Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Poster: Genome Sequencing & ESTs
Physical map based sequencing of gene rich islands in complex genomes provides an alternative strategy to whole genome sequencing. Using a fingerprinting method developed physical maps of several plant, animal and fungal genomes, and integrated them with gene maps. Using genetic markers we mapped two genes to 500 kbp interval, Rhg1 for resistance to soybean cyst nematode and Rfs2 for resistance to Fusarium solani f.sp. glycines causal agent of sudden death syndrome. Integrating EST libraries (60% of the genes) and predicted paralogs (40% of the genes) with the soybean physical map identified this interval as one of several gene rich islands. The interval was sequenced using anchored BACs from two cultivars. A high predicted gene density has been observed (1 gene per 10 kbp). Gene candidates were identified for Rhg1 and Rfs1 among predicted genes within intervals identified by substitution mapping. Predicted genes have been annotated by position in the genome and presence in EST libraries or in the transcriptome. We are testing the ability to detect predicted genes absent from the transcriptome in the hypo-methylated DNA or DNA bound to hyper-acetylated nucleosomes. Examining the sequence from the BACs carrying rhg1 for synteny in Arabidopsis showed that orthologs are predominantly from linkage groups II (5) and IV (5) although there are 1-3 orthologs from each linkage group. Comparing cultivar sequences we have found about 1 SNP per 2.1 kbp in genomic DNA, but two fold more SNPs around Rhg1. Sequencing of 10 Mbp to encompass one chromosome arm (encoding Rfs and Rfs3) and 1 Mbp of genomic DNA encompassing Rfs4 and Rfs5 on linkage groups C2 and I is proposed. Combining genome sequencing and substitution maps will annotate the 300-400 economically important soybean genes efficiently.