QTL Mapping And Candidate Genes Analysis Of Irregular Fruit Cracking In Tomato

Tomato（Solanum lycopersicum L.）,an important worldwide horticultural crop,is widely cultivated in China.Fruit cracking refers to the phenomenon of cracks on the surface of the fruit,which is very common in the tomato production process.It not only affects the appearance and quality,but also affects its sales,which is an urgent problem to be solved.In this experiment,the F₁ and F₂ offspring were obtained by crossing the cracking-susceptible（CS）germplasm accession‘S189’and the cracking-resistant（CR）germplasm accession‘R91’and subsequent self-crossing.Genomic DNA of 20 CS and20 CR F₂ individuals were evenly mixed as CS-pool and CR-pool,respectively.QTL-seq approach was applied to identify candidate QTLs,combined with traditional QTL analysis for verification.Afterwards,gene expression difference analysis was used to mine candidate genes related to irregular fruit cracking in tomato,and thus bioinformatics analysis was carried out.The main findings are as follows:（1）In the F₂ population,the rate of fruit cracking per plant showed continuous variation and obeyed a normal distribution,indicating that the irregular fruit cracking traits of tomato conformed to the characteristics of quantitative traits.（2）A total of 2 QTLs that regulated irregular fruit cracking in tomato were detected,which were physically located in the region of 38.75-42.14 Mb on chromosome 2 and the region of 49.07-49.48 Mb on chromosome 5.The 2 QTLs were temporarily designed as q CR2 and q CR5.（3）The linkage map of chromosome 2 was constructed using 43 polymorphic markers.Afterwards,traditional QTL analysis was carried out based on the fruit cracking rate of F₂ population.A major QTL was detected between the polymorphic markers sli2734and Bin3371,whose LOD score was 3.05 and contribution rate was 7.05%.The corresponding physical location of the major QTL was coincided with the q CR2’s region.According to the results from both QTL-seq and traditional QTL analysis,the candidate region was delimited between 39.55-39.94 Mb,eventually designated as q CR2.1.There were a total of 53 genes in this 387 Kb interval.（4）The mature fruit pericarps from the parents were used to analyze the differences at gene expression levels and thus 3 genes with significantly different expression levels were obtained,namely Solyc02g072400,Solyc02g072470 and Solyc02g076780.Among them,the expression levels of Solyc02g076780 between the parents were extremely significantly different.Solyc02g076780 played a role in ethylene regulation,which could be a key candidate gene for irregular fruit cracking in tomato.（5）The mature fruit pericarps from some F₂ individuals were used to analyze the differences at gene expression levels.The results showed that the average expression levels of Solyc02g076780 between the cracking-susceptible individuals and the cracking-resistant individuals were extremely significantly different,which further confirmed that Solyc02g076780 was the major gene that regulated irregular fruit cracking in tomato.（6）The bioinformatics analysis results of Solyc02g076780 showed that its protein had the Le-CTR1 domain,which could regulate ethylene-induced senescence and participate in the transduction of stress response signals.