Biological Sciences, University of
Canterbury, Christchurch, New Zealand
- Correspondence:
| | - Jiancheng Song
- School of Life Sciences, Yantai University,
Yantai, China
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35
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Fu Y, Cheng M, Li M, Guo X, Wu Y, Wang J. Identification and Characterization of PLATZ Transcription Factors in Wheat. Int J Mol Sci 2020; 21:E8934. [PMID: 33255649 PMCID: PMC7728089 DOI: 10.3390/ijms21238934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022] Open
Abstract
The PLATZ (plant AT-rich protein and zinc-binding protein) transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins. PLATZ has essential roles in seed endosperm development, as well as promoting cell proliferation duration in the earlier stages of the crops. In the present study, 62 TaPLATZ genes were identified from the wheat genome, and they were unequally distributed on 15 chromosomes. According to the phylogenetic analysis, 62 TaPLATZ genes were classified into six groups, including two groups that were unique in wheat. Members in the same groups shared similar exon-intron structures. The polyploidization, together with genome duplication of wheat, plays a crucial role in the expansion of the TaPLATZs family. Transcriptome data indicated a distinct divergence expression pattern of TaPLATZ genes that could be clustered into four modules. The TaPLATZs in Module b possessed a seed-specific expression pattern and displayed obvious high expression in the earlier development stage of seeds. Subcellular localization data of TaPLATZs suggesting that they likely perform a function as a conventional transcription factor. This study provides insight into understanding the structure divergence, evolutionary features, expression profiles, and potential function of PLATZ in wheat.
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Affiliation(s)
- Yuxin Fu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (M.C.); (M.L.); (X.G.)
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Mengping Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (M.C.); (M.L.); (X.G.)
- Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Ministry of Education, Chengdu 611130, China
| | - Maolian Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (M.C.); (M.L.); (X.G.)
- Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Ministry of Education, Chengdu 611130, China
| | - Xiaojiang Guo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (M.C.); (M.L.); (X.G.)
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (M.C.); (M.L.); (X.G.)
- Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Ministry of Education, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Use in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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36
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Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5808-5822. [PMID: 32725154 DOI: 10.1093/jxb/eraa355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Chuan Ge
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Wenyun Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Linyi Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Guan P, Shen X, Mu Q, Wang Y, Wang X, Chen Y, Zhao Y, Chen X, Zhao A, Mao W, Guo Y, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Peng H. Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2639-2653. [PMID: 32488301 DOI: 10.1007/s00122-020-03622-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/22/2020] [Indexed: 05/23/2023]
Abstract
This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population. Here, near-isogenic lines (NILs) in the ND3338 background were developed to dissect and validate the QTL cluster. Based on six independent BC3F3:4 heterogeneous inbred families, the 4B QTL cluster was divided into two linked QTL intervals (designated 4B.1 and 4B.2 QTL). For the 4B.1 QTL, the Rht-B1 gene, of which Rht-B1b allele reduces plant height (PH) by 21.18-29.34 cm (34.34-53.71%), was demonstrated to be the most likely candidate gene with pleiotropic effects on grain size and TGW. For the 4B.2 QTL, the NILJD6 consistently showed an increase in TGW of 3.51-7.68 g (8.84-22.77%) compared with NILND3338 across different field trials, along with a significant increase in PH of 2.26-6.71 cm (3.92-12.01%). Moreover, both QTL intervals had a larger effect on grain width than on grain length. Additionally, the first significant difference in 100-grain fresh weight and 100-grain dry weight between the NIL pairs of the 4B.1 QTL interval (Rht-B1) was observed at 6 days after pollination (DAP), while the differences were first visible at 30 DAP for the 4B.2 QTL interval. Collectively, our work provides a new example of QTL dissection for grain weight in wheat and lays a foundation for further map-based cloning of the major QTL that have potential applications in wheat molecular breeding for high yield.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yue Zhao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiyong Chen
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Weiwei Mao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yiwen Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Jiang C, Kan J, Ordon F, Perovic D, Yang P. Bymovirus-induced yellow mosaic diseases in barley and wheat: viruses, genetic resistances and functional aspects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1623-1640. [PMID: 32008056 DOI: 10.1007/s00122-020-03555-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/24/2020] [Indexed: 05/20/2023]
Abstract
Bymovirus-induced yellow mosaic diseases seriously threaten global production of autumn-sown barley and wheat, which are two of the presently most important crops around the world. Under natural field conditions, the diseases are caused by infection of soil-borne plasmodiophorid Polymyxa graminis-transmitted bymoviruses of the genus Bymovirus of the family Potyviridae. Focusing on barley and wheat, this article summarizes the achievements on taxonomy, geography and host specificity of these disease-conferring viruses, as well as the genetics of resistance in barley, wheat and wild relatives. Moreover, based on recent progress of barley and wheat genomics, germplasm resources and large-scale sequencing, the exploration and isolation of corresponding resistant genes from wheat and barley as well as relatives, no matter what a large and complicated genome is present, are becoming feasible and are discussed. Furthermore, the foreseen advances on cloning of the resistance or susceptibility-encoding genes, which will provide the possibility to explore the functional interaction between host plants and soil-borne viral pathogens, are discussed as well as the benefits for marker-assisted resistance breeding in barley and wheat.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China.
