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Boehm J, Cai X. Enrichment and Diversification of the Wheat Genome via Alien Introgression. PLANTS (BASEL, SWITZERLAND) 2024; 13:339. [PMID: 38337872 PMCID: PMC10857235 DOI: 10.3390/plants13030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome's polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.
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Affiliation(s)
- Jeffrey Boehm
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Xiwen Cai
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
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2
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Griffiths M, Liu AE, Gunn SL, Mutan NM, Morales EY, Topp CN. A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress ( Thlaspi arvense L.) accessions. FRONTIERS IN PLANT SCIENCE 2023; 14:1145389. [PMID: 37426970 PMCID: PMC10327891 DOI: 10.3389/fpls.2023.1145389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023]
Abstract
Introduction Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Methods Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing). Results Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. Discussion These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.
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3
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Thapa K, Shivam K, Khan H, Kaur A, Dua K, Singh S, Singh TG. Emerging Targets for Modulation of Immune Response and Inflammation in Stroke. Neurochem Res 2023; 48:1663-1690. [PMID: 36763312 DOI: 10.1007/s11064-023-03875-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
The inflammatory and immunological responses play a significant role after stroke. The innate immune activation stimulated by microglia during stroke results in the migration of macrophages and lymphocytes into the brain and are responsible for tissue damage. The immune response and inflammation following stroke have no defined targets, and the intricacies of the immunological and inflammatory processes are only partially understood. Innate immune cells enter the brain and meninges during the acute phase, which can cause ischemia damage. Activation of systemic immunity is caused by danger signals sent into the bloodstream by injured brain cells, which is followed by a significant immunodepression that encourages life-threatening infections. Neuropsychiatric sequelae, a major source of post-stroke morbidity, may be induced by an adaptive immune response that is initiated by antigen presentation during the chronic period and is directed against the brain. Thus, the current review discusses the role of immune response and inflammation in stroke pathogenesis, their role in the progression of injury during the stroke, and the emerging targets for the modulation of the mechanism of immune response and inflammation that may have possible therapeutic benefits against stroke.
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Affiliation(s)
- Komal Thapa
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India.,School of Pharmacy, Chitkara University, Rajpura, Himachal Pradesh, 174103, India
| | - Kumar Shivam
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Heena Khan
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Amarjot Kaur
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia.,Faculty of Health, Australian Research Centre in Complementary & Integrative Medicine, University of Technology Sydney, Ultimo, 2007, Australia
| | - Sachin Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India.
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4
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Leigh FJ, Wright TIC, Horsnell RA, Dyer S, Bentley AR. Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement. Heredity (Edinb) 2022; 128:291-303. [PMID: 35383318 PMCID: PMC9076643 DOI: 10.1038/s41437-022-00527-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 01/07/2023] Open
Abstract
Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.
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Affiliation(s)
- Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard A Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Sarah Dyer
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK. .,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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5
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Grewal S, Coombes B, Joynson R, Hall A, Fellers J, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines. THE PLANT GENOME 2022; 15:e20193. [PMID: 35102721 DOI: 10.1002/tpg2.20193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 05/23/2023]
Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
- Current address: Limagrain Europe, Clermont-Ferrand, France
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - John Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Cai-Yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Peter Isaac
- iDna Genetics Ltd., Norwich Research Park, Norwich, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
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6
