||To dissect the molecular mechanisms underlying plant height differences affected by qtph1.1, a major-effect quantitative trait locus controlling tomato plant height, the total transcriptome of young stems of near isogenic lines NIL-WT and NIL-qtph1.1 treated with GA3 or ethanol (CK) was analyzed using RNA-seq. NIL-WT and NIL-qtph1.1 were derived from the cross between fresh-market tomato inbred line SG-7 and cherry tomato TS-165. The SlGID1a genes of NIL-WT and NIL-qtph1.1 were homologous for SG-7 allele and TS-165 allele, respectively. The seeds of NIL-WT and NIL-qtph1.1 were germinated on culture plates and were sown in plastic pots (one seed per pot) in a glasshouse. After 4 weeks, the tomato plants were treated by spraying to runoff with 50 μM GA3 (Cat. No. G7645; Sigma, St Louis, Mo., USA). For the control (CK) solution, 1 mL 70% ethanol was added to 999 mL water. The GA treatment was performed once every two days. After three GA treatments, the sixth internodes were collected from the plants in the four groups. Each group comprised three biological replicates, and each replicate contained samples from five plants. A total of 12 samples were immediately frozen in liquid nitrogen and then stored at -80°C until RNA extraction. Total RNA was isolated using the Quick RNA Isolation Kit (Cat. No. BC1803, Huayueyang Biotech Co. Ltd., Beijing, China). Twelve RNA-seq libraries were constructed using the TruSeq RNA Library Prep Kit (Illumina Inc.) and were sequenced by Beijing Nuohe Zhiyuan Company.