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Molecular markers for shelf life improvement through transcriptomic

profiling of Tomato (Solanum lycopersicum L) Indian cultivar.


Ajay 1
Bhaskar , Biji. C. L. 2, Sunitha 2
P, K. K. Sabu 3 and Achuthsankar S. Nair2
1:
School of Biotechnology and Bioinformatics, D.Y. Patil University, Navi Mumbai, Maharashtra,
2: Department of Computational Biology and Bioinformatics, University of Kerala, Kerala, 3: Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical

Botanic Garden and Research Institute, Palode, Kerala


*Corresponding author’s email: ajaynair.nair5@gmail.com

ABSTRACT METHODS RESULTS


.

 In India, tomato (Solanum lycopersicum L) is one of the major vegetable crop


and India stands second to China for its production. Dinucleotide
Input Raw reads Trinucleotide
 The present study focuses on the prediction and development of EST-SSR
Tetranucleotide
Trinucleotide, 400, 69%
markers and differential expression analysis through the publically available Pentanucleotide
transcriptomic data. Quality control Hexanucleotide
using FastQC Dinucleotide, 170, 29%
 In this study we have utilized the ‘Tuxedo’ pipeline for downstream analysis. The
datasets are collected during various developmental stages of the plant.
BowTie2
 RNA sequences of Solanum lycopersicum L(Accession number: SRR363116 (Root), Reference Genome
Tetranucleotide, 5, 1%
SRR363117 (Stem), SRR363118 (Leaf), SRR363119 (Flower), SRR363120 (Fruit and Annotation Hexanucleotide, 5, 1%
Tophat2
Pentanucleotide, 2, 0%
mature), SRR363121 (Fruit breaker), SRR363122 (Fruit ripe) were retrieved from
European Nucleotide Archive. Fig.3: Distribution of different repeat classes in MIcroSAtellite Identification Tool
Aligned Reads
(BAM files)
Antioxidants
30390 Total number of genes
Controls
Carotenoids
Weight CuffDiff CuffLink
Differentially Expressed Genes

72 Upregulated Genes
Differentially expressed genes Transcripts from all
Improve 31 41
Vitamins and transcripts between the libraries Downregulated Genes
vision
two libraries

response to stimulus (GO:0050896) 5 X-axis : Biological Process


MISA
reproduction (GO:0000003) 1 Y-axis : No. of Genes
Cardiovascul Functional Annotation multicellular organismal process (GO:0032501) 1
Minerals ar diseases metabolic process (GO:0008152)
WebSat 18
localization (GO:0051179) 2
developmental process (GO:0032502) 1
Aid in Lower cellular process (GO:0009987)
digestion hypertension 14
NetPrimer cellular component organization(GO:0071840) 1
• Type a caption for the data content or pictures here. biological regulation (GO:0065007) 1
0 2 4 6 8 10 12 14 16 18 20
Fig.1: Health benefits of Tomato Fig.2: Workflow of Methodology Wet Lab Validation Fig.4: PANTHER GO Biological Process(Biological Process vs No. of Genes)

OBJECTIVES RESULTS CONCLUSIONS


Identify the differentially expressed genes between a mature • 582 SSRs were developed using MISA. • The results showed that genes like PG2, TBG6, ACS2, ACS4 play a crucial role
during the ripening may have important roles in shelf life .Understanding their
(Green) and ripe (Red) tomato. • The most frequent dinucleotide, trinucleotide and tetra nucleotides were CT,
roles during ripening process will lead us to design better strategy for controlling
AAG, TAAA.
Functional enrichment analysis in Tomato (Solanum the shelf life in agroindustry.
• A total of 284 SSRs were identified using WebSat. However, among the 284 SSRs
lycopersicum) that were identified 114 SSRs could not be used to design the primers as the • This translational genomic study of Solanum lycopersicum provides valuable
flanking sequences were too short. So 170 primers were designed using WEBSAT. information that can be used in population genetics, marker assisted selection for
Identification & Validation of EST-SSR Markers in Tomato Fruit breeding programs, Quantitative trait loci (QTL) analysis and for the estimation
Further these primers were validated using NetPrimer.
(Solanum lycopersicum). of genetic diversity.

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