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United States Department of Agriculture

Agricultural Research Service

Qijian Song

Research Geneticist

Soybean Genomics and Improvement Laboratory
Beltsville Agricultural Research Center
Bldg. 006  Rm. 100
10300 Baltimore Ave, 
Beltsville, MD 20705, USA
(301) 504-5337

Description of Research Activities


Research involves: Discovery of  genetic variants in soybean, wheat and common bean genomes through high throughput DNA and RNA sequence analysis; Development and application of molecular genetic markers and genomic research tools such as gene chips to identify QTL and genes controlling biotic and abiotic stress resistance, agronomic and quality traits; Identification of desirable genetic diversity for germplasm improvement; Application of knowledge of bioinformatics, biostatistics to breeding practice, genetics and genomics research; and Development of algorithms and computer programs for the genetic analysis of large datasets containing high throughput sequences and genotyping data.




Wen ZX, Boyse JF, Song QJ, Cregan PB, Wang DC. 2015. Genomic consequences of selection and genome-wide association mapping in soybean.  BMC Genomics 2015 16:671.

Hagerty HC, Cuesta-Marcos A, Cregan PB, Song QJ, McClean PE, Noffsinger S, Myers JR. 2015. Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris). Crop Sci. 55:1969-1977 doi: 10.2135/cropsci2014.11.0805.

Song QJ, Jia GF, Hyten DL, Jenkins J, Hwang EY, Schroeder S, Schmutz J, Jackson SA , McClean P, Cregan PB. 2015. SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research. G3: Genes| Genomes| Genetics  doi:10.1534/g3.115.020594.

Bandillo N, Jarquin D, Song QJ, Cregan PB, Nelson R, Specht J, Lorenz A. 2015. An association and population structure analysis on the USA Soybean Germplasm Collection. Plant Genome doi:10.3835/plantgenome2015.04.0024.

Song QJ, Hyten DL, Jia GF, Quigley CV., Fickus EW, Nelson RL, Cregan PB. 2015. Fingerprinting soybean germplasm and its utility in genomic research. G3 Genes Genomes Genetics  doi:10.1534/g3.115.019000.

SX Li, Song QJ, Ji PS, and Cregan PB. 2015. Draft Genome Sequence of Phomopsis longicolla Type Strain TWH P74, a Fungus Causing Phomopsis Seed Decay in Soybean. Journal submitted: Genome Announcements (genome A).  doi: 10.1128/genomeA.00010-15.

Pham AT, Harris D, Buck J, Serrano J, Abdel-Haleem H, Cregan PB, Song QJ, Boerma HR, and Li ZL. 2015. Fine Mapping and Characterization of Candidate Gene(s) that Control the Resistance to Frogeye Leaf Spot Disease in Soybean.  PLoS ONE DOI: 10.1371/journal.pone.0126753.

Zhang JP, Song QJ, Cregan PB, Nelson RL,Wu JX, and Jiang GL, 2015. Genome-wide association mapping of flowering time and maturity dates in early mature soybean germplasm. BMC Genomics 16(1), 217. DOI: 10.1186/s12864-015-1441-4. 

Vaughn JN, Nelson RL, Song QJ, Cregan PB, Boerma R, and Li ZL. 2014. The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.G3 Genes Genomes Genetics  doi:10.1534/g3.114.013433. 

Zhou L, Wang SB, He R, Geng QC, Wen J, Geng QC, Song QJ, Wu Z, Li GJ, Liu YQ,  Jian J, Niu Y, Zhang L, Ren WL, Zhang YM, 2015. Domestication-related loci and molecular mechanism for flowering time and seed size in soybean. Scientific Report doi:10.1038/srep09350.

Dhanapal AP, Ray JD, Hoyos-Villegas V, Singh SK, Smith JR, King CA, Purcell LC, Cregan PB, QJ Song, and Fritschi FB. 2014. Genome-wide association studies (GWAS) for carbon isotope signatures (?13C) in diverse soybean genotypes.  Theor and Applied Genetics 10.1007/s00122-014-2413-9.

Natarajan SS, Khan FH, Luthria DL, Tucker ML, Song QJ, Garrett WM. 2014. A comparison of protein and phenolic compounds in seed from GMO and non-GMO soybean. Data Mining in Genomics & Proteomics 5(3):161 doi:10.4172/2153-0602.1000161.