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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Chen L, Zhao J, Song J, Jameson PE. Cytokinin dehydrogenase: a genetic target for yield improvement in wheat. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:614-630. [PMID: 31782596 PMCID: PMC7004901 DOI: 10.1111/pbi.13305] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/19/2019] [Indexed: 05/04/2023]
Abstract
The plant hormone group, the cytokinins, is implicated in both qualitative and quantitative components of yield. Cytokinins have opposing actions in shoot and root growth-actions shown to involve cytokinin dehydrogenase (CKX), the enzyme that inactivates cytokinin. We revise and provide unambiguous names for the CKX gene family members in wheat, based on the most recently released wheat genome database, IWGSC RefSeq v1.0 & v2.0. We review expression data of CKX gene family members in wheat, revealing tissue-specific gene family member expression as well as sub-genome-specific expression. Manipulation of CKX in cereals shows clear impacts on yield, root growth and orientation, and Zn nutrition, but this also emphasizes the necessity to unlink promotive effects on grain yield from negative effects of cytokinin on root growth and uptake of mineral nutrients, particularly Zn and Fe. Wheat is the most widely grown cereal crop globally, yet is under-research compared with rice and maize. We highlight gaps in our knowledge of the involvement of CKX for wheat. We also highlight the necessity for accurate analysis of endogenous cytokinins, acknowledging why this is challenging, and provide examples where inadequate analyses of endogenous cytokinins have led to unjustified conclusions. We acknowledge that the allohexaploid nature of bread wheat poses challenges in terms of uncovering useful mutations. However, we predict TILLING followed by whole-exome sequencing will uncover informative mutations and we indicate the potential for stacking mutations within the three genomes to modify yield components. We model a wheat ideotype based on CKX manipulation.
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Affiliation(s)
- Lei Chen
- School of Life SciencesYantai UniversityYantaiChina
| | - Jiqiang Zhao
- School of Life SciencesYantai UniversityYantaiChina
| | | | - Paula E. Jameson
- School of Life SciencesYantai UniversityYantaiChina
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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Martinez SA, Shorinola O, Conselman S, See D, Skinner DZ, Uauy C, Steber CM. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:719-736. [PMID: 31993676 PMCID: PMC7021667 DOI: 10.1007/s00122-019-03503-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 05/09/2023]
Abstract
Using bulked segregant analysis of exome sequence, we fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3-A locus of chromosome 4A. Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 (ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat 'Zak.' ERA8 was mapped to chromosome 4A in a Zak/'ZakERA8' backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA-hypersensitive phenotype was strongly linked to a missense mutation in TaMKK3-A-G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an 'Otis'/ZakERA8 but not in a 'Louise'/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS-tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3-A-G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3-A-G1093A mutation.
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Affiliation(s)
- Shantel A Martinez
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | | | - Samantha Conselman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Deven See
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Daniel Z Skinner
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Camille M Steber
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA.
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42
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Sashidhar N, Harloff HJ, Jung C. Identification of phytic acid mutants in oilseed rape (Brassica napus) by large-scale screening of mutant populations through amplicon sequencing. THE NEW PHYTOLOGIST 2020; 225:2022-2034. [PMID: 31651044 DOI: 10.1111/nph.16281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/11/2019] [Indexed: 05/18/2023]
Abstract
Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants. We implemented a high-throughput next-generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2-PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene. A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2-PGK2 showed a significant reduction of phytic acid contents. We propose to use three-dimensional pooling combined with amplicon stacking and next-generation sequencing to identify mutations in polyploid oilseed rape in a fast and cost-effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2-PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.
