Construction Of Genomic Database And Genetic Dissection Of Metabolomic Traits In Lettuce

As a popular vegetable worldwide,lettuce(Lactuca sativa)has diversified genotypes and is rich in nutrition for daily consumption such as fibers,vitamins and amino acids.Resent,the high quality lettuce reference genome and multi-omics data for diverse lettuce accessions have been released.In order to better use these published data,it is necessary to summarize these omics data and provide a user friendly platform to assist researchers to obtain and analyze lettuce data.Here,we developed a web server of lettuce genomic database to reduce the difficulty of data acquisition and simplify the data analysis process.Plants produce a large number of metabolites during growth and development,which not only participate in plant growth and development and stress response,but also give plants a unique flavor and play an important role in the process of maintaining human health.In this study,we conducted metabolomics analysis on a large number of lettuce materials,and used the constructed lettuce genome database as a platform to integrate metabolome,transcriptome,and genome data to investigate the variation of metabolites during lettuce domestication process and their underling genetic basis and molecular mechanism.Main results are as follows:(1)We constructed a comprehensive lettuce genomic database.The database integrates240 RNA-seq data from different lettuce accessions,gene annotation information,eQTL and gene co-expression network,creating a search platform that can break the barrier between different omics data.This database also provides dozens of bioinformatics tools,including BLAST,Jbrowse,BSR-seq pipeline,QTL-seq pipeline,GWAS and differential expression and so on,to assist users to analyze lettuce genomic data.(2)Based on investigation of 77 primary metabolites in a panel of 189 lettuce accessions including major horticultural types and wild lettuce Lactuca serriola,we found that the primary metabolites in Lactuca serriola show different levels comparing with cultivated lettuce.Metabolites which have been under selection during lettuce domestication and subsequent cultivar differentiation were discovered using NANOVA,Tukey's test and Qst-Fst.Specifically,galactinol,malate,quinate and threonate were significantly affected by the domestication process and cultivar differentiation of lettuce.(3)We identified 154 loci significantly associated with the level of 51 primary metabolites.One of them,LG8749721 which encodes a galactinol synthase,is considered as a candidate gene that affects the contents of galactinol and raffinose in lettuce.Overexpression assay in tabacoo showed that LG8749721 can affect galactinol and raffinose contents in tabacoo.(4)A new pipeline is developed to detect metabolite related genes affected by domestication.Four candidate genes passed filter criteria and three of them are associated with quinate and chlorogenic acid.LG8763094 and LG5482522 are selected as the candidate genes due to the high correlation between their gene expression and metabolic levels.Abundant genetic variations were detected between cultivated and wild lettuce in the promoters of LG8763094 and LG5482522,which may affect their expression levels and lead to the accumulation of quinate and chlorogenic acid in L.serriola.Our study provides a comprehensive lettuce genome database and important genetic information of lettuce.The content of chlorogenic acid in cultivated lettuce is significantly lower than that in wild lettuce.chlorogenic acid contributes to human health,and this research provides important approach to imcrease its contents and improve the quality of lettuce in the future.