Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway
| Autor: | Carlo Fasano, Concita Cantarella, Teodoro Cardi, Giuseppe Mennella, Nunzio D’Agostino, Irma Terracciano |
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| Přispěvatelé: | Terracciano, Irma, Cantarella, Concita, Fasano, Carlo, Cardi, Teodoro, Mennella, Giuseppe, D'Agostino, Nunzio |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genotype Sequence analysis Science Genomics Single-nucleotide polymorphism Polymorphism Single Nucleotide Article 03 medical and health sciences INDEL Mutation Solanum lycopersicum Genetic variation Regulatory Elements Transcriptional Gene Carotenoid Plant Proteins Genetics chemistry.chemical_classification Multidisciplinary biology fungi Genetic Variation food and beverages Exons Sequence Analysis DNA biology.organism_classification Carotenoids 030104 developmental biology chemistry Genetic marker Medicine Solanum Metabolic Networks and Pathways |
| Zdroj: | Scientific Reports Scientific Reports, Vol 7, Iss 1, Pp 1-13 (2017) |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-017-06120-3 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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