Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

SNPS ANALYSIS OF HEXAPLOID WHEAT AND ITS APPLICATION TO GENE EXPRESSION PROFILING

¹ Kihara Institute for Biological Research and Graduate School of Integrated Science Yokohama City University, Maioka, Yokohama, Kanagawa, 244-0813, Japan

² National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan

Single nucleotide polymorphisms (SNPs) are the most frequently DNA variations, and quite useful for genotyping of strains and/or cultivars. In common wheat, polyploid nature makes it difficult to assign the sequence polymorphisms among the three genes into each of homoeologous chromosomes. Because, its transcriptome is a mixture of transcripts from A, B, D genome. In order to investigate SNPs analysis in hexaploid wheat, it is essential to assign each homoeologous gene sequence into the three homoeologous chromosome. We have developed an EST assembling method, namely phrap-blast-phrap (PBP) method that can distinguish the individual contigs of cDNAs transcribed from each of homeologous loci. The 112632 ESTs sequenced from 10 cDNA libraries of common wheat (Triticum aestivum cv. Chinese Spring) classified into 14906 gene groups, and specific SNPs haplotypes on each homeologous sequence were found. Pyrosequencing^TM method was adopted for chromosome assignment of each homoeologous sequence according to its SNPs haplotype in combination with Nulli-Tetra series of CS. About 90 gene groups were assigned into their each homoeologous chromosome. Most gene groups were transcribed from all three genomes but some genes located on specific genome were not expressed. Furthermore, according to the number of members belonging to each contig, the genome and tissue specific expression patterns were monitored. Person's correlation coefficient between contigs was calculated, and their relationships were visualized by virtual display. The correlation analysis showed genome and tissue specific gene expression patterns. This multidimensional analysis presented the whole profiling of transcriptome in hexaploid wheat.