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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species.

Hwang EY, Wei H, Schroeder SG, Fickus EW, Quigley CV, Elia P, Araya S, Dong F, Costa L, Ferreira ME, Cregan PB, Song Q.

G3 (Bethesda). 2019 Jul 9;9(7):2325-2336. doi: 10.1534/g3.119.400220.


Genome-wide Scan for Seed Composition Provides Insights into Soybean Quality Improvement and the Impacts of Domestication and Breeding.

Zhang J, Wang X, Lu Y, Bhusal SJ, Song Q, Cregan PB, Yen Y, Brown M, Jiang GL.

Mol Plant. 2018 Mar 5;11(3):460-472. doi: 10.1016/j.molp.2017.12.016. Epub 2018 Jan 2.


Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population.

Xavier A, Jarquin D, Howard R, Ramasubramanian V, Specht JE, Graef GL, Beavis WD, Diers BW, Song Q, Cregan PB, Nelson R, Mian R, Shannon JG, McHale L, Wang D, Schapaugh W, Lorenz AJ, Xu S, Muir WM, Rainey KM.

G3 (Bethesda). 2018 Feb 2;8(2):519-529. doi: 10.1534/g3.117.300300.


High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases.

Valentini G, Gonçalves-Vidigal MC, Hurtado-Gonzales OP, de Lima Castro SA, Cregan PB, Song Q, Pastor-Corrales MA.

Theor Appl Genet. 2017 Aug;130(8):1705-1722. doi: 10.1007/s00122-017-2920-6. Epub 2017 May 30.


Molecular Characterization of Resistance to Soybean Rust (Phakopsora pachyrhizi Syd. & Syd.) in Soybean Cultivar DT 2000 (PI 635999).

Vuong TD, Walker DR, Nguyen BT, Nguyen TT, Dinh HX, Hyten DL, Cregan PB, Sleper DA, Lee JD, Shannon JG, Nguyen HT.

PLoS One. 2016 Dec 9;11(12):e0164493. doi: 10.1371/journal.pone.0164493. eCollection 2016.


Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.

Phansak P, Soonsuwon W, Hyten DL, Song Q, Cregan PB, Graef GL, Specht JE.

G3 (Bethesda). 2016 Jun 1;6(6):1635-48. doi: 10.1534/g3.116.027656.


Phenotypic variation and identification of quantitative trait loci for ozone tolerance in a Fiskeby III × Mandarin (Ottawa) soybean population.

Burton AL, Burkey KO, Carter TE Jr, Orf J, Cregan PB.

Theor Appl Genet. 2016 Jun;129(6):1113-25. doi: 10.1007/s00122-016-2687-1. Epub 2016 Feb 26.


Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01.

Song Q, Jenkins J, Jia G, Hyten DL, Pantalone V, Jackson SA, Schmutz J, Cregan PB.

BMC Genomics. 2016 Jan 6;17:33. doi: 10.1186/s12864-015-2344-0.


Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max).

Zhang J, Song Q, Cregan PB, Jiang GL.

Theor Appl Genet. 2016 Jan;129(1):117-30. doi: 10.1007/s00122-015-2614-x. Epub 2015 Oct 30.


Genome-Wide Association Study of Ureide Concentration in Diverse Maturity Group IV Soybean [Glycine max (L.) Merr.] Accessions.

Ray JD, Dhanapal AP, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, King CA, Boykin D, Cregan PB, Song Q, Fritschi FB.

G3 (Bethesda). 2015 Sep 14;5(11):2391-403. doi: 10.1534/g3.115.021774.


Genomic consequences of selection and genome-wide association mapping in soybean.

Wen Z, Boyse JF, Song Q, Cregan PB, Wang D.

BMC Genomics. 2015 Sep 3;16:671. doi: 10.1186/s12864-015-1872-y.


SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

Song Q, Jia G, Hyten DL, Jenkins J, Hwang EY, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB.

G3 (Bethesda). 2015 Aug 28;5(11):2285-90. doi: 10.1534/g3.115.020594.


Fingerprinting Soybean Germplasm and Its Utility in Genomic Research.

Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB.

G3 (Bethesda). 2015 Jul 28;5(10):1999-2006. doi: 10.1534/g3.115.019000. Erratum in: G3 (Bethesda). 2016 Feb;6(2):495.


Confirmation of delayed canopy wilting QTLs from multiple soybean mapping populations.

