Identification of QTL for yield potential under heat stress conditions through a tomato MAGIC population

Abstract

High temperature severely limits tomato reproductive development and yield, particularly in tropical production systems. Pollen viability and fruit set are commonly used as indicators of reproductive heat tolerance, but much of the supporting evidence has been obtained under controlled conditions. Their relevance to breeding under variable open-field environments remains less clear. This study investigated reproductive performance and its genetic basis under open-field heat stress using a multi-parent advanced generation inter-cross (MAGIC) population. We developed a MAGIC population from eight Solanum lycopersicum parents combining heat tolerance and multiple disease resistances and evaluated 262 F5:6 lines under natural open-field heat stress. Flower number showed the highest heritability (0.64), followed by pollen viability (0.56), fruit number (0.48), and days to flowering (0.25), whereas fruit set showed negligible heritability (<0.01). Despite its moderate heritability, pollen viability was only weakly correlated with fruit set (r = 0.22). In contrast, fruit number was strongly correlated with fruit set (r = 0.86), supporting fruit number as a practical selection criterion for reproductive performance under open-field heat stress. Restriction enzyme-associated DNA sequencing generated 16,350 high-quality SNPs for genome-wide association analysis, which identified multiple QTLs for reproductive traits, several overlapping previously reported loci. A region on chromosome 6 at approximately 31-33 Mb was particularly notable because it was associated with multiple reproductive traits and coincided with a previously reported heat-responsive QTL region. Candidate-gene analysis highlighted floral developmental regulation, represented by positional candidates SlAGO7, ENO, and SlWUS, and cellular and protein homeostasis, supported by direct candidates including MON1, ECM29, and ubiquitin-related genes. Selection criteria established under controlled environments may not fully predict reproductive performance under open-field heat stress. Fruit number provides an integrative and moderately heritable indicator of realized reproductive success under field conditions. The identified QTLs and candidate genes provide targets for validation and development of heat-tolerant tomatoes adapted to tropical open-field production.