Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents,which undergo considerable variations during development and maturation.The molecular mechanisms underlying these variations remain unclear.In this study,we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism.We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids.Within these modules,based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction(RT-qPCR),we identified 7 genes involved in the metabolism of sugars and organic acids.Among these genes,Cla97C01G000640,Cla97C05G087120 and Cla97C01G018840(r^(2)=0.83 with glucose content)were identified as sugar transporters(SWEET,EDR6 and STP)and Cla97C03G064990(r^(2)=0.92 with sucrose content)was identified as a sucrose synthase from information available for other crops.Similarly,Cla97C07G128420,Cla97C03G068240 and Cla97C01G008870,having strong correlations with malic(r^(2)=0.75)and citric acid(r^(2)=0.85),were annotated as malate and citrate transporters(ALMT7,CS,and ICDH).The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon.These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.