title: Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data.
abstract: Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Chen
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, Hebei, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Tian
authors.affiliation: Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Tangshan Academy of Agricultural Sciences, Tangshan 036001, Hebei, China.
authors.forename: Zhenxing
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China.
authors.forename: Xiyu
authors.initials: X
authors.lastname: Hao
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Lixia
authors.initials: L
authors.lastname: Wang
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Suhua
authors.initials: S
authors.lastname: Wang
authors.affiliation: Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
authors.affiliation: Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China.
authors.forename: Liya
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China.
authors.forename: Fengxiang
authors.initials: F
authors.lastname: Yin
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Xuzhen
authors.initials: X
authors.lastname: Cheng
mesh_terms: D007887:Fabaceae / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers