Genic microsatellite markers in plants: features and applications

Varshney, Rajeev K.; Graner, Andreas; Sorrells, Mark E.

doi:10.1016/j.tibtech.2004.11.005

Cited by 1,642 publications

(1,458 citation statements)

References 62 publications

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“…In earlier reports, tri-nucleotide repeats were generally the most common motif found in both monocots [19] and dicots [17]. In the present investigation, tri-nucleotide repeat was also found to be the most abundant SSRs, followed by di-, tetra-, penta, and hexa-nucleotide (Table 1).…”

Section: Discussionsupporting

confidence: 79%

“…Moreover, due to their association with coding sequences, EST-SSRs can also lead to the direct gene tagging for QTL mapping of agronomically important traits and increase the efficiency of marker-assisted selection [15]. In addition, EST-SSRs show a higher level of transferability to closely related species than genomic SSR markers [13,16-18] and can be served as anchor markers for comparative mapping and evolutionary studies [19,20]. …”

Section: Introductionmentioning

confidence: 99%

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Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

et al. 2011

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BackgroundCurrently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.ResultsIn this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.ConclusionThis study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

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Section: Discussionsupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

et al. 2011

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“…Simple sequence repeats (SSR) were present in 56 (3.5%) of these sequences, a significantly lesser frequency than that reported for other plants (Varshney et al 2005). More than 50% of the SSRs were dinucleotide repeats; trinucleotide repeats being next most abundant category of repeats.…”

Section: Resultsmentioning

confidence: 71%

Development of EST-based new SSR markers in seabuckthorn

Jain

Ghangal

Grover

et al. 2010

Physiol Mol Biol Plants

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EST-based SSR markers were developed by screening a collection of 1584 clustered ESTs of seabuckthorn (Hippophae rhamnoides). PCR primers were designed for the amplification of 30 microsatellite loci. Two to five allelic bands were displayed by nine primer pairs in H. rhamnoides genotypes and by eleven primer pairs in H. salicifolia genotypes. None of the thirty primer pairs detected polymorphism in H. tibetana genotypes. Considering the high polymorphism detected in the tested genotypes and their direct origin from the genic regions, these EST-SSR markers hold immense promise in seabuckthorn genome analysis, molecular breeding and population genetics.

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“…Among the various molecular markers, microsatellites or simple sequence repeats (SSR) have shown to be very useful, because these markers showed high polymorphism, reproducible and easy to handle (Varshney et al 2005(Varshney et al , 2009Datta et al 2011). Though in lentil, a number of SSR markers have been developed (Hamwieh et al 2005;Kaur et al 2011;Datta et al 2011), availability of polymorphic SSR markers and their use in analysis of the genetic diversity is still limited in lentil compared to other pulses such as chickpea (Hamwieh et al 2005(Hamwieh et al , 2009Kaur et al 2011;Datta et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Kumar

Srivastva

Singh

et al. 2013

Physiol Mol Biol Plants

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Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had 'Precoz' gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers' preference.

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Genic microsatellite markers in plants: features and applications

Cited by 1,642 publications

References 62 publications

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

Development of EST-based new SSR markers in seabuckthorn

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

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