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Sertse D, Fetene A, Leon J, You FM, Cloutier S, McCartney CA. Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:237. [PMID: 39340687 DOI: 10.1007/s00122-024-04738-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.
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Affiliation(s)
- Demissew Sertse
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
| | - Aramde Fetene
- Department of Environmental Planning and Landscape Design, EiABC, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jen Leon
- Department of Plant Breeding, University of Bonn, Bonn, Germany
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curt A McCartney
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Cavalet-Giorsa E, González-Muñoz A, Athiyannan N, Holden S, Salhi A, Gardener C, Quiroz-Chávez J, Rustamova SM, Elkot AF, Patpour M, Rasheed A, Mao L, Lagudah ES, Periyannan SK, Sharon A, Himmelbach A, Reif JC, Knauft M, Mascher M, Stein N, Chayut N, Ghosh S, Perovic D, Putra A, Perera AB, Hu CY, Yu G, Ahmed HI, Laquai KD, Rivera LF, Chen R, Wang Y, Gao X, Liu S, Raupp WJ, Olson EL, Lee JY, Chhuneja P, Kaur S, Zhang P, Park RF, Ding Y, Liu DC, Li W, Nasyrova FY, Dvorak J, Abbasi M, Li M, Kumar N, Meyer WB, Boshoff WHP, Steffenson BJ, Matny O, Sharma PK, Tiwari VK, Grewal S, Pozniak CJ, Chawla HS, Ens J, Dunning LT, Kolmer JA, Lazo GR, Xu SS, Gu YQ, Xu X, Uauy C, Abrouk M, Bougouffa S, Brar GS, Wulff BBH, Krattinger SG. Origin and evolution of the bread wheat D genome. Nature 2024; 633:848-855. [PMID: 39143210 PMCID: PMC11424481 DOI: 10.1038/s41586-024-07808-z] [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: 11/15/2023] [Accepted: 07/10/2024] [Indexed: 08/16/2024]
Abstract
Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch's goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.
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Affiliation(s)
- Emile Cavalet-Giorsa
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrea González-Muñoz
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Adil Salhi
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Samira M Rustamova
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education of the Republic of Azerbaijan, Baku, Azerbaijan
| | - Ahmed Fawzy Elkot
- Wheat Research Department, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- International Maize and Wheat Improvement Centre (CIMMYT), c/o CAAS, Beijing, China
| | - Long Mao
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia
| | - Sambasivam K Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia
- Centre for Crop Health School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Amir Sharon
- Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Manuela Knauft
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Noam Chayut
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Dragan Perovic
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Alexander Putra
- Bioscience Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ana B Perera
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chia-Yi Hu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre d'anthropobiologie et de génomique de Toulouse (CAGT), Laboratoire d'Anthropobiologie et d'Imagerie de Synthèse, CNRS UMR 5288, Faculté de Médecine de Purpan, Toulouse, France
| | - Konstanze D Laquai
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Luis F Rivera
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Renjie Chen
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yajun Wang
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - W John Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Eric L Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Yi Ding
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Deng-Cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Firuza Y Nasyrova
- Institute of Botany, Plant Physiology and Genetics, Tajik National Academy of Sciences, Dushanbe, Tajikistan
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Meng Li
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Naveen Kumar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Wilku B Meyer
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Surbhi Grewal
- Nottingham Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, UK
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
| | - Harmeet Singh Chawla
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer Ens
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Steven S Xu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Yong Q Gu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Xianyang Xu
- Peanut and Small Grains Research Unit, USDA-ARS, Stillwater, OK, USA
| | | | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Canada
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Salvatore E, Samuela P, Paolo V, Giuseppina A, D'Attilia C, Francesca T, Francesco S, Pasquale DV. Identification and development of functional markers for purple grain genes in durum wheat (Triticum durum Desf.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:210. [PMID: 39198268 DOI: 10.1007/s00122-024-04710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/04/2024] [Indexed: 09/01/2024]
Abstract
KEY MESSAGE Two allelic variants of Pp-A3 and Pp-B1 were identified in purple durum wheat. Molecular markers at both loci were developed and validated on an independent panel, offering a breakthrough for wheat improvement. Purple wheats are a class of cereals with pigmented kernels of particular interest for their antioxidant and anti-inflammatory properties. Although two complementary loci (Pp-B1 and Pp-A3), responsible for purple pericarp have been pinpointed in bread wheat (Triticum aestivum L.), in durum wheat (Triticum durum Desf.) the causative genes along with functional and non-functional alleles are still unknown. Here, using a quantitative trait loci (QTL) mapping approach on a RIL population derived from purple and non-purple durum wheat genotypes, we identified three major regions on chromosomes 2A, 3A, and 7B explaining the highest phenotypic variation (> 50%). Taking advantage of the Svevo genome, a MYB was reannotated on chromosome 7B and reported as a candidate for Pp-B1. An insertion of ~ 1.6 kb within the first exon led to a non-functional allele (TdPpm1b), whereas the functional allele (TdPpm1a) was characterized and released for the first time in durum wheat. Pp-A3 was instead identified as a duplicated gene, of which only one was functional. The promoter sequencing of the functional allele (TdPpb1a) revealed six 261-bp tandem repeats in purple durum wheat, whereas one unit (TdPpb1b) was found in the yellow once. Functional molecular markers at both loci were developed to precisely discriminate purple and not purple genotypes, representing a valuable resource for selecting superior purple durum lines at early growth stages. Overall, our results expand the understanding of the function of MYB and bHLH activators in durum wheat, paving new ways to explore cis-regulatory elements at the promoter level.
