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Wang M, Cheng J, Wu J, Chen J, Liu D, Wang C, Ma S, Guo W, Li G, Di D, Zhang Y, Han D, Kronzucker HJ, Xia G, Shi W. Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits. Nat Genet 2024:10.1038/s41588-024-01762-2. [PMID: 38802564 DOI: 10.1038/s41588-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
Na+ exclusion from above-ground tissues via the Na+-selective transporter HKT1;5 is a major salt-tolerance mechanism in crops. Using the expression genome-wide association study and yeast-one-hybrid screening, we identified TaSPL6-D, a transcriptional suppressor of TaHKT1;5-D in bread wheat. SPL6 also targeted HKT1;5 in rice and Brachypodium. A 47-bp insertion in the first exon of TaSPL6-D resulted in a truncated peptide, TaSPL6-DIn, disrupting TaHKT1;5-D repression exhibited by TaSPL6-DDel. Overexpressing TaSPL6-DDel, but not TaSPL6-DIn, led to inhibited TaHKT1;5-D expression and increased salt sensitivity. Knockout of TaSPL6-DDel in two wheat genotypes enhanced salinity tolerance, which was attenuated by a further TaHKT1;5-D knockdown. Spike development was preserved in Taspl6-dd mutants but not in Taspl6-aabbdd mutants. TaSPL6-DIn was mainly present in landraces, and molecular-assisted introduction of TaSPL6-DIn from a landrace into a leading wheat cultivar successfully improved yield on saline soils. The SPL6-HKT1;5 module offers a target for the molecular breeding of salt-tolerant crops.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China.
- University of Chinese Academy of Sciences, Beijing, P. R. China.
| | - Jie Cheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Jiefei Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Dan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Chenyang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China
| | - Weiwei Guo
- Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, P. R. China
| | - Guangjie Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Dongwei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Yumei Zhang
- Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Herbert J Kronzucker
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, P. R. China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, P. R. China
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Hussain A, Khan AA, Aslam MQ, Nazar A, Zaman N, Amin A, Mahmood MA, Mukhtar MS, Rahman HUU, Farooq M, Saeed M, Amin I, Mansoor S. Comparative analysis, diversification, and functional validation of plant nucleotide-binding site domain genes. Sci Rep 2024; 14:11930. [PMID: 38789717 PMCID: PMC11126693 DOI: 10.1038/s41598-024-62876-5] [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: 10/26/2023] [Accepted: 05/22/2024] [Indexed: 05/26/2024] Open
Abstract
Nucleotide-binding site (NBS) domain genes are one of the superfamily of resistance genes involved in plant responses to pathogens. The current study identified 12,820 NBS-domain-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes are classified into 168 classes with several novel domain architecture patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR, etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2, etc.) and unique (highly specific to species; OG80, OG82, etc.) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6, and OG15 in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to cotton leaf curl disease (CLCuD). The genetic variation between susceptible (Coker 312) and tolerant (Mac7) Gossypium hirsutum accessions identified several unique variants in NBS genes of Mac7 (6583 variants) and Coker312 (5173 variants). The protein-ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of the cotton leaf curl disease virus. The silencing of GaNBS (OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful in understanding the plant adaptation mechanism.
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Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan.
| | - Aqsa Anwer Khan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Aquib Nazar
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Nadir Zaman
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Ayesha Amin
- Department of Biological Sciences, Superior University, Lahore, 54000, Pakistan
| | - Muhammad Arslan Mahmood
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - M Shahid Mukhtar
- Biosystems Research Complex, Department of Genetics & Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Hafiz Ubaid Ur Rahman
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammed Farooq
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Muhammed Saeed
- Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau Abteilung Phytopathologie, Paul-Ehrlich-Straße 22, 67653, Kaiserslautern, Germany
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- Jamil ur Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 74000, Pakistan.
