Dynamic Transcriptome Profiling of Mungbean Genotypes Unveil the Genes Respond to the Infection of Mungbean Yellow Mosaic Virus.

Yellow mosaic disease (YMD), incited by mungbean yellow mosaic virus (MYMV), is a primary viral disease that reduces mungbean production in South Asia, especially in India. There is no detailed knowledge regarding the genes and molecular mechanisms conferring resistance of mungbean to MYMV. Therefore, disclosing the genetic and molecular bases related to MYMV resistance helps to develop the mungbean genotypes with MYMV resistance. In this study, transcriptomes of mungbean genotypes, VGGRU-1 (resistant) and VRM (Gg) 1 (susceptible) infected with MYMV were compared to those of uninfected controls. The number of differentially expressed genes (DEGs) in the resistant and susceptible genotypes was 896 and 506, respectively. Among them, 275 DEGs were common between the resistant and susceptible genotypes. Functional annotation of DEGs revealed that the DEGs belonged to the following categories defense and pathogenesis, receptor-like kinases; serine/threonine protein kinases, hormone signaling, transcription factors, and chaperons, and secondary metabolites. Further, we have confirmed the expression pattern of several DEGs by quantitative real-time PCR (qRT-PCR) analysis. Collectively, the information obtained in this study unveils the new insights into characterizing the MYMV resistance and paved the way for breeding MYMV resistant mungbean in the future.

Detection of QTLs associated with mungbean yellow mosaic virus (MYMV) resistance using the interspecific cross of Vigna radiata × Vigna umbellata.

Mungbean (Vigna radiata) and ricebean (V. umbellata) were utilized to obtain an inter-specific recombinant inbred line (RIL) population with the objective of detecting quantitative trait loci (QTL) associated with mungbean yellow mosaic virus (MYMV) resistance. To precisely map QTLs, accurate genetic linkage maps are essential. In the present study, genotyping-by-sequencing (GBS) platform was utilized to develop the genetic linkage map. The map contained 538 single nucleotide polymorphism (SNP) markers, consisted of 11 linkage groups and spanned for 1291.7 cM with an average marker distance of 2.40 cM. The individual linkage group ranged from 90.2 to 149.1 cM in length, and the SNP markers were evenly distributed in the genetic linkage map, with 30-79 SNP markers per chromosome. The QTL analysis using the genetic map and 2 years (2015 and 2016) of phenotyping data identified five QTLs with phenotypic variation explained (PVE) from 10.11 to 20.04%. Of these, a QTL on chromosome 4, designated as qMYMV4-1, was major and stably detected in the same marker interval in both years. This QTL region harbours possible candidate genes for controlling MYMV resistance. The linkage map and QTL/gene (s) for MYMV resistance identified in this study should be useful for QTL fine mapping and cloning for further studies.

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species.

BACKGROUND: MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. FINDINGS: We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. CONCLUSIONS: BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php.

Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.