Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

Abstract

<jats:p>In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (<jats:italic>Olea europaea</jats:italic> L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.</jats:p>

Evolution and perspectives of cultivar identification and traceability from tree to oil and table olives by means of DNA markers

“…These microsatellites contained a long core of hexanucleotide SSR that allows wider separation among alleles, thus permitting accurate genotyping. Levels of polymorphism were similar to those of dinucleotide microsatellites, the only ones developed in the previous studies …”

“…Levels of polymorphism were similar to those of dinucleotide microsatellites, the only ones developed in the previous studies. 65 Being by far the most reproducible class of molecular markers, microsatellites have been considered the markers of election with the aim of developing a robust method for cultivar identification. Hence it was worth to work for standardizing protocols among laboratories.…”

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

“…In fact, EST-derived SSRs have been well documented in several plant species (Lima et al 2008;Feng et al 2009;Du et al 2013;Yao et al 2012;Xu et al 2012;Zhou et al 2014;Ferrao et al 2015). Lately, also, in olive, some EST-SSRs have been identified and used for paternity testing and mapping purposes (Essalouh et al 2014;de la Rosa et al 2013;Khadari et al 2014).…”

Venetian olive (Olea europaea) germplasm: disclosing the genetic identity of locally grown cultivars suited for typical extra virgin oil productions

“…Therefore, identification of olive varieties based on phenotypic traits has lead in the past to several confusions (Corrado et al 2009;Rotondi et al 2011). On the contrary, molecular markers have been successfully exploited for the characterisation of the olive germplasm and represent very accurate tools to screen, characterize and assess genetic identity of cultivars and to determine genetic diversity and relationships among cultivars (Hannachi et al 2008;El Bakkali et al 2013;Díez et al 2015), with applications in breeding programs and germplasm collection management (Belaj et al 2012;De la Rosa et al 2013;Saumitou-Laprade et al 2017). Microsatellite (simple sequence repeat, SSR) markers represent one of the most popular marker systems for olive DNA genotyping, since they are highly informative, reproducible within and transferable among laboratories, and are thus ideal for developing fingerprinting studies (Baldoni et al 2009;Gomes et al 2009;Muzzalupo et al 2009;Haouane et al 2011).…”