Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants.
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.
Department of Botany, University of Rajasthan, Jaipur 302004, India.
Shamshad Ul
SU
Haq
Department of Botany, University of Rajasthan, Jaipur 302004, India ; Department of Biosciences, Manipal University, Jaipur 302007, India.
Rohit
R
Jain
Department of Botany, University of Rajasthan, Jaipur 302004, India.
Meenakshi
M
Sharma
Department of Botany, University of Rajasthan, Jaipur 302004, India.
Sumita
S
Kachhwaha
Department of Botany, University of Rajasthan, Jaipur 302004, India ; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 302006, India.
S L
SL
Kothari