Hwang S, King CA, Ray JD, Cregan PB, Chen P, Carter TE Jr, Li Z, Abdel-Haleem H, Matson KW, Schapaugh W Jr, Purcell LC.

Theor Appl Genet. 2015 Oct;128(10):2047-65. doi: 10.1007/s00122-015-2566-1. Epub 2015 Jul 12.


Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm.

Zhang J, Song Q, Cregan PB, Nelson RL, Wang X, Wu J, Jiang GL.

BMC Genomics. 2015 Mar 20;16:217. doi: 10.1186/s12864-015-1441-4.


Identification of novel QTL governing root architectural traits in an interspecific soybean population.

Manavalan LP, Prince SJ, Musket TA, Chaky J, Deshmukh R, Vuong TD, Song L, Cregan PB, Nelson JC, Shannon JG, Specht JE, Nguyen HT.

PLoS One. 2015 Mar 10;10(3):e0120490. doi: 10.1371/journal.pone.0120490. eCollection 2015.


QTL for seed protein and amino acids in the Benning × Danbaekkong soybean population.

Warrington CV, Abdel-Haleem H, Hyten DL, Cregan PB, Orf JH, Killam AS, Bajjalieh N, Li Z, Boerma HR.

Theor Appl Genet. 2015 May;128(5):839-50. doi: 10.1007/s00122-015-2474-4. Epub 2015 Feb 12.


Erratum to: Genome-wide association study (GWAS) of carbon isotope ratio (δ(13)C) in diverse soybean [Glycine max (L.) Merr.] genotypes.

Dhanapal AP, Ray JD, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, Andy King C, Cregan PB, Song Q, Fritschi FB.

Theor Appl Genet. 2015 Feb;128(2):375-6. doi: 10.1007/s00122-014-2450-4. No abstract available.


Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes.

Dhanapal AP, Ray JD, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, Andy King C, Cregan PB, Song Q, Fritschi FB.

Theor Appl Genet. 2015 Jan;128(1):73-91. doi: 10.1007/s00122-014-2413-9. Epub 2014 Nov 4. Erratum in: Theor Appl Genet. 2015 Feb;128(2):375-6.


Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean.

Bello MH, Moghaddam SM, Massoudi M, McClean PE, Cregan PB, Miklas PN.

BMC Genomics. 2014 Oct 16;15:903. doi: 10.1186/1471-2164-15-903.


Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655.

Jiao Y, Vuong TD, Liu Y, Meinhardt C, Liu Y, Joshi T, Cregan PB, Xu D, Shannon JG, Nguyen HT.

Theor Appl Genet. 2015 Jan;128(1):15-23. doi: 10.1007/s00122-014-2409-5. Epub 2014 Oct 15.


Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean.

Wen Z, Tan R, Yuan J, Bales C, Du W, Zhang S, Chilvers MI, Schmidt C, Song Q, Cregan PB, Wang D.

BMC Genomics. 2014 Sep 23;15:809. doi: 10.1186/1471-2164-15-809.


The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.

Vaughn JN, Nelson RL, Song Q, Cregan PB, Li Z.

G3 (Bethesda). 2014 Sep 22;4(11):2283-94. doi: 10.1534/g3.114.013433.


A reference genome for common bean and genome-wide analysis of dual domestications.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA.

Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.


Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

Wang X, Jiang GL, Green M, Scott RA, Song Q, Hyten DL, Cregan PB.

Mol Genet Genomics. 2014 Oct;289(5):935-49. doi: 10.1007/s00438-014-0865-x. Epub 2014 May 27.


A roadmap for functional structural variants in the soybean genome.

Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO, Song Q, Cregan PB, Specht JE, Diers BW, Cannon SB, McHale LK, Stupar RM.

G3 (Bethesda). 2014 May 22;4(7):1307-18. doi: 10.1534/g3.114.011551.


A genome-wide association study of seed protein and oil content in soybean.

Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB.

BMC Genomics. 2014 Jan 2;15:1. doi: 10.1186/1471-2164-15-1.


Inheritance of soybean aphid resistance in 21 soybean plant introductions.

Fox CM, Kim KS, Cregan PB, Hill CB, Hartman GL, Diers BW.

Theor Appl Genet. 2014 Jan;127(1):43-50. doi: 10.1007/s00122-013-2199-1. Epub 2013 Sep 27.


Development and evaluation of SoySNP50K, a high-density genotyping array for soybean.

Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB.

PLoS One. 2013;8(1):e54985. doi: 10.1371/journal.pone.0054985. Epub 2013 Jan 25.


Identification of a second Asian soybean rust resistance gene in Hyuuga soybean.

Kendrick MD, Harris DK, Ha BK, Hyten DL, Cregan PB, Frederick RD, Boerma HR, Pedley KF.

Phytopathology. 2011 May;101(5):535-43. doi: 10.1094/PHYTO-09-10-0257.


High-throughput SNP discovery and assay development in common bean.

Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB.

BMC Genomics. 2010 Aug 16;11:475. doi: 10.1186/1471-2164-11-475.


High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence.

Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB.

BMC Genomics. 2010 Jan 15;11:38. doi: 10.1186/1471-2164-11-38.


Simple sequence repeat DNA markers in alfalfa and perennial and annual Medicago species.

Diwan N, Bhagwat AA, Bauchan GB, Cregan PB.

Genome. 1997 Dec;40(6):887-95.


High-throughput genotyping with the GoldenGate assay in the complex genome of soybean.

Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB.

Theor Appl Genet. 2008 May;116(7):945-52. doi: 10.1007/s00122-008-0726-2. Epub 2008 Feb 16.


A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis.

Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB.

Genetics. 2007 May;176(1):685-96. Epub 2007 Mar 4.


Highly variable patterns of linkage disequilibrium in multiple soybean populations.

Hyten DL, Choi IY, Song Q, Shoemaker RC, Nelson RL, Costa JM, Specht JE, Cregan PB.

Genetics. 2007 Apr;175(4):1937-44. Epub 2007 Feb 7.


BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification.

Yoon MS, Song QJ, Choi IY, Specht JE, Hyten DL, Cregan PB.

Theor Appl Genet. 2007 Mar;114(5):885-99. Epub 2007 Jan 12.


Impacts of genetic bottlenecks on soybean genome diversity.

Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB.

Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16666-71. Epub 2006 Oct 26.


SNP-PHAGE--High throughput SNP discovery pipeline.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP.

BMC Bioinformatics. 2006 Oct 23;7:468.


Abnormal leaf formation in soybean: genetic and environmental effects.

Orf JH, Chase K, Specht J, Choi IY, Cregan PB, Lark KG.

Theor Appl Genet. 2006 Jun;113(1):137-46. Epub 2006 Apr 22.


Application of machine learning in SNP discovery.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP.

BMC Bioinformatics. 2006 Jan 6;7:4.


Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea.

Van K, Hwang EY, Kim MY, Park HJ, Lee SH, Cregan PB.

J Hered. 2005 Sep-Oct;96(5):529-35. Epub 2005 Jun 30.


Development and mapping of microsatellite (SSR) markers in wheat.

Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB.

Theor Appl Genet. 2005 Feb;110(3):550-60. Epub 2005 Jan 18.


Comparison of four flow cytometric SNP detection assays and their use in plant improvement.

Lee SH, Walker DR, Cregan PB, Boerma HR.

Theor Appl Genet. 2004 Dec;110(1):167-74. Epub 2004 Nov 17.


A new integrated genetic linkage map of the soybean.

Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB.

Theor Appl Genet. 2004 Jun;109(1):122-8. Epub 2004 Feb 27.


QTL mapping of partial resistance in winter wheat to Stagonospora nodorum blotch.

Czembor PC, Arseniuk E, Czaplicki A, Song Q, Cregan PB, Ueng PP.

Genome. 2003 Aug;46(4):546-54.


Assignment of molecular linkage groups to soybean chromosomes by primary trisomics.

Zou JJ, Singh RJ, Lee J, Xu SJ, Cregan PB, Hymowitz T.

Theor Appl Genet. 2003 Aug;107(4):745-50. Epub 2003 May 29.


Single-nucleotide polymorphisms in soybean.

Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB.

Genetics. 2003 Mar;163(3):1123-34.


Characterization of trinucleotide SSR motifs in wheat.

Song QJ, Fickus EW, Cregan PB.

Theor Appl Genet. 2002 Feb;104(2-3):286-293.


Molecular mapping of the fasciation mutation in soybean, Glycine max (Leguminosae).

Karakaya HC, Tang Y, Cregan PB, Knap HT.

Am J Bot. 2002 Apr;89(4):559-65. doi: 10.3732/ajb.89.4.559.

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