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Peters Haugrud AR, Achilli AL, Martínez-Peña R, Klymiuk V. Future of durum wheat research and breeding: Insights from early career researchers. THE PLANT GENOME 2024:e20453. [PMID: 38760906 DOI: 10.1002/tpg2.20453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/20/2024]
Abstract
Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.
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Affiliation(s)
- Amanda R Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Ana Laura Achilli
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raquel Martínez-Peña
- Regional Institute of Agri-Food and Forestry Research and Development of Castilla-La Mancha (IRIAF), Agroenvironmental Research Center El Chaparrillo, Ciudad Real, Spain
| | - Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Xu B, Shen T, Chen H, Li H, Rehman SU, Lyu S, Hua L, Wang G, Zhang C, Li K, Li H, Lan C, Chen GY, Hao M, Chen S. Mapping and characterization of rust resistance genes Lr53 and Yr35 introgressed from Aegilops species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:113. [PMID: 38678511 PMCID: PMC11056342 DOI: 10.1007/s00122-024-04616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
Abstract
KEY MESSAGE The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the ph1b mutation obtained from the cross 98M71 × CSph1b, both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs.
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Affiliation(s)
- Binyang Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100000, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Shams Ur Rehman
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Shikai Lyu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Chaozhong Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kairong Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guo-Yue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China.
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Li H, Men W, Ma C, Liu Q, Dong Z, Tian X, Wang C, Liu C, Gill HS, Ma P, Zhang Z, Liu B, Zhao Y, Sehgal SK, Liu W. Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein. Nat Commun 2024; 15:2449. [PMID: 38503771 PMCID: PMC10951266 DOI: 10.1038/s41467-024-46814-7] [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: 04/21/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.
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Affiliation(s)
- Huanhuan Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Wenqiang Men
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Chao Ma
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qianwen Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, PR China
| | - Xiubin Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Chaoli Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250000, PR China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, PR China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Yue Zhao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [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: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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8
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Liu J, Wei L, Wu Y, Wang Z, Wang H, Xiao J, Wang X, Sun L. Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat. BMC Genomics 2024; 25:209. [PMID: 38408894 PMCID: PMC10895793 DOI: 10.1186/s12864-024-10114-7] [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: 10/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. RESULTS To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance. CONCLUSION Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.
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Affiliation(s)
- Jia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
- Jinhua Academy, Zhejiang Chinese Medical University, Jinhua, 321000, China
| | - Luyang Wei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Yirong Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Zongkuan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Jin Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
| | - Li Sun
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
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9
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Liu Y, Zheng C, Su X, Chen J, Li X, Sun C, Nizamani MM. Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits. BMC Genom Data 2024; 25:10. [PMID: 38287264 PMCID: PMC10826016 DOI: 10.1186/s12863-024-01197-y] [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: 09/28/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Krascheninnikovia ceratoides, a perennial halophytic semi-shrub belonging to the genus Krascheninnikovia (Amarathaceae), possesses noteworthy ecological, nutritional, and economic relevance. This species is primarily distributed across arid, semi-arid, and saline-alkaline regions of the Eurasian continent, encompassing Inner Mongolia, Xinjiang, Qinghai, Gansu, Ningxia, and Tibet. RESULTS We reported the comprehensive chloroplast (cp) genome of K. ceratoides, characterized by a circular conformation spanning 151,968 bp with a GC content of 36.60%. The cp genome encompassed a large single copy (LSC, 84,029 bp), a small single copy (SSC, 19,043 bp), and a pair of inverted repeats (IRs) regions (24,448 bp each). This genome harbored 128 genes and encompassed 150 simple sequence repeats (SSRs). Through comparative analyses involving cp genomes from other Cyclolobeae (Amarathaceae) taxa, we observed that the K. ceratoides cp genome exhibited high conservation, with minor divergence events in protein-coding genes (PCGs) accD, matK, ndhF, ndhK, ycf1, and ycf2. Phylogenetic reconstructions delineated K. ceratoides as the sister taxon to Atriplex, Chenopodium, Dysphania, and Suaeda, thus constituting a robust clade. Intriguingly, nucleotide substitution ratios (Ka/Ks) between K. ceratoides and Dysphania species for ycf1 and ycf2 genes surpassed 1.0, indicating the presence of positive selection pressure on these loci. CONCLUSIONS The findings of this study augment the genomic repository for the Amarathaceae family and furnish crucial molecular instruments for subsequent investigations into the ecological adaptation mechanisms of K. ceratoides within desert ecosystems.
