Mapping Quantitative Trait Loci(QTL) For Internode Length In Tomato

Tomato（Solanum Lycopersicum L.）is one of the most important vegetables around the world.Tomato architecture is defined as the three dimensional organization of the vegetative and reproductive organs,which strongly affects light interception and photosynthesis in the canopy and plays an extremely important role for overall yield and harvest index.In domesticated tomato,breeding efforts have focused on plant architecture modification,i.e.,“ideal-type breeding,”which has been adopted to improve crop adaptability to different environments and increase seed/fruit yield.Plant height and internode length are the major factors in plant architecture construction.Notably,one of the great successes of the Green Revolution was development of the varieties with reduced height and more robust stems.During modern breeding,plant architecture modifications aim to increase management and harvest convenience,to make favorable partition of carbon and nutrients between fruits and the other parts and to enhance efficiency of fertilizer and water use.Natural variation can be described as genetic variation within natural populations showed in nucleotide（SNP）changes and small insertions and deletions（InDels）.These nucleotide variations in the populations provide in vivo DNA platform to identify QTL in natural species.QTL detection through GWAS and QTL linkage mapping approaches provide direct identification method utilized to link genotype to a phenotype.Therefore,discovery of the genetic basis of tomato internode length gene will not only help to elucidate the molecular mechanism of tomato domestication and architecture,but also provide the theoretical basis for tomato molecular breeding.In this study,tomato wild type（S.pimpinellifolium）,RIL,and F₂ populations combined with GWAS and traditional QTL analysis methods were used to mapping the internode length QTL.The main results obtained are summarized below:1.A total of 190 tomato（S.pimpinellifolium）accessions were investigated for phenotypic and genotypic variations of internode length.Result shows that internodes length had highly significant differences（P≤0.001）across the 2 years,ranging from 3.17 to 13.27 cm in 2015,and 3.14 to 12.96 cm in 2016.In addition whole-genome sequencing of the 190 accessions was conducted,and obtained a total of 140 Gb of sequence,with an average depth of 0.6×and coverage of 37.4%of the reference genome,with a final set of 3692674 SNPs.In spite of the internode length variation among the accession,but no QTL was detected in both years of experiment.2.The solanum internode length（sil）candidate QTL has been analyzed in 200 tomato RIL populations derived from the S.lycopersicum cv.Moneymaker×S.pimpinellifolium accession PI365967.Compressed mixed linear model is used to detect associations between SNPs bin and traits which allowed identifying in total 21 QTLs.They were mapped respectively on 7 chromosomes.In particular,one Qil-13-p66470589 was repeatedly detected in the three seasons on chromosomes 4,and based on the gene annotation analysis cytochrome P450 CYP82D47-like may be a candidate for sil.3.Quantitative trait loci（QTL）for internode length traits in tomato（S.lycopersicum）was identified by F₂（957 plants）and F₃（320 plant）populations,originated from‘P502’（long internode）and‘Heinz-1706’（short internode）.One major QTL sil for internode length traits on chromosome 2 was identified,and sil accounted for 27.9%and 79.5%of the phenotypic variance for internodes length in F₂ and F₃,respectively.Refined map it is linked with a genetic distance of 2.385 cM and a physical distance of 36.1Kb between the nearest flanking markers D66 and HP633 in the population of F_2:3.According to the gene annotation information in the location region,terpene synthase TPS38（Gene ID:101261095）gene was considered as the candidate genes for internode length.