Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway

• Published in: Scientific reports 2017-07, Vol.7 (1), p.5616-13, Article 5616
• Main Authors: Terracciano, Irma, Cantarella, Concita, Fasano, Carlo, Cardi, Teodoro, Mennella, Giuseppe, D’Agostino, Nunzio
• Format: Article
• Language: English
• Subjects: 45/41; 631/449/2491; 631/449/711; Biological effects; Carotenoids; Carotenoids - biosynthesis; Exons; Fruits; Genetic diversity; Genetic Variation; Genotype; Genotypes; Health promotion; Humanities and Social Sciences; INDEL Mutation; Lycopene; Metabolic Networks and Pathways; multidisciplinary; Pigments; Plant breeding; Plant Proteins - genetics; Polymorphism, Single Nucleotide; Regulatory Elements, Transcriptional; Regulatory sequences; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods; Single-nucleotide polymorphism; Solanum lycopersicum; Solanum lycopersicum - genetics; Studies; Tomatoes; β-Carotene
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-06120-3

Tomato ( Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis - and trans -lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits.