Development of EST-SSR Markers in Tomato (Solanum Lycopersicum L)

Authors

  • Biji C L Department of Analytics, School of Computer Science Engineering and Technology, VIT University, Vellore, Tamil Nadu 632014
  • Ajay Bhaskar School of Biotechnology and Bioinformatics, D. Y. Patil University, Navi Mumbai, Maharashtra 410506
  • Priyanka B R Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581
  • Sunitha P Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581
  • Nadiya F Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562
  • Gouri Priya Ranjith Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562
  • Sakthipriya Mathavaraj Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562
  • Sabu K K Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562
  • Achuthsankar S. Nair Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581

Keywords:

EST SSR Markers, Shelf Life of Tomato, Gene database for tomato ripening, Marker Assisted Selection

Abstract

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 MicroSatellite 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

Author Biographies

  • Biji C L, Department of Analytics, School of Computer Science Engineering and Technology, VIT University, Vellore, Tamil Nadu 632014

    Biji C. L is the Associate Professor of Department of Analytics, School of Computer Science and Engineering, Vellore Institute of Technology, Vellore. Her research includes Machine Learning, Deep learning, Big data and Bioinformatics. She is passionate in developing insights from genomics data and that resulted in NCBI databank entries. She has a modest number of publications in high quality peer reviewed journals. She is fascinated with popular science communication and experiments with pedagogy. She has published a few popular scientific articles aimed at enlightening laymen.

  • Ajay Bhaskar, School of Biotechnology and Bioinformatics, D. Y. Patil University, Navi Mumbai, Maharashtra 410506

    Ajay Bhaskar is currently pursuing his Masters in Project Management from University College Dublin, Ireland. He has received the prestigious Indian Excellence Scholarship in University College Dublin to purse his Masters in Ireland. Due to his extraordinary performance in University College Ireland, he has been appointed as the Student Ambassador for UCD. He holds a Master’s degree in Clinical Research as well and did his B.Tech in Bioinformatics. Talking about his work experience, he worked as a Clinical Process Co-Ordinator in IQVIA for a period of 3.5 years.

  • Priyanka B R, Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581

    Priyanka. B.R. is the Bioinformatics Engineer of research and development team in Indx.Ai.  Her research area includes Cancer, Bio-marker discovery and Deep learning. She worked as a Project associate in NIIST and has worked in the identification of novel microbes from the brackish environment. She has completed ICMR fellowship from Madurai Kamaraj University, UGC-Centre of Potential for Excellence in Genomic Sciences and worked on the pathway activation functional genomics in liver cancer and sub-types of gastric cancer.

  • Sunitha P, Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581

    Sunitha P. is working as Assistant Professor at the Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram. She has been teaching in the field of Bioinformatics for over a decade. Her major research has been on the analysis of genes regulating the process of angiogenesis and has modest publication in this area. Her research work has contributed to the exhaustive re-construction of VEGFA-VEGFR2 signaling pathway which has been submitted in the Wikipathways.  Her other areas of interest are in Genomics, Transcriptomics including Next Generation sequence analysis, Small RNA analysis, Functional analysis and interpretation. She is interested in popular science communications.

  • Nadiya F, Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562

    Nadiya F is a PhD graduate in Biotechnology. She obtained her PhD degree in 2018 from University of Kerala and Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Thiruvananthapuram, India as the Research Center through KSCSTE fellowship, Govt of Kerala. For the PhD research programme she has done miRNA and trancriptome sequencing of Cardamom. She has more than 10 years of research experience in the field of plant genomics. She has 13 international publications and 4 book chapters to her credit. Her current area of research includes plant transcriptomics, Genome sequencing, Molecular diversity analysis and DNA barcoding.

  • Gouri Priya Ranjith, Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562

    Gouri Priya Ranjith is working as Assistant Professor at the Department of Botany, St. Thomas College, Thrissur. Research area includes plant functional genomics. She did her PhD from the Tropical Botanic Garden and Research Institute, Kerala. She has received research fellowship from KSCSTE. She is well trained in plant molecular biology techniques, plant micropropagation and phytochemistry.

  • Sakthipriya Mathavaraj, Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562

    Sakthipriya Mathavaraj is a PhD graduate in Biotechnology. She obtained her PhD degree from University of Kerala and Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Thiruvananthapuram, India as the Research Center through INSPIRE fellowship from the  Department of Science and Technology, Govt of India.  Research area includes Plant Molecular Biology, Genetic diversity studies, and GWAS. She worked as Assistant Professor at Department of Biotechnology, SRM Arts and Science College, Chennai, India. She completed short term fellowship from The James Hutton Institute, Dundee, Scotland, for this assignment she has received research grant from the Department of Biotechnology (DBT), India and British Council, UK. She qualified the ARS-NET examination.

  • Sabu K K, Biotechnology and Bioinformatics Division, JNTBGRI Pallode, Kerala, 695562

    Sabu K. K. is educated in the field of Plant Sciences and has working experience in plant genetics and genomics since 1995. His research interests include response of plants against environmental changes, natural variations in plant genetic resources and incorporation of genomics tools for big data analysis. As part of his post-doctoral research, he has carried out molecular breeding in rice and was instrumental in developing new rice varieties in Malaysia. Besides, miRNA and transcriptome sequencing were conducted in several plant species to understand genes regulating plant metabolism, yield and stress response. He has carried out several external funded research projects on bioprospecting and genetic variability analysis of several plant species. 8 PhDs were awarded under his guidance and 6 students are pursuing their PhDs. So far, over 50 MPhil, MSc, BSc and BTech students completed their dissertation projects and short-term training under his guidance. He has published 55 peer reviewed articles, 14 book chapters and 72 conference presentations in India and abroad.

  • Achuthsankar S. Nair, Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala 695581

    Achuthsankar S Nair is the senior Professor of Department of Computational Biology and Bioinformatics, University of Kerala. His research area includes machine learning, bio-sequence analysis, Travancore history and Carnatic music. He led various IT development projects as the Director of C-DIT, Govt of Kerala, for 3 years.  He authored more than 15 books in English and Malayalam. He is also a recipient of Kerala government's Young scientist award (1991), Engineering Teacher's National Award (1994) by ISTE, National Teacher's Award by Indian National Science Academy (INSA-2013), Vakkom Maulavi Foundation's Award for Excellence in Social Service (2014) and P.T Bhaskara Panicker Award (2019). He is a life member of Indian Society for Technical Education.

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Bioinformatics

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Published

2023-05-28

Issue

Vol. 10 No. 2 (2023): Bio Informatics

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