Multiomics Analysis Of Sweet Sorghum And Sorghum

Sorghum is an important crop in human life and a model organism for the study of C4 plants.The genome of sorghum has about 30,000 genes and 730 million nucleotides,which is 75% more than the rice genome.It is a crop with a relatively small genome in C4 plants known to date.Compared with non-sweet sorghum,sweet sorghum has its unique sugar metabolism accumulation mechanism.Discovery of sorghum regulatory genes and metabolic pathways related to sugar synthesis,transportation and accumulation will contribute to the genetic improvement design of its own sugar and carbon source distribution,as well as provide a reference for other important C4 crops such as sugarcane(Saccharum),miscanthus(Miscanthus),Switchgrass(Swtichgrass)and other important C4 crops.The genomes of sorghum related crops are relatively large,with more repetitive sequences and higher ploidy,while the sorghum genome has not undergone a whole-genome duplication event after the divergence of its common ancestor of gramineous plants.Relatively speaking,its genome has a low degree of repetition and complexity which is conducive to the discovery of gene function and related research of genomics.Therefore,the comparative analysis of multiple omics data related to sugar content of non-sweet sorghum and sweet sorghum will help to promote basic scientific research and genetic improvement of sorghum and related species.In this project,the sorghum pan-genome construction and the comparative analysis of sweet sorghum and non-sweet sorghum genomes are conducted on the existing sorghum genomes.In this way,the unique genes and structural variant genes in the sweet sorghum are found to construct the gene sets.Differential expression analysis of RNA-seq data in multi-samples and multi-period are used to construct gene co-expression network,screened and verified gene sets,and further screened sugar-related genes,and the results will help to reveal the difference of sugar content between sweet sorghum and non-sweet sorghum.The aim is to provide reference for future related research to sorghum variety improvement and breeding.Specifically,this study has obtained the following results:1.Genome level: Pan-genome construction was performed on the basis of existing sweet sorghum genome(Rio)and six closely related non-sweet sorghum genomes,resulting a 908 Mb sorghum pan-genome,followed by the classification of the constructed pen-genome gene families into(Core genes)and non-essential genes(Variable genes).Afterwards,GO(Gene Ontology)enrichment analysis was performed on genes in the presence/absence variation(PAVs)region and core/dispensible gene region in the pan-genome,obtaining the enrichment of gene functions of unique genes and core genes.Then,using the Rio genome as a template,high-impact SNPs(Single-nucleotide polymorphism)loci were screened out by analyzing the comparison results with other six genomes,and a gene set was constructed for the non-synonymous mutant genes;2.Transcriptome and metabolome: two sets of RNAs were collected.one of them was collected from 12 samples of sweet sorghum(Rio),non-sweet sorghum(BTx406)and their offspring(R9188)at different stages,the other was collected from sweet sorghum(No.1)and non-sweet sorghum(CK)samples from different tissues in the same period.gene co-expression analysis was performed using the collected RNA-seq data to obtain a gene co-expression network,and through the correlation analysis with the sucrose concentration change data in the corresponding period,the gene set related to sucrose metabolism was obtained,and the differential expression of the screened genes was further verified by self-testing RNA-seq data;3.Screening of genes related to sucrose transport and metabolism: The above-mentioned non-synonymous mutant gene set and the collected RNA-seq data were used to screen sucrose transporters and enzymes related to trehalose6-phosphate metabolism.finally one of SWEET gene and one of TPS gene were selected and both of them has the same non-synonymous SNPs locus in sweet sorghum and six other non-sweet sorghums,and the differential expression of these two genes was analyzed using self-test data.