Development and Characterization of Microsatellite Markers for the Cape Gooseberry Physalis peruviana

Simbaqueba, Jaime; Sánchez, P Alberto; Sanchez, Erika; Zarantes, Víctor Manuel Núñez; Chacón, María Isabel; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

doi:10.1371/journal.pone.0026719

Cited by 44 publications

(46 citation statements)

References 23 publications

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“…This fruit is native to the Andes, having transcended the history of periods pre-Incan and Incan [16,72]. Different chromosome numbers may exist among distinct genotypes, thus, it has been reported 2n = 24 for wild ecotypes, 2n = 32 for the ecotype grown in Colombia or 2n = 48 for the ecotype cultivated in Kenya [73,74]. It has remained intact and without apparent changes in the structure of their germplasm, having been described more than 80 wild species and many cultivars of different regions and countries.…”

Section: Botanical Aspectsmentioning

confidence: 99%

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Andean berries from Ecuador: A review on Botany, Agronomy, Chemistry and Health Potential

Carrillo‐Perdomo

Aller

Cruz-Quintana

et al. 2015

JBR

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Abstract. Interest in exploring new and exotic types of berries has grown in recent years. Highly valued for its unique flavor, texture and color, recent researches have shown that Andean berries are an important source of bioactive compounds. This article provides botanical and agronomic descriptions and reviews the chemical and biological activities of two types of berries (Physalis peruviana L. and Solanum betaceum C.) and one commonly known as a berry, Rubus glaucus B. All highly consumed in Ecuador and enjoying great popularity in Andean traditional medicine. Although both traditional folk medicine and composition of these berries suggest significant health benefits, few studies to date have investigated these potentials.

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Section: Botanical Aspectsmentioning

confidence: 99%

“…In Ecuador, the most produced varieties are "Kenian" and "Lojan", both with orange-yellow berries [76]. Although the collections held in genebanks have been partially evaluated for morphological and agronomic traits [74,[77][78][79], genetic diversity at the molecular level has been little studied [74,80].…”

Section: Botanical Aspectsmentioning

confidence: 99%

Andean berries from Ecuador: A review on Botany, Agronomy, Chemistry and Health Potential

Carrillo‐Perdomo

Aller

Cruz-Quintana

et al. 2015

JBR

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“…El país también ha avanzado en el conocimiento de la variabilidad genética de la uchuva, incluyendo la caracterización de germoplasma a escala morfo-agronómica para atributos vegetativos y de fruto (Trillos et al, 2008;Herrera et al, 2012) y molecular (Bonilla et al, 2008;Simbaqueba et al, 2011;Garzón et al, 2012). En citogenética, el conocimiento es todavía escaso; se destacan los estudios de Rodríguez y Bueno (2006) y Lagos (2006), quienes reportan variación en el número de cromosomas en algunos ecotipos de la especie, desde 2n = 24 hasta 2n = 48 con un número básico probable de X = 12.…”

Section: Introductionunclassified

Citogenética de genotipos de uchuva, Physalis peruviana L., y Physalis floridana Rydb., con respuesta diferencial a Fusarium oxysporum

