Polymorphic information content of SSR markers for Coffea spp.

Missio, Robson Fernando; Caixeta, E. T.; Zambolim, Eunize Maciel; Zambolim, Laércio; Cruz, Cosme Damião; Sakiyama, Ney Sussumu

doi:10.12702/1984-7033.v10n01a12

Cited by 20 publications

(19 citation statements)

References 13 publications

(18 reference statements)

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“…The total number of allele was 127, ranged from 2 to 8 alleles per locus, with an average of 4 alleles per locus (Table 2). Those values were similar to the results obtained by Missio et al (2010) on three coffee species by using of 33 SSR primers, which generate a total of 122 alleles and the average of 5.1 alleles per SSR locus.…”

Section: Resultssupporting

confidence: 88%

Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

Syafaruddin

Randriani

Dani

et al. 2014

JTIDP

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Robusta coffee (Coffea canephora) has been grown widely in Indonesia, especially in Bengkulu Province. For the last few decades, some farmers have been selected and developed several Robusta clones through plagiotropic shoot grafting technique to replace earlier coffee populations which were derived from seed. Hence, it would reduce the genetic diversity of Robusta coffee at farmer's field. To understand the genetic variability among 15 Robusta coffee genotypes selected by farmer, it is important to perform molecular analysis. Leaf samples of 15 Robusta coffee genotypes selected by farmer were collected from smallholder Robusta coffee plantations in Bengkulu Province. Genetic diversity analysis was conducted in the Germplasm, Breeding, and Biotechnology Laboratory of Indonesian Industrial and Beverage Crops Research Institute (IIBCRI), and Molecular Biology Laboratory, Indonesian Cereals Research Institute (ICERI). DNA samples were amplified using 34 SSRs markers. The result showed that 23 out of 34 SSRs markers had high polymorphism levels. Allele number per locus ranged from 2-8 with an average of 4 alleles per locus. Dendrogram analysis based on genetic similarity was obtained with score of about 0,44-0,79, and r score = 0,92 (good fit). Based on cluster analysis as well as PCoA analysis, there are three distinct groups of genotypes. Those three groups can be distinguished by specific character of leaf morphotype. Nevertheless, the majority of genotypes were clustered together into the single group. This indicates narrow genetic diversity among Robusta genotypes that selected by farmer.

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Section: Resultssupporting

confidence: 88%

Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

Syafaruddin

Randriani

Dani

et al. 2014

JTIDP

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“…This, because a higher PIC is related with the distribution and equilibrium of the population´s allelic frequencies (Missio et al, 2010), that allows to assert that the selected markers are reliable and effective to detect genetic variability in the cultivated yellow passion fruit genotypes in Colombia. The effectiveness of the markers reached 60% in the yellow passion fruit germplasm evaluated in comparison to what Oliveira et al (2005) reported.…”

Section: Discussionmentioning

confidence: 91%

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Ocampo¹,

Acosta-Barón²,

Fernández³

2017

Agron. colomb.

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Colombia is one of the leading producers of yellow passion fruit but the genetic studies based on molecular markers from commercial plantations have not been considered to select interesting market material. The goal of this study was to assess the genetic variability and the population structure of 51 Colombian commercial yellow passion fruit accessions (102 individuals), and to provide the necessary information for prospective selection and breeding programs. Thus, a total of six microsatellites were amplified with 58 alleles identified and an average of 9.66 alleles per locus, including nine private and 31 rare. Diversity indexes showed polymorphic information content values of 0.74 (PIC), an observed (Ho) and expected (He) heterozygosity average of 0.52 and 0.78, respectively. Spatial distribution showed the greatest allelic richness (11 to 14) in most of the Valle del Cauca accessions. The average genetic distance among accessions was 0.68, and the cluster analysis showed three main groups poorly supported (bootstrap <50%), with slight geographical structure and high differentiation between individuals of the same accession. Structure analysis indicated K=4 as the genetic structure's uppermost hierarchical level, while Bayesian clustering showed a division of individuals into four genetically distinct groups. The low geographic structure and high variability of the accessions could be explained by allogamy and seed exchange frequency among farmers. Results issued suggest a complementary agro-morphological assessment to establish total genetic variability and implement a breeding program through assisted selection of superior genotypes in search of more productive and resistant cultivars to phytosanitary problems.