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Affiliation(s)
- Esposito Salvatore
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), SS 673 Meters 25200, 71122, Foggia, Italy
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Via Università, 133, 80055, Portici, Italy
| | - Palombieri Samuela
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via Camillo de Lellis s.n.c., 01100, Viterbo, Italy
| | - Vitale Paolo
- International Maize and Wheat Improvement Center (CIMMYT), Edo. de Mexico, El Batan, Mexico
| | - Angione Giuseppina
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), SS 673 Meters 25200, 71122, Foggia, Italy
- Department of Agriculture, Food, Natural Science, Engineering (DAFNE), University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Chiara D'Attilia
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via Camillo de Lellis s.n.c., 01100, Viterbo, Italy
| | - Taranto Francesca
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Bari (CNR-IBBR), Via Amendola 165/A, 70126, Bari, Italy
| | - Sestili Francesco
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via Camillo de Lellis s.n.c., 01100, Viterbo, Italy
| | - De Vita Pasquale
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), SS 673 Meters 25200, 71122, Foggia, Italy.
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4
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Peracchi LM, Brew-Appiah RAT, Garland-Campbell K, Roalson EH, Sanguinet KA. Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum. BMC Genomics 2024; 25:816. [PMID: 39210247 PMCID: PMC11363449 DOI: 10.1186/s12864-024-10648-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance. RESULTS In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs. CONCLUSIONS Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.
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Affiliation(s)
- Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
| | - Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kimberly Garland-Campbell
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
- USDA-ARS Wheat Health, Genetics and Quality Research, Pullman, WA, 99164, USA
| | - Eric H Roalson
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA.
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5
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Yang X, Cheng X, Wang G, Song S, Ding X, Xiong H, Wang C, Zhao J, Li T, Deng P, Liu X, Chen C, Ji W. Cytogenetic identification and molecular mapping for the wheat-Thinopyrum ponticum introgression line with resistance to Fusarium head blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:191. [PMID: 39046492 DOI: 10.1007/s00122-024-04686-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: 03/26/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
KEY MESSAGE Xinong 511, a new wheat-Thinopyrum ponticum variety with excellent fusarium head blight resistance, the QTLs were mapped to the wheat chromosomes 5B and 7A with named QFhb.nwafu-5B and QFhb.nwafu-7A, respectively. Novel Fusarium head blight (FHB) resistance germplasms and genes are valuable for wheat improvement and breeding efforts. Thinopyrum ponticum, a wild relative of common wheat, is a valuable germplasm of disease resistance for wheat improvement and breeding. Xinong 511 (XN511) is a high-quality wheat variety widely cultivated in the Yellow and Huai Rivers Valley of China with stable FHB-resistance. Through analysis of pedigree materials of the wheat cultivar XN511, we found that the genetic material and FHB resistance from Th. ponticum were transmitted to the introgression line, indicating that the FHB resistance in XN511 likely originates from Th. ponticum. To further explore the genetic basis of FHB resistance in XN511, QTL mapping was conducted using the RILs population of XN511 and the susceptible line Aikang 58 (AK58). Survey with makers closely-linked to Fhb1, Fhb2, Fhb4, Fhb5, and Fhb7, indicated that both XN511 and the susceptible lines do not contain these QTL. Using bulked segregant analysis RNA-seq (BSR-Seq) and newly developed allele-specific PCR (AS-PCR) markers, QTLs in XN511 were successfully located on wheat chromosomes 5B and 7A. These findings are significant for further understanding and utilizing FHB resistance genes in wheat improvement.
