Abstract
BackgroundBakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses.ResultsA germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci.ConclusionsNew effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.
Highlights
Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses
Bakanae disease resistance in the Rice Germplasm Collection A virulent F. fujikuroi isolate was used to inoculate seeds of 138 rice accessions adapted to the Italian growing conditions, in order to explore their resistance to bakanae disease
Population structure of the Rice Germplasm Collection and genetic diversity analysis The model based analysis of the panel structure was performed with Structure coupled with Structure Harvester analysis of the results, taking into account the number of admixed varieties identified at each K value, as proposed by Courtois et al (2012)
Summary
Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. In various rice growing countries, significant yield losses caused by the disease can range from 50% to more than 70% (Ou 1985; Rood 2004). Bakanae is caused by one or more seed-borne Fusarium species, mainly F. fujikuroi (Wulff et al 2010), and the disease may infect rice plants from the pre-emergence stage to the mature stage, with severe infection of rice seeds resulting in poor germination or withering (Iqbal et al 2011). Mature rice plants are tall, frequently stunted, with an angle of leaf insertion wider than in healthy seedlings. Infected plants eventually die, while panicles on surviving plants do not develop any grains, resulting in yield loss (Desjardins et al 2000; Mew and Gonzales 2002; Ou 1985)
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