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United States Department of Agriculture

Agricultural Research Service

Selected Publications
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Song, Q.J., D.L. Hyten, C.V. Quigley, G.F. Jia, E.W. Fickus, P.B. Cregan. 2013. Development and Evaluation of a high-density Infinium beadchip SoySNP50K. PLoS ONE (

Du, J., Z. Tian, Y. Sui, M. Zhao, Q.-J. Song, S.B. Cannon, P. Cregan, and J. Ma. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the palaeopolyploid soybean. Plant Cell. DOI 10.1105/tpc.111.092759

Felicetti, E., Q.J. Song, G.F. Jia, P. Cregan, K.E. Bett and P.N. Miklas 2012. Simple sequence repeats linked with slow darkening trait in pinto bean discovered by SNP assay and whole genome sequencing. Crop Sci. 52:1600-1608.

Mamidi, S., C. Shireen, R.J. Goos, D.L Hyten, S.M. Moghaddam, P.B. Cregan, and P.E. McClean. 2011. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. The Plant Genome. 4:154-164.

Kendrick, M.D, D.K. Harris, B.K. Ha, D.L. Hyten, P.B. Cregan, R.D Frederick, H.R. Boerma and K.F. Pedley. 2011. Identification of a Second Asian Soybean Rust Resistance Gene in Hyuuga Soybean. Phytopathology 101:535-543.

Hyten, D.L, Q.-J. Song, E.W Fickus, C.V. Quigley1, J.-S. Lim, I.-Y. Choi, E.-Y. Hwang, M. Pastor-Corrales, and P.B. Cregan. 2010. High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475-482.

Gaitán-Solís, E., I.-Y. Choi, C. V. Quigley, P. B. Cregan and J. Tohme. 2008. Single nucleotide polymorphisms in common bean: their discovery and genotyping using a multiplex detection. The Plant Genome 1:125–134.

Hyten, D. L., J. R. Smith, R. D. Frederick, M. L. Tucker, Q. Song, and P. B. Cregan. 2009. Bulked segregant analysis using the GoldenGate Assay to locate the Rpp3 locus that confers resistance to Phakopsora pachyrhizi (Soybean Rust) in soybean. Crop Sci. 49: 265-271.

Hyten, D.L., S.B Cannon, Q.-J Song, N. Weeks, E.W. Fickus, R.C. Shoemaker, J.E Specht, A.D. Farmer, G.D. May and P.B. Cregan. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38 doi:10.1186/1471-2164-11-38

Schmutz, J. S.B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D.L. Hyten, Q.-J. Song, J.J. Thelen, J. Cheng, D. Xu, U. Hellsten, G.D. May, Y. Yu, T. Sakurai, T. Umezawa, M.K. Bhattacharyya, D. Sandhu, B Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X.-C. Zhang, K. Shinozaki, H.T. Nguyen, R.A. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R.C. Shoemaker and S.A. Jackson. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463:178-183.

Hyten, D.L., I-Y. Choi, Q.-J. Song, J.E. Specht, T.E. Carter, Jr., R.C. Shoemaker, E.-Y. Hwang, L.K. Matukumalli, and P.B. Cregan. 2010. A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Sci. 50:960-968.

Song, Q.-J., G.F. Jia, Y.-L. Zhu, D.M. Grant, E.-Y. Hwang, D.L. Hyten and P.B. Cregan. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci. 50:1550-1560.

Hyten, D.L. Q.-J. Song, I.-Y. Choi, M.-S. Yoon, J.E. Specht, L.K. Matukumalli, R.L. Nelson, R.C. Shoemaker, N.D. Young, and P.B. Cregan. 2008. High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor. Appl. Genet. 116:945-952.

Choi, I.-Y. D.L. Hyten, L.K. Matukumalli, Q.J. Song, J.M. Chaky, C.V. Quigley, K. Chase, K.G. Lark, R.S. Reiter, M.-S. Yoon, E.-Y. Hwang, S.-In Yi, N.D. Young, R.C. Shoemaker, C.P. van Tassell, J.E. Specht and P.B. Cregan. 2007. A soybean transcript map: gene distribution, haplotype and SNP analysis. Genetics 176: 685-696.

Hyten, D.L., I.-Y. Choi, Q.-J. Song, R.C. Shoemaker, R.L. Nelson , J.M. Costa, J.E. Specht and P.B. Cregan. 2007. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175: 1937-1944.

Hyten, D.L. G.L. Hartman, R.L. Nelson, R.D. Frederick, V.C. Concibido, J. Narvel, and P.B. Cregan. 2007. Map location of the Rpp1 locus that confers resistance to Phakopsora pachyrhizi (soybean rust) in soybean. Crop Sci. 47:837-840

Yoon, M.S., Q.-J. Song, I.-Y. Choi, J.E. Specht , D.L. Hyten, and P. B. Cregan. 2007. BARCSoySNP23: A panel of 23 selected SNPs for soybean cultivar identification. Theor. Appl. Genet. 114:885-899.

