GWAS-Guided Compact SNP Panels Enable Breeding-Relevant Prediction of Bolting and Flowering Timing of Lettuce

High temperatures accelerate bolting and shorten the vegetative phase, thereby reducing the marketable yield in lettuce(Lactuca sativa L.). Using the KNOU lettuce core collection (KLC; n = 288), which represents major horticultural types, we integrated genome-wide association studies (GWAS) with genotyping-by-target-sequencing (GBTS), a multiplex target amplicon sequencing approach, to develop compact SNP marker panels for breeding-relevant prediction of reproductive timing. The KLC was genotyped via genotyping-by-sequencing (GBS; 97,528 SNPs) and phenotyped across two spring-to-summer seasons to analyze cumulative temperature to bolting (CTTB) and cumulative temperature to anthesis (CTTA) under protected cultivation conditions, revealing broad variation and high heritability (H = 0.79 and 0.74, respectively). Multi-model GWAS consistently identified a major hotspot on chromosome 7 for both traits, whereas additional loci showed trait- and year-specific effects. A lead SNP on chromosome 7 was validated by KASP, confirming a consistent allelic effect across genetic backgrounds. GWAS-supported loci were converted into compact GBTS panels (CTTB-only, CTTA-only, and pooled), and their ability to predict genomic estimated breeding values (GEBVs) was evaluated via repeated 5-fold cross-validation. The pooled panel achieved the highest predictive performance for CTTB (up to R2 = 0.41 with random forest and R2 = 0.37 with RR-BLUP), outperforming the CTTB-only panel. In contrast, CTTA prediction was more moderate (up to R2 = 0.32). Overall, this GWAS-to-GBTS panel strategy provides a practical basis for low-cost, early selection of reproductive timing in lettuce breeding.