Sequence Variation Of A Wheat Introgression Line

The genome sequence variation is always accompanied with the evolutionary process of species. And the genome sequence variation is the source for the evolution of species. Our laboratory bred a wheat introgression cultivar Shanrong No.3(SR3) with tolerance to salt and drought, vigorous growth ability and high yield between the common wheat(Triticum aestivum L.) Jinan177(JN177) and Thinopyrum ponticum via the asymmetric somatic hybridization method. During asymmetric hybridization, the transient coexistence of two parents’genomes, the elimination of most of donor chromatins, and the introngression of several donor chromatin fragments into the recipient genome are acted as diploidization, which can cause a strong impact of genome, and produce systematic genomic variation. However, the characteristics and mechanisms of asymmetric hybridization-mediated of genomic variation as well as its difference from allopolyploidization-mediated genomic variation are not well known so far.Our previous analysis on molecular markers and functional genes showed genetic and epigenetic variations had taken place in the SR3genome, but the frequencies and characteristics of such variations are still unclear. In this study, we used the EST sequences of SR3and JN177from large-scale sequencing of cDNA library, to analyze variation frequencies of the total EST sequences and their5’-UTR, CDS and3’-UTR sequences, as well as those involved in different bioprocesses, with the aim to discover the rule for asymmetric somatic hybridization-mediated genomic variation.To systematically analyze sequence polymorphisms between SR3and JN177, and asymmetric hybridization mediated sequence polymorphisms, three groups of comparative analysis were conducted:JN177EST sequences as query to BlastN wheat EST assembled sequences (JN177-TC), SR3EST sequences to wheat EST assembled sequences (SR3-TC), SR3EST sequence as query to BlastN JN177EST sequences (SR3-JN177). The sequence alignments with identities not less than96%were extracted for analysis, of which SR3-JN177had2581sequences, SR3-TC7284, and JN177-TC5072.The SNP frequencies of JN177-TC、SR3-TC and SR3-JN177are9.84,9.83,11.85SNPs/kb EST, respectively, and their InDel frequenciesare3.07,3.58,5.43 InDels/kb EST. This shows that SR3genome occurred high frequency of genomic variation.The excellent traits of SR3are related to the alternation of the transcriptome and proteome, which results in the enhancement of antioxidation capacity and photosynthetic efficiency, and redox homeostatis. In order to understand the relationship between this change and genomic variation, we compared the polymorphisms of ESTs involved in biological processes of metabolism, gene expression, stress response, auxin biosynthesis and response, transfer, signal transduction and so on, according to the annotation information of Blast2GO. The results show that, the SNP frequencies of ESTs associated with these processes display diverse differential patterns, and their InDel frequencies are all similar to the overall ESTs. Among them, the SNP and InDel frequencies of chromatin assembly/disassembly and nucleosme assembly related ESTs are substantially lower in JN177-TC, and higher in SR3-TC and SR3-JN177, with a dramatic increase in SR3-JN177. This indicates that apart from DNA methylation, chromatin remodeling related genes take place a high frequency of variation, which also resulted in the epigenetic shift of DNA sequence and chromatin structure in SR3genome. This consequentially change the transcription patterns of SR3.The different regions of genes suffer from differential selection pressures during evolution. Therefore, we further analyzed the polymorphism differences of5’-UTR, CDS and3’-UTR in SR3and JN177EST sequences. The results show that, the SNP and InDel frequencies of5’-UTR and CDS are similar, while those of3’-UTR are higher; within InDels, the Deletion frequency of5’-UTR is higher, while the Insertion frequency of CDS and3’-UTR is higher; the frequencies of Deletions and Insertions in5’-UTR are more comparable than in CDS and3’-UTR, and in the latter two regions, the frequencies of Insertions are obviously higher than those of Deletions; the SNP frequencies of5’-UTR, CDS and3’-UTR are higher in JN177-TC than in SR3-TC, and the InDel frequencies of these regions are lower. All of these results indicate that, the variation is specific from each other in different regions of genes, and the evolutionary pattern of genes between allopolyploidy and asymmetric somatic hybrid are also different.