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 rep… Show more
“…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.…”
The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.
“…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.…”
The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.
“…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].…”
Section: Category Numbersmentioning
confidence: 99%
“…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.…”
Section: Development Of Microsatellite Markers Using 454 Pyrosequencingmentioning
confidence: 99%
“…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…”
Objectives: To discover and develop large-scale SSR markers of the P. miliaceum genome, which can be used in future genetic studies effectively.Result: 223,894 putative SSR sequences were identified by next-generation sequencing. A total of 56,694 primer pairs were successfully designed and 240 primer pairs were randomly selected for effectiveness validation. The expected heterozygosity and observed heterozygosity varied from 0.0447 to 0.7713 and from 0 to 0.9545, respectively and the mean of Shannon information index (I) was 0.7254. A UPGMA dendrogram indicated the high quality and effectiveness of these novel genomic SSR markers developed via next-generation sequencing technology.
Conclusion:A large repertoire of SSR markers were successfully developed by next-generation sequencing of the P. miliaceum genome which will be useful for the construction of genetic linkage maps, the identification of QTLs, and marker-assisted selection breeding.
“…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).…”
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