Elucidating the genetics of post-harvest shelf-life of cucumber fruits and identification of associated QTLs and candidate genes

Abstract

Cucumber is a perishable vegetable crop with limited storability, and development of genotypes with extended shelf-life will help in reducing post-harvest loss. One natural variant, DC-48 with extended shelf-life, was used to understand the genetics of the associated traits and identify the genomic regions and associated candidate genes. Scanning electron microscopy revealed differences in the structure of the epicarp in the genotypes. Programmed cell death (PCD) and appearance of senescence-related dark spots (SRDS) in the epicarp of the cucumber fruit with low shelf-life were also detected. Retention of green colour, absence of any shrinkage, retention of fruit firmness and slow change in the pH of the endocarp were essential traits associated with extended shelf-life. Single recessive gene govern retention of green colour while the remaining traits were polygenic. One QTL detected through QTL-seq on chromosome 4 was associated with retention of green colour spanning over a region of 5.01 Mb. Conventional mapping in F2 progenies with PCR-based markers also identified one QTL within the same region. RNA-seq and RT-PCR analysis at two different developmental stages revealed two genes in the QTL region namely, Csa_4G000860 with unknown function and Csa_4G016490 with acyl-transferase activity in the early and late developmental stages of the fruit, respectively associated with retention of green colour. Two PCR-based markers, InDel 861 and InDel 016, closely linked with retention of green colour can be used in marker-assisted back-cross introgression. This study provides greater insight into the molecular network associated with extended shelf-life in cucumber.