Uncovering candidate genes involved in postharvest ripening of tomato using the Solanum pennellii introgression line population by integrating phenotypic data, RNA-Seq, and SNP analyses

Abstract

Fruit shelf life in tomato (Solanum lycopersicum) and many other fleshy fruits is determined by several factors including cell wall structure, turgor, and cuticle properties. In this study, an introgression line (IL) population derived from a cross between Solanum pennellii (LA0716) and the S. lycopersicum cultivar M82 was used to identify candidate genes (CGs) that might be responsible for controlling tomato shelf life. IL4-2 and IL4-3-2 were identified as soft lines, IL5-1 and IL9-1-3 as firm lines based on their Br7 and Br14 firmness and shelf-life performance. To gain deeper insights into the genes that might play a regulatory key role in tomato shelf-life, transcriptome profiling was performed for the four ILs and M82 as the reference genome. A total of 5,580 Differentially Expressed Genes (DEGs) with 2,333 up-regulated and 3,247 down-regulated genes, were differentially expressed in IL4-2 vs M82, IL4-3-2 vs M82, IL5-1vs M82, and IL9-1-3 vs M82 combinations. Forty-two DEGs were selected as putative ripening related genes. The expression of nine genes potentially involved in ripening/softening process out of 42 DEGs was verified by qPCR. The RNA-Seq data was also used to discover SNPs between the ILs and the reference genome. The SNPs on CGs were converted to Cleaved Amplified Polymorphic Sequence (CAPS) markers which could be used in breeding programs in the future.