A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription

Fujimori, Shigeo; Washio, Takumi; Higo, Kenichi; Ohtomo, Yasuhiro; Murakami, Kazuo; Matsubara, Kazuo; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Kikuchi, Shoshi; Tomita, Masaru

doi:10.1016/s0014-5793(03)01041-x

Cited by 96 publications

(84 citation statements)

References 29 publications

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“…Among trinucleotide repeats, AAG repeats were most abundant. Both AG and AAG repeats are known to occur near or within genes and have been reported as the most abundant classes in plant ESTs (Fujimori et al 2003;Grover and Sharma 2004;Varshney et al 2005;). Primers could be designed for 30 of the microsatellites identified in this study.…”

Section: Resultsmentioning

confidence: 99%

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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Section: Resultsmentioning

confidence: 99%

Development of EST-based new SSR markers in seabuckthorn

Jain

Ghangal

Grover

et al. 2010

Physiol Mol Biol Plants

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“…While such a grouping for SciRoko and Sputnik can be called as natural (Reneker et al 2004), as it groups reverse complementary sequences together, the grouping in the output of MISA may be called as artificial due to the grouping of motifs which are considered complementary due to the readability from left to right on paper. Such results should be dealt with caution especially when strand specificities of microsatellite motifs are under consideration (Fujimori et al 2003).…”

Section: Microsatellite Search Approaches and Tools: User's Perspectivementioning

confidence: 99%

Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.

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“…They are proposed to act as cis-regulatory elements that can be recognised by transcription factors (Zhang et al 2006). Microsatellite repeats in the promoter can affect also its activation (Fujimori et al 2003). They may interfere with transcription activity, influencing the interaction with regulatory proteins by changing the distance between transcriptional factors binding sites .…”

Section: Role Of the Microsatellite (Ct) Repeatmentioning

confidence: 99%

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

Costa

Weg²,

Stella

et al. 2008

Tree Genetics & Genomes

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Fruit ripening can be considered as a complex set of biochemical and physiological changes occurring at the end of the developmental stage. Ripe fruit texture notably affects overall quality and consumer appreciation. Excessive softening limits shelf-life and storability, thereby increasing disease susceptibility and economic loss. Fruit softening is a process due to the depolymerisation of different polysaccharide classes, an event controlled by a synergic and coordinated action of several enzymes among which expansins play a fundamental role. To date, six expansin genes are known to be expressed during apple fruit ontogeny, from full bloom up to fruit ripening. We identified a novel expansin apple homolog (Md-Exp7) sharing high sequence similarity with specific-ripening expansin genes of other crops. A functional marker (MdExp7 SSR ) based on an SSR motif located within the untranslated region of the gene was developed and mapped on Linkage Group 1 of the apple and pear genomes in a region where one major apple QTL for fruit firmness had been previously identified. The allelic composition of 31 apple varieties for the SSR marker was associated with differences in fruit softening.

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A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription

Cited by 96 publications

References 29 publications

Development of EST-based new SSR markers in seabuckthorn

Development of EST-based new SSR markers in seabuckthorn

Searching microsatellites in DNA sequences: approaches used and tools developed

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

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