SNPs analysis of homoeologous genes by computing a large scale of expressed seque.i. tags in the hexaploid wheat

摘要

In order to carry out single nucleotide polymorphisms (SNPs) analyses, we classified a large number of wheat ESTs from the ten tissues in the wheat life cycle in silico. Each classified contig was inferred to correspond to independent homoeologous locus. These EST resources can apply for construction of cDNA microarray and SNPs analyses. Actually, cDNA microarrays are available. Whereas, alignment of those contigs enabled us to trace the SNP sites among homoeologues. By comparing SNPs among three homoeologous genes, we assigned 90 genes to each of the homoeologous chromosomes using a nullisomic-tetrasomic series of hexaploid wheat and Pyrosequencing~(TM). The relative expression of these genes in the ten tissues was determined and virtually displayed. It is remarkable that one of the three homoeologous genes of eleven genes was shut down throughout the life cycle. No preference for gene silencing in particular genomes or chromosomes was observed, suggesting that gene silencing after polyploidization takes place at the gene level, not at the chromosome or genome level.