QTL mapping and candidate gene identification of the full flowering date trait in olive trees (Olea Europaea L.)

Future climate models project that increases in global warming will have severe impacts on the flowering phenology of perennial fruit trees, including olive trees, a key species extensively cultivated in the Mediterranean region. Understanding the genetic factors regulating flowering is thus crucial to generate essential knowledge for the selection of suitable cultivars and for designing future olive breeding programs. Here we investigated genetic control of the full flowering date (FFD) trait through a quantitative trait loci (QTL) mapping approach. Two high-density parental genetic maps, with > 10k SNPs, were constructed based on an Olivière x Arbequina F1 hybrid olive progeny. Phenological observations of the same progeny were conducted across five environments (site × season), and the data served to compute best linear unbiased predictors (BLUPs) for FFD. Both FFD-based BLUPs and single-environment datasets were used to detect key QTLs, which were further explored through in silico candidate gene investigations. Analysis of the FFD distribution revealed high heritability with transgressive segregation. A total of 18 significant QTLs were identified in the BLUP analysis, and six were selected as the most relevant. Two QTLs were co-detected on the same linkage groups (LGs) of both parental genetic maps in the BLUP and some environment analyses: LG09 (qFDO9b/ qFDA9) and LG07 (qFDO7/ qFDA7). Moreover, four QTLs on LG3 (qFDA3), LG22 (qFDA22) and LG13 (qFDA13) on Arbequina map, and LG13 (qFDO13) on Olivière map were revealed in the BLUP and some single-environment analyses. qFDA13 and qFDA22 were characterized by high explained variance (14.67% and 11.66%, respectively) and additive effects (-1.09 and + 1.15, respectively). Candidate gene investigation revealed genes within key QTLs probably involved in transcription regulation, including WRKY71, RLT3, and ABSCISIC ACID-INSENSITIVE-5-LIKE, in addition to the FT-INTERACTING protein1 transport protein. This study aimed to elucidate the genetic control of the flowering date in olive trees. The key QTLs identified generated valuable knowledge on the genetic basis of the flowering date, which could be taken into account in future genetic and breeding research focused on developing new varieties better adapted to global warming.