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Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species

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Relation http://oar.icrisat.org/3015/
http://dx.doi.org/10.1007/s00122-006-0440-x
 
Title Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species
 
Creator Aggarwal, R K
Hendre, P S
Varshney, R K
Bhat, P R
Krishnakumar, V
Singh, L
 
Subject Genetics and Genomics
 
Description Genic microsatellites or EST–SSRs derived
from expressed sequence tags (ESTs) are desired
because these are inexpensive to develop, represent
transcribed genes, and often a putative function can be
assigned to them. In this study we investigated 2,553
coffee ESTs (461 from the public domain and 2,092
in-house generated ESTs) for identification and development
of genic microsatellite markers. Of these, 2,458
ESTs (all >100 bp in size) were searched for SSRs using
MISA—search module followed by stackPACK clustering
that revealed a total of 425 microsatellites in 331
(13.5%) non-redundant ESTs/consensus sequences
suggesting an approximate frequency of 1 SSR/2.16 kb
of the analysed coffee transcriptome. Identified microsatellites
mainly comprised of di-/tri-nucleotide repeats,
of which repeat motifs AG and AAG were the most
abundant. A total of 224 primer pairs could be designed
from the non-redundant SSR-positive ESTs (excluding
those with only mononucleotide repeats) for possible
use as potential genic markers. Of this set, a total of 24
(10%) primer pairs were tested and 18 could be validated
as usable markers. Sixteen of these markers
revealed moderate to high polymorphism information
content (PIC) across 23 genotypes of C. arabica and
C. canephora, while 2 markers were found to be
monomorphic. All the markers also showed robust
cross-species amplifications across 14 Coffea and 4
Psilanthus species. The apparent broad cross-species/
genera transferability was further confirmed by cloning
and sequencing of the amplified alleles. Thus, the study
provides an insight about the frequency and distribution
of SSRs in coffee transcriptome, and also demonstrates
the successful development of genic-SSRs. It is
expected that the potential markers described here
would add to the repertoire of DNA markers needed
for genetic studies in cultivated coffee and also related
taxa that constitute the important secondary genepool
for coffee improvement.
 
Publisher Springer Verlag
 
Date 2007
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/3015/1/Identification%2C_characterization_and_utilization_of_EST-derived_genic_microsatellite_markers_for_genome_analyses_of_coffee_and_related_species.pdf
Aggarwal, R K and Hendre, P S and Varshney, R K and Bhat, P R and Krishnakumar, V and Singh, L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. TAG Theoretical and Applied Genetics, 114 (2). pp. 359-372. ISSN 1432-2242