Study On Genomic Composition Variation And Gene Expression Patterns Of Wheat Allo-amphiploids

Transferring the excellent genes of wild relative species into wheat by distant hybridization is one of the important ways of wheat genetic improvement.The amphiploid of wheat and its wild relatives is an important bridge material for the transfer of alien excellent genes.The formation of amphiploid includes the process of hybridization and chromosome doubling,during the process,different species’genomes fuse together and interact with each other,resulting in abundant genetic variation.The study of the genome structure and gene expression pattern of amphiploid has great significance in exploring the genetic and evolutionary relationship between different species,cultivating new species,and improving wheat genetics.In this study,the octoploid triticale and wheat-Th.bessarabicum amphiploid as the materials,genomic variation and gene expression of wheat and wild relatives were studied.The main results obtained are as follows:1.Through the field phenotype statistics of Huixianhong,Jingzhou rye,F₁,and octoploid triticale,it was found that the phenotype and growth vigor of F₁ and octoploid triticale（plant height,internode length,spike length,number of spikelets）are mostly between the two parents,which is close to the phenotype of Huixianhong.The breaking internode force and wall thickness of internode of octoploid triticale were different from F₁,F₁ was between the two parents,and the octoploid triticale showed super-parent level,showing the phenomenon of heterosis.2.The results of FISH and GISH showed as expected F₁ and octoploid triticale contained14 wheat 7 rye chromosomes and 42 wheat 14 rye chromosomes,respectively.No obvious difference signal was found in the hybrid F₁ compared with the parental chromosome.Chromosome structural variation occurred on chromosomes 2A,4A,2B,and 7D in octoploid triticale.3.Transcriptome data analysis of different tissues and organs showed that after hybridization and polyploidization,gene expression in the A,B,and D sub genome was highly correlated with than in their parents,while the R sub genome was less correlated with parental gene expression,indicating the impact of gene expression patterns in R sub genome was much greater.4.Orthologous genes in the Chinese spring genome and the rye genome in the A,B,D,R genomes with the distribution of 1:1:1:1 were analyzed for gene expression bias and gene expression level.Through the biased expression of homologous genes in different tissues or organs were different between the parents,the bias of gene expression changed after polyploidization,and the Huixianhong gene was biased to express in hybrid F₁ and octoploid triticale.After doubling of F₁ to form octoploid triticale,the overall gene expression bias did not change,but it was found that about 20%of the homologous gene expression patterns had changed,and the expression bias to Huixianhong was in F₁ became balanced in the octoploid triticale,and the gene that was originally expressed in the balance in F₁ became bias to Huixianhong in the octoploid triticale.5.The expression levels dominance of genes in different tissues or organs showed that among the parental dominant types in the gene expression levels in hybrid F₁ and octoploid triticale,the number of genes that were consistent with the expression levels of Huixianhong genes was more than rye genes,indicating that the gene expression levels dominance of hybrid were similar to Huixianhong.Besides,the number of superparent up-regulated genes was greater than the number of superparent down-regulated genes in most tissues or organs.By comparing the distribution and expression of differentially expressed genes between F₁,octoploid triticale,and parents,it was found that Jingzhou rye genes were more down-regulated compared with their parents in all samples and most of these genes were distributed on 2A,3A,4A,2B,6B,6D,and 7D.6.The size of assembled the Th.bessarabicum genome through the De novo strategy is6.19G,and reach reference genome level.Through the annotation of repetitive sequences,a total of 4.5 Gb transposons were identified,accounting for 80.18%of the genome,and LTR retrotransposons accounted for about 59.59%,of which Copia and Gypsy families accounted for 15.79%and 43.65%,respectively.Through the evolutionary analysis of the Th.bessarabicum,it was found that the Th.elongtacum and the Th.bessarabicum were differentiated at about 48,000 years;through the collinear analysis,it was found that the aberration phenomenon was on the bessarabicum chromosomes 4,5,6,and 7.7.According to the result of FISH,the wheat bessarabicum diploid has 42 wheat chromosomes and 14 bessarabicum chromosomes.No obvious chromosomal variation was found between the chromosomes of wheat bessarabicum diploid and the parental chromosomes.After being treated with 250 mmol/L saline solution for 10 days and rehydrated for 3 days,the wheat bessarabicum diploid could still restore the original growth level,but the Chinese spring could not return to the normal level.The transcriptomes of roots and leaves were sequenced after treatment with 250 mmol/L salt solution at the Chinese spring,bessarabicum,and wheat bessarabicum diploid seedling stage.A total of 17 genes were filtered finally,which were all up-regulated in roots and leaves of bessarabicum,wheat bessarabicum diploid.8.By comparing the gene expression correlation between sub genome between wheat bessarabicum diploid and parents,it was found that the gene expression correlations of the A,B,and D sub genome were more related to the parental correlation,while the Eb sub genome was less related to the parent,indicating the impact of gene expression patterns in Eb sub genome was much greater.9.Genes bias expression was unchanged before and after treatment with salt solutions,and it was biased toward the Chinese spring part.By analyzing the expression levels of wheat bessarabicum diploid genes under different salt solutions,it was found that the expression levels were consistent with that of Chinese spring.Among the expression types,the number of genes in the super parent up-regulated type and ELD-Eb type increased after salt solution treatment,and it was speculated that these gene expression patterns may be related to the response to salt treatment.10.By comparing the distribution and expression of differentially expressed genes between the parts of Chinese spring and bessarabicum part in the diploid of wheat bessarabicum diploid,it was found that genes in some regions of the wheat chromosome were down-regulated.This phenomenon is similar to that of octoploid triticale,and most of these genes were on chromosome 5B.