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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] [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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Singh R, Kumar K, Purayannur S, Chen W, Verma PK. Ascochyta rabiei: A threat to global chickpea production. MOLECULAR PLANT PATHOLOGY 2022; 23:1241-1261. [PMID: 35778851 PMCID: PMC9366070 DOI: 10.1111/mpp.13235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 06/01/2023]
Abstract
UNLABELLED The necrotrophic fungus Ascochyta rabiei causes Ascochyta blight (AB) disease in chickpea. A. rabiei infects all aerial parts of the plant, which results in severe yield loss. At present, AB disease occurs in most chickpea-growing countries. Globally increased incidences of A. rabiei infection and the emergence of new aggressive isolates directed the interest of researchers toward understanding the evolution of pathogenic determinants in this fungus. In this review, we summarize the molecular and genetic studies of the pathogen along with approaches that are helping in combating the disease. Possible areas of future research are also suggested. TAXONOMY kingdom Mycota, phylum Ascomycota, class Dothideomycetes, subclass Coelomycetes, order Pleosporales, family Didymellaceae, genus Ascochyta, species rabiei. PRIMARY HOST A. rabiei survives primarily on Cicer species. DISEASE SYMPTOMS A. rabiei infects aboveground parts of the plant including leaves, petioles, stems, pods, and seeds. The disease symptoms first appear as watersoaked lesions on the leaves and stems, which turn brown or dark brown. Early symptoms include small circular necrotic lesions visible on the leaves and oval brown lesions on the stem. At later stages of infection, the lesions may girdle the stem and the region above the girdle falls off. The disease severity increases at the reproductive stage and rounded lesions with concentric rings, due to asexual structures called pycnidia, appear on leaves, stems, and pods. The infected pod becomes blighted and often results in shrivelled and infected seeds. DISEASE MANAGEMENT STRATEGIES Crop failures may be avoided by judicious practices of integrated disease management based on the use of resistant or tolerant cultivars and growing chickpea in areas where conditions are least favourable for AB disease development. Use of healthy seeds free of A. rabiei, seed treatments with fungicides, and proper destruction of diseased stubbles can also reduce the fungal inoculum load. Crop rotation with nonhost crops is critical for controlling the disease. Planting moderately resistant cultivars and prudent application of fungicides is also a way to combat AB disease. However, the scarcity of AB-resistant accessions and the continuous evolution of the pathogen challenges the disease management process. USEFUL WEBSITES https://www.ndsu.edu/pubweb/pulse-info/resourcespdf/Ascochyta%20blight%20of%20chickpea.pdf https://saskpulse.com/files/newsletters/180531_ascochyta_in_chickpeas-compressed.pdf http://www.pulseaus.com.au/growing-pulses/bmp/chickpea/ascochyta-blight http://agriculture.vic.gov.au/agriculture/pests-diseases-and-weeds/plant-diseases/grains-pulses-and-cereals/ascochyta-blight-of-chickpea http://www.croppro.com.au/crop_disease_manual/ch05s02.php https://www.northernpulse.com/uploads/resources/722/handout-chickpeaascochyta-nov13-2011.pdf http://oar.icrisat.org/184/1/24_2010_IB_no_82_Host_Plant https://www.crop.bayer.com.au/find-crop-solutions/by-pest/diseases/ascochyta-blight.
