DNA polymorphism among 18 species of Triticum–Aegilops complex using wheat EST–SSRs

Bandopadhyay, Rajib; Sharma, Shailendra; Rustgi, Sachin; Singh, Ravinder; Kumar, Ajay; Balyan, H. S.; Gupta, P. K.

doi:10.1016/j.plantsci.2003.09.022

Cited by 53 publications

(27 citation statements)

References 38 publications

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“…The high level of polymorphism (86%) in the set of Triticum durum and Ae. geniculata observed in this study corroborated with the results reported by Bandopadhyay et al (2004) on 18 Triticum-Aegilops complex species using wheat EST-SSRs, by Joshi & Nguyen (1993) on wheat and by Tao et al (1993) in Sorghum bicolor (L) Moench. The high level of polymorphism was probably due to the large number of primer used in this experiment.…”

Section: Discussionsupporting

confidence: 92%

Genetic diversity of Tunisian accessions ofAegilops geniculataRoth and durum wheats (Triticum durumDesf.) using RAPD markers

Mahjoub

Abdellaoui

Naceur

et al. 2010

Acta Botanica Gallica

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Abstract.-Genetic diversity of three durum wheat cultivars (Triticum durumDesf.) and thirteen Aegilops geniculata Roth accessions belonging to different regions of Tunisia (in North and Central) was evaluated using random amplified polymorphic DNA (RAPD) markers. Nineteen arbitrary universal primers were used for the amplification of random DNA sequences. Data were analysed with the SIMQUAL program using the NTSYS-pc. Phylogenetic diagram was drowning using the UPGMA algorithm. Results indicate an important inter-specific polymorphism between Aegilops and durum wheat. Ae. geniculata accessions revealed a high level of polymorphism (71.27%) than wheat cultivars (39.76%). Two main groups were represented by cluster and principal component analyses. The first group is formed by Ae. geniculata accessions and the second is constituted only by durum wheat cultivars. Consequently, RAPD markers separate clearly Ae. geniculata accessions and durum wheat cultivars.Key words : Aegilops geniculata -Triticum durum -polymorphism -RAPD. Résumé.-La diversité génétique de trois cultivars du blé dur (Triticum durumDesf.) et de treize accessions d'Aegilops geniculata Roth originaires de diffé-rentes régions de la Tunisie (nord et centre) a été évaluée en utilisant la technique RAPD. 19 amorces universelles arbitraires ont été utilisées pour l'amplification aléatoire des séquences de l'ADN. Les données statistiques ont été soumises au programme SIMQUAL du logiciel NTSYS-pc. Le diagramme phylogénétique a été réalisé par le sous-programme d'analyse UPGMA. Les résultats montrent un important polymorphisme interspécifique d'Ae. geniculata et de blé dur. Les accessions d'Ae. geniculata ont révélé un niveau élevé de polymorphisme (71.27%) par rapport à celui du blé (39.76%). Deux principaux groupes sont représentés par le dendrogramme de similarité et l'analyse en composantes principales. Le premier est formé par les accessions d'Ae. geniculata alors que le second n'est formé que par les cultivars du blé dur. En consé-quence, les marqueurs RAPD ont permis de séparer clairement les accessions d'Ae. geniculata et celles de cultivars du blé dur.

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Section: Discussionsupporting

confidence: 92%

Genetic diversity of Tunisian accessions ofAegilops geniculataRoth and durum wheats (Triticum durumDesf.) using RAPD markers

Mahjoub

Abdellaoui

Naceur

et al. 2010

Acta Botanica Gallica

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“…In fact, an estimated 2-5% of all plant-derived ESTs are thought to harbor SSRs (Kantety et al, 2002), although the actual frequency of SSR-bearing ESTs in any particular analysis is highly dependent on the search parameters (see below). Moreover, a large fraction of EST-SSRs (on the order of 80-90%) are typically found to be polymorphic (Bandopadhyay et al, 2004;Fraser et al, 2004;Pashley et al, 2006). Taking into account typical marker development attrition rates, it therefore seems likely that EST databases containing as few as 1000 sequences could provide enough markers to facilitate population genetic analyses.…”

Section: Est Resources and Ssr Frequenciesmentioning

confidence: 99%

“…This is particularly true in plants, where transferability among economically important crop taxa has been demonstrated on a number of occasions (Decroocq et al, 2003;Thiel et al, 2003;Bandopadhyay et al, 2004;Saha et al, 2004;Varshney et al, 2005b). Until recently, however, little attention had been paid to the potential for transferring EST-SSRs from well-characterized taxa to lesser studied relatives as a means for facilitating evolutionary analyses (but see Arnold et al, 2002;Ellis et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

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“…In general, EST-SSRs have been found to be significantly more transferable across taxonomic boundaries than traditional "anonymous" SSRs (Chagné et al, 2004;Gutierrez et al, 2005;Pashley et al, 2006). This transferability is particularly true in plants, where transferability among economically important crop taxa has been demonstrated on a number of occasions (Decroocq et al, 2003;Thiel et al, 2003;Bandopadhyay et al, 2004;Saha et al, 2004;Varshney et al, 2005). Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon but also in related taxa (Ellis and Burke, 2007).…”

Section: Introductionmentioning

confidence: 99%

Development of expressed sequence tag-simple sequence repeat markers for Chrysanthemum morifolium and closely related species

Sun

et al. 2015

Genet. Mol. Res.

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ABSTRACT. With the development of chrysanthemum breeding in recent years, an increasing number of wild species in genera related to Chrysanthemum were introduced to extend the genetic resources and facilitate the genetic improvement of chrysanthemums via hybridization. However, few simple sequence repeat (SSR) markers are available for marker-assisted breeding and population genetic studies of chrysanthemum and closely related species. Expressed sequence tags (ESTs) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequencebased markers. In this study, 25 EST-SSRs were successfully developed from Chrysanthemum EST sequences for Chrysanthemum morifolium and closely related species. In total, 4164 unigene sequences were assembled from 7180 ESTs of chrysanthemum in GenBank, which were subsequently used to screen for the presence of microsatellites with the Development of EST-SSR markers for chrysanthemum SSRIT software. The screening criteria were 8, 5, 4, and 3 repeating units for di-, tri-, tetra-, and penta-and higher-order nucleotides, respectively. Moreover, 310 SSR loci from 296 sequences were identified, and 198 primer pairs for SSR amplification were designed with the Primer Premier 5.0 software, of which 25 SSR loci showed polymorphic amplification in 52 species and varieties belonging to Chrysanthemum, Ajania, and Opisthopappus. The application of EST-SSR markers to the identification of intergeneric hybrids between Chrysanthemum and Ajania was demonstrated. Therefore, EST-SSRs can be developed for species that lack gene sequences or ESTs by utilizing ESTs of closely related species.

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DNA polymorphism among 18 species of Triticum–Aegilops complex using wheat EST–SSRs

Cited by 53 publications

References 38 publications

Genetic diversity of Tunisian accessions ofAegilops geniculataRoth and durum wheats (Triticum durumDesf.) using RAPD markers

Genetic diversity of Tunisian accessions ofAegilops geniculataRoth and durum wheats (Triticum durumDesf.) using RAPD markers

EST-SSRs as a resource for population genetic analyses

Development of expressed sequence tag-simple sequence repeat markers for Chrysanthemum morifolium and closely related species

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