Allele mining in tomato: sequence capture and targeted re-sequencing of genes belonging to the carotenoid biosynthetic pathway

The aim of this study is the identification of superior alleles in tomato genes belonging to the plastidial carotenoid biosynthetic pathway to be used in breeding programmes. To achieve this goal, we used sequence capture to re-sequence 34 genes playing a key role in carotenoid metabolism on a panel of 48 genotypes which differ for carotenoid content in the fruit as determined through RP-HPLC analysis.A set of 13,667 baits of 120 nucleotides in length were designed to target all exons and 5 kb upstream to the translation start site. The 48 genotypes were subjected to targeted sequence capturing approach through Agilent’s SureSelect solution phase hybridization and Illumina HiSeq1500 paired-end sequencing.