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Affiliation(s)
- Ritu Singh
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
| | - Kamal Kumar
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Department of Plant Molecular BiologyUniversity of Delhi (South Campus)New DelhiIndia
| | - Savithri Purayannur
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Weidong Chen
- Grain Legume Genetics and Physiology Research Unit, USDA Agricultural Research Service, and Department of Plant PathologyWashington State UniversityPullmanWashingtonUSA
| | - Praveen Kumar Verma
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Plant Immunity Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
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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. FRONTIERS IN PLANT SCIENCE 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] [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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Raman R, Warren A, Krysinska-Kaczmarek M, Rohan M, Sharma N, Dron N, Davidson J, Moore K, Hobson K. Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:877266. [PMID: 35665159 PMCID: PMC9159299 DOI: 10.3389/fpls.2022.877266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/08/2022] [Indexed: 05/05/2023]
Abstract
Ascochyta blight (AB), caused by a necrotrophic fungus, Ascochyta rabiei (syn. Phoma rabiei) has the potential to destroy the chickpea industry worldwide, due to limited sources of genetic resistance in the cultivated gene pool, high evolutionary potential of the pathogen and challenges with integrated disease management. Therefore, the deployment of stable genetic resistance in new cultivars could provide an effective disease control strategy. To investigate the genetic basis of AB resistance, genotyping-by-sequencing based DArTseq-single nucleotide polymorphism (SNP) marker data along with phenotypic data of 251 advanced breeding lines and chickpea cultivars were used to perform genome-wide association (GWAS) analysis. Host resistance was evaluated seven weeks after sowing using two highly aggressive single spore isolates (F17191-1 and TR9571) of A. rabiei. GWAS analyses based on single-locus and multi-locus mixed models and haplotyping trend regression identified twenty-six genomic regions on Ca1, Ca4, and Ca6 that showed significant association with resistance to AB. Two haplotype blocks (HB) on chromosome Ca1; HB5 (992178-1108145 bp), and HB8 (1886221-1976301 bp) were associated with resistance against both isolates. Nine HB on the chromosome, Ca4, spanning a large genomic region (14.9-56.6 Mbp) were also associated with resistance, confirming the role of this chromosome in providing resistance to AB. Furthermore, trait-marker associations in two F3 derived populations for resistance to TR9571 isolate at the seedling stage under glasshouse conditions were also validated. Eighty-nine significantly associated SNPs were located within candidate genes, including genes encoding for serine/threonine-protein kinase, Myb protein, quinone oxidoreductase, and calmodulin-binding protein all of which are implicated in disease resistance. Taken together, this study identifies valuable sources of genetic resistance, SNP markers and candidate genes underlying genomic regions associated with AB resistance which may enable chickpea breeding programs to make genetic gains via marker-assisted/genomic selection strategies.
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Affiliation(s)
- Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- *Correspondence: Rosy Raman,
| | - Annie Warren
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | | | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Nicole Dron
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - Jenny Davidson
- South Australian Research and Development Institute, Urrbrae, SA, Australia
| | - Kevin Moore
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - Kristy Hobson
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
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Getaneh G, Tefera T, Lemessa F, Ahmed S, Fite T, Villinger J. Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia. J Fungi (Basel) 2021; 7:jof7100820. [PMID: 34682241 PMCID: PMC8541683 DOI: 10.3390/jof7100820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.
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Affiliation(s)
- Gezahegne Getaneh
- Ambo Agricultural Research Center, Ethiopian Institute of Agricultural Research, Addis Ababa P.O. Box 2003, Ethiopia
- International Centre of Insect Physiology and Ecology (icipe), Addis Ababa P.O. Box 5689, Ethiopia; (T.T.); (T.F.)
- International Centre of Insect Physiology and Ecology (icipe), Nairobi P.O. Box 30772-00100, Kenya;
- Department of Horticulture and Plant Science, Jimma University, Jimma P.O. Box 307, Ethiopia;
- Correspondence: or
| | - Tadele Tefera
- International Centre of Insect Physiology and Ecology (icipe), Addis Ababa P.O. Box 5689, Ethiopia; (T.T.); (T.F.)
| | - Fikre Lemessa
- Department of Horticulture and Plant Science, Jimma University, Jimma P.O. Box 307, Ethiopia;
| | - Seid Ahmed
- ICARDA International Center of Agricultural Research, Rue Hafiane Cherkaoui, Agdal, Rabat P.O. Box 6299, Morocco;
| | - Tarekegn Fite
- International Centre of Insect Physiology and Ecology (icipe), Addis Ababa P.O. Box 5689, Ethiopia; (T.T.); (T.F.)
- International Centre of Insect Physiology and Ecology (icipe), Nairobi P.O. Box 30772-00100, Kenya;
- School of Plant Sciences, College of Agriculture and Environmental Sciences, Haramaya University, Dire Dawa P.O. Box 138, Ethiopia
| | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), Nairobi P.O. Box 30772-00100, Kenya;
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