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Zhang Q, Li Y, Li Y, Fahima T, Shen Q, Xie C. Introgression of the Powdery Mildew Resistance Genes Pm60 and Pm60b from Triticum urartu to Common Wheat Using Durum as a 'Bridge'. Pathogens 2021; 11:pathogens11010025. [PMID: 35055973 PMCID: PMC8778237 DOI: 10.3390/pathogens11010025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici (Bgt), has limited wheat yields in many major wheat-production areas across the world. Introducing resistance genes from wild relatives into cultivated wheat can enrich the genetic resources for disease resistance breeding. The powdery mildew resistance gene Pm60 was first identified in diploid wild wheat Triticum urartu (T. urartu). In this study, we used durum as a ‘bridge’ approach to transfer Pm60 and Pm60b into hexaploid common wheat. Synthetic hexaploid wheat (SHW, AABBAuAu), developed by crossing T. urartu (AuAu) with durum (AABB), was used for crossing and backcrossing with common wheat. The Pm60 alleles were tracked by molecular markers and the resistance to powdery mildew. From BC1F1 backcross populations, eight recombinant types were identified based on five Pm60-flanking markers, which indicated different sizes of the introgressed chromosome segments from T. urartu. Moreover, we have selected two resistance-harboring introgression lines with high self-fertility, which could be easily used in wheat breeding system. Our results showed that the durum was an excellent ‘bridge’ for introducing the target gene from diploid T. urartu into the hexaploid cultivated wheat. Moreover, these introgression lines could be deployed in wheat resistance breeding programs, together with the assistance of the molecular markers for Pm60 alleles.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Yinghui Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel;
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel;
| | - Qianhua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
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7
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Grewal S, Guwela V, Newell C, Yang CY, Ashling S, Scholefield D, Hubbart-Edwards S, Burridge A, Stride A, King IP, King J. Generation of Doubled Haploid Wheat- Triticum urartu Introgression Lines and Their Characterisation Using Chromosome-Specific KASP Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:643636. [PMID: 34054892 PMCID: PMC8155260 DOI: 10.3389/fpls.2021.643636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 05/07/2023]
Abstract
Wheat is one of the most important food and protein sources in the world and although, in recent years wheat breeders have achieved yield gains, they are not sufficient to meet the demands of an ever-growing population. Development of high yielding wheat varieties, resilient to abiotic and biotic stress resulting from climate change, has been limited by wheat's narrow genetic base. In contrast to wheat, the wild relatives of wheat provide a vast reservoir of genetic variation for most, if not all, agronomic traits. Previous studies by the authors have shown the transfer of genetic variation from T. urartu into bread wheat. However, before the introgression lines can be exploited for trait analysis, they are required to have stable transmission of the introgressions to the next generation. In this work, we describe the generation of 86 doubled haploid (DH) wheat-T. urartu introgression lines that carry homozygous introgressions which are stably inherited. The DH lines were characterised using the Axiom® Wheat Relative Genotyping Array and 151 KASP markers to identify 65 unique T. urartu introgressions in a bread wheat background. DH production has helped accelerate the breeding process and facilitated the early release of homozygous wheat-T. urartu introgression lines. Together with the KASP markers, this valuable resource could greatly advance identification of beneficial alleles that can be used in wheat improvement.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Veronica Guwela
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Claire Newell
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Alex Stride
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
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8
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McAusland L, Vialet-Chabrand S, Jauregui I, Burridge A, Hubbart-Edwards S, Fryer MJ, King IP, King J, Pyke K, Edwards KJ, Carmo-Silva E, Lawson T, Murchie EH. Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent. THE NEW PHYTOLOGIST 2020; 228:1767-1780. [PMID: 32910841 DOI: 10.1111/nph.16832] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/03/2020] [Indexed: 05/26/2023]
Abstract
The wild relatives of modern wheat represent an underutilized source of genetic and phenotypic diversity and are of interest in breeding owing to their wide adaptation to diverse environments. Leaf photosynthetic traits underpin the rate of production of biomass and yield and have not been systematically explored in the wheat relatives. This paper identifies and quantifies the phenotypic variation in photosynthetic, stomatal, and morphological traits in up to 88 wheat wild relative accessions across five genera. Both steady-state measurements and dynamic responses to step changes in light intensity are assessed. A 2.3-fold variation for flag leaf light and CO2 -saturated rates of photosynthesis Amax was observed. Many accessions showing higher and more variable Amax , maximum rates of carboxylation, electron transport, and Rubisco activity when compared with modern genotypes. Variation in dynamic traits was also significant; with distinct genus-specific trends in rates of induction of nonphotochemical quenching and rate of stomatal opening. We conclude that utilization of wild relatives for improvement of photosynthesis is supported by the existence of a high degree of natural variation in key traits and should consider not only genus-level properties but variation between individual accessions.
