title: Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek).
abstract: BACKGROUND
  Mungbean (Vigna radiata [L.] R. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Genomic and transcriptomic comparison of bruchid-resistant and -susceptible mungbean could reveal bruchid-resistant genes (Br) for this pest and give insights into the bruchid resistance of mungbean.
  
  
  RESULTS
  Flow cytometry showed that the genome size varied by 61 Mb (mega base pairs) among the tested mungbean accessions. Next generation sequencing followed by de novo assembly of the genome of the bruchid-resistant recombinant inbred line 59 (RIL59) revealed more than 42,000 genes. Transcriptomic comparison of bruchid-resistant and -susceptible parental lines and their offspring identified 91 differentially expressed genes (DEGs) classified into 17 major and 74 minor bruchid-resistance-associated genes. We found 408 nucleotide variations (NVs) between bruchid-resistant and -susceptible lines in regions spanning 2 kb (kilo base pairs) of the promoters of 68 DEGs. Furthermore, 282 NVs were identified on exons of 148 sequence-changed-protein genes (SCPs). DEGs and SCPs comprised genes involved in resistant-related, transposable elements (TEs) and conserved metabolic pathways. A large number of these genes were mapped to a region on chromosome 5. Molecular markers designed for variants of putative bruchid-resistance-associated genes were highly diagnostic for the bruchid-resistant genotype.
  
  
  CONCLUSIONS
  In addition to identifying bruchid-resistance-associated genes, we found that conserved metabolism and TEs may be modifier factors for bruchid resistance of mungbean. The genome sequence of a bruchid-resistant inbred line, candidate genes and sequence variations in promoter regions and exons putatively conditioning resistance as well as markers detecting these variants could be used for development of bruchid-resistant mungbean varieties.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. msliu@gate.sinica.edu.tw.
authors.forename: Mao-Sen
authors.initials: MS
authors.lastname: Liu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. tony.cy.kuo@gmail.com.|Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. tony.cy.kuo@gmail.com.
authors.forename: Tony Chien-Yen
authors.initials: TC
authors.lastname: Kuo
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. g874222@gate.sinica.edu.tw.
authors.forename: Chia-Yun
authors.initials: CY
authors.lastname: Ko
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. r00442023@ntu.edu.tw.|Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. r00442023@ntu.edu.tw.
authors.forename: Dung-Chi
authors.initials: DC
authors.lastname: Wu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. kyli.tw@gmail.com.|Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. kyli.tw@gmail.com.
authors.forename: Kuan-Yi
authors.initials: KY
authors.lastname: Li
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. lwj751205@gmail.com.|Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan. lwj751205@gmail.com.
authors.forename: Wu-Jui
authors.initials: WJ
authors.lastname: Lin
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. mygod1118@gmail.com.
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Lin
authors.affiliation: AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan. vivian.wang@worldveg.org.
authors.forename: Yen-Wei
authors.initials: YW
authors.lastname: Wang
authors.affiliation: AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan. roland.schafleitner@worldveg.org.
authors.forename: Roland
authors.initials: R
authors.lastname: Schafleitner
authors.affiliation: Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan. hflo@ntu.edu.tw.
authors.forename: Hsiao-Feng
authors.initials: HF
authors.lastname: Lo
authors.affiliation: Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. chienyuchen@ntu.edu.tw.
authors.forename: Chien-Yu
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. ochenlf@gate.sinica.edu.tw.
authors.forename: Long-Fang O
authors.initials: LF
authors.lastname: Chen
mesh_terms: D000818:Animals; D001517:Coleoptera; D004251:DNA Transposable Elements; D007887:Fabaceae / Q000235:genetics / Q000469:parasitology*; D015870:Gene Expression; D014644:Genetic Variation; D018745:Genome, Plant; D010935:Plant Diseases / Q000235:genetics*; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements