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Selection Pressure and Founder Effects Constrain Genetic Variation in Differentiated Populations of Soilborne Bymovirus Wheat yellow mosaic virus (Potyviridae) in China

First, second, fifth, and seventh authors: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MoA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; first and sixth authors: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, Henan Province, China; third author: Department of Biological Sciences, School of Biosciences, College of Natural sciences, Makerere University, P.O. Box 7062, Kampala, Uganda; and fourth author: Rothamsted Research, Harpenden, Herts AL5 2JQ, UK.

To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average F_ST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.