Liberato

Sánchez-Betancourt

Argüelles-Cárdenas

et al. 2015

CTA

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GENÉTICA VEGETAL Y BIODIVERSIDAD RESUMENEl marchitamiento vascular ocasionado por el hongo Fusarium oxysporum se considera el principal limitante en la producción de uchuva (Physalis peruviana) en Colombia. Se han identificado genotipos de P. peruviana y la especie relacionada P. floridana con diferentes niveles de reacción a F. oxysporum. En el presente estudio, se evaluaron los genotipos con el fin de complementar el conocimiento de la diversidad citogenética en Physalis y el diseño de estrategias de hibridación como apoyo al mejoramiento del cultivo de la uchuva. Se determinó el número de cromosomas en células en división mitótica de ápices radicales de plantas cultivadas in vitro, para lo cual se estimó como hora mitótica promedio las 12:00 para P. peruviana, y las 10:00 para P. floridana. Se encontraron dotaciones cromosómicas de 2n = 4x = 48 y 2n = 2x = 24 para cada una de las dos especies. Adicionalmente, se realizó un análisis por citometría de flujo, en el cual se detectó variación en el contenido de ADN nuclear en P. peruviana con 2,33 pg para el genotipo 2n = 24 y entre 5,77 y 8,12 pg para los genotipos 2n = 48. En P. floridana el contenido de ADN fue 2,29 pg para el genotipo con número cromosómico 2n = 24 y 4,03 pg para el genotipo 2n = 48. Se encontró un efecto significativo (α = 0,01) del número de cromosomas sobre el contenido de ADN nuclear para las dos especies.Palabras claves: cariotipo, citometría de flujo, conteo cromosómico. ABSTRACTVascular wilt caused by the fungus Fusarium oxysporum is considered the main constraint of cape gooseberry, Physalis peruviana, production in Colombia. P. peruviana and P. floridana genotypes with differential resistance responses against F. oxysporum have been identified previously. In the present study, the genotypes were evaluated in order to complement the knowledge of cytogenetics diversity in Physalis and to design hybridization strategies to support breeding of cape gooseberry crop. The chromosome number in mitotic dividing cells from root-tips of tissue culture plantlets was determined, from which the average mitotic hour was estimated at 12:00 hours for P. peruviana and 10:00 for P. floridana. Chromosomic complements of 2n = 4x = 48 and 2n = 2x = 24 were found for each one of the two species. Additionally, flow cytometry analyses detected variation within P. peruviana with a nuclear DNA content of 2.33 pg for the 2n = 24 genotype and variations ranged from 5.77 to 8.12 pg for 2n = 48 genotypes. In P. floridana DNA content was 2.29 pg in the 2n = 24 genotype and 4.03 pg in the 2n = 48 genotype. There was a significant effect (α = 0.01) of the number of chromosomes on nuclear DNA content for the two species.

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“…On the other hand, simple repeats (sometimes known as microsatellites) are highly variable DNA sequences, usually less than 100 base pairs long, composed of short tandem repeats of 1–6 nucleotides. Typically, simple repeats have co-dominant inheritance, making them the markers of choice in a variety of applications, such as the characterization and certification of genetic materials in genetic mapping and breeding programs [9, 10]. …”

Section: Introductionmentioning

confidence: 99%

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps

Spouge

Mariño-Ramírez

Sheetlin

2014

IJBRA

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Background Some biological sequences contain subsequences of unusual composition, e.g., some proteins contain DNA binding domains, transmembrane regions, and charged regions; and some DNA sequences contain repeats. Requiring time linear in the length of an input sequence, the Ruzzo-Tompa (RT) Algorithm finds subsequences of unusual composition, using a sequence of scores as input and the corresponding “maximal segments” as output. (Loosely, maximal segments are the contiguous subsequences having greatest total score.) Just as gaps improved the sensitivity of BLAST, in principle gaps could help tune other tools, to improve sensitivity when searching for subsequences of unusual composition. Results Call a graph whose vertices are totally ordered a “totally ordered graph”. In a totally ordered graph, call a path whose vertices are in increasing order an “increasing path”. The input of the RT Algorithm can be generalized to a finite, totally ordered, weighted graph, so the algorithm then locates maximal segments, corresponding to increasing paths of maximal weight. The generalization permits penalized deletion of unfavorable letters from contiguous subsequences, so the generalized Ruzzo-Tompa algorithm can find subsequences with greatest total gapped scores. The search for inexact simple repeats in DNA exemplifies some of the concepts. For some limited types of repeats, RepWords, a repeat-finding tool based on the principled use of the Ruzzo-Tompa algorithm, performed better than a similar extant tool. Conclusions With minimal programming effort, the generalization of the Ruzzo-Tompa algorithm given in this article could improve the performance of many programs for finding biological subsequences of unusual composition.

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Development and Characterization of Microsatellite Markers for the Cape Gooseberry Physalis peruviana

Cited by 44 publications

References 23 publications

Andean berries from Ecuador: A review on Botany, Agronomy, Chemistry and Health Potential

Andean berries from Ecuador: A review on Botany, Agronomy, Chemistry and Health Potential

Citogenética de genotipos de uchuva, Physalis peruviana L., y Physalis floridana Rydb., con respuesta diferencial a Fusarium oxysporum

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps

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