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Affiliation(s)
- Yuping Liu
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Changyuan Zheng
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
| | - Jinyuan Chen
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Xiaoli Li
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Chenglin Sun
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, Guizhou, China.
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10
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Qiu Y, Han Z, Liu N, Yu M, Zhang S, Chen H, Tang H, Zhao Z, Wang K, Lin Z, Han F, Ye X. Effects of Aegilops longissima chromosome 1S l on wheat bread-making quality in two types of translocation lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:2. [PMID: 38072878 DOI: 10.1007/s00122-023-04504-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Two wheat-Ae. longissima translocation chromosomes (1BS·1SlL and 1SlS·1BL) were transferred into three commercial wheat varieties, and the new advanced lines showed improved bread-making quality compared to their recurrent parents. Aegilops longissima chromosome 1Sl encodes specific types of gluten subunits that may positively affect wheat bread-making quality. The most effective method of introducing 1Sl chromosomal fragments containing the target genes into wheat is chromosome translocation. Here, a wheat-Ae. longissima 1BS·1SlL translocation line was developed using molecular marker-assisted chromosome engineering. Two types of translocation chromosomes developed in a previous study, 1BS·1SlL and 1SlS·1BL, were introduced into three commercial wheat varieties (Ningchun4, Ningchun50, and Westonia) via backcrossing with marker-assisted selection. Advanced translocation lines were confirmed through chromosome in situ hybridization and genotyping by target sequencing using the wheat 40 K system. Bread-making quality was found to be improved in the two types of advanced translocation lines compared to the corresponding recurrent parents. Furthermore, 1SlS·1BL translocation lines displayed better bread-making quality than 1BS·1SlL translocation lines in each genetic background. Further analysis revealed that high molecular weight glutenin subunit (HMW-GS) contents and expression levels of genes encoding low molecular weight glutenin subunits (LMW-GSs) were increased in 1SlS·1BL translocation lines. Gliadin and gluten-related transcription factors were also upregulated in the grains of the two types of advanced translocation lines compared to the recurrent parents. This study clarifies the impacts of specific glutenin subunits on bread-making quality and provides novel germplasm resources for further improvement of wheat quality through molecular breeding.
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Affiliation(s)
- Yuliang Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Institute of Cotton Sciences, Shanxi Agricultural University, Yuncheng, 044000, China
| | - Zhiyang Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ningtao Liu
- Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161600, China
| | - Mei Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuangxi Zhang
- Crop Research Institute, Ningxia Academy of Agri-Forestry Sciences, Yinchuan, 750105, China
| | - Haiqiang Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huali Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Zhao
- Institute of Cotton Sciences, Shanxi Agricultural University, Yuncheng, 044000, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhishan Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fangpu Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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11
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Sharma PK, Ahmed HI, Heuberger M, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Yadav IS, Kathiresan N, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Abrouk M, Gu YQ, Poland J, Krattinger SG, Lazo GR, Tiwari VK. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Oxford) 2023; 2023:baad079. [PMID: 37971714 PMCID: PMC10653128 DOI: 10.1093/database/baad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.
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Affiliation(s)
- Parva Kumar Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesus Quiroz-Chavez
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | | | - Cristobal Uauy
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Yong Q Gu
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
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12
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Puccio G, Ingraffia R, Giambalvo D, Frenda AS, Harkess A, Sunseri F, Mercati F. Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families. FRONTIERS IN PLANT SCIENCE 2023; 14:1302337. [PMID: 38023895 PMCID: PMC10665861 DOI: 10.3389/fpls.2023.1302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.
