Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
Charkes R. Yesudas1 , Jeffry L Shultz1 , Hong Bin Zhang2 , Gane Ka-Shu Wong3 , David Lightfoot1
Homologous regions can be detected in soybean genomic DNA with most markers. Homeologs to microsatellite markers vary in number from 2 to more than 6. Homology varies by chromosome from 2-14 regions on other chromosomes. Presented is a complete set of 20x20 (reciprocal and self) linkage group comparisons. DNA sequence to 5 fold coverage of several pairs of BAC clones taken from different gene rich homologous regions is presented. One region showed conservation above 99.9% over 140 Kbp. Genetic diversity was found in gene coding regions (eg. a lipocalin ortholog). Alignments suggest that sequence divergence is lower than the sequencing error rate over large regions so that the sequence assemblers cannot separate the sequences in most regions. Regions with homologs to markers from 2 regions of the genome were much more diverse. Therefore, the 25% of the genome that is highly conserved and duplicated will not be easily resolved by shotgun sequencing of the soybean genome but must be approached clone by clone but the 75% that is diverged is sufficiently diverged to allow assembly from shotgun reads. We conclude that: Initially the duplicated portion of the genome need be sequenced for one copy reducing cost for clone by clone approaches by 25%. Paralogs should be inferred from QTL for identical traits that are positioned in homologous regions. Trait maps should be re-examined in light of the new map of homologs. Assignments of QTL and BACs to linkage groups by marker amplification are putative. Supported by NSF9872635, USB2218-6218.