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Affiliation(s)
- Xiaoying Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaofang Cheng
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Guangyi Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Siyuan Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xu Ding
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Hui Xiong
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changyou Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Tingdong Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Pingchuan Deng
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Xinlun Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Chunhuan Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China.
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6
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Li J, Li J, Cheng X, Yang Z, Pang Y, Wang C, Wu J, Ji W, Chen X, Zhao J. The addition of Psathyrostachys Huashanica Keng 6Ns large segment chromosomes has positive impact on stripe rust resistance and plant spikelet number of common wheat. BMC PLANT BIOLOGY 2024; 24:685. [PMID: 39026182 PMCID: PMC11256485 DOI: 10.1186/s12870-024-05395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Developing novel germplasm by using wheat wild related species is an effective way to rebuild the wheat resource bank. The Psathyrostachys huashanica Keng (P. huashanica, 2n = 2x = 14, NsNs) is regarded as a superior species to improve wheat breeding because of its multi-resistance, early maturation and numerous tiller traits. Introducing genetic components of P. huashanica into the common wheat background is the most important step in achieving the effective use. Therefore, the cytogenetic characterization and influence of the introgressed P. huashanica large segment chromosomes in the wheat background is necessary to be explored. RESULTS In this study, we characterized a novel derived line, named D88-2a, a progeny of the former characterized wheat-P. huashanica partial amphiploid line H8911 (2n = 7x = 49, AABBDDNs). Cytological identification showed that the chromosomal composition of D88-2a was 2n = 44 = 22II, indicating the addition of exogenous chromosomes. Genomic in situ hybridization demonstrated that the supernumerary chromosomes were a pair of homologues from the P. huashanica and could be stably inherited in the common wheat background. Molecular markers and 15 K SNP array indicated that the additional chromosomes were derived from the sixth homoeologous group (i.e., 6Ns) of P. huashanica. Based on the distribution of the heterozygous single-nucleotide polymorphism sites and fluorescence in situ hybridization karyotype of each chromosome, this pair of additional chromosomes was confirmed as P. huashanica 6Ns large segment chromosomes, which contained the entire short arm and the proximal centromere portion of the long arm. In terms of the agronomic traits, the addition line D88-2a exhibited enhanced stripe rust resistance, improved spike characteristics and increased protein content than its wheat parent line 7182. CONCLUSIONS The new wheat germplasm D88-2a is a novel cytogenetically stable wheat-P. huashanica 6Ns large segment addition line, and the introgressed large segment alien chromosome has positive impact on plant spikelet number and stripe rust resistance. Thus, this germplasm can be used for genetic improvement of cultivated wheat and the study of functional alien chromosome segment.
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Affiliation(s)
- Jiaojiao Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Xueni Cheng
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610000, China
| | - Yuhui Pang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jun Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinhong Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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7
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Evans C, Mogg SL, Soraru C, Wallington E, Coates J, Borrill P. Wheat NAC transcription factor NAC5-1 is a positive regulator of senescence. PLANT DIRECT 2024; 8:e620. [PMID: 38962173 PMCID: PMC11217990 DOI: 10.1002/pld3.620] [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: 02/02/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024]
Abstract
Wheat (Triticum aestivum L.) is an important source of both calories and protein in global diets, but there is a trade-off between grain yield and protein content. The timing of leaf senescence could mediate this trade-off as it is associated with both declines in photosynthesis and nitrogen remobilization from leaves to grain. NAC transcription factors play key roles in regulating senescence timing. In rice, OsNAC5 expression is correlated with increased protein content and upregulated in senescing leaves, but the role of the wheat ortholog in senescence had not been characterized. We verified that NAC5-1 is the ortholog of OsNAC5 and that it is expressed in senescing flag leaves in wheat. To characterize NAC5-1, we combined missense mutations in NAC5-A1 and NAC5-B1 from a TILLING mutant population and overexpressed NAC5-A1 in wheat. Mutation in NAC5-1 was associated with delayed onset of flag leaf senescence, while overexpression of NAC5-A1 was associated with slightly earlier onset of leaf senescence. DAP-seq was performed to locate transcription factor binding sites of NAC5-1. Analysis of DAP-seq and comparison with other studies identified putative downstream target genes of NAC5-1 which could be associated with senescence. This work showed that NAC5-1 is a positive transcriptional regulator of leaf senescence in wheat. Further research is needed to test the effect of NAC5-1 on yield and protein content in field trials, to assess the potential to exploit this senescence regulator to develop high-yielding wheat while maintaining grain protein content.