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Affiliation(s)
- Lorna McAusland
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | | | - Iván Jauregui
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | | | - Stella Hubbart-Edwards
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Michael J Fryer
- School of Life Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Ian P King
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Julie King
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Kevin Pyke
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | | | | | - Tracy Lawson
- School of Life Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Erik H Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
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9
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Baker L, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge AJ, Przewieslik-Allen AM, Wilkinson PA, King IP, King J. Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2213-2226. [PMID: 32313991 PMCID: PMC7311493 DOI: 10.1007/s00122-020-03591-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/31/2020] [Indexed: 05/23/2023]
Abstract
One hundred and thirty four introgressions from Thinopyrum elongatum have been transferred into a wheat background and were characterised using 263 SNP markers. Species within the genus Thinopyrum have been shown to carry genetic variation for a very wide range of traits including biotic and abiotic stresses and quality. Research has shown that one of the species within this genus, Th. elongatum, has a close relationship with the genomes of wheat making it a highly suitable candidate to expand the gene pool of wheat. Homoeologous recombination, in the absence of the Ph1 gene, has been exploited to transfer an estimated 134 introgressions from Th. elongatum into a hexaploid wheat background. The introgressions were detected and characterised using 263 single nucleotide polymorphism markers from a 35 K Axiom® Wheat-Relative Genotyping Array, spread across seven linkage groups and validated using genomic in situ hybridisation. The genetic map had a total length of 187.8 cM and the average chromosome length was 26.8 cM. Comparative analyses of the genetic map of Th. elongatum and the physical map of hexaploid wheat confirmed previous work that indicated good synteny at the macro-level, although Th. elongatum does not contain the 4A/5A/7B translocation found in wheat.
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Affiliation(s)
- Lauren Baker
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Surbhi Grewal
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Cai-Yun Yang
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stella Hubbart-Edwards
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Duncan Scholefield
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephen Ashling
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Amanda J Burridge
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | | | - Paul A Wilkinson
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Ian P King
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Julie King
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
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10
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Grewal S, Othmeni M, Walker J, Hubbart-Edwards S, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Development of Wheat- Aegilops caudata Introgression Lines and Their Characterization Using Genome-Specific KASP Markers. FRONTIERS IN PLANT SCIENCE 2020; 11:606. [PMID: 32477394 PMCID: PMC7240103 DOI: 10.3389/fpls.2020.00606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 05/23/2023]
Abstract
Aegilops caudata L. [syn. Ae. markgrafii (Greuter) Hammer], is a diploid wild relative of wheat (2n = 2x = 14, CC) and a valuable source for new genetic diversity for wheat improvement. It has a variety of disease resistance factors along with tolerance for various abiotic stresses and can be used for wheat improvement through the generation of genome-wide introgressions resulting in different wheat-Ae. caudata recombinant lines. Here, we report the generation of nine such wheat-Ae. caudata recombinant lines which were characterized using wheat genome-specific KASP (Kompetitive Allele Specific PCR) markers and multi-color genomic in situ hybridization (mcGISH). Of these, six lines have stable homozygous introgressions from Ae. caudata and will be used for future trait analysis. Using cytological techniques and molecular marker analysis of the recombinant lines, 182 KASP markers were physically mapped onto the seven Ae. caudata chromosomes, of which 155 were polymorphic specifically with only one wheat subgenome. Comparative analysis of the physical positions of these markers in the Ae. caudata and wheat genomes confirmed that the former had chromosomal rearrangements with respect to wheat, as previously reported. These wheat-Ae. caudata recombinant lines and KASP markers are useful resources that can be used in breeding programs worldwide for wheat improvement. Additionally, the genome-specific KASP markers could prove to be a valuable tool for the rapid detection and marker-assisted selection of other Aegilops species in a wheat background.
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Affiliation(s)
- Surbhi Grewal
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Manel Othmeni
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Jack Walker
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Stella Hubbart-Edwards
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Cai-yun Yang
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Duncan Scholefield
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Stephen Ashling
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Peter Isaac
- IDna Genetics Ltd., Norwich Research Park, Norwich, United Kingdom
| | - Ian P. King
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Julie King
- Division of Plant and Cop Sciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Nottingham, United Kingdom
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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12
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Han G, Liu S, Jin Y, Jia M, Ma P, Liu H, Wang J, An D. Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.). BMC Genomics 2020; 21:206. [PMID: 32131733 PMCID: PMC7057559 DOI: 10.1186/s12864-020-6624-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/25/2020] [Indexed: 02/01/2023] Open
Abstract
Background Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding. Results In the present study, five rye cultivars including Imperial, German White, Jingzhouheimai, Baili and Guyuan were sequenced by specific-locus amplified fragment sequencing (SLAF-seq) to develop large-scale rye-specific markers. Based on SLAF-seq and bioinformatics analyses, a total of 404 universal PCR-based and a whole set of Kompetitive allele-specific PCR (KASP) markers specific for the 14 individual rye chromosome arms were developed and validated. Additionally, two KASP markers specific for 1RS and 2RL were successfully applied in the detection of 1RS translocations in a natural population and 2RL chromosome arms in wheat-rye derived progenies that conferred adult resistance to powdery mildew. Conclusion The 404 PCR-based markers and 14 KASP markers specific for the 14 individual rye chromosome arms developed in this study can enrich the marker densities for gene mapping and accelerate the utilization of rye-derived genes in wheat improvement. Especially, the KASP markers achieved high-throughput and accurate detection of rye chromatin in wheat background, thus can be efficiently used in marker-assisted selection (MAS). Besides, the strategy of rye-specific PCR-based markers converting into KASP markers was high-efficient and low-cost, which will facilitate the tracing of alien genes, and can also be referred for other wheat relatives.