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Affiliation(s)
- Guglielmo Puccio
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Dario Giambalvo
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alfonso S. Frenda
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Francesco Sunseri
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
- Department Agraria , University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
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13
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Luo X, Yang Y, Lin X, Xiao J. Deciphering spike architecture formation towards yield improvement in wheat. J Genet Genomics 2023; 50:835-845. [PMID: 36907353 DOI: 10.1016/j.jgg.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.
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Affiliation(s)
- Xumei Luo
- 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; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, 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; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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14
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- 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
| | - Lingfeng Miao
- 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
| | - Yongming Chen
- 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
| | - Huiru Peng
- 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
| | - Weilong Guo
- 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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15
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Polturak G, Misra RC, El-Demerdash A, Owen C, Steed A, McDonald HP, Wang J, Saalbach G, Martins C, Chartrain L, Wilkinson B, Nicholson P, Osbourn A. Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis. Nat Commun 2023; 14:6977. [PMID: 37914713 PMCID: PMC10620232 DOI: 10.1038/s41467-023-42464-3] [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: 07/17/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Isoflavones are a group of phenolic compounds mostly restricted to plants of the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and in nodulation. Their well-studied health promoting attributes have made them a prime target for metabolic engineering, both for bioproduction of isoflavones as high-value molecules, and in biofortification of food crops. A key gene in their biosynthesis, isoflavone synthase, was identified in legumes over two decades ago, but little is known about formation of isoflavones outside of this family. Here we identify a specialized wheat-specific isoflavone synthase, TaCYP71F53, which catalyzes a different reaction from the leguminous isoflavone synthases, thus revealing an alternative path to isoflavonoid biosynthesis and providing a non-transgenic route for engineering isoflavone production in wheat. TaCYP71F53 forms part of a biosynthetic gene cluster that produces a naringenin-derived O-methylated isoflavone, 5-hydroxy-2',4',7-trimethoxyisoflavone, triticein. Pathogen-induced production and in vitro antimicrobial activity of triticein suggest a defense-related role for this molecule in wheat. Genomic and metabolic analyses of wheat ancestral grasses further show that the triticein gene cluster was introduced into domesticated emmer wheat through natural hybridization ~9000 years ago, and encodes a pathogen-responsive metabolic pathway that is conserved in modern bread wheat varieties.
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Affiliation(s)
- Guy Polturak
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | | | - Amr El-Demerdash
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Division of Organic Chemistry, Department of Chemistry, School of Sciences, Mansoura University, Mansoura, 35516, Egypt
| | - Charlotte Owen
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andrew Steed
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hannah P McDonald
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - JiaoJiao Wang
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | | | - Carlo Martins
- Proteomics Facility, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Barrie Wilkinson
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Paul Nicholson
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
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16
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Adhikari L, Raupp J, Wu S, Koo DH, Friebe B, Poland J. Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1268370. [PMID: 37915516 PMCID: PMC10616851 DOI: 10.3389/fpls.2023.1268370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
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Affiliation(s)
- Laxman Adhikari
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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17
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Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
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18
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Papon N, Lasserre-Zuber P, Rimbert H, De Oliveira R, Paux E, Choulet F. All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity. THE PLANT GENOME 2023; 16:e20347. [PMID: 37243411 DOI: 10.1002/tpg2.20347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x = AABBDD) and a single genome for Triticum durum (4x = AABB), Triticum dicoccoides (4x = AABB), Triticum urartu (2x = AA), and Aegilops tauschii (2x = DD). We show that 5%-34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di-, tetra-, and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.
