Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes

Morgante, Michèle; Hanafey, Michael K.; Powell, W.

doi:10.1038/ng822

Cited by 1,028 publications

(1,003 citation statements)

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“…This observation is in agreement with previous reports [32,37]. EST-derived SSRs; AG/CT repeats have been studied widely in eukaryotes, particularly in plants, and found to be highly abundant and highly polymorphic [38,39]. For P. papatasi , the number of published SSR markers is very limited compared with other major insect vectors, including species of Anopheles and Aedes [14].…”

Section: Discussionsupporting

confidence: 90%

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

Hamarsheh

Amro

2011

Parasites Vectors

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BackgroundPhlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs), or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers.ResultsSimple sequence repeats (SSRs) were characterized in P. papatasi expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.ConclusionThe first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

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Section: Discussionsupporting

confidence: 90%

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

Hamarsheh

Amro

2011

Parasites Vectors

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“…In contrast, the most frequent tri-nucleotide repeat motifs were (AAC/TTG)n in wheat, (AGG/TCC)n in rice, and (CCG/GGC)n in maize, barley and sorghum [31,36,37]. The abundance of the tri-nucleotide CCG repeat motif was favored overwhelmingly in cereal species [31,36,38] and also considered as a specific feature of monocot genome, which may be due to the high GC content and consequent codon usage bias [5,39]. But interestingly, in this study, the second most dominant tri-nucleotide repeat motif was CCG/CGG (5.8%), following AAG/CTT.…”

Section: Discussionmentioning

confidence: 99%

“…DNA simple sequence repeats, also known as microsatellites, are tandem repeats of 2-6 bp DNA core sequences, which are widely distributed in both non-coding and transcribed sequences, commonly known as genomic-SSRs and EST-SSRs [5]. With the advantages of being PCR-based, reliable, co-dominant, multi-allelic, chromosome specific, and highly informative, SSRs are useful for many applications in plant genetics and breeding such as construction of high-density linkage maps, genetic diversity analysis, cultivar identification, and marker-assisted selection.…”

Section: Introductionmentioning

confidence: 99%

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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“…In cereals also, TNRs were recorded and the most frequent followed by DNRs and TTNRs when MNRs were excluded (Varshney et al 2005). CCG/CGG was relatively rare in dicotyledonous plants (Morgante et al 2002). Tri motifs were harbored in exons.…”

Section: Genetic Diversitymentioning

confidence: 99%

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta¹,

Sankar²,

Sreelakshmi³

et al. 2016

Physiol Mol Biol Plants

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Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSRcontaining ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.

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Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes

Cited by 1,028 publications

References 34 publications

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

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

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

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