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Plant height is an important agronomic trait in crops. Several genes underlying tomato ( Solanum lycopersicum ) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which,  qtph1.1  ( QTL for tomato plant height 1.1 ),  qtph3.1  and  qtph12.1  were major QTLs and explained 15, 16, and 12% of phenotypic variation (R 2 ), respectively. The  qtph1.1  was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40),  Solyc01g098390  encoding GA receptor SlGID1a was the putative candidate gene. The  SlGID1a  gene underlying the  qtph1.1  locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the  qtph1.1  locus (NIL- qtph1.1 ) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL- qtph1.1  could not be rescued by exogenous GA 3  treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL- qtph1.1  and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height