Wang XZ, Jiang GL, Song QJ, Cregan PB, Scott RA, Zhang JP,Yen Y, and Brown M. 2014. Quantitative trait loci analysis of seed sulfur containing amino acids in two recombinant inbred line populations of soybean. Euphytica DOI 10.1007/s10681-014-1223-0.

Lee S, Freewalt KR., McHale LK, Song QJ, Jun TH, Michel AP, Dorrance AE, and Mian R. 2014.   A high resolution genetic linkage map of soybean based on 357 recombinant inbred lines and genotyped with BARCSoySNP6K. Molecular Breeding 35(2), 1-7.

Wen ZX, Tan RJ, Yuan JZ, Bales C, Du WY, Zhang SC, Chilvers M, Schmidt C, Song QJ, Cregan PB, Kull L, Wang DC. 2014. Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean. BMC Genomics 15:809. DOI: 10.1186/1471-2164-15-809.

Wang XZ, Jiang GL, Green M, Scott RA, Song QJ, Hyten DL, and Cregan PB. 2014. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred populations of soybean.Molecular Genetics and Genomics, 1-15.DOI 10.1007/s00438-014-0865-x. 

Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO, Song QJ,  Cregan PB, Specht JE, Diers BW, Cannon SB, McHale LK and Stupar RM. 2014. A roadmap for functional structural variants in the soybean genome. G3. Genes Genomes Genetics doi: 10.1534/g3.114.011551.

Cook DE, Bayless A, Wang K, Guo XL, Song QJ, Jiang JM, Bent AF, 2014. Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode. Plant Physiology DOI:10.1104/pp.114.235952.

Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song QJ, Schultz Q, Qi LL. 2014. A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12. PLoS ONE 9(7): e98628. doi:10.1371/journal.pone.0098628.

Hwang EY, Song QJ,  Jia GF, Specht JE, Hyten DL, Costa J, and Cregan PB. 2014. A genome-wide association study to identify loci associated with seed protein concentration in soybean. BMC Genomics 2014, 15:1 doi:10.1186/1471-2164-15-1.

Schmutz J, McClean P, Mamidi S, Wu A, Cannon S, Grimwood J, Jenkins J, Shu S, Song QJ, Chavarro C, 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 J, Kudrna D, Lee R, Manon RMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA., Cregan PB, Rokhsar DS, Jackson SA. A reference genome and domestication of common bean. 2014. Nature Genetics  46: 707-713. doi:10.1038/ng.3008.

Zeng A, Chen P, Shi A, Wang D, Zhang B, Orazaly M, Jaureguy L, Florez L, Brye K, Song QJ and Cregan P. 2014. Identification of quantitative trait loci for sucrose content in soybean seed. Crop Science54: 2: 554-564doi:10.2135/cropsci2013.01.0036

Moghaddam SM,  Song QJ, Mamidi S, Lee R, Cregan P, Osorno JM, McClean PE. 2014. Developing Market class Specific InDel Markers from Next Generation Sequence Data in Phaseolus vulgaris L. Front. Plant Sci. 5:185. DOI: 10.3389/fpls.2014.00185 .

Zhang ZN, Hao J, Yuan J, Song QJ, Hyten DL, Cregan PB, Zhang GR, Gu CH, Li M, Wang DC. 2014. Phytophthora Root Rot Resistance in Soybean E00003. Crop Sci 54: 2: 492-499. doi: 10.2135/cropsci2012.11.0631.

Akond M, Liu SM, Schoener L, Anderson JA, Kantartzi SK, Meksem KL, Song QJ, Wang DC, Wen ZX, Lightfoot DA, and Kassem MA. 2013. A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array.  Journal of Plant Genome Sciences 1(3):80-89.

Zhang GR, Bales-Arcelo G. Liu M.,Mensah C, Gu CH,  Song QJ, Hyten D, Cregan P, Wang DC. 2013. Mapping soybean aphid resistance genes in PI 567598B. Theoretical Applied Genetics 126:2081-2091.

Song QJ, Hyten DL, Quigley CV, Jia GF, Fickus EW, Cregan PB. 2013. Development and Evaluation of a high-density Infinium beadchip SoySNP50K. PLoS ONE 8(1): e54985. doi:10.1371/journal.pone.0054985.

