Emergence of Southern Rice Black-Streaked Dwarf Virus in the Centuries-Old Chinese Yuanyang Agrosystem of Rice Landraces

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.

Keywords: Honghe Hani rice terraces system; Southern rice black-streaked dwarf virus; host genotyping; rice; virus emergence; virus prevalence.

Figure 1

(A) Neighbor-Net split decomposition network indicating the relationships between rice accessions based on 12,112 analyzed SNPs. Plant samples assigned to the HY, MH and TIL indica variety groups are labelled in purple, blue and orange, respectively. Plant samples that were not assigned to one of the three variety groups (“outlier varieties”) are labelled in black. Characters A to J or P1 to P10 (e.g., YYT5-J or Plot-23-P2) refer to individual plants that were collected from each rice field (7–10 plants were collected in each field, Table 1) (B) Ancestry proportions within accessions for sNMF models [26] from K = 2 to K = 15 ancestral populations. Each horizontal bar represents the proportion of ancestry within a single accession, with colors corresponding to ancestral populations.

Figure 2

Maximum-likelihood phylogenetic trees of partial SRBSDV segment 8 sequences (624 nt in length). Branches with less than 50% bootstrap support were collapsed. Branches associated with a black dot have bootstrap supports above 90% whereas those with white dots have bootstrap supports above 70%. Variety group of the samples, the village where the plant sample was collected and the host plant are depicted on the right of the phylogenetic tree. Variety groups: traditional indica landraces group (TIL); Hongyang improved modern variety group (HY) and modern hybrid variety group (MH). Villages: grey star, Huangcaolin village; black star, Malizhai village and white star, Dayutang village.