Study Of Watermelon Fruit Quality And Evolution Based On Transcriptome And Genome Comparison

Watermelon is an important fruit crop grown worldwide.It originated in the tropical deserts of Africa.From wild watermelon to cultivated waterrmelon,the fruit quality and ripening characteristics have undergone drastic changes,resulting in modern high-quality cultivated watermelons and rich and varied types.However,the expression patterns and genome evolution basis of these changes is still unclear.In this study,transcriptome and genome comparison of cultivated watermelon and wild watermelon were compared and phylogenetic analysis was conducted to explore important genes and their expression patterns in watermelon quality and ripening evolution.The main results are listed as follows.1.The genome sequence of wild watermelon PI296341-FR was constructed and the total length was 362.1 Mb,including 23,274 genes.Genome recombination hotspot analysis revealed that there was a recombination hotspot in the 11 Mb region of chromosome 2 and the genome recombination in 12-20 Mb region was significantly inhibited.The recombination frequency of the 2.5 Mb region of chromosome 7 was also significantly higher than other regions.These unusual recombination indicate that the two chromosomes may play an important role in genome evolution.2.3.97 M SNPs and 0.68 M InDel were identified between 97103 genome and PI296341-FR genome.870 and 643 PAVs were found in 97103 and PI296341-FR.Combining the transcriptome data of fruit development,we found 4,495 genes with encoding mutations and expressed in fruit flesh.5,423 genes with length variation of encoded proteins were expressed in fruit flesh.Many fruit quality development and ripening regulation related genes,such as AGA,HDA1,PSY,CHYB,LCYB,PME,ACS,ACO,ERF,were included.57 genes unique in 97103 genome are expressed in its flesh tissue,including BG,potassium transporters and limonene synthase.53 genes unique in PI296341-FR genome are expressed in its flesh tissue,including stress-enhancing proteins.Na+/H+ antiporter and thioredoxin.These genes formed the genetic variation basis for the fruit quality and ripening characteristics between cultivated watermelon and wild watermelon.3.641 transcription factors with non-synonymous mutations were identified between 97103 genome and PI296341-FR genome,of which 281 transcription factors were expressed in fruit tissues.The main types include MYB,bHLH,bZIP,AP2-EREBP,C3H,C2H2,HB and CCAAT,GRAS,NAC.These transcription factors are the important candidates for the differential gene expression regulation related to watermelon fruit development and ripening.4.During the fruit development of cultivated watermelon 97103 and wild watermelon PI296341-FR,2,452,826 and 322 genes were differentially expressed in the flesh and the mesocarp of 97103 fruits and PI296341-FR flesh.The AGA,IAI,UGGP gene and MFS sugar transporter are the important genes contributing to the sugar accumulation difference between 97103 and PI296341-FR fruits.PSY,CHYB,NCED and CCD genes play the important role in fruit flesh color development of 97103 and PI296341-FR.The differential expression of cellulose,pectin and lignification related genes,including 4CL,CESA,PME,PMEI,PGI and MANA,affected the fruit flesh texture of cultivated watermelon and wild watermelon flesh.ACS,ACO and ethylene signaling transduction genes ETR and ERF play the key role in the ethylene-induced fruit ripening and softening.5.Total of 73 genes including bHLH transcription factor,ACO,BG,PG and potassium transporter were specifically expressed in 97103 fruit flesh,which may play the important role in the quality development and fruit ripening regulation of cultivated watermelon.83 genes including heat shock protein,disease-associated protein and receptor kinase were specifically expressed in the flesh of PI296341-FR.These genes may be involved in the stress response and resistance-related regulation of fruit in wild watermelon.6.We identified 24.7 M SNPs based on genomic variation analysis of 323 representative watermelon accessions.The phylogenetic tree was constructed based on the SNP variation loci and the evolutionary relationships among the species within the genus citrullus were clarified.Based on the genome wide association analysis of fruit quality traits,we found that the α-galactosidase gene and the sugar transporter gene TST2 may contribute to sugar accumulation in watermelon fruit flesh.The lycopene p-cyclase gene is a key candidate gene in watermelon fruit flesh color determination.The bHLH transcription factor is a key candidate gene determining the bitterness taste of watermelon fruit.7.The evolution,domestication and improvement scenario of watermelon fruit quality development and ripening characteristics and the key selected genes from wild watermelon to cultivated watermelon were modelled.In the evolution stage from C.colocynthis to C.mucosospermus,the photosynthate unloading gene AGA,cell expansion gene EXL5 and histone deacetylase gene HDA1 participated in evolution from the non-ripening and small fruit of C.colocynthis to the preliminary ripening big fruit of C.mucosospermus.In the domestication stage from C.mucosospermus to C.lanatus landrace,the bHLH transcription factor is the key candidate gene determining the bitterness of watermelon fruit.The sugar transporter SWEET3 is involved in the domestication selection for fruit flesh sweetness traits.In the improvement stage from C.lanatus landrace to C.latanus cultivated,sugar transporter TST2 was further selected and formed the modern cultivated watermelon with high-quality fruit.The sequential selection of these genes has driven the fruit quality and ripening evolution from wild watermelon to cultivated watermelon.This study preliminarily clarified the gene expression and selection evolution patterns of the differences in the fruit quality and ripening characteristics between cultivated and wild watermelons,providing important clues for the ultimate elucidation of the molecular mechanisms of watermelon quality development and fruit ripening,and for the effective utilization of the excel lent genetic resources in wild and cultivated watermelons.The theoretical basis for watermelon quality improvement and molecular breeding was laid based on this study.