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Affiliation(s)
- Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyu Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuli Jin
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Mengshu Jia
- School of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Pengtao Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,School of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Jing Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China. .,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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13
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Grewal S, Hubbart‐Edwards S, Yang C, Devi U, Baker L, Heath J, Ashling S, Scholefield D, Howells C, Yarde J, Isaac P, King IP, King J. Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:743-755. [PMID: 31465620 PMCID: PMC7004896 DOI: 10.1111/pbi.13241] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/17/2019] [Indexed: 05/23/2023]
Abstract
For future food security, it is important that wheat, one of the most widely consumed crops in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. For trait discovery, it is necessary that each introgression is homozygous and hence stable. Breeding programmes rely on efficient genotyping platforms for marker-assisted selection (MAS). Recently, single nucleotide polymorphism (SNP)-based markers have been made available on high-throughput Axiom® SNP genotyping arrays. However, these arrays are inflexible in their design and sample numbers, making their use unsuitable for long-term MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP™) assays that are comparatively cost-effective and efficient for low-density genotyping of introgression lines. However, due to the polyploid nature of wheat, KASP assays for homoeologous SNPs can have difficulty in distinguishing between heterozygous and homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that can differentiate between heterozygotes and homozygotes, we PCR-amplified and sequenced genomic DNA from potential single-copy regions of the wheat genome and compared them to orthologous copies from different wild relatives. A panel of 620 chromosome-specific KASP assays have been developed that allow rapid detection of wild relative segments and provide information on their homozygosity and site of introgression in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that can be used for genotyping introgression lines. These multipurpose KASP assays represent a powerful tool for wheat breeders worldwide.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Stella Hubbart‐Edwards
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Urmila Devi
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Lauren Baker
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Jack Heath
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Caroline Howells
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | | | - Peter Isaac
- IDna Genetics Ltd.Norwich Research ParkNorwichUK
| | - Ian P. King
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Julie King
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
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14
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Huang D, Zheng Q, Melchkart T, Bekkaoui Y, Konkin DJF, Kagale S, Martucci M, You FM, Clarke M, Adamski NM, Chinoy C, Steed A, McCartney CA, Cutler AJ, Nicholson P, Feurtado JA. Dominant inhibition of awn development by a putative zinc-finger transcriptional repressor expressed at the B1 locus in wheat. THE NEW PHYTOLOGIST 2020; 225:340-355. [PMID: 31469444 PMCID: PMC6916588 DOI: 10.1111/nph.16154] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 05/22/2023]
Abstract
Awns, bristle-like structures extending from grass lemmas, provide protection against predators, contribute to photosynthesis and aid in grain dispersal. In wheat, selection of awns with minimal extension, termed awnletted, has occurred during domestication by way of loci that dominantly inhibit awn development, such as Tipped1 (B1), Tipped2 (B2), and Hooded (Hd). Here we identify and characterize the B1 gene. B1 was identified using bulked segregant RNA-sequencing of an F2 durum wheat population and through deletion mapping of awned bread wheat mutants. Functional characterization was accomplished by gene overexpression while haplotype analyses assessed B1 polymorphisms and genetic variation. Located on chromosome 5A, B1 is a C2H2 zinc finger encoding gene with ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. Constitutive overexpression of B1 in awned wheat produced an awnletted phenotype with pleiotropic effects on plant height and fertility. Transcriptome analysis of B1 overexpression plants suggests a role as transcriptional repressor, putatively targeting pathways involved in cell proliferation. Haplotype analysis revealed a conserved B1 coding region with proximal polymorphisms and supported the contention that B1 is mainly responsible for awnletted wheats globally. B1, predominantly responsible for awn inhibition in wheat, encodes a C2H2 zinc finger protein with EAR motifs which putatively functions as a transcriptional repressor.
