Genome-wide meta-QTL approach identifies consensus loci associated with agriculturally important tomato fruit traits

Using 82 different QTL mapping populations investigated in prior studies, we identified 99 high-confidence meta-QTL regions along with potential candidate genes associated with fruit quality traits in tomato. The genetic analysis of economically important quantitative traits is essential for the development of new cultivars that exhibit improved yield and quality, including disease resistance and enhanced flavor. Meta-QTL (MQTL) analyses allow for the integration of QTL data from multiple independent studies, revealing chromosomal regions consistently associated with traits of interest. In this study, we identified reliable and consistent QTLs for eight agronomically important fruit traits in the cultivated tomato through MQTL analysis of 1,438 QTLs reported in 82 independent mapping populations. Our analysis helped identify 99 consensus MQTLs, distributed across all 12 tomato chromosomes, with almost 4 times narrower confidence intervals (CI) than in the original studies. We identified the most promising candidate genes (CGs) located within each MQTL interval based on the potential function of their orthologous genes in Arabidopsis thaliana. These newly identified CGs complement previously characterized genes and candidate genes with GWAS signals from prior studies. Our research has identified consistent QTLs and CGs in unstressed conditions, offering valuable resources for enhancing fruit-related traits. We further discuss these CGs regarding their potential to improve fruit-related traits in tomato breeding programs.