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Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana.

Simbaqueba J, Sánchez P, Sanchez E, Núñez Zarantes VM, Chacon MI, Barrero LS, Mariño-Ramírez L - PLoS ONE (2011)

Bottom Line: The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana.We obtained an amplification rate of 83% and a polymorphic rate of 22%.Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research (CORPOICA), Bogota, Colombia.

ABSTRACT
Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

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SSR alleles in eight Physalis genotypes and four polymorphic loci.The polymorphic SSR loci were visualized in 6% polyacrylamide gels, samples 1–8 correspond to the work code shown in Table 1. M = Molecular size marker, 10 bp DNA Ladder (Invitrogen, Carlsbad, CA).
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pone-0026719-g001: SSR alleles in eight Physalis genotypes and four polymorphic loci.The polymorphic SSR loci were visualized in 6% polyacrylamide gels, samples 1–8 correspond to the work code shown in Table 1. M = Molecular size marker, 10 bp DNA Ladder (Invitrogen, Carlsbad, CA).

Mentions: The SSR loci selected for primer design were located at UTRs and identified with an imperfect repeat search to increase the probabilities for finding polymorphisms within the individuals analyzed. Using this strategy a total of 162 primers pairs were designed. A successful PCR amplification was obtained for 138 (83%) of the 162 primers designed from microsatellite loci using seven P. peruviana and one P. floridana genotype (Table 1). Polymorphisms among the eight genotypes were observed for 30 (22%) loci whereas the remaining 108 loci were monomorphic (Figure 1, Tables 3 and 4).


Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana.

Simbaqueba J, Sánchez P, Sanchez E, Núñez Zarantes VM, Chacon MI, Barrero LS, Mariño-Ramírez L - PLoS ONE (2011)

SSR alleles in eight Physalis genotypes and four polymorphic loci.The polymorphic SSR loci were visualized in 6% polyacrylamide gels, samples 1–8 correspond to the work code shown in Table 1. M = Molecular size marker, 10 bp DNA Ladder (Invitrogen, Carlsbad, CA).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198794&req=5

pone-0026719-g001: SSR alleles in eight Physalis genotypes and four polymorphic loci.The polymorphic SSR loci were visualized in 6% polyacrylamide gels, samples 1–8 correspond to the work code shown in Table 1. M = Molecular size marker, 10 bp DNA Ladder (Invitrogen, Carlsbad, CA).
Mentions: The SSR loci selected for primer design were located at UTRs and identified with an imperfect repeat search to increase the probabilities for finding polymorphisms within the individuals analyzed. Using this strategy a total of 162 primers pairs were designed. A successful PCR amplification was obtained for 138 (83%) of the 162 primers designed from microsatellite loci using seven P. peruviana and one P. floridana genotype (Table 1). Polymorphisms among the eight genotypes were observed for 30 (22%) loci whereas the remaining 108 loci were monomorphic (Figure 1, Tables 3 and 4).

Bottom Line: The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana.We obtained an amplification rate of 83% and a polymorphic rate of 22%.Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research (CORPOICA), Bogota, Colombia.

ABSTRACT
Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

Show MeSH