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Affiliation(s)
- Niharika Sashidhar
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
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43
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Lavergne FD, Broeckling CD, Brown KJ, Cockrell DM, Haley SD, Peairs FB, Pearce S, Wolfe LM, Jahn CE, Heuberger AL. Differential Stem Proteomics and Metabolomics Profiles for Four Wheat Cultivars in Response to the Insect Pest Wheat Stem Sawfly. J Proteome Res 2020; 19:1037-1051. [PMID: 31995381 DOI: 10.1021/acs.jproteome.9b00561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Common wheat (Triticum aestivum L.) is a global staple crop, and insect pests can impact grain yield. The wheat stem sawfly (Cephus cinctus, WSS) is a major wheat pest, and while partial resistance has been deployed by breeding for a solid-stem trait, this trait is affected by environment. Here, a proteomics and metabolomics study was performed on four wheat cultivars to characterize a molecular response to WSS infestation. The cultivars Hatcher (hollow-stem partially tolerant), Conan (semisolid-stem-resistant), and Denali and Reeder (hollow-stem-susceptible) were infested with WSS, and changes in stem proteins and metabolites were characterized using liquid chromatography-mass spectrometry. The proteome was characterized as 1830 proteins that included five major biological processes, including metabolic processes and response to stimuli, and the metabolome (1823 metabolites) spanned eight chemical superclasses, including alkaloids, benzenoids, and lipids. All four varieties had a molecular response to WSS following infestation. Hatcher had the most distinct changes, whereby 62 proteins and 29 metabolites varied in metabolic pathways involving enzymatic detoxification, proteinase inhibition, and antiherbivory compound production via benzoxazinoids, neolignans, and phenolics. Taken together, these data demonstrate variation in the wheat stem molecular response to WSS infestation and support breeding for molecular resistance in hollow-stem cultivars.
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Affiliation(s)
- Florent D Lavergne
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Corey D Broeckling
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado 80523, United States.,Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kitty J Brown
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Darren M Cockrell
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Scott D Haley
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Frank B Peairs
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Courtney E Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado 80523, United States.,Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
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Guo H, Xiong H, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Functional mutation allele mining of plant architecture and yield-related agronomic traits and characterization of their effects in wheat. BMC Genet 2019; 20:102. [PMID: 31888475 PMCID: PMC6937682 DOI: 10.1186/s12863-019-0804-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Wheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. Plant architecture and yield-related features are important agronomic traits for wheat breeders and mining favorable alleles of these traits will improve wheat characteristics. RESULTS Here we used 190 wheat phenotypic mutants as material and by analyzing their SNP variation and phenotypic data, mutation alleles for plant architecture and yield-related traits were identified, and the genetic effects of these alleles were evaluated. In total, 32 mutation alleles, including three pleiotropic alleles, significantly associated with agronomic traits were identified from the 190 wheat mutant lines. The SNPs were distributed on 12 chromosomes and were associated with plant height (PH), tiller number, flag leaf angle (FLA), thousand grain weight (TGW), and other yield-related traits. Further phenotypic analysis of multiple lines carrying the same mutant allele was performed to determine the effect of the allele on the traits of interest. PH-associated SNPs on chromosomes 2BL, 3BS, 3DL, and 5DL might show additive effects, reducing PH by 10.0 cm to 31.3 cm compared with wild type, which means that these alleles may be favorable for wheat improvement. Only unfavorable mutation alleles that reduced TGW and tiller number were identified. A region on chromosome 5DL with mutation alleles for PH and TGW contained several long ncRNAs, and their sequences shared more than 90% identity with cytokinin oxidase/dehydrogenase genes. Some of the mutation alleles we mined were colocalized with previously reported QTLs or genes while others were novel; these novel alleles could also result in phenotypic variation. CONCLUSION Our results demonstrate that favorable mutation alleles are present in mutant resources, and the region between 409.5 to 419.8 Mb on chromosome 5DL affects wheat plant height and thousand grain weight.
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Affiliation(s)
- Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yuping Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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Sestili F, Garcia-Molina MD, Gambacorta G, Beleggia R, Botticella E, De Vita P, Savatin DV, Masci S, Lafiandra D. Provitamin A Biofortification of Durum Wheat through a TILLING Approach. Int J Mol Sci 2019; 20:E5703. [PMID: 31739436 PMCID: PMC6888361 DOI: 10.3390/ijms20225703] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
Macro- and micronutrients, essential for the maintenance of human metabolism, are assimilated daily through the diet. Wheat and other major cereals are a good source of nutrients, such as carbohydrates and proteins, but cannot supply a sufficient amount of essential micronutrients, including provitamin A. As vitamin A deficiency (VAD) leads to several serious diseases throughout the world, the biofortification of a major staple crop, such as wheat, represents an effective way to preserve human health in developing countries. In the present work, a key enzyme involved in the branch of carotenoids pathway producing β-carotene, lycopene epsilon cyclase, has been targeted by a Targeting Induced Local Lesions in Genomes (TILLING) approach in a "block strategy" perspective. The null mutant genotype showed a strong reduction in the expression of the lcyE gene and also interesting pleiotropic effects on an enzyme (β-ring hydroxylase) acting downstream in the pathway. Biochemical profiling of carotenoids in the wheat mutant lines showed an increase of roughly 75% in β-carotene in the grains of the complete mutant line compared with the control. In conclusion, we describe here the production and characterization of a new wheat line biofortified with provitamin A obtained through a nontransgenic approach, which also sheds new light on the molecular mechanism governing carotenoid biosynthesis in durum wheat.
