Elucidating the genetic aspect of yellow shoulder disorder in tomato (Solanum lycopersicum) by QTL-seq and linkage mapping

Abstract

The color and color uniformity of the fruits are of paramount importance to fresh consumption and the tomato processing industry. This is mostly because consumers often associate vibrant and uniform colors with freshness and quality. Yellow shoulder disorder (YSD) characterized by discolored yellow or green sectors on fruit skin is one of the major concerns for tomato producers worldwide since YSD symptoms adversely affect market value and consumer appeal. Therefore, YSD has been studied for a long time, but the genetic aspect of the problem has not been a major focus and hence, it has remained mostly unknown. So, the objective of this research was to identify the genetic components of the YSD. An F2 mapping population was developed and phenotyped for the YSD Visual Score. The F2 plants showing extreme phenotypes were selected and bulks were created. After whole genome sequencing of these bulks, three Quantitative Trait Loci (QTL)s namely YSD1.1 on chromosome 1, YSD3.1 on chromosome 3, and YSD11.1 on chromosome 11 were identified using QTL-seq and traditional linkage mapping. These three QTLs explained approximately 20 % of the phenotypic variation in the F2 mapping population. Further, candidate genes in each QTL interval were identified based on their expression profile and genetic polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) on genic/intergenic regions. These genes involve in fruit ripening, cell wall modification, lipid metabolism and starch degradation. The present study reports the first QTLs associated with YSD resistance and 17 KASP markers that can be used in marker-assisted selection for YSD in tomato.