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Kohlmeier MG, Farquharson EA, Ballard RA, O’Hara GW, Terpolilli JJ. Complete genome sequence of Rhizobium leguminosarum bv. viciae SRDI969, an acid-tolerant, efficient N 2-fixing microsymbiont of Vicia faba. Microbiol Resour Announc 2023; 12:e0048923. [PMID: 37526441 PMCID: PMC10508120 DOI: 10.1128/mra.00489-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023] Open
Abstract
We report the complete genome sequence of Rhizobium leguminosarum bv. viciae SRDI969, an acid-tolerant, efficient nitrogen-fixing microorganism of Vicia faba. The 6.8 Mbp genome consists of a chromosome and four plasmids, with the symbiosis and nitrogen fixation genes encoded on the chromosome.
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Affiliation(s)
- MacLean G. Kohlmeier
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Elizabeth A. Farquharson
- South Australian Research and Development Institute, Urrbrae, South Australia, Australia
- University of Adelaide, School of Agriculture, Food and Wine, Adelaide, South Australia, Australia
| | - Ross A. Ballard
- South Australian Research and Development Institute, Urrbrae, South Australia, Australia
- University of Adelaide, School of Agriculture, Food and Wine, Adelaide, South Australia, Australia
| | - Graham W. O’Hara
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Jason J. Terpolilli
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, Perth, Western Australia, Australia
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Henares BM, Blake SN, Farfan-Caceres L, Tahghighi H, Debler JW, Russ MH, Farquharson EA, Rose JA, Khani M, Davidson JA, Kamphuis LG, Lee RC. Virulence Profiles and Genome-Wide Association Study for Ascochyta lentis Isolates Collected from Australian Lentil-Growing Regions. Phytopathology 2023; 113:1515-1524. [PMID: 36935379 DOI: 10.1094/phyto-10-22-0397-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ascochyta lentis, the causal organism of Ascochyta blight (AB) of lentil (Lens culinaris), has been shown to produce an avirulence effector protein that mediates AB resistance in certain lentil cultivars. The two known forms of the effector protein were identified from a biparental mapping population between isolates that have reciprocal virulence on 'PBA Hurricane XT' and 'Nipper'. The effector AlAvr1-1 was described for the PBA Hurricane XT-avirulent isolate P94-24 and AlAvr1-2 characterized in the PBA Hurricane XT-virulent isolate AlKewell. Here, we performed a genome-wide association study to identify other loci associated with AB for a differential set of lentil cultivars from a diverse panel of isolates collected in the Australian lentil-growing regions from 2013 to 2020. The chromosome 3 AlAvr1 locus was strongly associated with the PBA Hurricane XT, 'Indianhead', and Nipper disease responses, but one other genomic region on chromosome 11 was also associated with the Nipper disease trait. Our results corroborate earlier work that identified the AlAvr1 locus for field-collected isolates that span the period before release and after widespread adoption of PBA Hurricane XT. A multiplex PCR assay was developed to differentiate the genes AlAvr1-1 and AlAvr1-2 to predict PBA Hurricane XT avirulence and pathotype designation in the diversity panel. Increasing numbers of the PBA Hurricane XT-virulent pathotype 2 isolates across that time indicate strong selection for isolates with the AlAvr1-2 allele. Furthermore, one other region of the A. lentis genome may contribute to the pathogen-host interaction for lentil AB.
