Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek)

Abstract

BackgroundMungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean.ResultWe have generated and characterized a total of 470,024 genome shotgun sequences covering 100.5 Mb of the mungbean (Vigna radiata (L.) Wilczek) genome using 454 sequencing technology. We identified 1,493 SSR motifs that could be used as potential molecular markers. Among 192 tested primer pairs in 17 mungbean accessions, 60 loci revealed polymorphism with polymorphic information content (PIC) values ranging from 0.0555 to 0.6907 with an average of 0.2594. Majority of microsatellite markers were transferable in Vigna species, whereas transferability rates were only 22.90% and 24.43% in Phaseolus vulgaris and Glycine max, respectively. We also used 16 SSR loci to evaluate phylogenetic relationship of 35 genotypes of the Asian Vigna group. The genome survey sequences were further analyzed to search for gene content. The evidence suggested 1,542 gene fragments have been sequence tagged, that fell within intersected existing gene models and shared sequence homology with other proteins in the database. Furthermore, potential microRNAs that could regulate developmental stages and environmental responses were discovered from this dataset.ConclusionIn this report, we provided evidence of generating remarkable levels of diverse microsatellite markers and gene content from high throughput genome shotgun sequencing of the mungbean genomic DNA. The markers could be used in germplasm analysis, accessing genetic diversity and linkage mapping of mungbean.

Development of Species-Specific Microsatellite Markers for Broomcorn Millet (Panicum miliaceum L.) via High-Throughput Sequencing

“…454 GS-FLX technology (next-generation sequencing) provides new opportunities for microsatellite isolation due to its high throughput, low cost of operation, and more thorough representation of the genome [15,41]. To date, several crops have developed high-throughput and novel genomic SSR markers via 454 GS-FLX sequencing [18][19][20][21]42]. In this study, massively parallel sequencing technology was adopted and hoped to discovery numerous SSR with high quality from genome of broomcorn millet quickly.…”

“…For SSR development, approximately equivalent weights of 7-dayold leaves (15)(16)(17)(18)(19)(20) of each genotype were collected and pooled. Total genomic DNA was extracted using a cetyltrimethylammonium bromide (CTAB) method as modified by Edward et al [22].…”

“…In conjunction with selective hybridization, NGS technologies can be used in highthroughput applications to develop and identify sequences that flank simple sequence repeat (SSR) regions. Species-specific SSR markers in mung beans [18], endangered dwarf bulrushes [19], fava beans [20], and grass peas [21] have been identified using this method and can be…”

High Throughput Marker Development and Application in Horticultural Crops

“…Although genic SSRs tend to be less polymorphic than SSR repeats in non-coding DNA, they are more easily transferable to related species, as the primers often reside in coding regions. There are several recent papers that report generating SSR markers from next generation sequences, including Tangphatsornruang et al (2009) …”

Re-evaluation of the Mungbean [Vigna radiata (L.) Wilczek] Genotypes for Resistance to Mungbean Yellow Mosaic Virus (MYMV) under Screen-House Conditions

“…It belongs to the subgenus Ceratotropis in the genus Vigna and is a self-pollinating diploid grain legume (2n=22) with a genome size of 579 Mb (Arumuganathan and Earle, 1991). Due to its protein rich edible seeds, its ability to fix nitrogen, drought tolerance, and early maturity, it is widely planted in various cropping systems (Tangphatsornruang et al, 2009). It is a good source of dietary protein with high contents of folate and iron compared with many other legumes crops (Keatinge et al, 2011).…”