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Affiliation(s)
- Catherine Evans
- Department of Crop GeneticsJohn Innes CentreNorwichUK
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | | | | | | | - Juliet Coates
- School of BiosciencesUniversity of BirminghamBirminghamUK
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8
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John-Bejai C, Trethowan R, Revell I, de Groot S, Shezi L, Koekemoer F, Diffey S, Lage J. Identifying the seeds of heterotic pools for Southern and Eastern Africa from global elite spring wheat germplasm. FRONTIERS IN PLANT SCIENCE 2024; 15:1398715. [PMID: 38993941 PMCID: PMC11236601 DOI: 10.3389/fpls.2024.1398715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024]
Abstract
Hybrid breeding can increase the competitiveness of wheat (Triticum aestivum L.) in Sub-Saharan Africa by fostering more public-private partnerships and promoting investment by the private sector. The benefit of hybrid wheat cultivars in South Africa has previously been demonstrated but due to the high cost of hybrid seed production, hybrid breeding has not received significant attention in the past decade. Considering the renewed commitment of the private sector to establish wheat as a hybrid crop globally, coupled with significant research investment into enhancement of outcrossing of wheat, hybrid wheat breeding in Southern and Eastern Africa should be revisited. Our study aimed to identify genetically distinct germplasm groups in spring wheat that would be useful in the establishment of heterotic pools targeting this region. Multi-environment yield testing of a large panel of F1 test hybrids, generated using global elite germplasm, was carried out between 2019 and 2020 in Argentina, Africa, Europe, and Australia. We observed significant genotype by environment interactions within our testing network, confirming the distinctiveness of African trial sites. Relatively high additive genetic variance was observed highlighting the contribution of parental genotypes to the grain yield of test hybrids. We explored the genetic architecture of these parents and the genetic factors underlying the value of parents appear to be associated with their genetic subgroup, with positive marker effects distributed throughout the genome. In testcrosses, elite germplasm from the International Maize and Wheat Improvement Center (CIMMYT) appear to be complementary to the genetically distinct germplasm bred in South Africa. The feasibility of achieving genetic gain via heterotic pool establishment and divergence, and by extension the viability of hybrid cultivars in Sub-Saharan Africa, is supported by the results of our study.
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Affiliation(s)
| | - Richard Trethowan
- The Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | - Isobella Revell
- The Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | | | - Lindani Shezi
- Wheat Breeding, Sensako (Syngenta), Bethlehem, South Africa
| | | | | | - Jacob Lage
- Wheat Breeding, KWS UK Ltd, Thriplow, United Kingdom
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9
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Gauley A, Pasquariello M, Yoshikawa GV, Alabdullah AK, Hayta S, Smedley MA, Dixon LE, Boden SA. Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time. Curr Biol 2024; 34:2330-2343.e4. [PMID: 38781956 PMCID: PMC11149547 DOI: 10.1016/j.cub.2024.04.029] [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: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
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Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia
| | - Abdul Kader Alabdullah
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Laura E Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.
