Genome Duplication in Soybean (Glycine subgenus soja)

INVESTIGATIONS

Genome Duplication in Soybean (Glycine subgenus soja)

R. C. Shoemaker, K. Polzin, J. Labate, J. Specht, E. C. Brummer, T. Olson, N. Young, V. Concibido, J. Wilcox, J. P. Tamulonis, G. Kochert and H. R. Boerma
Department of Agronomy and USDA-ARS Field Crops Research, Iowa State University, Ames, Iowa 50011

Restriction fragment length polymorphism mapping data from nine populations (Glycine max X G. soja and G. max X G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

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				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]

				I.-Y. Choi, D. L. Hyten, L. K. Matukumalli, Q. Song, J. M. Chaky, C. V. Quigley, K. Chase, K. G. Lark, R. S. Reiter, M.-S. Yoon, et al. A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis Genetics, May 1, 2007; 176(1): 685 - 696. [Abstract] [Full Text] [PDF]

				A. J. Cardinal, J. W. Burton, A. M. Camacho-Roger, J. H. Yang, R. F. Wilson, and R. E. Dewey Molecular Analysis of Soybean Lines with Low Palmitic Acid Content in the Seed Oil Crop Sci., February 6, 2007; 47(1): 304 - 310. [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]

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				J. A. Udall and J. F. Wendel Polyploidy and Crop Improvement Crop Sci., November 1, 2006; 46(Supplement_1): S-3 - S-14. [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]

				J. A. Schlueter, B. E. Scheffler, S. D. Schlueter, and R. C. Shoemaker Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.) Genetics, October 1, 2006; 174(2): 1017 - 1028. [Abstract] [Full Text] [PDF]

				T. Nakazato, M.-K. Jung, E. A. Housworth, L. H. Rieseberg, and G. J. Gastony Genetic Map-Based Analysis of Genome Structure in the Homosporous Fern Ceratopteris richardii Genetics, July 1, 2006; 173(3): 1585 - 1597. [Abstract] [Full Text] [PDF]

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				J. G. Walling, R. Shoemaker, N. Young, J. Mudge, and S. Jackson Chromosome-Level Homeology in Paleopolyploid Soybean (Glycine max) Revealed Through Integration of Genetic and Chromosome Maps Genetics, March 1, 2006; 172(3): 1893 - 1900. [Abstract] [Full Text] [PDF]

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				P. D. Rabinowicz, R. Citek, M. A. Budiman, A. Nunberg, J. A. Bedell, N. Lakey, A. L. O'Shaughnessy, L. U. Nascimento, W. R. McCombie, and R. A. Martienssen Differential methylation of genes and repeats in land plants Genome Res., October 1, 2005; 15(10): 1431 - 1440. [Abstract] [Full Text] [PDF]

				K. Komatsu, S. Okuda, M. Takahashi, R. Matsunaga, and Y. Nakazawa QTL Mapping of Antibiosis Resistance to Common Cutworm (Spodoptera litura Fabricius) in Soybean Crop Sci., August 26, 2005; 45(5): 2044 - 2048. [Abstract] [Full Text] [PDF]

				J.-Y. Lin, B. H. Jacobus, P. SanMiguel, J. G. Walling, Y. Yuan, R. C. Shoemaker, N. D. Young, and S. A. Jackson Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile Genetics, July 1, 2005; 170(3): 1221 - 1230. [Abstract] [Full Text] [PDF]

				B. E. Pfeil, J. A. Schlueter, R. C. Shoemaker, and J. J. Doyle Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families Syst Biol, June 1, 2005; 54(3): 441 - 454. [Abstract] [Full Text] [PDF]

				P. Yin and A. J. Hartemink Theoretical and practical advances in genome halving Bioinformatics, April 1, 2005; 21(7): 869 - 879. [Abstract] [Full Text] [PDF]

				H. Zhu, H.-K. Choi, D. R. Cook, and R. C. Shoemaker Bridging Model and Crop Legumes through Comparative Genomics Plant Physiology, April 1, 2005; 137(4): 1189 - 1196. [Full Text] [PDF]

				R. T. Nelson, D. Grant, and R. C. Shoemaker ESTminer: a suite of programs for gene and allele identification Bioinformatics, March 1, 2005; 21(5): 691 - 693. [Abstract] [Full Text] [PDF]