Metabolome Changes And Genetic Basis In Tomato Breeding

Tomato(Solanum lycopersicum)is the most widely cultivated fruit and vegetable crop in the world and an important source of human dietary fiber and nutrients.After the domestication and improvement of the wild tomato,the yield and fruit weight of tomato have been significantly improved.The breeding history of tomato mainly includes the four major stages of domestication,improvement,divergence and introgression.Cherry tomato(S.lycopersicum var.cerasiforme)is considered the probable ancestor of the big-fruited tomato and was likely domesticated from the red-fruited wild species Solanum pimpinellifolium.Cultivated tomatoes undergo a variety of divergence during the breeding process,the emergence of red fruits and pink fruits is a typical example.In addition,modern breeding introgressed gene fragments of good traits of wild resources into the genome of cultivated tomato.These breeding behaviors have an important influence on the metabolomes of tomato.This study systematically studied the Changes in the metabolomes of tomato and its biochemical and genetic basis in four major breeding stages.In order to explore the influence of human breeding behaviors on the metabolomes of tomato and to analyze the important metabolic pathways and regulatory networks related to tomato nutritional quality,we analyzed genomics,transcriptomes and metabolomes of610 different accessions of tomato resources worldwide.A total of 26 million genome mutation sites,over 30,000 gene expression levels,and 980 metabolite contents were obtained.Using mGWAS,eQTL and co-expression analysis methods,such as found 3,526 signal sites that regulate and control 514 metabolites,more than 90000 eQTL loci,and230000 groups of metabolites content was significantly associated with gene expression;In addition,SNP shared by mGWAS and eQTL was constructed to construct the networks of metabolite-SNP-gene in tomato fruit,including 371 metabolites,970 SNPs and 535 genes.This study provided the source of big data for the study of the molecular mechanism of tomato metabolomes,which greatly promoted the development of plant functional genomics.In the process of domestication,the weight of tomato fruit has increased a hundredfold.We conducted metabolomic analysis of the tomato population and found that there were significant changes in the contents of 389 and 614 metabolites in the domestication and improvement stages,respectively.By constructing a segregating population to simulate the tomato breeding process,it was found that about 30%and 28%of the metabolites were affected by the weight selection in these two stages.Then the different introgression lines and transgenic plants of fruit weight gene fw11.3 was used to reveal the effect of the hitchhiking genes on the tomato metabolome.The taste of tomato also changed significantly during domestication.The results showed that the content of SGAs,a toxic anti-nutritional factor with astringent taste,gradually decreased during the breeding process from wild tomato to cultivated tomato.Further analysis revealed that the natural variation of SGAs was controlled by five major genetic loci,and these loci were strongly selected during domestication and improvement.One of the most effective loci was a gene cluster containing cytochrome P450,acyl-CoA dehydrogenase,and UDP-glucosyltransferase on chromosome 10 to be tested in vitro experiments.A SNP(ch01:64501127)that introduces a premature stop codon was found in the exon of a UDP-glycosyltransferase(Solyc10g085230),and significantly reduced the content of SGAs in cultivated tomato fruits.Selection for low SGA alleles at both SW29 and SW246 can reduce the three SGAs to 20.9%.In order to study the metabolomic differences and genetic basis of red and pink fruits,we compared all pericarp metabolites in 44 pink BIG lines and 191 red BIG lines,identifying 122 metabolites that were significantly different.CRISPR/Cas9 technology was used to knock out SlMYB12 to create pink fruit mutants,and it was found that the content of flavonoids in tomato fruits was greatly reduced by metabolomic analysis.Transcriptome analysis revealed that multiple structural genes of polyamines and SGAs metabolic pathways were differentially expressed,further validating the novel regulatory functions of SlMYB12.The rich genetic and phenotypic variation of wild resources is used in tomato breeding,and most of the resistance genes in modern tomato varieties come from wild tomatoes.By analyzing disease-resistant resources and segregating populations in different backgrounds,we confirmed the impact of the application of the tobacco mosaic virus gene(Tm-2~a)on tomato metabolomes.In this study,a multi-omics approach was used to perform a comprehensive analysis of the breeding process.The anti-nutritional factor and nutritional factor of tomato were ameliorated by means of metabolomics-assisted breeding.This study provides a theoretical basis for the cultivation of new tomato varieties,and its large data resources will also promote the improvement of tomato nutrition and health quality.