Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

Nicot, Nathalie; Chiquet, V.; Gandon, B.; Amilhat, L.; Legeai, Fabrice; Leroy, Philippe; Bernard, Michel; Sourdille, Pierre

doi:10.1007/s00122-004-1685-x

Cited by 169 publications

(125 citation statements)

References 27 publications

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“…This higher polymorphism level for gSSRs was expected, because it is known that genomic DNA has higher variability than the more conserved transcribed region (Nicot et al, 2004). Another reason for lower polymorphism levels of the new SSRs is more likely to be their repeats motifs.…”

Section: Discussionmentioning

confidence: 75%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions ('Stark Early Orange' (SEO), 'Hacıhaliloğlu' (HH), 'Perfection' , 'Iğdır' , 'Roxana' , 'Esen1' , and 'Esen2'), which yielded a total number of transcripts ranging from 30,363 for 'SEO' to 59,751 for 'Iğdır' . The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in the transcript pool and 14,722 di-, tri-tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions, including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri-and tetranucleotide repeats.

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Section: Discussionmentioning

confidence: 75%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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“…The frequency of EST-SSRs was 13.1%. Previous studies have shown that the EST-SSR frequencies of ginkgo, jatropha, poplar, and eucalyptus are 5.97, 6.51, 17.73, and 17.73%, respectively (Nicot et al, 2004;Yadav et al, 2011). The results of our present study differ markedly from these previous findings, possibly because of the different SSR search programs used and variations in the software parameter settings.…”

Section: Discussionmentioning

confidence: 95%

Characterization of ESTs from black locust for gene discovery and marker development

Wang

Lü²,

Yuan

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Black locust (Robinia pseudoacacia L.) is an ecologically and economically important species. However, it has relatively underdeveloped genomic resources, and this limits gene discovery and marker-assisted selective breeding. In the present study, we obtained large-scale transcriptome data using a next-generation sequencing platform to compensate for the lack of black locust genomic information. Increasing the amount of transcriptome data for black locust will provide a valuable resource for multi-gene phylogenetic analyses and will facilitate research on the mechanisms whereby conserved genes and functions are maintained in the face of species divergence. We sequenced the black locust transcriptome from a cDNA library of multiple tissues and individuals on an Illumina platform, and this produced 108,229,352 clean sequence reads. The high-quality overlapping expressed sequence tags (ESTs) 12684-12691 (2015) were assembled into 36,533 unigenes, and 4781 simple sequence repeats were characterized. A large collection of high-quality ESTs was obtained, de novo assembled, and characterized. Our results markedly expand the previous transcript catalogues of black locust and can gradually be applied to black locust breeding programs. Furthermore, our data will facilitate future research on the comparative genomics of black locust and related species.

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“…Because there are many GA and GT repeat motifs in wheat, eight wheat varieties have been scanned with designed primers using these motifs (Koike et al, 2006). GA was also shown to be the most abundant motif in grasses (Temnykh et al, 2001;Kantety et al, 2002;Nicot et al, 2004;Parida et al, 2006). It was revealed that the GA repeat motif has the highest polymorphism rate (approx.…”

Section: Discussionmentioning

confidence: 99%

Assessing wheat (Triticum aestivum) genotypes for “Yr” resistance genes using conserved regions and simple-sequence motifs

Çabuk

Aydin²,

Uncuoğlu³

2011

Genet. Mol. Res.

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ABSTRACT. Analysis of DNA sequence variation among genotypes is useful for differentiation of wheat accessions, selection strategies and genetic development of crop plants. We screened molecular markers for yellow rust resistance genes (Yr7, Yr9, Yr15, Yr18, Yr26, and YrH52), which are in the gene-rich regions of wheat chromosomes 1B, 2B, and 7D, to investigate DNA sequence differences and repeat motifs and numbers between wheat cultivars resistant (Izgi2001, Sonmez2001, PI178383) and susceptible (Aytin98, ES14, Harmankaya99) to yellow rust. The F 2 individuals derived from the crosses were evaluated for yellow rust resistance at both the seedling and adult stages to identify DNA markers genetically linked to yellow rust resistance. The most repeated motif was found to be GA and the least repeated motif TAGA among the cultivars. When we examined DNA sequence differences (insertion, deletion and single nucleotide changes), the molecular markers Xgwm526 (Yr7) and Xgwm273 (YrH52) were found to have the most conserved regions and Yr15 (Xgwm413) the least conserved regions among the cultivars. This DNA sequence information can be used for selection of suitable parents, creating mapping populations and developing molecular markers associated with yellow rust resistance in plant breeding programs.

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Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

Cited by 169 publications

References 27 publications

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Characterization of ESTs from black locust for gene discovery and marker development

Assessing wheat (Triticum aestivum) genotypes for “Yr” resistance genes using conserved regions and simple-sequence motifs

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