Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek)

BMC Plant Biology

Research Article

Yen-Wei Wang¹  Roland Schafleitner¹  Chien-Yu Chen²  Hsiao-Feng Lo³  Ching-Ping Lin⁴  Chia-Yun Ko⁴  Mao-Sen Liu⁴  Long-Fang O. Chen⁴  Tony Chien-Yen Kuo⁵  Kuan-Yi Li⁵  Dung-Chi Wu⁵  Wu-Jui Lin⁶ 

[1] AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, 74151, Tainan, Taiwan;Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, 106, Taipei, Taiwan;Department of Horticulture and Landscape Architecture, National Taiwan University, 106, Taipei, Taiwan;Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan;Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan;Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, 106, Taipei, Taiwan;Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan;Department of Horticulture and Landscape Architecture, National Taiwan University, 106, Taipei, Taiwan;

关键词: Vigna radiata;    Callosobruchus;    Next generation sequencing;    Differential expressed gene;    Nucleotide variation;    Molecular marker;   

DOI  :  10.1186/s12870-016-0736-1

 received in 2015-09-10, accepted in 2016-02-09,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMungbean (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.ResultsFlow 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.ConclusionsIn 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.

【 授权许可】

CC BY   
© Liu et al. 2016