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Nelson MN, Książkiewicz M, Rychel S, Besharat N, Taylor CM, Wyrwa K, Jost R, Erskine W, Cowling WA, Berger JD, Batley J, Weller JL, Naganowska B, Wolko B. The loss of vernalization requirement in narrow-leafed lupin is associated with a deletion in the promoter and de-repressed expression of a Flowering Locus T (FT) homologue. New Phytol 2017; 213:220-232. [PMID: 27418400 DOI: 10.1111/nph.14094] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/05/2016] [Indexed: 05/19/2023]
Abstract
Adaptation of Lupinus angustifolius (narrow-leafed lupin) to cropping in southern Australian and northern Europe was transformed by a dominant mutation (Ku) that removed vernalization requirement for flowering. The Ku mutation is now widely used in lupin breeding to confer early flowering and maturity. We report here the identity of the Ku mutation. We used a range of genetic, genomic and gene expression approaches to determine whether Flowering Locus T (FT) homologues are associated with the Ku locus. One of four FT homologues present in the narrow-leafed lupin genome, LanFTc1, perfectly co-segregated with the Ku locus in a reference mapping population. Expression of LanFTc1 in the ku (late-flowering) parent was strongly induced by vernalization, in contrast to the Ku (early-flowering) parent, which showed constitutively high LanFTc1 expression. Co-segregation of this expression phenotype with the LanFTc1 genotype indicated that the Ku mutation impairs cis-regulation of LanFTc1. Sequencing of LanFTc1 revealed a 1.4-kb deletion in the promoter region, which was perfectly predictive of vernalization response in 216 wild and domesticated accessions. Linkage disequilibrium rapidly decayed around LanFTc1, suggesting that this deletion caused the loss of vernalization response. This is the first time a legume FTc subclade gene has been implicated in the vernalization response.
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Affiliation(s)
- Matthew N Nelson
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Naghmeh Besharat
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Candy M Taylor
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Katarzyna Wyrwa
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Ricarda Jost
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for AgriBiosciences, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - William Erskine
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Centre for Plant Genetics and Breeding, School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Jens D Berger
- Centre for Plant Genetics and Breeding, School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- CSIRO Agriculture, Private Bag No. 5, Wembley, WA, 6913, Australia
| | - Jacqueline Batley
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Barbara Naganowska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bogdan Wolko
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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Mair WJ, Deng W, Mullins JGL, West S, Wang P, Besharat N, Ellwood SR, Oliver RP, Lopez-Ruiz FJ. Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51. Front Microbiol 2016; 7:1279. [PMID: 27594852 PMCID: PMC4990540 DOI: 10.3389/fmicb.2016.01279] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/03/2016] [Indexed: 12/18/2022] Open
Abstract
Pyrenophora teres f. sp. teres is the cause of net form of net blotch (NFNB), an economically important foliar disease in barley (Hordeum vulgare). Net and spot forms of net blotch are widely controlled using site-specific systemic fungicides. Although resistance to succinate dehydrogenase inhibitors and quinone outside inhibitors has been addressed before in net blotches, mechanisms controlling demethylation inhibitor resistance have not yet been reported at the molecular level. Here we report the isolation of strains of NFNB in Australia since 2013 resistant to a range of demethylase inhibitor fungicides. Cyp51A:KO103-A1, an allele with the mutation F489L, corresponding to the archetype F495I in Aspergillus fumigatus, was only present in resistant strains and was correlated with resistance factors to various demethylase inhibitors ranging from 1.1 for epoxiconazole to 31.7 for prochloraz. Structural in silico modeling of the sensitive and resistant CYP51A proteins docked with different demethylase inhibitor fungicides showed how the interaction of F489L within the heme cavity produced a localized constriction of the region adjacent to the docking site that is predicted to result in lower binding affinities. Resistant strains also displayed enhanced induced expression of the two Cyp51A paralogs and of Cyp51B genes. While Cyp51B was found to be constitutively expressed in the absence of fungicide, Cyp51A was only detected at extremely low levels. Under fungicide induction, expression of Cyp51B, Cyp51A2, and Cyp51A1 was shown to be 1.6-, 3,- and 5.3-fold higher, respectively in the resistant isolate compared to the wild type. These increased levels of expression were not supported by changes in the promoters of any of the three genes. The implications of these findings on demethylase inhibitor activity will require current net blotch management strategies to be reconsidered in order to avoid the development of further resistance and preserve the lifespan of fungicides in use.
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Affiliation(s)
- Wesley J Mair
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
| | - Weiwei Deng
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
| | | | - Samuel West
- Institute of Life Science, School of Medicine, Swansea University Swansea, UK
| | - Penghao Wang
- School of Veterinary and Life Sciences, Murdoch University Murdoch, WA, Australia
| | - Naghmeh Besharat
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
| | - Simon R Ellwood
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
| | - Richard P Oliver
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
| | - Francisco J Lopez-Ruiz
- Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University Bentley, WA, Australia
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Mason AS, Rousseau-Gueutin M, Morice J, Bayer PE, Besharat N, Cousin A, Pradhan A, Parkin IAP, Chèvre AM, Batley J, Nelson MN. Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis. Genetics 2016; 202:513-23. [PMID: 26614742 PMCID: PMC4788232 DOI: 10.1534/genetics.115.183210] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.
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Affiliation(s)
- Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia
| | | | - Jérôme Morice
- IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France
| | - Philipp E Bayer
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Naghmeh Besharat
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Anouska Cousin
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Aneeta Pradhan
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
| | - Anne-Marie Chèvre
- IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France
| | - Jacqueline Batley
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia
| | - Matthew N Nelson
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom
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