Plant Biotechnology
   Molecular Biology and Genetics
Electronic Journal of Biotechnology ISSN: 0717-3458 Vol. 13 No. 5, Issue of September 15, 2010
© 2010 by Pontificia Universidad Católica de Valparaíso -- Chile Received February 21, 2010 / Accepted May 5, 2010
DOI: 10.2225/vol13-issue5-fulltext-3  
RESEARCH ARTICLE

Detection of single nucleotide polymorphisms in the conserved ESTs regions of Gossypium arboreum

Tayyaba Shaheen
 Plant Genomics and Molecular Breeding Labs
National Institute for Biotechnology and Genetic Engineering
PO Box 577, Jhang Road
Faisalabad, Pakistan 

Yusuf Zafar
Plant Genomics and Molecular Breeding Labs
National Institute for Biotechnology and Genetic Engineering
PO Box 577, Jhang Road
Faisalabad, Pakistan 

Mehboob-ur-Rahman*
 Plant Genomics and Mol Breeding Labs
National Institute for Biotechnology and Genetic Engineering
PO Box 577, Jhang Road
Faisalabad, Pakistan
E-mail: mehboob_pbd@yahoo.com

*Corresponding author

Financial support: This research was funded by Higher Education Commission (HEC) through a project under the scheme of PYI award (2007-2010) and indigenous PhD scholarship scheme through a PhD student grant.

Keywords: conserved regions, Gossypium arboretum, SNPs.

Abbreviations:

ESTs: expressed sequence tags
Indels: insertions and deletions
MAS: marker-assisted selection
QTL: quantitative trait locus
SNPs: single nucleotide polymorphisms
Abstract   Full Text

Exploring genetic variation in Gossypium arboreum L. germplasm is useful as it contains many important genes conferring resistance to different stresses. In limited earlier studies, low level of genetic diversity was found by using conventional DNA marker systems which may impede future genome mapping studies. In the present investigation, we explored the extent of Single Nucleotide Polymorphisms (SNP) among 30 conserved regions of Expressed Sequence Tags (EST) of low copy genes between two genotypes of G. arboreum. A total of 27 SNPs including 21 substitutions and 6 Insertions and deletions (Indels) in 7804 bp were found between these genotypes with a frequency of one SNP per 371 bp and one Indel after every 1300 bp. Out of these SNPs, 52% were transitions, whilst 48% SNPs were transversion. In conclusion, SNPs are expedient markers that can explore polymorphism in highly conserved sequences where other markers are not effective.
Supported by UNESCO / MIRCEN network