Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Uses Of The Soybean Sequence Ready Physical Map

Jeffry Shultz¹ , N Lavu¹ , Chet Langin¹ , Kay Shopinski¹ , S Kazi¹ , R Bashir¹ , J Iqbal¹ , J Afzal¹ , C Town⁴ , K Meksem² , H Zhang³ , C Wu⁵ , David Lightfoot¹

¹  Genomics Core Facility, Southern. Illinois University, Carbondale, IL62901.USA. ga4082@siu,edu

²  Plants and Microbes Genomics and Genetics lab; Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Room 176. Carbondale, IL 62901-4415. Fax: 618 453 7457; E-mail: meksemk@siu.edu;

³  Texas A&M Univ., College Station, TX USA

⁴  TIGR, Maryland USA

⁵  Pioneer Hibred, IO USA

The second ever dicot complete marker anchored physical map of the soybean has been constructed, see http://bioinformatics.siu.edu. Map development lead to major discoveries in genome structure, genome architecture, gene distribution, gene family evolution, educational tools and research methods for polyploid genomes. Marker integration showed the genetic map of soybean was gapped. Markers were shown to have homeologs in the genome that could be mapped. One thousand additional microsatellite markers were developed. Four thousand resistance gene analogs were placed on the map. Gene density estimates correlated with idiotypes of chromosomes . Gap filling in the soybean physical map was required diverse BAC libraries. BAC end sequence derived microsatellite markers were essential tools for the physical maps of this polyploid genome. HICF was shown to be ineffective in separating the duplicated and highly conserved regions. Homeologous contigs proved the relationships between soybean chromosome is complex but useful for improving QTL maps. Gbrowse was adapted to show homeologous genomic regions. DNA sequences showed that homoelogous regions often share identity above the base call error rate for hundreds of Kbp. Divergent regions exist and are interspersed. Gbrowse was found useful to present the map to the community. The minimum tiling path contained gene like sequences on 63% of clones. Mapping with EST probes located gene rich islands in sub-telomeric regions. Little conserved synteny was measured with Arabidopsis thaliana slightly more with Medicago truncatulata. Maps are compared by C-MAP and through LIS at NCR from GFF files we have provided. Supported by NSF 9872635