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“…Además, el aumento de PIC está relacionado con la distribución y equilibrio de las frecuencias alélicas en la población (MISSIO et al, 2010), lo cual permite afirmar que los marcadores seleccionados son confiables y efectivos para detectar diversidad genética en genotipos de granadilla.…”

Section: Discussionunclassified

Caracterizacion y analisis de la variabilidad genética de la granadilla (Passiflora ligularis juss.) en Colombia empleando marcadores microsatélites

Bernal-Parra¹,

Ocampo

Fernández

2014

Rev. Bras. Frutic.

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RESUMEN-La granadilla es la segunda especie en importancia económica del género Passiflora y Colombia es el principal productor del mundo con 53.000 t/año. Son pocos los estudios sobre la diversidad intraespecifica en la especie que permitan establecer las relaciones genéticas entre individuos. El objetivo de esta investigación fue explorar la variabilidad genética de la granadilla cultivada en Colombia por medio de marcadores microsatélites. Diez marcadores microsatélites fueron evaluados en 41 accesiones (82 individuos) provenientes de los principales departamentos productores. Un total de cinco microsatélites fueron amplificados con 66 alelos identificados y un promedio de 12,2, entre ellos 7 únicos y 13 raros. Los índices de diversidad mostraron un contenido de información polimórfica de 0,74 (PIC), y una heterocigocidad promedio observada (Ho) y esperada (He) de 0,98 y 0,96 bajo condiciones de equilibrio de Hardy-Weinberg. La distancia genética promedio dentro y entre poblaciones fue de 0,65 y 0,80, siendo Boyacá, Valle del Cauca y Putumayo los más distantes (>0,87). Los análisis de clasificación arbórea (nj) y factorial de correspondencia múltiple (AFCM) revelaron poca estructuración geográfica de las accesiones y dispersión de los individuos de un mismo origen. La carencia de estructuración y la alta variabilidad intraespecífica podría explicarse por el fenómeno de alogamia presente en la especie y el intercambio de semillas entre productores. En conclusión, estos resultados sugieren una evaluación agromorfológica complementaria que permita establecer la variabilidad genética total e implementar un programa de mejoramiento genético por medio de la selección asistida de genotipos superiores en búsqueda de cultivares más productivos y resistentes a problemas fitosanitarios que afectan los cultivos. Palabras clave: Passiflora, fruta, marcadores moleculares, variabilidad intraespecífica, fitomejoramiento. CHARACTERIZATION AND ANALYSIS OF THE GENETIC VARIABILITY OF SWEET PASSION FRUIT (Passiflora ligularis Juss.) IN COLOMBIA USING MICROSATELLITE MARKERSABSTRACT-Sweet passion fruit is the second economically important species of the genus Passiflora and Colombia is the largest producer in the world with 53,000 t/year. There are however, few studies on intraspecific diversity within the species that establish genetic relationships between individuals. The objective of this research was to explore the genetic variability of cultivated sweet passion fruit in Colombia using microsatellite markers. Ten microsatellite markers were evaluated in 41 accessions (82 individuals) from the main producing departments in the country. A total of five microsatellites were amplified with 66 alleles identified and an average of 12.2, including 7 unique and 13 rare. Diversity indexes showed a polymorphic information content of 0.74 (PIC), and an observed (Ho) and expected (He) heterozygosity average of 0.98 and 0.96 under Hardy-Weinberg equilibrium conditions. The average genetic distance within and among populations was 0.65 and ...

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Polymorphic information content of SSR markers for Coffea spp.

Abstract: -

Cited by 20 publications

References 13 publications

Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Caracterizacion y analisis de la variabilidad genética de la granadilla (Passiflora ligularis juss.) en Colombia empleando marcadores microsatélites

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