 Felicetti E, Song QJ, Cregan P, Bett K, and Miklas P. 2012. Simple sequence repeats linked with slow dark trait in pinto bean discovered by SNP assay and whole genome sequencing. Crop Science. 52:1600-1608.

Du JC, Sui Y, Song QJ, Cannon S, Cregan P, and Ma JX, 2012. Pericentromeric Effects in Shaping the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Palaeopolyploid Soybean (Glycine max (L.).  Plant Cell 24(1):21-32.

Kim KS, Unfried JR, Hyten DL, Frederick RD, Hartman GL, Nelson RL, Song QJ, and Diers B. 2012. Molecular Mapping of a Gene Conferring Resistance to Asian Soybean Rust in Soybean PI 561356 and SNP Haplotype Analysis of the Rpp1 Region in 39 Soybean accessions. Theoretical Applied Genetics 125:1339-1352.

van Berkum P. Elia P, Song QJ, Eardly BD. 2012 Development and application of a multilocus sequence analysis method for the identification of genotypes within the genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr).  Molecular Plant Microbe Interactions 25(3):321-330.

Hyten DL, Song QJ, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Corrales MP, and Cregan PB. 2010. High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475.

Chiu EYH, Lin UH, Wu W, Song QJ, Chang PFL, Gao LY, Chou CC, and Ueng PP. 2010. Alternative splicing and genetic diversity of the white collar-1 (wc-1) gene in cereal Phaeosphaeria pathogens. European Journal of Plant Pathology 127:351-363.

Hyten DL, Choi IK, Song QJ, Specht JE, Carter TE, Shoemaker RC, Hwang EY, Matukumalli LK, and Cregan PB. 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 Science 50:960-968.

Schmutz, J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song QJ, Thelen JJ, Cheng J, Xu D, Hellsten U, May G, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan PB, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, and Jackson SA. 2010. A genome sequence of paleopolyploid soybean (Glycine max) Nature 463:178-183.

Natarajan S, Luthria D, Song QJ, and Cregan PB, 2010, Determination of Seed Storage Proteins and Total Isoflavones in Wild and Cultivated Soybeans. Journal of Plant Biochemistry and Biotechnology 19(1): 115-118.

Hyten DL, Cannon SB, Song QJ, Weeks N, Fickus EC, Shoemaker RC, Specht JE, May GD, and Cregan PB. 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(1):38.

Song QJ, Jia GF, Zhu YL, Hwang EY, Hyten DL, and Cregan PB. 2010. Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean. Crop Science 50:1950-1960.

Malkus A, Song QJ, Cregan PB, Arseniuk E and Ueng PP. 2009. Genetic linkage map of Phaeosphaeria nodorum, the causal agent of stagonospora nodorum blotch disease of wheat. European Journal of Plant Pathology European Journal of Plant Pathology 124:681-690.

Hyten DL, Smith JR, Frederick RD, Tucker ML, Song QJ, and Cregan PB. 2009. Bulk Segregate Analysis using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Phakopsora pachyrhizi (Soybean Rust) in Soybean. Crop Science 49:265-271

Johnson ES, Bekele FL, Brown SJ, Song QJ, Motamayor JC, Zhang D, Meinhardt LW and Schnell RJ. 2009. Population structure and genetic diversity of the Trinitario cacao (Theobroma cacao L.) from Trinidad and Tobago. Crop Science 49: 564-572.

Puthoff PD, Neelam A, Ehrenfried ML, Scheffler BE, Ballard L, Song QJ, Campbell KB, Cooper B, and Tucker ML. 2008. Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi. Phytopathology 98(10):1126-1135.

Hyten DL, Song QJ, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, and Cregan PB. 2008. High-throughput genotyping with the GoldenGate assay in the highly complex genome of soybean. Theoretical Applied Genetics 116:945-952.

Reszka E, Arseniuk E, Song QJ, Cregan PB, and Ueng PP. 2007. QTL analysis of partial resistance to Stagonospora nodorum blotch in winter triticale cultivars Pinokio and Bogo. Plant Pathology Bulletin 16:161-167.

Li WB, Song QJ, Brlansky RH, and Hartung JS. 2007. Genetic diversity, worldwide proliferation and identification of citrus bacteria canker pathogens. Proceedings of National Academy of Sciences 104(47):18427-18432.

