Publications by authors named "Phil Salisbury"

5 Publications

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Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.).

Sci Rep 2020 03 10;10(1):4416. Epub 2020 Mar 10.

NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.

Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the 'ascospore shower' test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.
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http://dx.doi.org/10.1038/s41598-020-61211-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064481PMC
March 2020

Stable Quantitative Resistance Loci to Blackleg Disease in Canola ( L.) Over Continents.

Front Plant Sci 2018 23;9:1622. Epub 2018 Nov 23.

IGEPP, INRA, Agrocampus Ouest, Université Rennes, Le Rheu, France.

The hemibiotrophic fungus, is the most devastating pathogen, causing blackleg disease in canola ( L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by 'Darmor-' but 'Yudal' also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that which is present in 'Darmor-' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference 'Darmor-' genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies.
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http://dx.doi.org/10.3389/fpls.2018.01622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265502PMC
November 2018

A multiplex PCR for rapid identification of species in the triangle of U.

Plant Methods 2017 15;13:49. Epub 2017 Jun 15.

Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia.

Background: Within the Brassicaceae, six species from the genus are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six species are described by U's triangle model. Extensive shared traits and diverse morphotypes among species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species. Molecular genotyping based on simple sequence repeat (SSR) marker sequencing or the Illumina Infinium 60K single nucleotide polymorphism (SNP) array has been used to identify species and assess genetic diversity of collections. However, these methods are technically challenging, expensive and time-consuming, making them unsuitable for routine or rapid screening of accessions for germplasm management. A cheaper, faster and simpler method for species identification is described here.

Results: A multiplex polymerase chain reaction (MPCR) consisting of new and existing primers specific to the A, B and C genomes was able to reliably distinguish all six species in the triangle of U with 16 control samples of known species identity. Further validation against 120 accessions previously genotyped showed that the MPCR is highly accurate and comparable to more advanced techniques such as SSR marker sequencing or the Illumina Infinium 60K SNP array. In addition, the MPCR was sensitive enough to detect seed contaminations in pooled seed samples of accessions.

Conclusion: A cheap and fast multiplex PCR assay for identification of species in the triangle of U was developed and validated in this study. The MPCR assay can be readily implemented in any basic molecular laboratory and should prove useful for the management of germplasm collections in genebanks.
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http://dx.doi.org/10.1186/s13007-017-0200-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472915PMC
June 2017

Genome-wide Association Study Identifies New Loci for Resistance to in Canola.

Front Plant Sci 2016 24;7:1513. Epub 2016 Oct 24.

Marcroft Grains Pathology, Horsham VIC, Australia.

Key message "We identified both quantitative and quantitative resistance loci to , a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to One of the novel loci identified for the first time, , conveys adult plant resistance in canola." Blackleg, caused by , is a significant disease which affects the sustainable production of canola (). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to . Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned / genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to . One of the novel loci identified for the first time, , conveys adult plant resistance and mapped within 13.2 kb from gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of genes of and on the sequenced genome of cv. Darmor-. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to in canola.
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http://dx.doi.org/10.3389/fpls.2016.01513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075532PMC
October 2016

Pterostilbene Is a Potential Candidate for Control of Blackleg in Canola.

PLoS One 2016 23;11(5):e0156186. Epub 2016 May 23.

Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia.

Two stilbenes, resveratrol and pterostilbene, exhibit antifungal activity against Leptosphaeria maculans, the fungal pathogen responsible for blackleg (stem canker) in canola (Brassica napus). In vitro studies on the effect of these stilbenes on L. maculans mycelial growth and conidia germination showed that pterostilbene is a potent fungicide and sporicide, but resveratrol only exerted minor inhibition on L. maculans. Cell viability of hyphae cultures was markedly reduced by pterostilbene and SYTOX green staining showed that cell membrane integrity was compromised. We demonstrate that pterostilbene exerts fungicidal activity across 10 different L. maculans isolates and the compound confers protection to the blackleg-susceptible canola cv. Westar seedlings. The potential of pterostilbene as a control agent against blackleg in canola is discussed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156186PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877020PMC
July 2017
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