Association between molecular and quantitative variability in a tomato broad cross identified by sequence-specific markers developed from transcriptomic polymorphism for the sHSP cluster in chromosome six

Abstract

Advances in plant sequencing have revolutionized breeding strategies, but implementing them in large-scale programs remains expensive. A more practical strategy uses genomic and transcriptomic data from parental lines to develop molecular markers, such as Insertion/Deletion (InDel) markers, for application in segregating generations. In this manner, the approach provides a cost-effective and efficient means of identifying quantitative trait loci (QTLs) by linking molecular polymorphisms to phenotypic traits. In the present study, we phenotypically characterized two consecutive segregating tomato populations (F4 and F5). Interestingly, the organoleptic traits displayed higher narrow-sense heritability (h2 ), whereas the morphological traits showed lower heritability values. Within a specific genomic region on chromosome six, where small Heat Shock Proteins (sHSPs) are differentially expressed, we identified a structural polymorphism that was used to develop a diagnostic InDel marker. The marker enabled the detection and validation of QTLs associated with fruit weight and fruit height in both populations, F4 and F5. Because the InDel marker exhibited unexpected behavior, we further examined the region using Oxford Nanopore Technologies (ONT), which provided structural resolution and a more precise understanding of the underlying genetic variation.