Variation analysis and quantitative trait loci mapping of 16 free amino acid traits in the tea plant (Camellia sinensis)

The levels of free amino acids (FAAs) and the timing of bud flush (TBF) are among the the most economic traits of tea plants (Camellia sinensis). Investigating the genetic variation characteristics of FAAs and their potential associations with TBF is critical for the breeding of new tea cultivars with high economic value. In this study, we utilized the ‘Emei Wenchun’ (♀) × ‘Chuanmu 217’ (♂) filial 1 (F1) genetic population (n = 208) and measured their FAA contents in the “one bud and two leaves” samples across two spring seasons and one summer season using high-performance liquid chromatography combined with the Waters AccQ-Tag method. The sprouting index (SPI) was observed over two springs to quantify the TBF trait. A genetic map previously constructed based on the same population was employed for quantitative trait loci (QTL) mapping. A total of 16 FAAs were measured, and the average total FAA contents were 28.1 and 25.4 mg/g (dry weight) in the two spring seasons and 14.29 mg/g in the summer season. Within the population, the coefficients of variation (CV) for the FAAs ranged from 23 to 41% within each season, and the correlation coefficients (r) varied from 0.15 to 0.35 across seasons. ANOVA analyses revealed that 13 out of the 16 FAAs exhibited significant genetic variation, with the estimated broad-sense heritability (h2) ranging between 10.33% and 57.10%. Interestingly, three FAAs and the total FAA contents showed significant positive correlations (r = 0.21–0.34, P < 0.01) with the SPI trait in both spring seasons. QTL mapping identified 13 FAA-associated QTLs distributed across eight linkage groups. Within the F1 population, the FAAs exhibited considerable variation across seasons, their heritabilities were generally low (most ≤ 50%). There was a weak but significant positive correlation between FAAs and TBF. Additionally, 13 FAA-associated QTLs were identified. The results of this study enhance our understanding of the genetic variation characteristics of FAAs and provide insights for breeding tea cultivars with both higher FAAs and earlier TBF.