High-throughput novel microsatellite marker of faba bean via next generation sequencing

Abstract

BackgroundFaba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required.ResultsA library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology.ConclusionsLarge scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts.

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

“…These data were in agreement with previous analysis of Yang et al (2012) which revealed relationship between faba bean germplasm from diverse geographic origin using SSR markers. For some population (P19, P20 and P21), data showed incomplete relationship between the origin of the populations and the molecular clusters.…”

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

“…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].…”

“…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.…”

“…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…”

Translational Genomics in Agriculture: Some Examples in Grain Legumes

“…For example, 250,393 SSRs were identified from 247 faba bean accessions (Yang et al, 2012) using 454/FLX sequencing technology. Beyond providing SSR markers, these transcriptome assemblies have been used for identification of SNPs from NGS datasets generated from two or more genotypes (Table 2).…”