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Affiliation(s)
- Daiqing Huang
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Qian Zheng
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Tancey Melchkart
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - David J. F. Konkin
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Martial Martucci
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Frank M. You
- Ottawa Research and Development CentreAgriculture and Agri‐Food Canada960 Carling AvenueOttawaONK1A 0C6Canada
| | - Martha Clarke
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Nikolai M. Adamski
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Catherine Chinoy
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Andrew Steed
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Curt A. McCartney
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Adrian J. Cutler
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Paul Nicholson
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - J. Allan Feurtado
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
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15
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Cseh A, Megyeri M, Yang C, Hubbart-Edwards S, Scholefield D, Ashling SS, King IP, King J, Grewal S. Development of a New A m -Genome-Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat-Triticum monococcum Introgression Lines. THE PLANT GENOME 2019; 12:1-7. [PMID: 33016586 DOI: 10.3835/plantgenome2018.12.0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/24/2019] [Indexed: 06/11/2023]
Abstract
We identified 1247 polymorphic single nucleotide polymorphisms between Triticum monococcum and wheat. We identified 191 markers validated across all seven chromosomes of T. monococcum. Detected a T. monococcum introgression in leaf-rust-resistant lines. Cultivated einkorn wheat (Triticum monococcum L. subsp. monococcum, 2n = 2x = 14, Am Am ) and its wild relative T. monococcum subsp. aegilopoides are important sources of economically useful genes that can be exploited for wheat (Triticum aestivum L.) breeding. Einkorn has excellent resistance to fungal diseases and gene transfer is relatively simple via standard breeding methods. To fulfill the growing demand by modern prebreeding programs for a cost-effective high-throughput procedure for accurately detecting introgressed chromosomes or chromosome segments from T. monococcum into wheat, we used the Axiom Wheat-Relative Genotyping Array and developed a set of Am genome-specific exome-based single nucleotide polymorphism (SNP) markers suitable for rapid identification of T. monococcum chromatin in a wheat background. We identified 1247 polymorphic SNPs between T. monococcum and wheat. We identified 191 markers across all seven chromosomes of T. monococcum that are also present on an existing Triticum urartu Thum. ex Gandil. genetic map and potentially ordered them on the basis of the high macrocollinearity and conservation of marker order between T. monococcum and T. urartu. The marker set has been tested on leaf-rust-resistant BC3 F4 progenies of wheat-T. monococcum hybrids. Two markers (AX-94492165, AX-95073542) placed on the distal end of the chromosome arm 7AL detected a T. monococcum introgression into wheat. The SNP marker set thus proved highly effective in the identification of T. monococcum chromatin in a wheat background, offering a reliable method for screening and selecting wheat-T. monococcum introgression lines, a procedure that could significantly speed up prebreeding programs.
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Affiliation(s)
- Andras Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462, Martonvasar, Hungary
| | - Maria Megyeri
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462, Martonvasar, Hungary
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Stephen S Ashling
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, Univ. of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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16
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Devi U, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge A, King IP, King J. Development and characterisation of interspecific hybrid lines with genome-wide introgressions from Triticum timopheevii in a hexaploid wheat background. BMC PLANT BIOLOGY 2019; 19:183. [PMID: 31060503 PMCID: PMC6501383 DOI: 10.1186/s12870-019-1785-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/17/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Triticum timopheevii (2n = 4x = 28; AtAtGG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines, T. timopheevii can contribute to wheat's narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines. RESULTS A whole genome introgression approach, exploiting homoeologous recombination in the absence of the Ph1 locus, has resulted in the transfer of different chromosome segments from both the At and G genomes of T. timopheevii into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from T. timopheevii, thereby allowing the generation of a genetic map of T. timopheevii containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the At and G genomes of T. timopheevii. The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of T. timopheevii and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the At and G genomes of T. timopheevii that have been previously only detected through cytological techniques. CONCLUSIONS In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of T. timopheevii in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat-T. timopheevii hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions.
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Affiliation(s)
- Urmila Devi
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Surbhi Grewal
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Cai-Yun Yang
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stella Hubbart-Edwards
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Duncan Scholefield
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stephen Ashling
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ian P King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Julie King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK.
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