Structural Variation Of Polyploid Peanut Genome And Its Homoeolog Expression Patterns

Polyploids are ubiquitous across angiosperms and a major force in genome evolution,speciation and crop domestication.Among them,allotetraploids are formed by crossing different species of ancestral diploids,and special evolutionary conditions often divide them into two subgenomes,which are widely used to study the gene expression remodeling events caused by polyploidization.After polyploidization,the subgenomes within allotetraploids often contain part of homoeologs with differential expression and bias,and the dominant homoeologs is often the key to the regulation and differentiation of phenotypic traits,which is of great practical significance for clarifying the objectives of crop breeding and gene editing.The allotetraploid cultivated peanut(Arachis hypogaea L.),a globally important oil crop,formatted by the hybridization of two wild ancestral diploids A.duranensis(A genome)and A.ipaensis(B genome).To study the expression pattern of homoeologs in polyploid plants and to investigate the identification of functional genes with genetic transformation significance in peanut,the complete genome of cultivated peanut species Arachis hypogaea var.fastigiata was used for comparative analysis with transcriptome data from different tissues and developmental stages.The following were the key findings.1.The synteny comparison between cultivated peanut and the ancestral diploid revealed large chromosomal structural variation(SV)in some regions of the genomes.Chromosomes A5/05,A7/07,A8/08 and A9/09 between peanut subgenome A and A.duranensis and B8/08,B10/10 between subgenome B and A.ipaensis are differentiated by a large inversion in one arm.Between subgenomes A and B 06/16 have one inversion,01/11,05/15 and 09/19 are differentiated by two large inversions and chromosomes 17/18 have undergone reciprocal translocations relative to 07/08.To investigate the potential effects of structural variation on allotetraploids,enrichment analysis of SV region genes revealed that the functions of subgenome A and A.duranensis region genes mainly included positive regulation of fatty acid biosynthetic and metabolic process,cadmium ion transmembrane transport activity and site of DNA damage,while the functions of subgenome B and A.ipaensis region genes mainly included positive regulation of leaf senescence and development,ubiquitin protein ligase binding and site double-strand breaking.The functions of genes in subgenome A and B regions mainly include the participation in positive regulation of fatty acid biosynthetic process,cell wall hydroxyproline-rich glycoprotein metabolic process,cellular potassium ion homeostasis and chromatin DNA binding.2.Differential expression analysis was used on the expression data of different tissues and developmental stages of cultivated peanut to explore the homoeolog expression bias(HEB)of subgenomes.Overall,the number of homoeologs with A subgenome expression bias was not significantly different from the number with B subgenome expression bias(2,399 and2,536 for A and B,respectively).When different tissues and developmental stages were considered separately,the number of DEGs differed significantly only in the Nodule.In addition,the number of DEGs that were highly asymmetrically differentially expressed did not differ.3.In order to identify genes with key functions or significance among the structural variants,genes were screened for the presence of homoeolog expression bias and RPKM expression values greater than 10 in all treatments,and the representative genes obtained were Arachis112773.m1,which is involved in calcium binding,and Arachis056328.m1.The latter showed abnormally high expression values in Root,Flower,and Seed Patte stages 6,7,and 8.To further identify functional genes of evolutionary importance in cultivated peanut,Ka/Ks values(ratio of non-synonymous mutations to synonymous mutations)were calculated among homoeologs in the subgenomes,and a specific pair of genes Arachis008103.m1 and Arachis014643.m1 was identified with Ka/Ks values greater than 1 in the SV region and the presence of HEB.The expression of these genes was biased toward subgenome A in Root and subgenome B in Seed Patte stages7 and 8,there was no expression bias in the rest of the treatments.Its protein is predicted to be abundant in late embryogenesis development and its function is predicted to be in response to water deprivation,freezing and protein stabilization.The expression bias present in all genes except this homoeologs was same across multiple treatments.4.In particular,genes with functions of auxin polar transport,calcium ion binding,zinc ion binding,response to water deprivation and freezing,and protein stabilization have been identified,such as Arachis102399.m1,Arachis112773.m1,Arachis103236.m2,Arachis008103.m1,Arachis014643.m1,etc.At the same time,genes with significant effects on different tissues and developmental stages were also identified,such as Arachis056328.m1,Arachis078529.m1,Arachis103236.m2,Arachis079443.m1 and so on.The above obtained genes can be used for further genetic transformation or gene editing exploration in the future.In this research,the structural variation of cultivated peanut and its ancestral diploids was described and the pattern of homoeolog expression among subgenomes was explored.The discovery of homoeologs in regions of structural variation has important theoretical implications for the study of allotetraploid polyploidization events,subgenomic coevolution and regulation patterns of homoeolog expression.In combination with expression,genes Arachis112773.m1,Arachis056328.m1,Arachis008103.m1,and Arachis014643.m1 with functions affecting phenotypic traits in cultivated peanut were identified,which can be used as target genes for gene editing and for crop breeding improvement and peanut genetic engineering,etc.provide realistic value.