First Report of Dwarf Disease in Foxtail Millet (Setaria italica) Caused by Barley Yellow Striate Mosaic Virus in China

Abstract

Foxtail millet (Setaria italica) is an important cereal crop with high drought resistance and widely cultivated in northern China. Virus disease in foxtail millet is a serious problem because of yield decrease and difficulty in control. In Korea, rice black-streaked dwarf virus, rice stripe virus, and barley virus G have been detected on foxtail millet, whereas in China only barley yellow dwarf virus has been reported on foxtail millet (Oh et al. 2017; Pei et al. 1984). In the summer of 2018, a foxtail millet variety, Yugu18, showed virus-like symptoms of dwarfing, shortening of internode, stunting, and head sterility in Shijiazhuang of Hebei province, with an incidence of about 15%. To identify the viral diseases on foxtail millet, 10 samples showing the above virus-like symptoms were collected and stored at –80°C for RNA extraction. Total RNA of the samples was extracted by TRIzol Reagent (Invitrogen, Carlsbad, CA), and then the 10 RNA samples were combined into one sample for further detection and next-generation sequencing (NGS) was performed with an Illumina HiSeq 2000 sequencer. The whole NGS procedure was implemented by Majorbio Bio-Pharm Technology Company (Shanghai, China). In the pooled sample, 56 viral contigs matching barley yellow striate mosaic virus (BYSMV) were obtained in the range of 30 to 1,259 bp, and the NGS results were confirmed by the following reverse transcription PCR (RT-PCR) assay. First, a BYSMV-specific primer set (5′-TTTGATGATGATGTCCCTG-3′ and 5′- GATGTATTCTTCTCTTCTCC-3′) was designed according to the determined phosphoprotein (P) gene sequence of BYSMV in wheat (GenBank accession no. KP163566), and each of the above 10 RNA samples was analyzed by RT-PCR assay. In the RT-PCR assay, seven out of 10 samples produced a single amplicon of the expected size (∼600 bp), and three randomly selected positive products were sequenced. Nucleotide BLAST search indicated that the three sequences showed 99% identity with the BYSMV P gene from a wheat isolate. The sequences of the BYSMV P gene in foxtail millet were submitted to GenBank with the accession number MN434075, MN434076, and MN434077. BYSMV belongs to genus Cytorhabdovirus, which was first reported in Italy and was recently found on wheat and rice in China (Appiano et al. 1974; Wang et al. 2015). In this study, BYSMV was detected in samples of foxtail millet with virus-like symptoms through RNA sequencing using NGS and confirmed by RT-PCR. To our knowledge, this is the first report of BYSMV on foxtail millet in China. According to our observation, the yield of foxtail millet decreased by almost 10% with a great quantity of head sterility in Shijiazhuang because of virus infection, and this disease may become a serious threat to foxtail millet production in other regions of China. Further studies will be carried out to identify the pathological properties, host range, and resistance germplasm resources in foxtail millet. Therefore, the identification of BYSMV on foxtail millet has great significance in providing an appropriate strategy for monitoring, prevention, and control of dwarf disease in China.