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Affiliation(s)
- Nathan Papon
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Hélène Rimbert
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Etienne Paux
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Frédéric Choulet
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
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19
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Page R, Huang S, Ronen M, Sela H, Sharon A, Shrestha S, Poland J, Steffenson BJ. Genome-wide association mapping of rust resistance in Aegilops longissima. FRONTIERS IN PLANT SCIENCE 2023; 14:1196486. [PMID: 37575932 PMCID: PMC10413114 DOI: 10.3389/fpls.2023.1196486] [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: 03/29/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023]
Abstract
The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
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Affiliation(s)
- Rae Page
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Shuyi Huang
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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20
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Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)-The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
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21
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Raskina O, Shklyar B, Nevo E. The Influence of Edaphic Factors on DNA Damage and Repair in Wild Wheat Triticum dicoccoides Körn. ( Poaceae, Triticeae). Int J Mol Sci 2023; 24:6847. [PMID: 37047823 PMCID: PMC10094829 DOI: 10.3390/ijms24076847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
A complex DNA repair network maintains genome integrity and genetic stability. In this study, the influence of edaphic factors on DNA damage and repair in wild wheat Triticum dicoccoides was addressed. Plants inhabiting two abutting microsites with dry terra rossa and humid basalt soils were studied. The relative expression level of seven genes involved in DNA repair pathways-RAD51, BRCA1, LigIV, KU70, MLH1, MSH2, and MRE11-was assessed using quantitative real-time PCR (qPCR). Immunolocalization of RAD51, LigIV, γH2AX, RNA Polymerase II, and DNA-RNA hybrid [S9.6] (R-loops) in somatic interphase nuclei and metaphase chromosomes was carried out in parallel. The results showed a lower expression level of genes involved in DNA repair and a higher number of DNA double-strand breaks (DSBs) in interphase nuclei in plants growing in terra rossa soil compared with plants in basalt soil. Further, the number of DSBs and R-loops in metaphase chromosomes was also greater in plants growing on terra rossa soil. Finally, RAD51 and LigIV foci on chromosomes indicate ongoing DSB repair during the M-phase via the Homologous Recombination and Non-Homologous End Joining pathways. Together, these results show the impact of edaphic factors on DNA damage and repair in the wheat genome adapted to contrasting environments.
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Affiliation(s)
- Olga Raskina
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Boris Shklyar
- Bioimaging Unit, Faculty of Natural Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
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22
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Zhu S, Liu C, Gong S, Chen Z, Chen R, Liu T, Liu R, Du H, Guo R, Li G, Li M, Fan R, Liu Z, Shen QH, Gao A, Ma P, He H. Orthologous genes Pm12 and Pm21 from two wild relatives of wheat show evolutionary conservation but divergent powdery mildew resistance. PLANT COMMUNICATIONS 2023; 4:100472. [PMID: 36352792 PMCID: PMC10030366 DOI: 10.1016/j.xplc.2022.100472] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/23/2022] [Accepted: 11/07/2022] [Indexed: 05/04/2023]
Abstract
Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease that threatens wheat production worldwide. Pm12, which originated from Aegilops speltoides, a wild relative of wheat, confers strong resistance to powdery mildew and therefore has potential use in wheat breeding. Using susceptible mutants induced by gamma irradiation, we physically mapped and isolated Pm12 and showed it to be orthologous to Pm21 from Dasypyrum villosum, also a wild relative of wheat. The resistance function of Pm12 was validated via ethyl methanesulfonate mutagenesis, virus-induced gene silencing, and stable genetic transformation. Evolutionary analysis indicates that the Pm12/Pm21 loci in wheat species are relatively conserved but dynamic. Here, we demonstrated that the two orthologous genes, Pm12 and Pm21, possess differential resistance against the same set of Bgt isolates. Overexpression of the coiled-coil domains of both PM12 and PM21 induces cell death in Nicotiana benthamiana leaves. However, their full-length forms display different cell death-inducing activities caused by their distinct intramolecular interactions. Cloning of Pm12 will facilitate its application in wheat breeding programs. This study also gives new insight into two orthologous resistance genes, Pm12 and Pm21, which show different race specificities and intramolecular interaction patterns.
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Affiliation(s)
- Shanying Zhu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Cheng Liu
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shuangjun Gong
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zhaozhao Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rong Chen
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Tianlei Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Renkang Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Haonan Du
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rui Guo
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Genying Li
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Renchun Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Anli Gao
- School of Life Sciences, Henan University, Kaifeng 475004, China.
