Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Journal of genetics

A. Chandrasekar²  Aikkal Riju²  S. Elain Apshara¹  M. K. Rajesh²  P. T. P. Fasila Sherin²  Vadivel Arunachalam1² 

[1] Central Plantation Crops Research Institute, Regional Station, Vittal 574 243, India$$;Central Plantation Crops Research Institute, Kasaragod 671 124, India$$

关键词: genome;    in silico;    simple sequence repeats;    Malvales;    Theobroma cacao L.;   

DOI  :  

学科分类：生物科学（综合）

来源: Indian Academy of Sciences

【 摘 要 】

Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (>5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.

【 授权许可】

Unknown