Nutrients and soil structure influence furovirus infection of wheat

Soil-borne wheat mosaic virus (SBWMV) and Soil-borne cereal mosaic virus (SBCMV), genus Furovirus, family Virgaviridae, cause significant crop losses in cereals. The viruses are transmitted by the soil-borne plasmodiophorid Polymyxa graminis. Inside P. graminis resting spores, the viruses persist in the soil for long time, which makes the disease difficult to combat. To open up novel possibilities for virus control, we explored the influence of physical and chemical soil properties on infection of wheat with SBWMV and SBCMV. Moreover, we investigated, whether infection rates are influenced by the nutritional state of the plants. Infection rates of susceptible wheat lines were correlated to soil structure parameters and nutrient contents in soil and plants. Our results show that SBWMV and SBCMV infection rates decrease the more water-impermeable the soil is and that virus transmission depends on pH. Moreover, we found that contents of several nutrients in the soil (e.g. phosphorous, magnesium, zinc) and in planta (e.g. nitrogen, carbon, boron, sulfur, calcium) affect SBWMV and SBCMV infection rates. The knowledge generated may help paving the way towards development of a microenvironment-adapted agriculture

Quality characteristics of European avena genetic resources collections

International audienceThe research project "Avena genetic resources for quality in human consumption" (AVEQ, 2007-2011) aimed at the agronomic and qualitative evaluation of European oat germplasm; for this purpose a working collection with more than 600 accessions, including modern commercial cultivars and wild species, was used. The working collection was split in two groups and field grown in 2008 and 2009 in seven different locations: Estonia, Sweden, Poland, France, Italy, Romania and Bulgaria. For each accession morphological and technological traits were registered. The results of this study indicated that modern varieties are significantly superior to old varieties and wild accessions in terms of yield and grain technological quality (seed weight and test weight). A wide variability was observed for quantitative and qualitative traits, and some genotypes potentially interesting for breeding programs were identified

Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Sensitivity to lodging of oat varieties has been reduced in the last decades through the introduction of dwarfing genes. However, lodging may still cause significant yield loss, underscoring the need for new oat varieties with higher levels of lodging tolerance. In the present study, we analysed lodging and plant height in a collection of European oat accessions including landraces, old and modern varieties, in order to perform a genome-wide association study (GWAS) for identifying markers associated to lodging tolerance. This collection has been recently genotyped by the Infinium 6K SNP array for oat and SNP data were analysed as continuous intensity ratios, rather than as discrete genotypes (Tumino et al. 2016, Theor Appl Genet 129, pp. 1711–1724). Phenotypes for lodging severity, plant height and growth habit were collected under natural conditions in eight European countries. Plant height correlated to lodging severity as previously observed in many studies, explaining about 30% of lodging variation. GWAS analyses detected six significant associations for lodging and two for plant height. These results indicate that GWAS can successfully be used for identifying markers associated to lodging in oat, even though lodging is a quantitative trait influenced by several plant characteristics.</p

Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios

Key message: Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option.Abstract: Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward’s clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits

Fusarium genetic traceability: role for mycotoxin control in small grain cereals agro-food chains

Risks associated with mycotoxin contamination of cereals, that are included in the ten major staple foods and greatly contribute to the dietary energy intake, are of worldwide relevance. In small grain cereals, mycotoxins are produced by fungi such as Aspergillus, Penicillium, Alternaria and Fusarium that colonize the plant in the field and can grow during the post-harvest period, producing several classes of mycotoxins. The identification of mycotoxigenic fungal species and strains is essential for developing effective strategies for control. For this purpose, genetic traceability has proved to be a valuable tool that can be applied along the whole production chain, starting in the field for early diagnosis of FHB (Fusarium Head Blight) disease to the final processing steps, such as malting or pasta making. In this paper, DNA-based analytical tools that are currently available for the identification and quantification of mycotoxigenic fungal species and strains are reviewed, with particular emphasis on Fusarium, and their possible applications in mycotoxin control in small grain cereal chains are discussed