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Affiliation(s)
- Francesco Sestili
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Maria Dolores Garcia-Molina
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Gianluca Gambacorta
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (P.D.V.)
| | - Ermelinda Botticella
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (P.D.V.)
| | - Daniel Valentin Savatin
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Stefania Masci
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
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Ingvardsen CR, Massange-Sánchez JA, Borum F, Uauy C, Gregersen PL. Development of mlo-based resistance in tetraploid wheat against wheat powdery mildew. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3009-3022. [PMID: 31317234 DOI: 10.1007/s00122-019-03402-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/11/2019] [Indexed: 05/12/2023]
Abstract
Powdery mildew is a severe disease in wheat. In barley, durable resistance exists, based on non-functionality of the Mlo gene. As a model to analyse the effects of mutagenesis in the homoeologous Mlo genes of wheat, we developed mlo-based powdery mildew resistance in tetraploid durum wheat. To obtain Mlo mutations, we screened a TILLING population developed in tetraploid wheat "Kronos" for which the captured exome sequence of > 1500 lines is available. This resulted in 23 mutants for Mlo-A1 and 26 non-redundant mutants for Mlo-B1. Two Mlo-A1 and four Mlo-B1 mutants were crossed to obtain eight F2 mutant lines that showed a range of phenotypes from susceptibility to full resistance. Pot experiments under semi-field conditions confirmed the resistance levels for six of the mutants without any signs of adverse pleiotropic effects. Resistance ranking was similar across six powdery mildew isolates, indicating no isolate specificity of the mlo-based resistance. The effect of mutations in the Mlo-B1 gene was stronger than in the Mlo-A1 gene, probably reflecting differences in wild-type Mlo gene expression levels. Strong partial resistance effects were observed with single mlo-B1 mutations hence, revealing a dosage effect of mlo mutant alleles. Two of the four mlo-B1 mutations (W163* and P335L) were very strong; however, the highest combined effect was observed with the MloA-P335S/MloB-P335L combination, suggesting that non-functional, but full-length Mlo proteins might have the strongest effect compared with nonsense mutations. Our results show that mlo-based resistance might offer possibilities to introduce durable protection in tetraploid wheat against powdery mildew.
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Affiliation(s)
- Christina R Ingvardsen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
| | - Julio A Massange-Sánchez
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
- CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark.
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Harrington SA, Overend LE, Cobo N, Borrill P, Uauy C. Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence. BMC PLANT BIOLOGY 2019; 19:407. [PMID: 31533618 PMCID: PMC6749658 DOI: 10.1186/s12870-019-2022-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/06/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND NAC transcription factors contain five highly conserved subdomains which are required for protein dimerisation and DNA binding. Few residues within these subdomains have been identified as essential for protein function, and fewer still have been shown to be of biological relevance in planta. Here we use a positive regulator of senescence in wheat, NAM-A1, to test the impact of missense mutations at specific, highly conserved residues of the NAC domain on protein function. RESULTS We identified missense mutations in five highly conserved residues of the NAC domain of NAM-A1 in a tetraploid TILLING population. TILLING lines containing these mutations, alongside synonymous and non-conserved mutation controls, were grown under glasshouse conditions and scored for senescence. Four of the five mutations showed a significant and consistent delay in peduncle senescence but had no consistent effects on flag leaf senescence. All four mutant alleles with the delayed senescence phenotype also lost the ability to interact with the homoeolog NAM-B1 in a yeast two-hybrid assay. Two of these residues were previously shown to be involved in NAC domain function in Arabidopsis, suggesting conservation of residue function between species. Three of these four alleles led to an attenuated cell death response compared to wild-type NAM-A1 when transiently over-expressed in Nicotiana benthamiana. One of these mutations was further tested under field conditions, in which there was a significant and consistent delay in both peduncle and leaf senescence. CONCLUSIONS We combined field and glasshouse studies of a series of mutant alleles with biochemical analyses to identify four residues of the NAC domain which are required for NAM-A1 function and protein interaction. We show that mutations in these residues lead to a gradient of phenotypes, raising the possibility of developing allelic series of mutations for traits of agronomic importance. We also show that mutations in NAM-A1 more severely impact peduncle senescence, compared to the more commonly studied flag leaf senescence, highlighting this as an area deserving of further study. The results from this integrated approach provide strong evidence that conserved residues within the functional domains of NAC transcription factors have biological significance in planta.
