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BackgroundRice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers.ResultsThe contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance.ConclusionsIt was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0131-4) contains supplementary material, which is available to authorized users.

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The effect of two-component rice cultivar mixtures on the control of rice blast disease was studied in three different experiments under rainfed upland conditions in the Madagascar Highlands. The mixtures involved a susceptible cultivar (either susceptible or very susceptible) and a resistant cultivar in different mixture arrangements (random or row mixtures) and with different proportions of the susceptible cultivar (50, 20 and 16AE7%), which were compared to the susceptible cultivar grown in a pure stand. The effect of these mixtures on the incidence and severity of leaf and panicle blast was measured weekly, and on yield and yield components at harvest time. The mixture effect was more efficient in reducing disease with a proportion of 16AE7% susceptible component than with a proportion of 50%. Blast epidemic was significantly reduced in all three experiments. However, under high blast pressure, there was no reduction in the disease by the end of the epidemic and yields of the susceptible cultivar were almost zero whatever the mixture. In two other experiments performed under lower blast pressure, disease incidence and severity were significantly lower in mixtures, and yields of the susceptible cultivars grown in mixtures were higher than those of their respective pure stands. Cultivar mixtures are a promising strategy that could contribute to a more sustainable cultivation of rice under upland conditions in the context of subsistence agriculture in Madagascar, where all cropping operations are manual.

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