1. Transcriptome characterization and large-scale identification of SSR/SNPmarkers in symbiotic nitrogen fixation crop faba bean (Vicia faba L.)
- Author
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Hyung-Jin Baek, Jung Yoon Yi, Sundan Suresh, Joon-Hyeong Cho, Sok-Young Lee, Jong Wook Chung, Myung-Chul Lee, Sebastin Raveendar, Gyu-Taek Cho, and Tae-Sung Kim
- Subjects
Genetics ,Ecology ,Contig ,Sequence assembly ,food and beverages ,Forestry ,Biology ,Vicia faba ,Transcriptome ,454 pyrosequencing,gene ontology,molecular marker,transcriptome analysis ,chemistry.chemical_compound ,chemistry ,Molecular marker ,Pyrosequencing ,Functional genomics ,Orthologous Gene ,Food Science - Abstract
We used 454 sequencing technology for faba bean transcriptome, which yielded 29.61 Mb sequence data. A total of 81,333 raw sequence reads were obtained and assembled by de novo sequence assembly. The contig distributions in three nonmutually exclusive gene ontology classifications and clusters of orthologous gene classes were assigned, which were also used to identify genes related to nitrogen fixation. Furthermore, a set of 1729 reads with simple sequence repeat (SSR) motifs were identified. Subsets of 55 SSR primer pairs were selected to validate SSR marker assay. Fifty-five primer pairs were used to amplify from one or more of the template genotypes, the single nucleotide polymorphism (SNP) types manifested high confidence differences, and 1946 SNPs, 145 insertion-deletions, and 110 variants were observed with more than one nucleotide among the detected SNPs. This study provides large-scale identification of the faba bean transcriptome resources for functional genomics studies and the development of molecular markers, which will certainly lead to crop improvement.
- Published
- 2015