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
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23
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Yang Y, Cui L, Lu Z, Li G, Yang Z, Zhao G, Kong C, Li D, Chen Y, Xie Z, Chen Z, Zhang L, Xia C, Liu X, Jia J, Kong X. Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat. PLANT COMMUNICATIONS 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
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Affiliation(s)
- Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Licao Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Marone MP, Singh HC, Pozniak CJ, Mascher M. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes. PLANT METHODS 2022; 18:128. [PMID: 36461065 PMCID: PMC9719158 DOI: 10.1186/s13007-022-00964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects. RESULTS We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive. CONCLUSION Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly .
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Affiliation(s)
- Marina Püpke Marone
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
| | - Harmeet Chawla Singh
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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25
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Molecular characterization and evolutionary relationships of avenin-like b gene in Aegilops speltoides. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lu Y, Ha M, Li X, Wang J, Mo R, Zhang A. Distribution, expression of hexaploid wheat Fes1s and functional characterization of two TaFes1As in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1037989. [PMID: 36325559 PMCID: PMC9621618 DOI: 10.3389/fpls.2022.1037989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Hexaploid wheat is a major food crop and is sensitive to heat stress. It is necessary to discover genes related to thermotolerance in wheat. Fes1s is a class of nucleotide exchange factor of heat shock protein 70s, proven to be participated in heat response in human, yeast, and Arabidopsis. However, little is known about Fes1s in hexaploid wheat. In this study, we identified nine Fes1s in hexaploid wheat (TaFes1s) and found that they present as three triads. A phylogenetic relationship analysis revealed that these Fes1s grouped into Fes1A, Fes1B and Fes1C subclades, and Fes1As and Fes1Bs were divergent in monocots, but possibly not in dicots. The sequences, gene structures and protein motifs of TaFes1s homoeologues within a triad were highly conserved. Through cis-elements analysis including heat shock elements, and miRNA targets prediction, we found that regulation of three TaFes1s homoeologues may be different, while the expression patterns of three homoeologues were similar. The expression levels of TaFes1As were higher than those of TaFes1Bs and TaFes1Cs, and based on these expressions, TaFes1As were chosen for functional characterization. Intriguingly, neither TaFes1A-5A nor TaFes1A-5D could not rescue the thermotolerance defect of Arabidopsis fes1a mutants at seedling stage, but in the transgenic plants seed germination was accelerated under normal and heat stress condition. The functional characterization indicated that roles of Fes1As would be different in Arabidopsis and hexaploid wheat, and function retention of TaFes1As may occur during wheat evolution. In conclusion, our study comprehensively characterized the distribution and expression of Fes1s in hexaploid wheat and found that two TaFes1As could accelerate seed germination under normal and heat stress condition.
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Affiliation(s)
- Yunze Lu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Mingran Ha
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Xinming Li
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Junzhe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ruirui Mo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Aihua Zhang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae. FRONTIERS IN PLANT SCIENCE 2022; 13:980764. [PMID: 36325551 PMCID: PMC9621091 DOI: 10.3389/fpls.2022.980764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D (Abdolmalaki et al., 2019) XcrXcr and 2n = 6x = 42, D1D (Abdolmalaki et al., 2019) XcrXcrD2D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Darrier B, Colas I, Rimbert H, Choulet F, Bazile J, Sortais A, Jenczewski E, Sourdille P. Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number. PLANTS (BASEL, SWITZERLAND) 2022; 11:2281. [PMID: 36079661 PMCID: PMC9460588 DOI: 10.3390/plants11172281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022]
Abstract
Understanding meiotic crossover (CO) variation in crops like bread wheat (Triticum aestivum L.) is necessary as COs are essential to create new, original and powerful combinations of genes for traits of agronomical interest. We cytogenetically characterized a set of wheat aneuploid lines missing part or all of chromosome 3B to identify the most influential regions for chiasma formation located on this chromosome. We showed that deletion of the short arm did not change the total number of chiasmata genome-wide, whereas this latter was reduced by ~35% while deleting the long arm. Contrary to what was hypothesized in a previous study, deletion of the long arm does not disturb the initiation of the synaptonemal complex (SC) in early meiotic stages. However, progression of the SC is abnormal, and we never observed its completion when the long arm is deleted. By studying six different deletion lines (missing different parts of the long arm), we revealed that at least two genes located in both the proximal (C-3BL2-0.22) and distal (3BL7-0.63-1.00) deletion bins are involved in the control of chiasmata, each deletion reducing the number of chiasmata by ~15%. We combined sequence analyses of deletion bins with RNA-Seq data derived from meiotic tissues and identified a set of genes for which at least the homoeologous copy on chromosome 3B is expressed and which are involved in DNA processing. Among these genes, eight (CAP-E1/E2, DUO1, MLH1, MPK4, MUS81, RTEL1, SYN4, ZIP4) are known to be involved in the recombination pathway.
