Data_Sheet_1_SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.docx

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 (R2), 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 GA3 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.

株高是作物重要的农艺性状。目前已有多个调控番茄（Solanum lycopersicum）株高突变体的基因被克隆，但在番茄中被鉴定的株高数量性状基因仍较为有限。本研究在番茄中鉴定到7个调控株高的数量性状位点（quantitative trait loci, QTL），其中qtph1.1（番茄株高QTL 1.1）、qtph3.1与qtph12.1为主效QTL，分别可解释15%、16%及12%的表型变异（R²）。研究进一步将qtph1.1定位至1号染色体上18.9 kb的区间内。基于番茄注释基因组（版本SL2.50，注释版本ITAG2.40），编码赤霉素（gibberellin, GA）受体SlGID1a的Solyc01g098390即为该位点的候选基因。qtph1.1位点所在的SlGID1a基因存在一处单核苷酸多态性（single nucleotide polymorphism, SNP），该变异导致蛋白序列中的氨基酸发生改变。携带qtph1.1位点的近等基因系（near-isogenic line, NIL-qtph1.1）相较于野生型近等基因系（NIL-WT），节间长度与细胞长度均更短。NIL-qtph1.1的矮化表型无法通过外源施加赤霉素3（GA3）得以恢复。转录组分析与实时荧光定量反转录PCR（real-time quantitative reverse transcription PCR, qPCR）结果显示，NIL-qtph1.1与NIL-WT的茎组织中，多个参与赤霉素与生长素生物合成及信号转导的基因存在差异表达。本研究结果可为解析番茄株高的分子调控机制奠定基础。