The Genome Of Brassica Rapa Crops And Bioinfomatic Analyses For The Important Agronomic Traits Related Genes

Brassica rapa crops are known as the cruciferae family of Brassica plants,which mainly contain three subspecies,including Chinese cabbage(B.rapa ssp.pekinensis),Non-heading Chinese cabbage(B.rapa ssp.chinensis)and turnip(B.rapa ssp.rapa).The Chinese cabbage genome was recently sequenced and assembled,which provides the important reference genome for the re-sequencing of B.rapa crops.The genomics research of B.rapa is lagged behind the other model plants,especially the follow-up study of B.rapa genomics has not been carried out.So it is very important to systematically conduct the B.rapa genomics research and establish the follow-up research methods.In this study,we re-sequenced the B.rapa crops and analyzed the evolution of the relationship and leaf shape development mechanism among them.Combining the re-sequencing data,we conduct the genome-wide association study for 14 important agronomic traits,and a lot of agronomic traits related genes are detected.The expression profile is constructed for three accessions at the five key growth stages.A large number of gene related with the growth stages were identified.Through transcriptome sequencing for different temperature treatments,we obtain a lot of low and high temperature significantly related genes.Using the genomic information,we conducted the genome-wide analysis of the several important gene family in Chinese cabbage,and several of the key genes for functional analysis.The results are as follows:1.In this study,we re-sequenced the genome of 129 B.rapa accessions and identified single nucleotide polymorphisms(SNPs),insertions/deletions,and structure variations.We detected 20 candidate genes related to leaf margin by FST,three of which overlapped with quantitative trait loci and verified by eQTL,including BrCycD3,BrGRF2 and BrAS1.Furthermore,genome-wide association study(GWAS)detected 17 genes related to leaf development,among which,6 genes were also overlapped with the known QTLs.Two genes,BrKAN3 and BrAS1 were identified by combining FST and GWAS,which involved in leaf morphological differences.They contained large effect variations in the FST divergence regions,and also contained the significant SNPs identified by GWAS.2.We conducted a genome-wide association study for 14 important agronomic traits using the SNPs identified by genome re-sequencing for 96 non-heading Chinese cabbage(NHCC)accessions.The results showed that there were 729 association signals,and the identified loci explained about 45%of the phenotypic variation.Among of them,16 loci related with the leaf margin and chlorophyll content.Moreover,real-time reverse-transcription PCR showed that six important candidate genes were associated with the two traits.In addition,the first high-density haplotype map of NHCC was constructed to assist the GWAS.This is the first comprehensive and systematic GWAS of NHCC,and establishes an efficient platform for performing GWAS.This study provides a rich source of data for genetic and breeding research in NHCC and other horticultural crops.3.We investigated the differential expressions of genes that control adaptability and development in plants growing in the natural environment to study underlying mechanisms of their expression.Using digital gene expression tag profiling,we found thousands of genes that exhibited significant differences in expression levels at five developmental stages among three non-heading Chinese cabbage cultivars.Through comparative analysis and previous reports,we identified several candidate genes associated with late flowering,self-incompatibility,cold tolerance,and leaf color.Two genes related to cold tolerance were verified using quantitative real-time PCR.This analysis will provide a wealth of resources for studying the gene expression of different growth stages in B.rapa crops.4.We conducted comprehensive analysis for cold and heat treatments in NHCC using RNA-seq.Totally,136,189 unigenes with N50 length of 1,705 bp,and a total length of 153.1 Mb were obtained.We performed a temperature decrease course differential gene expression analysis,and the results showed that only few genes continuously decreased or increased in expression accompanying temperature decrease.However,the expression of majority genes remained unchanged over the temperature decrease process.A total of 14,329 differentially expressed genes(DEGs)were detected under at least one treatment.Among which,10 DEGs were detected in all treatments,including 7 up-regulated and 3 down-regulated.The enrichment analysis showed that 25 and 33 genes were enriched under cold and heat treatments,respectively.In addition,10,001 LncRNAs were identified,and 968,7 belonged to novel LncRNAs.Furthermore,we constructed a co-expression network for LncRNAs and protein-coding genes.This study systematic and comprehensive analyzed the NHCC transcriptome,which provides a valuable resource for genetic and genomic studies under abiotic stress in future for B.rapa.5.We conducted systematic and comprehensive analysis of several major gene families of Chinese cabbage,including Hsf,AP2/ERF,bHLH,GRAS,NAC,CO and SNARE.In this study,we used the Hsf as example to illustrate how in-depth study a gene family using the bioinformatics tools.In this study,35 BrHsf genes were identified from Chinese cabbage,which could be classified into 3 groups according to the phylogenetic comparisons with Arabidopsis and rice.Thirty-three BrHsf genes mapped on chromosomes were further assigned to 3 subgenomes and 8 ancestral karyotypes.Chinese cabbage and Arabidopsis shared 22 orthologous gene pairs.The expansion of BrHsf genes mainly resulted from genome triplication.Comparative analysis showed that the most Hsf genes were in Chinese cabbage among the five species analyzed.The expression patterns of BrHsf genes were different in 6 tissues based on RNA-seq.qRT-PCR analysis showed that the expression level of BrHsf genes were affected by cold,heat or other several various abiotic stresses.In conclusion,this comprehensive analysis of BrHsf genes will provide rich resources,aiding the determination of Hsfs functions in plant heat resistance.