Fine Mapping And Candidate Gene Analysis Of Tomato All-flesh Fruit

The locular gel forming is an important process and typical characterization for tomato(solanum lycopersicum)fruit developments.During the early stages of tomato fruit development,the peripheral part of the columella(or placental tissue)develops into locular tissue,surrounding the seeds and appearances jelly-like in the ripening fruit.The locular tissue plays a key role in fruit development,texture changing,flavor composition,and seeds development.From the research of physiological and biochemical changes in the forming of locular gel,it was recognized that hydrolases,plant hormones and cyclin factors play an important role in the formation of locular gel.Even the formation of locular number and its mechanism has been studied.However,the detailed mechanism of the differentiation and formation of locular gel for fleshy fruit are still unclear.The all-flesh tomato(alf)lost the function of forming the locular gel.It's inner structure of fruit looks like eggplant(Solanum melongena).The main difference between all-flesh tomato and wild types is whether they have locular gel or not.In this study,the characterizations and genetics analysis of all-flesh tomato were studied.By genetic method,the mutant gene was mapped and the candidate gene was analysed.The main results are as follows:1.Through genetics analysis of all-flesh tomato revealed that the mutant trait was controlled by a single recessive gene.By analysis of locular tissue characterization and their paraffin section,the changes of locular morphological and cell wall were known.In the wild type,the locular gel was formatted and its cell wall was broken at 25DPA(Day after anthesis).In all-flesh tomato,the locular cell wall was still intact,and the size and arrangement was similar with placenta cell.The seeds of all-flesh tomato fruit were decreased especially after 25 DPA.2.By the BSA-seq the mutant gene was mapped,and the result was confirmed with GWAS.The alf trait was fine mapped by linkage analysis with molecular markers which were obtained by sequence data.As a result,the alf gene was mapped to 184.2Kb,the physical location was SL3.0 ch06:40418964-40603185.According to the tomato genome annotation(SL3.0),twenty-nine genes were predicted in the mapped region.3.The differentially expressed genes(DEGs)of the locular tissue among all-flesh tomato and normal tomato were found based on transcriptome sequence.The transcription factor activity is the major difference in the molecular function of 25 DPA locular tissues between all-flesh and normal tomato fruits.The gene express characterization was checked by Quantitative Real-time PCR.Gene Solyc06g064840 was highly expressed in locular tissue(include seeds)in the wild types,and the difference was significant.Solyc06g064840 belongs to the AGAMOUS-like MADS-box transcription factor,which was specific expressed in locular tissues and seeds,that will be the cause of the all-flesh phenotype of this mutant.4.The class D clade including AGAMOUS-like genes are involved in the development of seed,ovule,and funiculus.They also regulate expansion and ripening process of flesh fruit.According to theNCBI database,Solyc06g064840 was predicted to be AGAMOUS-like MADS-box protein AGL11 isoform X1,for its highly conserved MADS-box region and the relatively conserved K-box region.Solyc06g064840 has very high similarity with the reported tobacco(Nicotiana tabacum)TAGL11 and petunia(Petunia hybrida)D class genes fbp11 & fbp7.Solyc06g064840 also is similar to the arabidopsis(Arabidopsis thaliana)D class genes(STK)and tomato AGAMOUS genes.Phylogenetic analysis showed that Solyc06g064840 displays very high evolution homology with the AGL clade genes of potata(Solanum tuberosum),eggplant and pepper(Capsicum annuum).5.In this study,we demonstrated a deletion of 416 base pairs located at 374 base pairs upstream from 5'UTR of Solyc06g064840.The deletion contains cis-actings such as TATA-box and CAAT-box,which may affect the express of Solyc06g064840,and then cause the alf trait of all-flesh tomato.The tomato all-flesh trait was controlled by a single recessive gene,which indicating that the function loss of one site can affect the formation of berry components.To study the all-flesh tomato,the molecular mechanism of differentiation and formation of fruit locular gel will be uncovered,and also would provide a basis for the further understanding of fruit formation,development,evolution and genetic evolution in different fleshy species.Furthermore,it will contribute to clear the effects of locular gel formation on tomato fruit physiological and flavor quality,and even provide theoretical basis for illustrating the flavor composition and improvement in tomato breeding program.