Originally published as Genetics Published Articles Ahead of Print on August 3, 2006.

Genetics, Vol. 174, 1017-1028, October 2006, Copyright © 2006
doi:10.1534/genetics.105.055020

Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)

Jessica A. Schlueter^*, Brian E. Scheffler, Shannon D. Schlueter^* and Randy C. Shoemaker^,1

^* Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USDA-ARS MSA Genomics Laboratory, Stoneville, Mississippi 38776 and USDA-ARS-CICGR, Ames, Iowa 50011

¹ Corresponding author: USDA-ARS-CICGR, G401 Agronomy Hall, Iowa State University, Ames, IA 50011.
E-mail: rcsshoe{at}iastate.edu

The paleopolyploid soybean genome was investigated by sequencing homeologous BAC clones anchored by duplicate N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes. The homeologous BACs were genetically mapped to linkage groups C1 and C2. Annotation of the 173,747- and 98,760-bp BACs showed that gene conservation in both order and orientation is high between homeologous regions with only a single gene insertion/deletion and local tandem duplications differing between the regions. The nucleotide sequence conservation extends into intergenic regions as well, probably due to conserved regulatory sequences. Most of the homeologs appear to have a role in either transcription/DNA binding or cellular signaling, suggesting a potential preference for retention of duplicate genes with these functions. Reverse transcriptase–PCR analysis of homeologs showed that in the tissues sampled, most homeologs have not diverged greatly in their transcription profiles. However, four cases of changes in transcription were identified, primarily in the HCBT gene cluster. Because a mapped locus corresponds to a soybean cyst nematode (SCN) QTL, the potential role of HCBT genes in response to SCN is discussed. These results are the first sequenced-based analysis of homeologous BACs in soybean, a diploidized paleopolyploid.

This article has been cited by other articles:

				K. Van, D. H. Kim, C. M. Cai, M. Y. Kim, J. H. Shin, M. A. Graham, R. C. Shoemaker, B.-S. Choi, T.-J. Yang, and S.-H. Lee Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome DNA Res, April 1, 2008; 15(2): 93 - 102. [Abstract] [Full Text] [PDF]

				J. A. Schlueter, B. E. Scheffler, S. Jackson, and R. C. Shoemaker Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana J. Hered., March 2, 2008; (2008) esn010v1. [Abstract] [Full Text] [PDF]

				N. M. Springer and R. M. Stupar Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid Maize PLANT CELL, August 1, 2007; 19(8): 2391 - 2402. [Abstract] [Full Text] [PDF]

				A. M. Missaoui, D. V. Phillips, and H. R. Boerma DNA Marker Analysis of 'Davis' Soybean and Its Descendants for the Rcs3 Gene Conferring Resistance to Cercospora sojina Crop Sci., May 31, 2007; 47(3): 1263 - 1270. [Abstract] [Full Text] [PDF]

				J. A. Schlueter, I. F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Siegfried, B. A. Roe, S. D. Schlueter, B. E. Scheffler, and R. C. Shoemaker The FAD2 Gene Family of Soybean:: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome Crop Sci., January 1, 2007; 47(Supplement_1): S-14 - S-26. [Abstract] [Full Text] [PDF]

				S. A. Jackson, D. Rokhsar, G. Stacey, R. C. Shoemaker, J. Schmutz, and J. Grimwood Toward a Reference Sequence of the Soybean Genome: A Multiagency Effort Crop Sci., November 1, 2006; 46(Supplement_1): S-55 - S-61. [Abstract] [Full Text] [PDF]

International Access Link

Online ISSN: 1943-2361  Print ISSN: 0016-6731
Copyright 2009 by the Genetics Society of America
phone: 412-268-1812   fax: 412-268-1813   email: genetics-gsa{at}andrew.cmu.edu