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Affiliation(s)
- Bernadette M Henares
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Sara N Blake
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Lina Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Hediyeh Tahghighi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Michelle H Russ
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Elizabeth A Farquharson
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Jade A Rose
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Mohsen Khani
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Jennifer A Davidson
- Pulse and Oilseed Pathology, Plant Health & Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA 5064 Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Blake SN, Lee RC, Russ MH, Farquharson EA, Rose JA, Herdina, Goonetilleke SN, Farfan-Caceres LM, Debler JW, Syme RA, Davidson JA. Phenotypic and Genotypic Diversity of Ascochyta fabae Populations in Southern Australia. Front Plant Sci 2022; 13:918211. [PMID: 35982697 PMCID: PMC9380778 DOI: 10.3389/fpls.2022.918211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/06/2022] [Indexed: 09/22/2023]
Abstract
Ascochyta fabae Speg. is a serious foliar fungal disease of faba bean and a constraint to production worldwide. This study investigated the phenotypic and genotypic diversity of the A. fabae pathogen population in southern Australia and the pathogenic variability of the population was examined on a differential set of faba bean cultivars. The host set was inoculated with 154 A. fabae isolates collected from 2015 to 2018 and a range of disease reactions from high to low aggressiveness was observed. Eighty percent of isolates collected from 2015 to 2018 were categorized as pathogenicity group (PG) PG-2 (pathogenic on Farah) and were detected in every region in each year of collection. Four percent of isolates were non-pathogenic on Farah and designated as PG-1. A small group of isolates (16%) were pathogenic on the most resistant differential cultivars, PBA Samira or Nura, and these isolates were designated PG-3. Mating types of 311 isolates collected between 1991 and 2018 were determined and showed an equal ratio of MAT1-1 and MAT1-2 in the southern Australian population. The genetic diversity and population structure of 305 isolates were examined using DArTseq genotyping, and results suggest no association of genotype with any of the population descriptors viz.: collection year, region, host cultivar, mating type, or PG. A Genome-Wide Association Study (GWAS) was performed to assess genetic association with pathogenicity traits and a significant trait-associated genomic locus for disease in Farah AR and PBA Zahra, and PG was revealed. The high frequency of mating of A. fabae indicated by the wide distribution of the two mating types means changes to virulence genes would be quickly distributed to other genotypes. Continued monitoring of the A. fabae pathogen population through pathogenicity testing will be important to identify any increases in aggressiveness or emergence of novel PGs. GWAS and future genetic studies using biparental mating populations could be useful for identifying virulence genes responsible for the observed changes in pathogenicity.
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Affiliation(s)
- Sara N. Blake
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michelle H. Russ
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Elizabeth A. Farquharson
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Jade A. Rose
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Herdina
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Shashi N. Goonetilleke
- Crop Improvement, Plant Health and Biosecurity, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Lina M. Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Johannes W. Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Robert A. Syme
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Jennifer A. Davidson
- Pulse and Oilseed Pathology, Plant Health and Biosecurity, Crop Sciences, South Australian Research and Development Institute, Adelaide, SA, Australia
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Sadras VO, Lake L, Li Y, Farquharson EA, Sutton T. Phenotypic plasticity and its genetic regulation for yield, nitrogen fixation and δ13C in chickpea crops under varying water regimes. J Exp Bot 2016; 67:4339-51. [PMID: 27296246 DOI: 10.1093/jxb/erw221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We measured yield components, nitrogen fixation, soil nitrogen uptake and carbon isotope composition (δ(13)C) in a collection of chickpea genotypes grown in environments where water availability was the main source of yield variation. We aimed to quantify the phenotypic plasticity of these traits using variance ratios, and to explore their genetic basis using FST genome scan. Fifty-five genes in three genomic regions were found to be under selection for plasticity of yield; 54 genes in four genomic regions for the plasticity of seeds per m(2); 48 genes in four genomic regions for the plasticity of δ(13)C; 54 genes in two genomic regions for plasticity of flowering time; 48 genes in five genomic regions for plasticity of nitrogen fixation and 49 genes in three genomic regions for plasticity of nitrogen uptake from soil. Plasticity of yield was related to plasticity of nitrogen uptake from soil, and unrelated to plasticity of nitrogen fixation, highlighting the need for closer attention to nitrogen uptake in legumes. Whereas the theoretical link between δ(13)C and transpiration efficiency is strong, the actual link with yield is erratic due to trade-offs and scaling issues. Genes associated with plasticity of δ(13)C were identified that may help to untangle the δ(13)C-yield relationship. Combining a plasticity perspective to deal with complex G×E interactions with FST genome scan may help understand and improve both crop adaptation to stress and yield potential.
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Affiliation(s)
- Victor O Sadras
- South Australian Research and Development Institute, Waite Campus, Australia
| | - Lachlan Lake
- South Australian Research and Development Institute, Waite Campus, Australia
| | - Yongle Li
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Australia
| | | | - Tim Sutton
- South Australian Research and Development Institute, Waite Campus, Australia
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