Simple sequence repeat (SSR) vs. sequence-related amplified polymorphism (SRAP) markers for Cynara cardunculus characterization

Abstract

A little is known about the genetic variability present in globe artichoke, cultivated and wild cardoons. This knowledge is very important for efficient genetic resources utilization, and to gain a better understanding of genetic structure of this botanical varieties. With the aims to determine genetic distances between Cynara cardunculus accessions and to compare two molecular markers systems for their efficiency to differ between botanical varieties, a molecular characterization of sixteen accessions from different geographical origins was performed. Seven SSR and seven SRAP markers were used for varieties characterization and to calculate genetic distances between them. Both distance matrices were subjected to cluster analysis. Exclusive SSR alleles were found for globe artichoke and for wild cardoon, but non exclusive alleles were found for cultivated cardoon. For both markers systems two major groups were identified, one of them included mostly globe artichoke accessions and the other one grouped mainly cardoons. The differences observed in the sub-cluster conformation with each marker systems may be due to intrinsic characteristics of the markers. Concluding, both kind of molecular markers are valuable tools for studying genetic distances between C. cardunculus accessions although they give different information. Nevertheless, SSR electrophoretic profiles are simpler to score than SRAP markers because they consist of just a few bands. As well, bands are highly informative because of the great number of alleles existing in population and they are codominant markers. In addition, SSR's use would reduce time and costs.Additional key words: cardoon; genetic resources; genetic variability; globe artichoke. ResumenMarcadores SSR (simple sequence repeat) vs. SRAP (sequence-related amplified polymorphism) en la caracterización de Cynara cardunculus En la actualidad existe poca información acerca de la variabilidad genética presente en alcachofa y cardos (silvestres y cultivados). Conocer esta variabilidad es importante para utilizar eficientemente los recursos genéticos disponibles y comprender la estructura genética de estas variedades botánicas. Con el objetivo de determinar las distancias genéticas entre accesiones de Cynara cardunculus y comparar dos sistemas de marcadores moleculares en cuanto a su eficiencia para establecer diferencias entre las variedades, se realizó la caracterización molecular de 16 accesiones de diferentes orígenes geográficos. Para ello se utilizaron siete primers SSR y siete SRAP. Se calcularon las distancias genéticas y ambas matrices fueron sometidas a análisis de agrupamiento. Se encontraron alelos SSR exclusivos para alcachofa y cardo silvestre, pero no para cardo cultivado. El análisis de agrupamiento con ambos marcadores permitió identificar dos grandes grupos, el primero incluyó mayoritariamente accesiones de alcachofa mientras que el segundo agrupó a la mayoría de los cardos. Las diferencias observadas en la formación de sub-grupos con ambos sistemas se deberían a carac...

Genetic variability in wild cardoon (Cynara cardunculus L. var. sylvestris) revealed by SSR markers and morphological traits

“…Wild cardoon SSR polymorphism showed that all populations were clearly distinguished from each other suggesting high performance of the SSR as molecular tools for genetic identification. Similar studies using microsatellites to analyze populations of Cynara showed high levels of polymorphism (Casadevall et al, 2011;Gatto et al, 2013). Overall, the results of molecular markers analysis revealed a high gene diversity of wild cardoon populations (He = 0.77) and supported those found by Khaldi et al (2012) for Tunisian wild cardoon genotypes.…”

Genetic diversity and population structure of a Peruvian Coffea arabica L. collection

“…Moreover, the electrophoresis in agarose gel used in SRAP markers is faster and less laborious than the electrophoresis in polyacrylamide gel for microsatellites. On the other hand, Casadevall et al (2011), using microsatellites and SRAP markers to study the genetic diversity of Cynara cardunculus, recommended to use microsatellite markers for their easy visualization and codominance information. The fact that in this study as well as in our research (Table 6) the estimators of genetic diversity obtained by SRAP appear lower than those obtained by microsatellite might be due to the characteristics of the marker system.…”

Comparison of different methodologies in order to perform a representative Cynara cardunculus L. core collection

“…In previous studies (Cravero, Martin and Cointry, 2007;Casadevall, Martin and Cravero, 2011), the variability available between some accessions, belonging to the local C. cardunculus collection, was evaluated using Sequence Related Amplified Polymorphism (SRAP) (Li and Quiros, 2001). Those studies proved that SRAP is also a helpful tool to detect genetic diversity in this species and to classify accessions into groups based on their genetic distance values.…”