Caracterización molecular de materiales cultivados de gulupa (Passiflora edulis f. edulis)

Fonseca-Trujillo, Natalia; Márquez-Cardona, María del Pilar; Moreno-Osorio, Jairo Hernán; Terán-Pérez, Wilson; Schuler-García, Ingrid

doi:10.11144/javeriana.sc14-2-3.cmdm

Cited by 8 publications

(6 citation statements)

References 6 publications

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“…The only exception is accession “Gulupa” from Colombia. This accession, however, is believed to have been originally collected in Brazil and later introduced in Colombia [ 47 , 48 ] and was, therefore, also used in the analysis. These ten P. edulis accessions were genotyped with a random sample of 60 di- and tri-nucleotide microsatellites.…”

Section: Methodsmentioning

confidence: 99%

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

et al. 2017

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BackgroundThe Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few Passiflora species. We describe the use of NGS technology to partially assemble the P. edulis genome in order to develop hundreds of new microsatellite markers.ResultsA total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite sequences was selected for PCR primer development. Panels of di- and tri-nucleotide repeat markers were then tested in P. edulis germplasm accessions for validation. DNA polymorphism was detected in 74% of the markers (PIC = 0.16 to 0.77; number of alleles/locus = 2 to 7). A core panel of highly polymorphic markers (PIC = 0.46 to 0.77) was used to cross-amplify PCR products in 79 species of Passiflora (including P. edulis), belonging to four subgenera (Astrophea, Decaloba, Distephana and Passiflora). Approximately 71% of the marker/species combinations resulted in positive amplicons in all species tested. DNA polymorphism was detected in germplasm accessions of six closely related Passiflora species (P. edulis, P. alata, P. maliformis, P. nitida, P. quadrangularis and P. setacea) and the data used for accession discrimination and species assignment.ConclusionA database of P. edulis DNA sequences obtained by NGS technology was examined to identify microsatellite repeats in the sour passion fruit genome. Markers were submitted to evaluation using accessions of cultivated and wild Passiflora species. The new microsatellite markers detected high levels of DNA polymorphism in sour passion fruit and can potentially be used in genetic analysis of P. edulis and other Passiflora species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3881-5) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

et al. 2017

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“…In Colombia, genetic diversity studies on Passiflora, such as those carried out by Fonseca-Trujillo et al (2009), who used ISSR markers, have characterized the cultivated gulupa materials collected in the Departments of Boyacá, Cundinamarca and Huila, finding that these molecular markers were efficient at detecting polymorphisms in this species (89%), evidencing broad genetic diversity that is distributed in the areas where gulupa is grown. The gulupa materials evaluated in this study showed high genetic diversity, probably because of the propagation method, origin and short time of establishment of these crops in this country.…”

Section: Meneses Et Al 2019)mentioning

confidence: 99%

Characterization of the genetic diversity in Passiflora spp. in the Boyacá Department, Colombia

Martínez

Morillo

Reyes-Ardila

2020

Chil. j. agric. res.

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Passiflora is a group of species of economic importance in Colombia because of their productive potential and nutritional, pharmaceutical and industrial properties; therefore, it is necessary to study the genetic diversity of the species cultivated in principal productive departments, such as Boyacá. The use of molecular markers has become a fundamental tool for germplasm characterization, which effectively complements morphological and agronomic information. This research aimed to characterize the genetic diversity of Passiflora spp. grown in the Department of Boyacá using inter-simple sequence repeat (ISSR) markers. The eight ISSRs generated a total 138 bands with molecular weights between 250 and 1350 kb. With a similarity coefficient of 0.60, seven groups were formed, showing lax distribution of the individuals. The percentage of polymorphic loci was between 56% (TG) and 90% (AG). The average value of heterozygosity was 0.56 with a genetic differentiation coefficient (FST) of 0.16, which indicated great genetic diversity but without a defined population structure. The AMOVA showed that 64% of the observed genetic variation was due to the component within the groups. The results suggested levels of hierarchy and subdivision finer than those considered in this study, in addition to a complementary morphoagronomic characterization that established the total genetic diversity, which can be used to implement a breeding program for more productive cultivars that are resistant to the principal phytosanitary problems.

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“…La caracterización a través marcadores moleculares es una herramienta valiosa que tiene varias ventajas, como su independencia del medio ambiente y el alto nivel de polimorfismo que se puede encontrar distribuido por el genoma (Fonseca-Trujillo et al, 2009). Los microsatélites o SSR's, secuencias simples de ADN con motivos de 1 a 6 nucleótidos repetidos en tándem, se usan como marcadores y poseen características útiles para estudiar la diversidad genética de una población.…”

Section: Introductionunclassified

Selección de marcadores microsatélites (SSR’s) para el análisis de variabilidad genética en siete cultivares de arracacha (Arracacia xanthorrhiza)

2016

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RESUMENLa arracacha (Arracacia xanthorrhiza Bancroft) es una Apiaceae con raíces tuberosas reservantes ricas en un fino y nutritivo almidón. Los microsatélites o SSR's, secuencias simples de ADN con motivos de 1 a 6 nucleótidos repetidos en tándem, poseen características útiles para estudiar la diversidad genética de una población. En el municipio de Boyacá, Boyacá, los agricultores identificaron mediante diferencias fenotípicas siete cultivares de arracacha. Esta investigación busca identificar los loci polimórficos y reproducibles para siete cultivares nativos de arracacha entre un conjunto de 14 loci SSR's diseñados a partir de un cultivar ecuatoriano. Se amplificó y evaluó el ADN de de los cultivares de arracacha con diferentes concentraciones de MgCl 2 y temperaturas de anillamiento para cada locus microsatélite. Los productos amplificados se separaron en geles de poliacrilamida al 6, 10 y 12%. La estandarización para cada locus logró reducir las bandas inespecíficas en un 80% y evidenciaron una resolución óptima de las bandas en poliacrilamida al 12%. Se detectó que 5 loci no son aptos para el análisis de la variabilidad de arracacha debido a que loci son monomórficos, mientras que 1 locus polimórfico presenta exceso de bandas inespecíficas. Se identificaron fragmentos polimórficos reproducibles en 9 loci microsatélites y se confirmó su uso para el análisis de la variabilidad genética de los cultivares nativos de arracacha: paliverde, palirrusia, palinegra, yema de huevo, blanca de tarro, yucatana y amarilla de tarro.Palabras claves: estandarización, marcadores moleculares, cultivares, PCR. RESEARCH ARTICLE

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Caracterización molecular de materiales cultivados de gulupa (Passiflora edulis f. edulis)

Cited by 8 publications

References 6 publications

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

Characterization of the genetic diversity in Passiflora spp. in the Boyacá Department, Colombia

Selección de marcadores microsatélites (SSR’s) para el análisis de variabilidad genética en siete cultivares de arracacha (Arracacia xanthorrhiza)

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