Microsatellites

Development of novel simple sequence repeat markers from a genomic sequence survey database and their application for diversity assessment in Jatropha curcas germplasm from Guatemala

R. S. Raposo, Souza, I. G. B., Veloso, M. E. C., Kobayashi, A. K., Laviola, B. G., and Diniz, F. M., Development of novel simple sequence repeat markers from a genomic sequence survey database and their application for diversity assessment in Jatropha curcas germplasm from Guatemala, vol. 13, pp. 6099-6106, 2014.

The last few years have seen a significant increase in the number of large-scale sequencing projects generating whole genome databases. These sequence databases can be surveyed (genome sequence survey) for tandem repeats as an alternative means to develop microsatellites for monitoring and selecting natural populations and cultivars of Jatropha curcas. A total of 100 tandem repeats were revealed from mining 368 genomic surveyed sequences available in the Kazusa DNA Research Institute database.

Isolation, characterization, and cross-transferability of microsatellite markers from the whitebacked planthopper (Sogatella furcifera)

L. Zhang, Li, G., He, G. C., Zhu, L. L., Qin, R., and Jing, S. L., Isolation, characterization, and cross-transferability of microsatellite markers from the whitebacked planthopper (Sogatella furcifera), vol. 13, pp. 6248-6252, 2014.

The whitebacked planthopper Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) is one of the most harmful pests of rice. In this study, 18 polymorphic microsatellite markers were developed from S. furcifera genomic libraries using the fast isolation by amplified fragment length polymorphism of sequences containing repeat protocols. Microsatellite polymorphism was investigated using 32 individuals from one natural population.

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

E. C. M. Lanes, Viana, J. M. S., Paes, G. P., Paula, M. F. B., Maia, C., Caixeta, E. T., and Miranda, G. V., Population structure and genetic diversity of maize inbreds derived from tropical hybrids, vol. 13, pp. 7365-7376, 2014.

The objectives of this study were to identify the population structure and to assess the genetic diversity of maize inbreds. We genotyped 81 microsatellite loci of 90 maize inbreds that were derived from tropical hybrids and populations. The population structure analysis was based on a Bayesian approach. Each subpopulation was characterized for the effective number of alleles, gene diversity, and number of private alleles. We also performed an analysis of molecular variance and computed a measure of population differentiation (FST).

Development and characterization of microsatellite markers for the Chinese endangered medicinal plant Tetrastigma hemsleyanum

Y. H. Wang, Chen, N., Zhang, Y. C., and Fu, C. X., Development and characterization of microsatellite markers for the Chinese endangered medicinal plant Tetrastigma hemsleyanum, vol. 13, pp. 9062-9067, 2014.

Tetrastigma hemsleyanum (Vitaceae) is an endangered medicinal plant endemic to China. Because of its widely known efficacy for treating many health problems, wild resources of this species are currently undergoing a rapid decline. Few studies have been conducted examining the population genetics or development of microsatellite loci for this plant. In this study, 14 microsatellite loci were isolated and characterized for T. hemsleyanum using a double-suppression PCR method. Polymorphisms were tested with a total of 50 individuals from 2 natural populations.

Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae)

M. Ogrzewalska, Bajay, M. M., Schwarcz, K., Bajay, S. K., Telles, M. P. C., Pinheiro, J. B., Zucchi, M. I., Pinter, A., and Labruna, M. B., Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae), vol. 13, pp. 9622-9627, 2014.

Amblyomma aureolatum (Pallas) is the main vector of the bacterium Rickettsia rickettsii, the etiological agent of Brazilian spotted fever. This disease is the most lethal human spotted fever rickettsiosis in the world. Microsatellite loci were isolated from a dinucleotide-enriched library produced from A. aureolatum sampled in Southeastern Brazil. Eight polymorphic microsatellites were further characterized among 38 individuals sampled from São Paulo metropolitan region.

Genetic relationship of cowpea (Vigna unguiculata) varieties from Senegal based on SSR markers

F. A. Badiane, Gowda, B. S., Cissé, N., Diouf, D., Sadio, O., and Timko, M. P., Genetic relationship of cowpea (Vigna unguiculata) varieties from Senegal based on SSR markers, vol. 11, pp. 292-304, 2012.

Genetic diversity and phylogenetic relationships among 22 local cowpea (Vigna unguiculata) varieties and inbred lines collected throughout Senegal were evaluated using simple sequence repeat molecular markers. A set of 49 primer combinations were developed from cowpea genomic/expressed sequence tags and evaluated for their ability to detect polymorphisms among the various cowpea genotypes. Forty-four primer combinations detected polymorphisms, with the remaining five primer sets failing to yield PCR amplification products.

Multiplex PCR panel of microsatellite markers for the tambaqui, Colossoma macropomum, developed as a tool for use in conservation and broodstock management

I. G. Hamoy and Santos, S., Multiplex PCR panel of microsatellite markers for the tambaqui, Colossoma macropomum, developed as a tool for use in conservation and broodstock management, vol. 11. pp. 141-146, 2012.

The tambaqui, Colossoma macropomum, native to Brazil, is widely used in aquaculture systems. We developed a multiplex PCR panel for this species, comprising 12 microsatellite loci. This panel was used to genotype 73 specimens collected from Juruti, a city in the Brazilian Amazon. The mean number of alleles per locus was 8.8, the mean observed heterozygosity was 0.76, and the combined power of discrimination and the combined power of exclusion were 0.99999999999999993 and 0.999991762, respectively.

Estimation of taurindicine hybridization of American Zebu cattle in Brazil

P. Ripamonte, Baccaglini, M., César, A. S. M., César, A. S. M., Figueiredo, L. G. G., Balieiro, J. C. C., Caetano, A. R., and Meirelles, F. V., Estimation of taurindicine hybridization of American Zebu cattle in Brazil, vol. 11, pp. 393-403, 2012.

Our objective was to estimate Bos primigenius taurus introgression in American Zebu cattle. One hundred and four American Zebu (Nellore) cattle were submitted to mtDNA, microsatellite and satellite analysis. Twenty-three alleles were detected in microsatellite analysis, averaging 4.6 ± 1.82/locus. Variance component comparisons of microsatellite allele sizes allowed the construction of two clusters separating taurus and indicus. No significant variation was observed when indicus and taurus mtDNA were compared.

Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers

M. Marulanda, López, A. M., and Uribe, M., Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers, vol. 11, pp. 322-331, 2012.

The species Rubus glaucus, also known as the Andean or “Castilla” blackberry, is one of nine edible species of this genus that grow naturally in Central and South America. In Colombia, this species is the most important of all Rubus species for agricultural and commercial purposes. We used 20 SSRs developed for other Rubus species to characterize 44 Colombian R. glaucus genotypes, collected from eight different departments, and to look for molecular differences between thornless and thorny cultivated blackberries.

Characterization of microsatellite markers in cassava based on microsatellite-AFLP technique

S. Whankaew, Sraphet, S., Thaikert, R., Smith, D. R., and Triwitayakorn, K., Characterization of microsatellite markers in cassava based on microsatellite-AFLP technique, vol. 11, pp. 1319-1326, 2012.

We developed molecular markers for cassava based on the microsatellite-amplified fragment length polymorphism (M-AFLP) technique. Twenty primer pairs were developed and used for the analysis of 48 samples of Manihot species, consisting of M. esculenta (33), M. esculenta ssp flabellifolia (3), M. chlorosticta (3), M. carthaginensis (3), M. filamentosa (3), and M. tristis (3).

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