Comparative Analysis of Fruit Transcriptome in Tomato (Solanum lycopersicum) Genotypes with Contrasting Lycopene Contents

Abstract

Carotenoid metabolism is regulated by several genes encoding carotenoid biosynthetic pathway enzymes. In the present study, a fruit transcriptome in tomato (Solanum lycopersicum) was compared between high lycopene accumulating genotype EC-521086 and low lycopene accumulating genotype VRT-32-1 at three different stages (green, breaker and red) of fruit ripening. This analysis led to the identification of 2,558 differentially expressed genes at three stages of fruit ripening. Among these genes, 123 were carotenoid-correlated genes. Quantitative RT-PCR analysis revealed high expression of genes encoding enzymes involved in lycopene biosynthesis like IPP isomerase, phytoene synthase, phytoene desaturase, z-carotene desaturase; and comparatively lower expression of genes encoding enzymes involved in lycopene catabolism like lycopene cyclase, carotenoid e-ring hydroxylase, zeaxanthin epoxidase, violaxanthin de-epoxidase and neoxanthin synthase in EC-521086, thereby possibly explaining the high lycopene content in EC-521086 as compared with the low lycopene genotype VRT-32-1. Further, the EC-521086 genotype exhibited high expression of the TOMATO AGAMOUS-LIKE 1 (TAGL1) MADS box gene—a positive regulator of lycopene accumulation—at breaker stage, and low expression of the ethylene receptor LeETR4 gene—a negative regulator of trans-lycopene and β-carotene accumulation, at the red stage of fruit ripening. Our results clearly demonstrate the role of specific genes in accumulation of high lycopene in the EC-521086 tomato genotype during the fruit ripening processes.