1. Notes:2.3: EST-SSR Marker resources for groundnut
Sameer Khanal*, Shunxue Tang, Ervin Nagy, Yufang Guo, Yan Li,
Vadim Beilinson, Phillip San Miguel, Baozhu Guo, Niels Nielsen,
Thomas Stalker, Marie-Michele Cordonnier-Pratt, Lee H Pratt,
Virgil Ed Johnson, Christopher A Taylor, Graham B Wiley, Simone
L. Macmil, Bruce Roe, Koppolu Ravi, Gautami Naidu, David
Hoisington, Rajeev Varshney, and Steven J Knapp
* Department of Crop and Soil Science and Institute of Plant Breeding,
Genetics, and Genomics, The University of Georgia, Athens, Georgia,
30602, USA; e-mail: sameer@uga.edu
Narrow genetic diversity and a deficiency of polymorphic DNAmarkers
have hindered genetic mapping and the application of translational
genomics approaches and marker-assisted selection in groundnut
(Arachis hypogaea). We developed and mined a groundnut EST
database for simple sequence repeats (SSRs), assessed the frequency of
polymorphic SSRs in ESTs, and developed 2,054 EST-SSR markers. We
assembled 71,448 long-read (Sanger) ESTs and 304,215 short-read (454)
ESTs into 37,914 unigenes, identified 7,413 perfect repeats, designed
and tested primers for 80 EST-SSRs sampled from broad spectrum
of motifs and repeat lengths, and screened 58 EST-SSR markers for
polymorphisms among elite and exotic germplasm accessions. Of the 58
EST-SSR markers, 55 were polymorphic, 32 were polymorphic among
elite lines (mean heterozygosity = 0.18), 27 were polymorphic among
four elite x elite mapping populations, and 48 were polymorphic in
two diploid mapping populations. The frequency of polymorphic EST-
SSRs seems to be sufficient for developing the critical mass of DNA
markers needed for routine genetic mapping and marker-assisted
selection applications in groundnut. The EST-SSR markers described
here are currently being screened for polymorphisms and mapped in
multiple diploid and tetraploid mapping populations and could play an
important role in breaking the DNA marker bottleneck in groundnut.
Related GCP project—SP2 Commissioned G4008.06: SNP discovery,
validation, and mapping in groundnut
22
Poster abstracts, GCP Annual Research Meeting 2008