Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0736-1) contains supplementary material, which is available to authorized users.
Highlights
Genome size of different mungbean cultivars and wild relatives The genome size estimated by cytometry ranged from about 494 to 555 mega base pairs (Mb) (Table 1) in the lines under investigation
We found about a 20-Mb difference in genome size between wild mungbean TC1966 (494 Mb) and the cultivar NM92 (517 Mb)
For genomic comparison and to facilitate research on bruchid resistance of mungbean, we sequenced and assembled the draft genome of the bruchid-resistant line recombinant inbred line 59 (RIL59), whose bruchid-resistant genes (Br) gene was inherited from the wild mungbean accession TC1966
Summary
The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. Bruchids (Callosobruchus spp.), the bean weevils, cause serious damage to and loss of legume seeds, including mungbean, during storage [6]. A few insectinfested seeds are needed for the initial inoculum for population build-up during grain storage [7]. Bruchid development from eggs to pupae takes place in a single seed, the larva being the most destructive stage. The emerging adults deposit eggs on the seed, causing rapid multiplication of the pest during storage and resulting in up to 100 % of grain loss
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