Identification of QTLs and candidate genes controlling berry size in table grape by integrating QTL and transcriptomic analysis

Grape berry size is one of important external quality attributes affecting consumers’ preference, but also a component of yield, and thus one of the major concerns of grapevine breeders. However, as a complex quantitative trait under polygenic control, its genetic mechanism is still not fully understood. In the present work, berry weight, berry length and berry diameter of the grapes of 160 F1 progenies from an interspecific cross between ‘Moldova’ (V. labruscana × V. vinifera) and ‘Ruiduxiangyu’ (V. vinifera) were evaluated at the mature stage over four consecutive years. The significant QTLs and the underlying candidate genes for berry size related traits were identified by integrating with QTL mapping, RNA-seq, phylogenetic, and allelic variants analyses. 15 QTLs mainly on the Chr5, 11, and 17 linked to the trait of berry weight, 17 QTLs contributed to the trait of berry length, and 8 QTLs associated with berry diameter were detected based on high density genetic linkage maps over four years respectively. 6 prominent candidate genes including VIT_05s0020g03980 (protein IQ-DOMAIN 14-like), VIT_08s0032g01110 (putative axial regulator YABBY 2-like), VIT_15s0021g02460 (putative cell number regulator 6), VIT_17s0053g00700 (unnamed protein), VIT_17s0053g00990 (predicted expansin-A15) and VIT_11s0052g00840 (PREDICTED AP2-like ethylene-responsive transcription factor AIL5-like) were further highlighted underlying the QTLs. The results obtained in this study provide new insights into berry size variation in grapevine.