Choi IY, Hyten DL, Specht JE, Matukumalli LK, Song QJ, Quigley CV, Lee MS, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Costa JM, and Cregan PB. 2007. Single Nucleotide Polymorphism Discovery in Soybean Genes and the Creation of a Transcript Map. Genetics 2007 176(1):685-96

Hyten DL, Choi IY, Song QJ, Shoemaker RC, Nelson RL, Costa JM, Specht JE, and Cregan PB. 2007. Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations. Genetics 175:1937-1944.

Yoon MS, Song QJ, Choi IY, Specht JE, and PB Cregan. 2007. BARCSOYSNP23: a selected panel of SNPs for soybean cultivar identification. Theoretical Applied Genetics 114:885-899.

Matthews BF, MacDonald MH, Lewers KS, Song QJ, and Cregan PB. 2007. Registration of soybean "Minimax" germplasm. Journal of Plant Registration 1(2):97-98.

Hyten DL, Song QJ, Zhu YL, Choi IY, Nelson R, Costa J, Specht JE, Shoemaker RC, and Cregan PB. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of National Academy of Sciences 103 (45): 16666-16671.

Reszka E, Arseniuk E, Malkus A, Chung KR, Song QJ, and Ueng PP. 2006. A New Biotype of Phaeosphaeria sp.of Uncertain Affinity Causing Stagonospora Leaf Blotch Disease in Cereals in Poland. Plant Dis. 90:113, published on-line as DOI: 10.1094/PD-90-0113B.

Song QJ, Shi JR, Singh S, Fickus EW, Costa J, Gill BS, Cregan PB, and Ward R. 2005. Development and mapping of microsatellite markers in wheat. Theoretical Applied Genetics 110: 550-560.

Arseniuk E, Czembor PC, Czaplicki A, Song QJ, Cregan PB, Hoffman DL, and Ueng PP. 2004. QTL analysis of partial resistance to stagonospora nodorum blotch in wheat. Euphytica 137:225-231.

Song QJ, Marek LF, Shoemaker RC, Lark KG, Specht JE, Concibido VC, Delannay X, and Cregan PB. 2004. A new integrated genetic linkage map of the soybean. Theoretical Applied Genetics 109:122-128

Ueng PP, O'Neil, Arseniuk E, Cunfer BM, Song QJ. 2003. Transposition and aggressiveness in a Phaeosphaeria nodorum sexual cross. Plant Pathology Bulletin 12:149-156.

Czembor PC, Arseniuk E, Czaplicki A, Song QJ, Cregan PB, and Ueng PP. 2003. QTL mapping of partial resistance in winter wheat to stagonospora nodorum blotch. Genome 46(4):546-554.

 Song QJ, Fickus EW, and PB Cregan. 2002. Characterization of trinucleotide microsatellites in wheat. Theoretical Applied Genetics 104: 286-293.

Zhu YL, Song QJ. Hyatt SM, Grimm DR, Fickus EW, Young ND, and Cregan PB. 2001. Single nucleotide polymorphism (SNPs) in soybean. Genetics 163:1123-1134.

Anderson JA, Stack RW, Liu S, Waldron BL, Fjeld AD, Coyne C, Moreno-Sevilla, Fetch JM, Song QJ, Cregan PB, and RC Frohberg. 2001. DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theoretical Applied Genetics 102:1164-1168.

 Song QJ, Quigley CV, Carter TC, Nelson RL, Boerma HR, Strachan J, and Cregan PB. 1999. A selected set of trinucleotide simple sequence repeat markers for soybean variety identification. Plant Varieties and Seed 12:207-220.

 Song QJ, and Kim NS. 1999. Production, utilization, and quality improvement of soybean in South Korea. Soybean Science 18(1):89-93.

 Song QJ, Shim KM, Heo NK, and Kim NS. 1998. Genotype fingerprinting, differentiation and association between morphological traits and SSR loci of Korean soybean landraces. Plant Resources 1(2):81-91.

 Song QJ, and Kim NS. 1998. SSRFING: A BASIC program for plant fingerprinting and association with SSR information. Korea Journal of Genetics 20(1): 29-34.

