1Department of Analytics, School of Computer Science Engineering and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
2Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, 695581, India
3School of Biotechnology and Bioinformatics, D. Y. Patil University, Navi Mumbai, Maharashtra, 410506, India
4Biotechnology and Bioinformatics Division, JNTBGRI, Palode, Kerala, 695562, India
Online Published on 16 January, 2024.
The present study focuses on the development of EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat) markers in tomato from the transcriptomic sequences. A database of the genes linked with ripening of tomatoes has also been developed. Transcriptome sequences SSR36311, SSR363117, SSR363118, SSR363119, SSR363120, SSR363121 and SSR363122 were retrieved from European Nucleotide Archive databases. After performing quality check using FastQC, the downstream analysis was done using Tuxedo pipeline. With the assembled transcriptomic sequences, ESTs (Expressed Sequence Tag) were identified using EST trimmer of Micro Satellite identification (MISA) tool. A total of 582 EST-SSR primers were designed using WebSat. Among them 20 SSR primers were synthesized and validated using six tomato varieties such as Pusa Ruby, Pusa Gaurav, Pusa Sheetal, F1 Roman, Vellayani Vijaya and S-22. The study would add information on the genetic resources of tomatoes thus helping in improving new cultivars.
Genbank Submission: MH370148.1, MH370149.1, MH370150.1, MH370151.1
EST SSR Markers, Shelf Life of Tomato, Gene database for tomato ripening, Marker Assisted Selection
