Abstract
Southern rice black-streaked dwarf virus (SRBSDV), which causes severe disease symptoms in rice (Oriza sativa L.) has been emerging in the last decade throughout northern Vietnam, southern Japan and southern, central and eastern China. Here we attempt to quantify the prevalence of SRBSDV in the Honghe Hani rice terraces system (HHRTS)—a Chinese 1300-year-old traditional rice production system. We first confirm that genetically diverse rice varieties are still being cultivated in the HHRTS and categorize these varieties into three main genetic clusters, including the modern hybrid varieties group (MH), the Hongyang improved modern variety group (HY) and the traditional indica landraces group (TIL). We also show over a 2-year period that SRBSDV remains prevalent in the HHRTS (20.1% prevalence) and that both the TIL (17.9% prevalence) and the MH varieties (5.1% prevalence) were less affected by SRBSDV than were the HY varieties (30.2% prevalence). Collectively we suggest that SRBSDV isolates are freely moving within the HHRTS and that TIL, HY and MH rice genetic clusters are not being preferentially infected by particular SRBSDV lineages. Given that SRBSDV can cause 30–50% rice yield losses, our study emphasizes both the need to better monitor the disease in the HHRTS, and the need to start considering ways to reduce its burden on rice production.
Highlights
Southern rice black-streaked dwarf virus (SRBSDV) causes the emergent rice black-streaked dwarf disease that has for the last decade been threatening rice-growing areas of northern Vietnam, southern Japan and southern, central and eastern China [1,2,3,4]
We first confirm that genetically diverse rice varieties are still being cultivated in the Honghe Hani rice terraces system (HHRTS) and categorize these varieties into three main genetic clusters: the traditional indica landraces group (TIL); the Hongyang group (HY) that contains improved modern varieties sharing recent ancestry with the TIL varieties; and the modern hybrid varieties group (MH) that includes commercial varieties usually grown outside the HHRTS
Rice genotyping-by-sequencing confirmed that the HHRTS hosts a large diversity of rice varieties, including traditional indica or japonica local rice subspecies and modern indica varieties that are widely grown in other regions of China and elsewhere in South-East Asia (Table 1)
Summary
Southern rice black-streaked dwarf virus (SRBSDV) causes the emergent rice black-streaked dwarf disease that has for the last decade been threatening rice-growing areas of northern Vietnam, southern Japan and southern, central and eastern China [1,2,3,4]. The long term cultivation of genetically diverse HHRTS landraces may have led today to the situation where two different lineages of the rice blast fungus, Pyricularia oryzae, are each locally adapted to either the indica or the japonica rice landraces that are grown in the terraces [11]. This specialization of different P. oryzae populations may limit the spread of this pathogen in the HHRTS, which, by extension, has reduced the impact of rice blast on rice yields in the terraces [11]. We attempt to both quantify the prevalence of SRBSDV in the HHRTS and determine whether this emergent virus has a greater impact on modern high yielding rice varieties than it does on traditional HHRTS landraces. Prevalence) and the MH varieties (5.1% prevalence) were less affected by SRBSDV than were the HY varieties (30.2% prevalence)
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