Identification of a novel quantitative trait locus improving fruit set in chili pepper (Capsicum annuum) under high-temperature greenhouse conditions

• qFS6 , a QTL on chromosome 6, regulates high-temperature fruit set in chili pepper. • No association was found between qFS6 and pollen germination or dispersal. • qFS6 provides valuable insights for breeding programs for high-temperature tolerance. High temperatures in greenhouses significantly reduce fruit set, impacting yields. Like other Solanaceae crops, Capsicum exhibits a poor fruit set under heat stress. A previous study identified ‘Takanotsume’ (‘TK’) as having a superior fruit set under high temperatures. In this study, we aimed to identify the genetic factors underlying in high-temperature fruit set. Genome-wide association studies and quantitative trait locus (QTL) analysis consistently identified a major QTL, qFS6 , on chromosome 6 associated with high-temperature fruit set, encompassing a candidate genomic interval of approximately 1.8 Mb. Neither fruit set nor qFS6 showed a significant association with pollen germination or pollen dispersal under high temperatures, suggesting that a causal gene of qFS6 does not contribute to improvements in male reproductive traits under heat stress. These results indicate that qFS6 may enhance fruit set under high temperatures through alternative pathways independent of male reproductive capacity. Furthermore, no significant differences in sugar content (sucrose, glucose, and fructose) of flowers on the day of flowering under high temperatures were observed among F 3 progenies carrying different qFS6 genotypes, suggesting that sugar metabolism is also unlikely to be involved in the improvement of fruit set by qFS6 . The identification of a novel QTL, qFS6 , provides valuable insights for breeding programs to improve high-temperature tolerance in chili pepper.