Hyten, D.L., Q.-J. Song, Y.-L. Zhu, I.-Y. Choi, R.L. Nelson, J.M. Costa, J.E. Specht, R.C. Shoemaker, and P.B. Cregan. 2006 Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U.S.A. 103:16666-16671.

Song, Q.J., L.F. Marek, R.C. Shoemaker, K.G. Lark, V.C. Concibido, X. Delannay, J.E. Specht, and P.B. Cregan. 2004. A new integrated genetic linkage map of the soybean. Theor. Appl. Genet. 109:122-128.

Zhu, Y.-L, Q.-J. Song, D.L. Hyten, C.P. Van Tassell, L.K. Matukumalli, D.R. Grimm, S.M. Hyatt, E.W. Fickus, N.D. Young, and P.B. Cregan. 2003. Single nucleotide polymorphisms (SNPs) in soybean. Genetics 163: 1123-1134.

Song, Q.J., E.W. Fickus, and P.B. Cregan. 2002. Characterization of trinucleotide SSR motifs in wheat. Theor. Appl. Genet. 104:286-293.

Anderson, J.A., R.W. Stack, S. Liu, B.L. Waldron, A.D. Fjeld, C. Coyne, B. Moreno-Sevilla, J. Mitchell Fetch, Q.J. Song, P.B. Cregan, and R.C. Frohberg. 2001. DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theor. Applied Genet. 102:1164-1168.

Demirbas, A., B.G. Rector, D.G. Lohnes, R.J. Fioritto, G.L. Graef, P.B. Cregan, R.C. Shoemaker, and J.E. Specht.2001. Simple sequence repeat markers linked to the soybean Rps genes for phytophthora resistance. Crop Sci. 41:1220-1227.

Cregan P.B., K.P. Kollipara, S.J. Xu, R.J. Singh and T. Hymowitz. 2001. The use of SSR markers to associate primary trisomics with linkage groups in soybean. Crop Sci. 41:1262-1267.

Song, Q., C.V. Quigley, T.E. Carter, R.L. Nelson, H.R. Boerma, J. Strachan, and P.B. Cregan. 1999. A selected set of trinucleotide simple sequence repeat markers for soybean variety identification. Plant Varieties and Seeds 12:207-220.

Grant, D., P.B. Cregan and R.C. Shoemaker. 2000. Genome organization in dicots: I. Synteny between soybean and Arabidopsis and evidence of segmental duplication in Arabidopsis Proc. Natl. Acad. Sci. USA 97:4168-4173.

Diwan, N., J.H. Bouton, G. Kochert, and P.B. Cregan. 2000. Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa. Theor. Appl. Genet. 101:165-172.

Cregan, P.B., J. Mudge, E.W. Fickus, D. Danesh, R. Denny, and N.D. Young. 1999. Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor. Appl. Genet. 99:811-818.

Cregan P.B., T. Jarvik, A.L. Bush, R.C. Shoemaker, K.G. Lark, A.L. Kahler, N. Kaya, T.T. VanToai, D.G. Lohnes, J. Chung, and J.E. Specht. 1999. An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464-1490.

Cregan,P.B, J. Mudge, E.W. Fickus, L.F. Marek, D. Danesh, R.. Denny, R.C. Shoemaker, B.F. Matthews, T. Jarvik, and N.D. Young. 1999. Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor. Appl. Genet. 98:919-928.

Mudge, J., P.B. Cregan,J.P. Kenworthy, W.J. Kenworthy, J.H. Orf, N.D. Young. 1997. Two microsatellite markers that flank the major soybean cyst nematode resistance locus.Crop Sci. 1611-1615.

Diwan, N., and P.B. Cregan. 1997. Automated sizing of fluorescent labeled simple sequence repeat markers to assay genetic variation in soybean. Theor. Appl. Genet. 95:723-733.

Akkaya, M.S., R.C.Shoemaker, J. E. Specht, A.A. Bhagwat, and P.B. Cregan. 1995. Integration of simple sequence repeat (SSR) DNA markers into a soybean linkage map. Crop Sci.35:1439-1445.

Jiang, Rongwen, M.S.Akkaya, U. Lavi, and P.B. Cregan. 1995. The use of microsatellite DNA markers for soybean genotype identification. Theor. Appl. Genet. 90:43-48.

Cregan, P.B., A.A.Bhagwat, M.S. Akkaya, and J. Rongwen. 1994. Microsatellite fingerprinting and mapping of soybean. Methods Cell. Mol. Biol. 5:49-61.

Akkaya, M.S., A.A. Bhagwat, and P.B. Cregan. 1992. Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132:1131-1139.

Cregan, P.B. 1992. Simple sequence repeat DNA length polymorphisms. Probe 2:18-22.



Last Modified: 3/4/2013
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