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Affiliation(s)
| | | | - Nicolas Cobo
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Philippa Borrill
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Harrington SA, Overend LE, Cobo N, Borrill P, Uauy C. Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence. BMC PLANT BIOLOGY 2019; 19:407. [PMID: 31533618 DOI: 10.1101/573881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/06/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND NAC transcription factors contain five highly conserved subdomains which are required for protein dimerisation and DNA binding. Few residues within these subdomains have been identified as essential for protein function, and fewer still have been shown to be of biological relevance in planta. Here we use a positive regulator of senescence in wheat, NAM-A1, to test the impact of missense mutations at specific, highly conserved residues of the NAC domain on protein function. RESULTS We identified missense mutations in five highly conserved residues of the NAC domain of NAM-A1 in a tetraploid TILLING population. TILLING lines containing these mutations, alongside synonymous and non-conserved mutation controls, were grown under glasshouse conditions and scored for senescence. Four of the five mutations showed a significant and consistent delay in peduncle senescence but had no consistent effects on flag leaf senescence. All four mutant alleles with the delayed senescence phenotype also lost the ability to interact with the homoeolog NAM-B1 in a yeast two-hybrid assay. Two of these residues were previously shown to be involved in NAC domain function in Arabidopsis, suggesting conservation of residue function between species. Three of these four alleles led to an attenuated cell death response compared to wild-type NAM-A1 when transiently over-expressed in Nicotiana benthamiana. One of these mutations was further tested under field conditions, in which there was a significant and consistent delay in both peduncle and leaf senescence. CONCLUSIONS We combined field and glasshouse studies of a series of mutant alleles with biochemical analyses to identify four residues of the NAC domain which are required for NAM-A1 function and protein interaction. We show that mutations in these residues lead to a gradient of phenotypes, raising the possibility of developing allelic series of mutations for traits of agronomic importance. We also show that mutations in NAM-A1 more severely impact peduncle senescence, compared to the more commonly studied flag leaf senescence, highlighting this as an area deserving of further study. The results from this integrated approach provide strong evidence that conserved residues within the functional domains of NAC transcription factors have biological significance in planta.
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Affiliation(s)
| | | | - Nicolas Cobo
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Philippa Borrill
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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Shorinola O, Kaye R, Golan G, Peleg Z, Kepinski S, Uauy C. Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform. G3 (BETHESDA, MD.) 2019; 9:2799-2809. [PMID: 31352407 PMCID: PMC6723138 DOI: 10.1534/g3.119.400537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022]
Abstract
Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.
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Affiliation(s)
- Oluwaseyi Shorinola
- Bioscience Eastern and Central Africa - International Livestock Research Institute, Nairobi, PO Box 30709, Kenya
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan Kaye
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Guan P, Di N, Mu Q, Shen X, Wang Y, Wang X, Yu K, Song W, Chen Y, Xin M, Hu Z, Guo W, Yao Y, Ni Z, Sun Q, Peng H. Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2367-2379. [PMID: 31119311 DOI: 10.1007/s00122-019-03359-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent through marker-assisted selection. Based on five independent BC3F3:4 segregating populations derived from BC3F3 plants with different heterozygous segments for the target QTL site and the results of genotyping analysis performed using the Wheat660 K SNP array, it was possible to delimit the QTL region to a physical interval of approximately 6.5 Mb (677.11-683.61 Mb, IWGSC Ref Seq v1.0). Field trials across multiple environments showed that NILsJD6 had a consistent effect on increasing the TGW by 5.16-27.48% and decreasing the grain number per spike (GNS) by 3.98-32.91% compared to the corresponding NILsND3338, which exhibited locus-specific TGW-GNS trade-offs. Moreover, by using RNA sequencing (RNA-Seq) of whole grains at 10 days after pollination stage of multiple NILs, we found that differentially expressed genes between the NIL pairs were significantly enriched for cell cycle and the replication of chromosome-related genes, hence affecting cell division and cell proliferation. Overall, our results provide a basis for map-based cloning of the major QTL and determining the mechanisms underlying TGW-GNS trade-offs in wheat, which would help to fine-tune these two components and maximize the grain yield for breeders.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Na Di
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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