Distribution and Genetic Diversity of Barley yellow striate mosaic virus in Northern China
【Abstract】[Objective] The objective of this study is to clarify the distribution and genetic diversity of Barley yellow striate mosaic virus (BYSMV) in major wheat production areas in northern China, and to provide a theoretical basis for the early warning, prevention and control of epidemic diseases. [Method] During 2008–2016, about 864 suspected virus-infected samples were collected from 66 districts in Hebei, Shandong, Jiangsu, Anhui, Henan, Shaanxi and Shanxi provinces and all the three viruses including BYSMV, Rice black-streaked dwarf virus (RBSDV) and Northern cereal mosaic virus (NCMV) were identified using one-step multiplex RT-PCR. L and N gene fragments of BYSMV were obtained by RT-PCR amplification and cloned, and then determined by nucleotide sequence analysis. The sequences were analyzed by softwares of MEGA, DnaSP, and PAML to elucidate the phylogenesis and genetic diversity of BYSMV isolates. [Result] A total of 336 samples collected from 48 districts in seven provinces were detected with BYSMV and the detection rate was 38.89%. The virus was mainly distributed in Shaanxi, Hebei, Shanxi and Shandong. In addition, it was also distributed in Henan and northern Anhui. Xuzhou and Pizhou in Jiangsu Province were only localized. The phylogenetic analysis showed that the population could be divided into two subgroups (I and II) based on fragments of L and N genes. The isolates in subgroup I were derived from all seven provinces, but the isolates in subgroup II were only from Shaanxi and Shanxi provinces. It was indicated that Iran isolate was related to the subgroup II isolates based on the phylogenesis of L gene sequence. The clustering of the isolates was related to their geographical origins, and not to the host plants or sampling dates. The genetic analysis by using 7 softwares of the RDP package showed that there was no evidence supporting the recombination. The selection pressure analysis showed that the ω (dN/dS) values varied from 0.02 to 0.19 which were far less than 1 within or between subgroups. It was indicated that the population was undergoing purifying selection. The haplotype diversity (Hd) values (0.909 09 and 0.995 24) of L and N gene fragments were greater than 0.5 and the nucleotide diversity (π) values (0.013 24 and 0.012 24) were higher than 0.005, indicating that there was a high level of genetic diversity in the population of BYSMV in China. The genetic differentiation based on L and N gene fragments showed that the fixation indices FST (0.322 01 and 0.373 26) of eastern and western subpopulations were greater than 0.25. The difference of statistical test was significant, which indicated that the BYSMV population in eastern and western regions was seriously differentiated. The Nm values (0.53 and 0.42) were less than 1, which indicated that the limited gene flow was the main reason of genetic differentiation. [Conclusion] BYSMV was widely distributed in the wheat production areas of northern China, and occurred in Hebei, Shandong, Jiangsu, Anhui, Henan, Shaanxi and Shanxi provinces on different levels. The population of BYSMV had a high level of genetic diversity in China, and there was a severe genetic differentiation between the eastern and western subpopulations.
【Keywords】 Barley yellow striate mosaic virus (BYSMV); phylogenesis; genetic diversity; selection pressure; genetic differentiation;
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