title: Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers.
abstract: Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens.
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Mina
authors.initials: M
authors.lastname: Yu
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Yu
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Huanhuan
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Yahui
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Xiaole
authors.initials: X
authors.lastname: Yin
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Huiwen
authors.initials: H
authors.lastname: Bo
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China. Electronic address: liuyf@jaas.ac.cn.
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D006999:Hypocreales / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D012275:Oryza / Q000382:microbiology*; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D005819:Genetic Markers
keywords: Genome; Simple sequence repeats; Ustilaginoidea virens