Microsatellite marker-based identification of mother plants for the reliable propagation of olive (<i>Olea europaea</i>L.) cultivars in Australia

Rehman, Aziz Ur; Mailer, Rodney J.; Belaj, Angjelina; Rosa, Raúl de la; Raman, Harsh

doi:10.1080/14620316.2012.11512925

Cited by 8 publications

(4 citation statements)

References 21 publications

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“…Various DNA markers have been used in these studies including restriction fragment length polymorphism (RFLP) (Bazakos et al 2012;Besnard and Berville 2002), amplified fragment length polymorphism (AFLP) (Albertini et al 2011;Angiolillo et al 1999;Baldoni et al 2006), random amplified polymorphic DNA (RAPD) (Awan et al 2011;Leva and Petruccelli 2012;Parra-Lobato et al 2012), sequence-characterized amplified regions (SCAR) (Marieschi et al 2011), DaRT (Domínguez-García et al 2012, SSR (Beghe et al 2011;Biton et al 2012;Corrado et al 2011;Delgado-Martinez et al 2012;Ercisli et al 2011;Rehman et al 2012;Rotondi et al 2011) and single nucleotide polymorphism (SNP) Hakim et al 2010;Macedo et al 2009;Muleo et al 2009;Reale et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

et al. 2015

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The olive (Olea europaea L.) was domesticated in the Mediterranean area over 6000 years ago and is currently one of the area's most important oleaginous crops. Due to its economic, cultural and ecological importance, breeding programs aimed at obtaining new olive cultivars have been developed in most olive-producing countries. An efficient breeding program requires a large and genetically variable germplasm collection. In this study, we used nextgeneration sequencing technology for the identification of 145,974 single nucleotide polymorphism (SNPs) loci. A subset of 138 SNPs was then used to analyze the genetic relationships between 119 cultivars making up most of the Israeli germplasm collection. The various cultivars did not cluster according to their geographic origin but rather showed a high correlation with their function (oil, table or dual purpose). Comparison of genetic diversity between 15 cultivars using SSRs and SNPs revealed that for the purposes of analyzing genetic variation between olive cultivars, the SSR marker seems more suitable. However, based on the analysis of several trees of the same cultivar sampled from different nurseries, the SNP marker proved to be a more reliable criterion for cultivar identification. This study presents the most comprehensive SNP analysis of olive phylogeny to date. Based on the rapid development of SNP genotyping methods over the last few years, we believe that in the near future, we will be able to genotype many sample genomes using the appropriate SNPs at a reasonably low cost. Therefore, we can expect that in the future, SNPs will definitely be the marker of choice for biodiversity analysis as well as for gene cloning and QTL identification in olives.

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Section: Introductionmentioning

confidence: 99%

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

et al. 2015

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“…Olive genotyping is currently based on microsatellite markers (SSR), that have shown high efficiency for the identification of olive cultivars coming from olive groves ( Beghè et al, 2011 ; Rehman et al, 2012 ; Fernández et al, 2015 ), or from regional ( Marra et al, 2013 ; Mousavi et al, 2017b ), national ( Fendri et al, 2010 ; Chalak et al, 2014 ; Muzzalupo et al, 2014 ) and international collections ( Sarri et al, 2006 ; Haouane et al, 2011 ; Trujillo et al, 2014 ). These markers have largely superseded the traditional morphological description ( Barranco and Rallo, 2000 ; Caruso et al, 2014 ; Messora et al, 2017 ) and other major molecular techniques (RFLP, RAPD and AFLP) used in olive ( Belaj et al, 2003b , 2016 ; Bracci et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management

et al. 2018

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Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre ‘Alameda del Obispo’ (Córdoba, Spain), one of the world’s largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross ‘Picual’ × ‘Arbequina’ cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.

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“…The results have shown that SSRs are convenient to assess routinely the crosses and to check self-incompatibility in olive cultivars (Diaz et al 2006). Rehman et al (2012) used nuclear SSR to distinguish Australian olive genotypes; the results supported the use of SSRs as a tool for cultivar differentiation and identification as well as reliable identification of mother plants for commercial propagation. Biton et al (2012), using microsatellite data of different cultivars and phenotypic data of the corresponding hybrids, evidenced the presence of significant correlation in terms of genetic distance between cultivars and F 1 performance for three traits: percentage of dry fruit weight, oil content and commercial oil production.…”

Section: Paternity Analysismentioning

confidence: 68%

Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding

Sebastiani

Busconi

2017

Plant Cell Rep

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The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic. The present paper represents an update of a previous review work published in this journal in 2011. The review is again mainly focused on DNA markers, whose application still constitutes a relevant percentage of the most recently published researches. Since the olive genomic era has recently started, the latest results in this field are also being discussed.

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Microsatellite marker-based identification of mother plants for the reliable propagation of olive (Olea europaeaL.) cultivars in Australia

Cited by 8 publications

References 21 publications

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management

Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding

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