Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.)

Rallo, Pilar; Dorado, Gabriel; Martín, António

doi:10.1007/s001220051571

Cited by 201 publications

(161 citation statements)

References 20 publications

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“…The enriched library prepared in the present study indeed resulted in a higher percentage (45%) of microsatellites, but redundancy problems further reduced the actual percentage to 30%. Problems of redundancy in enriched libraries have been reported in other crops (Rallo et al, 2000;Mba et al, 2001) as well as sesame (Dixit et al, 2005). The AG/TC class of dinucleotide repeats was the most abundant in the enriched library as well as in the ESTderived SSRs, as has been the case in other crops (Ferguson et al, 2004;Lichtenzveig et al, 2005).…”

Section: Discussionmentioning

confidence: 89%

Development of microsatellite markers in sesame (Sesamum indicum L.)

Badri¹,

Yepuri²,

Anuradha³

et al. 2014

Turk J Agric For

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Sesame (Sesamum indicum L.) is an important oilseed crop with high-quality seed oil and many antioxidant properties. Owing to its commercial and medicinal values, there is a renewed interest among agricultural scientists in this ancient crop. Efforts to strengthen the sesame-specific marker base have been initiated in the recent past; however, the available number of microsatellite markers is still not sufficient for the development of high-resolution genetic linkage maps for important agronomic traits and there is a need to increase the number of informative DNA markers in sesame. In the present study, we developed 25 microsatellite markers by employing the selective hybridization strategy and 95 mining expressed sequence tags of the NCBI database. This new set of microsatellite markers was characterized and screened for genetic diversity in an array of 16 sesame germplasms. Of the 120 SSRs, 92 were polymorphic, consisting of 18 SSRs from selective hybridization and 74 from the EST data set. The number of alleles per microsatellite locus ranged from 2 to 5, with an average of 3.11 alleles. The allele size ranged widely (100-510 bp) among the primer pairs. Polymorphic information content estimates ranged from 0.2982 to 0.912. Jaccard's similarity coefficient ranged from 0.21 to 0.82. The potential of the markers was assessed by diversity analysis using the sequential hierarchical agglomerative nonoverlapping clustering technique of the unweighted pair group method of arithmetic means on a set of 16 genotypes of sesame, including 2 wild species. Results supported the hypothesis that S. malabaricum could be the immediate progenitor of the cultivar species and that S. mulayanum is distinct from S. malabaricum and S. indicum, while suggesting hardly any diversity among the cultivars.

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Section: Discussionmentioning

confidence: 89%

Development of microsatellite markers in sesame (Sesamum indicum L.)

Badri¹,

Yepuri²,

Anuradha³

et al. 2014

Turk J Agric For

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“…Later, amplified fragment length polymorphism (AFLP) markers were found to be useful for the assessment of genetic diversity between olive cultivars, wild genotypes, and Olea species (Angiolillo et al, 1999;Owen et al, 2005;Ercisli et al, 2009). Simple sequence repeat (SSR) markers are another choice of marker technology for the characterization of olive genotypes and a considerable number of SSR markers have been developed for the olive genome in recent years (e.g., Rallo et al, 2000;Sefc et al, 2000;Ipek et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

et al. 2015

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ABSTRACT. The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization.

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“…Alleles differing by one or three nucleotides from each other were preserved for diversity analysis, even when observed on loci harboring blocks of dinucleotides (Figure 3(b), allele 217), especially considering the high level of polyploidy of the studied plant species. It has been done before for kiwi [30] and olive tree [35]. Besides, different numbers of repeats but also indels in the flanking regions of the blocks were found while transferring primers from Brassica rapa to other species of the same genus [36].…”

Section: Resultsmentioning

confidence: 95%

Microsatellites and the Polyploid Guarana Plant: Diversity under a Sea of Alleles

Angelo

Lira²,

Amado³

et al. 2014

OJGen

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Repeat blocks, microsatellites or simple sequence repeats (SSRs) can produce good co-dominant molecular markers for genetic diversity analysis and the determination of self-pollination rates in progenies originating from open pollination of selected genotypes. The enrichment of guarana genomic libraries was underway when it was confirmed that we are working with a complex polyploid species with 210 chromosomes. The probes (CA) 12 , (CT) 12 and (TC) 14 were used to finish the enrichment of four libraries for repeat blocks and the screening of a databank of expressed sequence tags (ESTs) from guarana seeded-fruits was accomplished as well. Fifteen clonal cultivars were genotyped with three replicas at 10 out of 27 identified loci using the 59 alleles that passed the reproducibility criterion. A large number of short repeat blocks were identified and this was considered to be a consequence of the recent polyploidization event. However, blocks with eight or more repeats ideal for genotyping were scarce. Annealing of most probes to short blocks by partial complementarity could explain the scarcity of longer blocks in genomic libraries but cannot explain why they were rare in the ESTs. Due to the complexity of the genotypes, alleles were treated as dominant traits. ESTs harboring repeat blocks had the functional annotation renewed. Locus GRN07 is inserted in a homologue of the MOTHER OF FLOWERING LOCUS T AND TFL1 (MFT), in which 3'-UTR displays clear post-transcriptional regulatory features. MFT and its variants are probably involved in the determination of seed germination and embryo growth characteristics. Other accessed loci can be involved in plant architecture and defense reactions. It was concluded that the alleles described in the present work can be used to distinguish guarana culti-* Corresponding author. P. C. S. Angelo et al. 191 vars and possibly to analyze segregation using the progenies of controlled pollinations between divergent genitors. Also, the fingerprints obtained can be added to the morphological and agronomic descriptors of the cultivars.

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Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.)

Cited by 201 publications

References 20 publications

Development of microsatellite markers in sesame (Sesamum indicum L.)

Development of microsatellite markers in sesame (Sesamum indicum L.)

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

Microsatellites and the Polyploid Guarana Plant: Diversity under a Sea of Alleles

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