Genome‐wide association mapping of <i>Fusarium langsethiae</i> infection and mycotoxin accumulation in oat (<i>Avena sativa</i> L.)

Isidro-Sánchez, Julio; Cusack, Kane D’Arcy D’Arcy; Verheecke‐Vaessen, Carol; Kahla, Amal; Bekele, Wubishet A.; Doohan, Fiona M.; Magan, Naresh; Medina, Ángel

doi:10.1002/tpg2.20023

Cited by 13 publications

(10 citation statements)

References 72 publications

(104 reference statements)

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“…The resistance against FHB is known to be complex and impacted by several minor genes. Only a few quantitative trait loci (QTL) are currently determined against FHB in oats ( Bjørnstad et al, 2017 , Isidro-Sánchez et al., 2020 ). In contrast to previous genetic studies that are based on heavy field phenotyping, the phenotyping method presented in this study provides information from the specific plant tissue.…”

Section: Discussionmentioning

confidence: 99%

“…The resistance of oats to both DON ( Tekle et al., 2018 ) and T-2/HT-2-producing fungi ( Isidro-Sánchez et al., 2020 ) can be assessed in artificially inoculated field trials but several trials are needed to get consistent cultivar rankings ( Tekle et al., 2018 ; Hautsalo et al., 2020 ). Controlled environments can provide more consistent estimates for the disease, but these results do not necessarily fit for selecting cultivars that would have resistance in variable field conditions ( Hautsalo et al., 2020 ) due to the complex nature of FHB disease resistance.…”

Section: Introductionmentioning

confidence: 99%

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Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance

et al. 2023

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Oat-based value-added products have increased their value as healthy foodstuff. Fusarium head blight (FHB) infections and the mycotoxins accumulated to the oat seeds, however, pose a challenge to oat production. The FHB infections are predicted to become more prevalent in the future changing climates and under more limited use of fungicides. Both these factors increase the pressure for breeding new resistant cultivars. Until now, however, genetic links in oats against FHB infection have been difficult to identify. Therefore, there is a great need for more effective breeding efforts, including improved phenotyping methods allowing time series analysis and the identification of molecular markers during disease progression. To these ends, dissected spikelets of several oat genotypes with different resistance profiles were studied by image-based methods during disease progression by Fusarium culmorum or F. langsethiae species. The chlorophyll fluorescence of each pixel in the spikelets was recorded after inoculation by the two Fusarium spp., and the progression of the infections was analyzed by calculating the mean maximum quantum yield of PSII (Fv/Fm) values for each spikelet. The recorded values were (i) the change in the photosynthetically active area of the spikelet as percentage of its initial size, and (ii) the mean of Fv/Fm values of all fluorescent pixels per spikelet post inoculation, both indicative of the progression of the FHB disease. The disease progression was successfully monitored, and different stages of the infection could be defined along the time series. The data also confirmed the differential rate of disease progression by the two FHB causal agents. In addition, oat varieties with variable responses to the infections were indicated.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance

et al. 2023

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“…In previous research conducted on large panels of oat lines based on DArT or GBS markers, a weak population structure within the analyzed accessions has been observed [ 30 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ]. Authors have claimed that oat, despite having four recognizable types (naked, covered, spring, and winter), has not shown an obvious structure of a population.…”

Section: Discussionmentioning

confidence: 99%

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More Than a Century of Polish Breeding

Koroluk

Sowa

Boczkowska

et al. 2023

IJMS

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This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.

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“…F. langsethiae Fe2391 strain was selected as this strain, originating from the UK, has been previously characterized as potent producer of T-2 and HT-2 toxin [ 6 , 29 ].…”

Section: Methodsmentioning

confidence: 99%

De novo genome assembly and functional annotation for Fusarium langsethiae

et al. 2022

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Background Fusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies. Results The F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology. Conclusions We developed a high-quality genome assembly of a total length of 59 Mb and N50 of 3.51 Mb. Raw sequence reads and assembled genome is publicly available and can be downloaded from: GenBank under the accession JAFFKB000000000. All commands used to generate this assembly are accessible via GitHub: https://github.com/FadyMohareb/fusarium_langsethiae.

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Genome‐wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.)

Cited by 13 publications

References 72 publications

Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance

Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More Than a Century of Polish Breeding

De novo genome assembly and functional annotation for Fusarium langsethiae

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