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10
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Ndreca B, Huttly A, Bibi S, Bayon C, Lund G, Ham J, Alarcón-Reverte R, Addy J, Tarkowská D, Pearce S, Hedden P, Thomas SG, Phillips AL. Stacked mutations in wheat homologues of rice SEMI-DWARF1 confer a novel semi-dwarf phenotype. BMC PLANT BIOLOGY 2024; 24:384. [PMID: 38724935 PMCID: PMC11080193 DOI: 10.1186/s12870-024-05098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Semi-dwarfing alleles are used widely in cereals to confer improved lodging resistance and assimilate partitioning. The most widely deployed semi-dwarfing alleles in rice and barley encode the gibberellin (GA)-biosynthetic enzyme GA 20-OXIDASE2 (GA20OX2). The hexaploid wheat genome carries three homoeologous copies of GA20OX2, and because of functional redundancy, loss-of-function alleles of a single homoeologue would not be selected in wheat breeding programmes. Instead, approximately 70% of wheat cultivars carry gain-of-function mutations in REDUCED HEIGHT 1 (RHT1) genes that encode negative growth regulators and are degraded in response to GA. Semi-dwarf Rht-B1b or Rht-D1b alleles encode proteins that are insensitive to GA-mediated degradation. However, because RHT1 is expressed ubiquitously these alleles have pleiotropic effects that confer undesirable traits in some environments. RESULTS We have applied reverse genetics to combine loss-of-function alleles in all three homoeologues of wheat GA20OX2 and its paralogue GA20OX1 and evaluated their performance in three years of field trials. ga20ox1 mutants exhibited a mild height reduction (approximately 3%) suggesting GA20OX1 plays a minor role in stem elongation in wheat. ga20ox2 mutants have reduced GA1 content and are 12-32% shorter than their wild-type segregants, comparable to the effect of the Rht-D1b 'Green Revolution' allele. The ga20ox2 mutants showed no significant negative effects on yield components in the spring wheat variety 'Cadenza'. CONCLUSIONS Our study demonstrates that chemical mutagenesis can expand genetic variation in polyploid crops to uncover novel alleles despite the difficulty in identifying appropriate mutations for some target genes and the negative effects of background mutations. Field experiments demonstrate that mutations in GA20OX2 reduce height in wheat, but it will be necessary to evaluate the effect of these alleles in different genetic backgrounds and environments to determine their value in wheat breeding as alternative semi-dwarfing alleles.
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Affiliation(s)
- Barbora Ndreca
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Alison Huttly
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Sajida Bibi
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Nuclear Institute for Agriculture and Biology, Faisalabad, Punjab, Pakistan
| | - Carlos Bayon
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - George Lund
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Joshua Ham
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | - John Addy
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
| | - Stephen Pearce
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Peter Hedden
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
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11
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Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, Swarbreck D, Collins J, Yao E, Sen TZ, Wilson M, Yant L, King IP, King J. Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii. Sci Data 2024; 11:420. [PMID: 38653999 PMCID: PMC11039740 DOI: 10.1038/s41597-024-03260-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.
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Affiliation(s)
- Surbhi Grewal
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.
| | - Cai-Yun Yang
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Duncan Scholefield
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Stephen Ashling
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Sreya Ghosh
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Joanna Collins
- Genome Reference Informatics Team, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Eric Yao
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- 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
| | - Taner Z Sen
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- 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
| | - Michael Wilson
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Ian P King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Julie King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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12
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Sun S, Bakkeren G. A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1369299. [PMID: 38681221 PMCID: PMC11046709 DOI: 10.3389/fpls.2024.1369299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.
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Affiliation(s)
- Sherry Sun
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Center, Summerland, BC, Canada
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13
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Afshari-Behbahanizadeh S, Puglisi D, Esposito S, De Vita P. Allelic Variations in Vernalization ( Vrn) Genes in Triticum spp. Genes (Basel) 2024; 15:251. [PMID: 38397240 PMCID: PMC10887697 DOI: 10.3390/genes15020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity.