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Affiliation(s)
- Benoit Darrier
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
- Syngenta, Toulouse Innovation Centre 12 Chemin de l’Hobit, 31790 Saint-Sauveur, France
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hélène Rimbert
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Frédéric Choulet
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Jeanne Bazile
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Aurélien Sortais
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Pierre Sourdille
- UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5, INRAE–Université Clermont-Auvergne, Chemin de Beaulieu, 63000 Clermont-Ferrand, France
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30
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Levy AA, Feldman M. Evolution and origin of bread wheat. THE PLANT CELL 2022; 34:2549-2567. [PMID: 35512194 PMCID: PMC9252504 DOI: 10.1093/plcell/koac130] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
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Tian X, Chen Q, Ma C, Men W, Liu Q, Zhao Y, Qian J, Fan Z, Miao J, He J, Sehgal SK, Li H, Liu W. Development and Characterization of Triticum aestivum- Aegilops longissima 6S l Recombinants Harboring a Novel Powdery Mildew Resistance Gene Pm6Sl. FRONTIERS IN PLANT SCIENCE 2022; 13:918508. [PMID: 35720614 PMCID: PMC9201914 DOI: 10.3389/fpls.2022.918508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew of wheat is a foliar disease that is spread worldwide. Cultivation of resistant varieties is the most effective, economical, and environmentally friendly strategy to curb this disease. Powdery mildew resistance genes (Pm) are the primary resources for resistance breeding, and new Pm genes are in constant demand. Previously, we identified Aegilops longissima chromosome 6Sl#3 as a carrier of powdery mildew resistance and designated the resistance gene as Pm6Sl. Here, we reported the design of 24 markers specific to 6Sl#3 on the basis of the full-length cDNA sequences of 6Sl#3 donor Ae. longissma accession TA1910, and the development of wheat-Ae. longissima 6Sl#3 introgression stocks by ph1b-induced homoeologous recombination. Further, 6Sl#3 introgression lines were identified and characterized by integration analysis of powdery mildew responses, in situ hybridization, and molecular markers and Pm6Sl was mapped to a distal interval of 42.80 Mb between markers Ael58410 and Ael57699 in the long arm of 6Sl#3. Two resistant recombinants, R43 (T6BS.6BL-6Sl#3L) and T27 (Ti6AS.6AL-6Sl#3L-6AL), contained segments harboring Pm6Sl with less than 8% of 6Sl#3 genomic length, and two markers were diagnostic for Pm6Sl. This study broadened powdery mildew resistance gene resources for wheat improvement and provided a fundamental basis for fine mapping and cloning of Pm6Sl to further understand its molecular mechanism of disease resistance.
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Affiliation(s)
- Xiubin Tian
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qifan Chen
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chao Ma
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqiang Men
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qianqian Liu
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yue Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiajun Qian
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Ziwei Fan
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jingnan Miao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jinqiu He
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Huanhuan Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenxuan Liu
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 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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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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