 Zhu CS, Gai JY, and Song QJ. 1998. A preliminary study on recurrent selection for yield in soybeans. Jiansu Journal of Agricultural Sciences 14(2):80-84.

 Song QJ, Wu TX, Wang MJ, and Gai JY. 1998. Inheritance of a recently discovered soybean virescent mutant "NJ93V", Soybean Genetics Newsletter 25:41-42.

 Wang MJ, Song QJ and Gai JY. 1998. Inheritance of tofu output in the cross Guanyundaheidou X Linhexiao yeqing. Soybean Genetics Newsletter 25:44-45.

 Zhu CS, Gai JY, and Song QJ. 1997. A study of genetic variability of four soybean intermating populations with nuclear male sterility. Journal of Chinese Oil Crops 19(3):18-22.

 Song QJ and Wu TX. 1997. Population improvement methods and techniques using recessive male sterile mutant. Soybean Science 16(1):80-84.

 Song QJ, Wu TX and Gai JY. 1997. Computer code for the first difference nearest neighbour analysis. Computer and Agriculture (4):26-30.

 Song QJ, Wu TX, and Gai JY. 1996. Selection effectiveness in a recent constructed random?mated soybean population processing ms1 gene for genetic male sterility. Soybean Genetics Newsletter 23:85?88.

 Song QJ, Wu TX, and Gai JY. 1996. Effects of maturity selection in recurrent selection populations on morphological, other agronomic characters and ratio of male?sterile plants. Scientica Agricultura Sinica 29(3):49?54.

 Song QJ, Wu TX and Gai JY. 1996. Canonical correlation analysis and path coefficient analysis of protein content, oil content and yield of summer soybean landrace population from Southern China. Soybean Science 15(1):11?16.

 Qiu JS, Gai JY, and Song QJ. 1996. Advances of soybean genetics and breeding during the 8th?Five?Year National Research Program and the strategy for the next five years. Soybean Report 1:1?3.

 Song QJ, Wu TX, and Gai JY. 1995. Distribution of seed size, protein content, fatty content in wild and landrace soybeans. Soybean Genetics Newsletter 22:76?79.

 Song QJ, Gai JY, and Ma YH. 1995. Genetic variability of agronomic and quality characters of landrace soybean from Mid?Yangtze River Valley. Soybean Genetics Newsletter 22:80? 82.

 Song QJ, Wu TX, and Gai JY. 1995. Studies on problems related to genetics and uses of male sterility. Soybean Science: 14(2):137?142.

Song QJ, Wu TX, and Gai JY. 1995. Effects of planting density and spacing on yield and agronomy traits. Soybean Science 14(1):42?47.

Song QJ, Gai JY, and Ma YH.1994. Genetic variability & heterosis of protein and oil content in soybean. Acta Agricultura Sinica 20(5):542?547.

Song QJ, Wu TX, Gai JY, and Ma YH. 1994. Statistical analysis and computer program for generalized block design. Application of Computer in Agriculture 1:25?30.

Song QJ, Wu TX, Gai JY, and Ma YH. 1994. Statistical analysis and computer program for nearest block design. Application of Computer in Agriculture 3:11?16.

Song QJ, Wu TX, Yang D, Gai JY, and Ma YH. 1993. Synthesis of a high protein content & seed yield population with male?sterile gene. Scientica Agricultura Sinica 1:164?166.

 Song QJ, Gai JY, and Ma YH. 1991. Combining ability of protein content, fatty content in soybean. Acta Agronomica Sinica 17(2):128?136.

Song QJ, Wu TX. 1991. A computer program for analysis of circulent partial diallel designs. Application of Computer in Agriculture 1:37?44.

Song QJ, Gai JY and Ma YH. 1990. A study on ecological characterization of protein content and oil content in soybean. Soybean Science 9(2):121?129.

Song QJ, Wu TX. 1990. Genetic variability of protein content, oil content in soybean. 1990, Agronomy Abroad?Soybean 4:7?10.

Song QJ, Gai JY, and Ma YH. 1989. A study on the genetic characterization of protein and oil content of soybean. Scientica Agricultura Sinica 22(6):24?29.

 Song QJ, Gai JY, and Ma YH. 1987. Characteristics and genetic variability of soybean landrace population from the Middle Yangtze Valley. Journal of Nanjing Agricultural University 3:29?36.


Last Modified: 8/12/2016
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