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Affiliation(s)
- Sanaz Afshari-Behbahanizadeh
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Damiano Puglisi
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), 80055 Portici, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
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14
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Liu X, Xu Z, Feng B, Zhou Q, Guo S, Liao S, Ou Y, Fan X, Wang T. Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1356687. [PMID: 38362452 PMCID: PMC10867189 DOI: 10.3389/fpls.2024.1356687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024]
Abstract
Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Insitute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuhao Ou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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15
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Zeng V, Uauy C, Chen Y. Identification of a novel SNP in the miR172 binding site of Q homoeolog AP2L-D5 is associated with spike compactness and agronomic traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:13. [PMID: 38142253 DOI: 10.1007/s00122-023-04514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 12/25/2023]
Abstract
KEY MESSAGE This study found that the compact spike locus of ANK-15 is on chromosome 5D instead of 2B. We have identified a new allele of AP2L-D5 as the candidate causal polymorphism. Spike architecture is a key determinant of wheat yield, a crop which supports much of the human diet but whose yield gains are stagnating. Spike architecture mutants offer opportunities to identify genetic factors contributing to inflorescence development. Here, we investigate the locus underlying the compact spike phenotype of mutant line ANK-15 by conducting mRNA-sequencing and genetic mapping using ANK-15 and its non-compact spike near-isogenic line Novosibirskaya 67 (N67). Previous literature has placed the compact spike locus of ANK-15 to chromosome 2B. However, based on the single nucleotide polymorphisms (SNPs) identified using mRNA-seq data, we were unable to detect polymorphisms between N67 and ANK-15 in the putative chromosome 2B region. We performed differential expression analysis of developing rachis and found that AP2L-D5, the D homoeolog of the domestication Q gene, is upregulated in ANK-15 in comparison to N67. ANK-15 carries a SNP in the microRNA172 binding site of AP2L-D5, which is predicted to lead to higher expression of AP2L-D5 due to decreased miRNA172-mediated degradation. Furthermore, we performed genetic mapping using an ANK-15 × N67 F2 population and found a single quantitative trait locus on chromosome 5D coinciding with the position of AP2L-D5. This result suggests that AP2L-D5 is likely the underlying causal gene for the compact spike phenotype in ANK-15. We performed a field trial to investigate the effect of the AP2L-D5 allele on agronomic traits and found that the AP2L-D5 allele from ANK-15 is associated with a significant reduction in height, increased thousand grain weight (TGW), and increased grain width.
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Affiliation(s)
- Victoria Zeng
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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16
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Muqaddasi QH, Muqaddasi RK, Ebmeyer E, Korzun V, Argillier O, Mirdita V, Reif JC, Ganal MW, Röder MS. Genetic control and prospects of predictive breeding for European winter wheat's Zeleny sedimentation values and Hagberg-Perten falling number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:229. [PMID: 37874400 PMCID: PMC10598174 DOI: 10.1007/s00122-023-04450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/16/2023] [Indexed: 10/25/2023]
Abstract
KEY MESSAGE Sedimentation values and falling number in the last decades have helped maintain high baking quality despite rigorous selection for grain yield in wheat. Allelic combinations of major loci sustained the bread-making quality while improving grain yield. Glu-D1, Pinb-D1, and non-gluten proteins are associated with sedimentation values and falling number in European wheat. Zeleny sedimentation values (ZSV) and Hagberg-Perten falling number (HFN) are among the most important parameters that help determine the baking quality classes of wheat and, thus, influence the monetary benefits for growers. We used a published data set of 372 European wheat varieties evaluated in replicated field trials in multiple environments. ZSV and HFN traits hold a wide and significant genotypic variation and high broad-sense heritability. The genetic correlations revealed positive and significant associations of ZSV and HFN with each other, grain protein content (GPC) and grain hardness; however, they were all significantly negatively correlated with grain yield. Besides, GPC appeared to be the major predictor for ZSV and HFN. Our genome-wide association analyses based on high-quality SSR, SNP, and candidate gene markers revealed a strong quantitative genetic nature of ZSV and HFN by explaining their total genotypic variance as 41.49% and 38.06%, respectively. The association of known Glutenin (Glu-1) and Puroindoline (Pin-1) with ZSV provided positive analytic proof of our studies. We report novel candidate loci associated with globulins and albumins-the non-gluten monomeric proteins in wheat. In addition, predictive breeding analyses for ZSV and HFN suggest using genomic selection in the early stages of breeding programs with an average prediction accuracy of 81 and 59%, respectively.
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Affiliation(s)
- Quddoos H Muqaddasi
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany.
- KWS SAAT SE & Co. KGaA, Einbeck, 37574, Germany.
