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Abstract
Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables worldwide, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit. Further, Reactive Oxygen Species (ROS) are critical players in BER development which, combined with perturbed calcium homeostasis, greatly affect the severity of the disorder. However, the genetic inheritance of the disorder has not been explored adequately due to its complexity and high genotype-by-environment interaction. The availability of a high-quality reference tomato genome as well as the whole genome resequencing of many accessions has recently permitted the genetic dissection of BER in segregating populations derived from crosses between cultivated tomato accessions. In this study, using QTL-seq and linkage-based QTL mapping approaches, four loci associated with BER Incidence were identified at chromosome (chr)3 (BER3.1 and BER3.2), chr 4 (BER4.1) and chr 11 (BER11.1). Using recombinant screening and progeny testing approaches, BER3.2, BER4.1 and BER11.1 were narrowed downed to 1.58 Mb, 190 Kb, and 338 Kb, respectively. Two fruit weight genes, FW3.2/SlKLUH and FAS/SlCLV3, were associated with BER3.2 and BER11.1, respectively. BER4.1 underlies a potential novel gene controlling BER. In addition to genetic dissection of BER, we also analyzed chlorophyll content index trait in one of the populations developed for BER. Chlorophylls are the major color-capturing pigments found in plants that allow them to photosynthesize. Due to their critical relevance in photosynthesis, chlorophylls have been studied extensively, but not all regulatory steps have been elucidated in plants. In this study, we mapped a major locus on chr 4 that explained 39.6 PVE% in the F2 population. Genetic analysis showed that the locus was controlled by a single recessive locus, which was named CCI4.1. Further finemapping and progeny testing narrowed CCI4.1 locus to a 32 Kb interval. Based on expression analyses, putative orthology with Arabidopsis genes and proposed function, Solyc04g010285 and Solyc04g010290 were proposed to be plausible candidates for CCI in tomato.