Rice brown spot (BS) is a chronic disease that affects millions of hectares of rice every growing season, grown by some of the most resource-poor farmers. Despite its widespread occurrence and impact, much still needs to be understood about BS. Reported yield losses in relative terms vary widely from 4 to 52 %. However, accurate, systematic estimates are lacking. BS is conventionally perceived as a secondary problem that reflects rice crops that experience physiological stresses, e.g. drought and poor soil fertility, rather than a true infectious disease. Much remains to be understood about the mechanisms leading to epidemics and crop losses. Quantitative and qualitative knowledge gaps exist in our understanding of the epidemiological processes, sources of resistance and biocontrol methods. In this review we identify several of these gaps, which if filled, could lead to a strong impact on the management of brown spot. We also use the architecture of a simulation model to position and prioritize these knowledge gaps, assess the epidemiological consequences of disease management options on

The specificity between pathotypes of Pyricularia oryzae and genera of gramineous plants is governed by gene-for-gene interactions. Here, we show that avirulence genes involved in this host specificity have undergone different modes of functional losses dependent on, or affected by genomic compartments harboring them. The avirulence of an Eleusine pathotype on wheat is controlled by five genes including PWT3 which played a key role in the evolution of the Triticum pathotype (the wheat blast fungus). We cloned another gene using an association of its presence/absence with pathotypes, and designated it as PWT6. PWT6 was widely distributed in a lineage composed of Eleusine/Eragrostis isolates, but completely absent in a lineage composed of Lolium/Triticum isolates. On the other hand, PWT3 homologs were present in all isolates, and their loss of function in Triticum isolates was caused by insertions of transposable elements or nucleotide substitutions. Analyses of whole genome sequences of representative isolates revealed that these two genes were located in different genomic compartments; PWT6 was located in a repeat-rich region while PWT3 was located in a repeat-poor region. These results suggest that the course of differentiation of the pathotypes in P. oryzae appears to be illustrated as processes of functional losses of avirulence genes, but that modes of the losses are affected by genomic compartments in which they reside.