| | - Roop Kamal Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | | | | | | | - Vilson Mirdita
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1B, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
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Wold-McGimsey F, Krosch C, Alarcón-Reverte R, Ravet K, Katz A, Stromberger J, Mason RE, Pearce S. Multi-target genome editing reduces polyphenol oxidase activity in wheat ( Triticum aestivum L.) grains. FRONTIERS IN PLANT SCIENCE 2023; 14:1247680. [PMID: 37786514 PMCID: PMC10541959 DOI: 10.3389/fpls.2023.1247680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Introduction Polyphenol oxidases (PPO) are dual activity metalloenzymes that catalyse the production of quinones. In plants, PPO activity may contribute to biotic stress resistance and secondary metabolism but is undesirable for food producers because it causes the discolouration and changes in flavour profiles of products during post-harvest processing. In wheat (Triticum aestivum L.), PPO released from the aleurone layer of the grain during milling results in the discolouration of flour, dough, and end-use products, reducing their value. Loss-of-function mutations in the PPO1 and PPO2 paralogous genes on homoeologous group 2 chromosomes confer reduced PPO activity in the wheat grain. However, limited natural variation and the proximity of these genes complicates the selection of extremely low-PPO wheat varieties by recombination. The goal of the current study was to edit all copies of PPO1 and PPO2 to drive extreme reductions in PPO grain activity in elite wheat varieties. Results A CRISPR/Cas9 construct with one single guide RNA (sgRNA) targeting a conserved copper binding domain was used to edit all seven PPO1 and PPO2 genes in the spring wheat cultivar 'Fielder'. Five of the seven edited T1 lines exhibited significant reductions in PPO activity, and T2 lines had PPO activity up to 86.7% lower than wild-type. The same construct was transformed into the elite winter wheat cultivars 'Guardian' and 'Steamboat', which have five PPO1 and PPO2 genes. In these varieties PPO activity was reduced by >90% in both T1 and T2 lines. In all three varieties, dough samples from edited lines exhibited reduced browning. Discussion This study demonstrates that multi-target editing at late stages of variety development could complement selection for beneficial alleles in crop breeding programs by inducing novel variation in loci inaccessible to recombination.
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Affiliation(s)
- Forrest Wold-McGimsey
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Caitlynd Krosch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Rocío Alarcón-Reverte
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - John Stromberger
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Richard Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
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18
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Kamel AM, Metwally K, Sabry M, Albalawi DA, Abbas ZK, Darwish DBE, Al-Qahtani SM, Al-Harbi NA, Alzuaibr FM, Khalil HB. The Expression of Triticum aestivum Cysteine-Rich Receptor-like Protein Kinase Genes during Leaf Rust Fungal Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:2932. [PMID: 37631144 PMCID: PMC10457733 DOI: 10.3390/plants12162932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Understanding the role of cysteine-rich receptor-like kinases (CRKs) in plant defense mechanisms is crucial for enhancing wheat resistance to leaf rust fungus infection. Here, we identified and verified 164 members of the CRK gene family using the Triticum aestivum reference version 2 collected from the international wheat genome sequencing consortium (IWGSC). The proteins exhibited characteristic features of CRKs, including the presence of signal peptides, cysteine-rich/stress antifungal/DUF26 domains, transmembrane domains, and Pkinase domains. Phylogenetic analysis revealed extensive diversification within the wheat CRK gene family, indicating the development of distinct specific functional roles to wheat plants. When studying the expression of the CRK gene family in near-isogenic lines (NILs) carrying Lr57- and Lr14a-resistant genes, Puccinia triticina, the causal agent of leaf rust fungus, triggered temporal gene expression dynamics. The upregulation of specific CRK genes in the resistant interaction indicated their potential role in enhancing wheat resistance to leaf rust, while contrasting gene expression patterns in the susceptible interaction highlighted potential susceptibility associated CRK genes. The study uncovered certain CRK genes that exhibited expression upregulation upon leaf rust infection and the Lr14a-resistant gene. The findings suggest that targeting CRKs may present a promising strategy for improving wheat resistance to rust diseases.
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Affiliation(s)
- Ahmed M. Kamel
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo 11241, Egypt
| | - Khaled Metwally
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo 11241, Egypt
| | - Mostafa Sabry
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo 11241, Egypt
| | - Doha A. Albalawi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia (D.B.E.D.)
| | - Zahid K. Abbas
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia (D.B.E.D.)
| | - Doaa B. E. Darwish
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia (D.B.E.D.)
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
| | - Salem M. Al-Qahtani
- Biology Department, University College of Tayma, University of Tabuk, P.O. Box 741, Tabuk 47512, Saudi Arabia
| | - Nadi A. Al-Harbi
- Biology Department, University College of Tayma, University of Tabuk, P.O. Box 741, Tabuk 47512, Saudi Arabia
| | - Fahad M. Alzuaibr
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia (D.B.E.D.)
| | - Hala B. Khalil
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo 11241, Egypt
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
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