Song Lab

Song Lab

Ecological and Evolutionary Plant Systems Biology

PUBLICATIONS

Peer-Reviewed Journal Publications

[^ Undergraduate students; # Graduate students; & Contributing Equally; * Corresponding author]

  • Quang Tri Le&, Xuebo Zhao&, Ping Yates#&, Henry W. Schmidt, Matias Kirst, Qiuyun Jenny Xiang, Tran Chau, Song Li, Zhangjun Fei*, Bao-Hua Song*. 2026. A chromosome-scale reference genome and single-nucleus root atlas reveal the cellular and molecular basis of coastal adaptation in sand bean. bioRxiv: https://www.biorxiv.org/content/10.64898/2026.08.27.747562v1.
  • Ping Yates#&, Zhengzhi Tan#&, Sibesh Maharjan#&, Sixue Chen, M. Shahid. Mukhtar, and Bao-Hua Song*. 2026. Integrative Multi-Omics Reveals Constitutive Preparedness and Rapid Phytochemical Defense against Soybean Cyst Nematode in Wild Soybean.
  • Ping Yates#&, Yatendra Singh#&, Sixue Chen, M. Shahid. Mukhtar*, and Bao-Hua Song*. 2026. A Decadal Perspective on Crop Wild Relatives in the Multi-omics and Single-Cell Era. Journal of Integrative Plant Biology. Under revision.
  • Poslinski H^., Tramell J, Hatley M#, Song B-H*. 2026. Persistence of soybean cyst nematode resistance in wild soybean under combined drought and nematode stress. UReCA. Under Review.
  • Hengyou Zhang&, Neha Mittal&#, Xu Li, Zenglu Li, Chunying Li, Han-Yi Chen, Eric Davis, Changbao Li, Qijian Song, Yong-qiang Charles An, and Bao-Hua Song* 2026. Phenolic chemical defense contributes to resistance against multiple soybean cyst nematode populations in wild soybean. Under revision.
  • Melissa Hately#, Earl Taliercio, Larry Leamy, Qijian Song, Hengyou Zhang*, and Bao-Hua Song*. 2026. Wild QTL: Resistance to Soybean Cyst Nematodes in Wild Soybean (Glycine soja).
  • Poslinski H^., Hatley, M.#, Tramel J., Hartle A., Song B-H*. 2025. Harnessing Phytochemicals in Sustainable and Green Agriculture. Journal of Agriculture and Food Research 2025, 101633, ISSN 2666-1543, https://doi.org/10.1016/j.jafr.2025.101633.
  • Stupar et al., 2024. Soybean genomics research community strategic plan: A vision for 2024–2028. The plant Genome, e20516. https://doi.org/10.1002/tpg2.20516.
  • Yates P.#, Janiol J., Li C., Song B-H*. 2024. Nematocidal Potential of Phenolic Acids: A Phytochemical Seed-Coating Approach to Soybean Cyst Nematode Management. Plants 2024, 13, 319. https://doi.org/10.3390/plants13020319
  • Yasmin F#&, Zhang H&,  Leamy L,  Wang B,  Winnike J,  Reid RW,  Brouwer CR,  Song B-H*. 2024. Genetic basis and selection of glyceollin induction in wild soybean. Frontiers in Plant Sciences. 2024 Feb 28;15:1240981. doi: 10.3389/fpls.2024.1240981. PMID: 38481402; PMCID: PMC10933117.
  • Zhang, Y.; Wang, L.; Song, B.-H.; Zhang, D.; Zhang, H. 2024. Genome-Wide Identification, Characterization, and Expression Analysis of the Amino Acid Permease Gene Family in Soybean. Agronomy, 14, 52. https://doi.org/10.3390/agronomy14010052
  • Interdisciplinary Plant Science Consortium. 2023. Inclusive collaboration across plant physiology and genomics: Now is the time!. Plant Direct, 7( 5), e493. https://doi.org/10.1002/pld3.493
  • Goettel W, Zhang H, Li Y, ZQiao Z, Jiang H, Hou D, Song Q, Pantalone VR, Song B-H, Yu D, An Y-Q. 2022. POWR1, a Key Domestication Gene Pleiotropically Regulating Seed Quality and Yield in Soybean. Nature Communication. 13, 3051.  https://doi.org/10.1038/s41467-022-30314-7
  • (Selected for Editors’ Highlights by the editors at Nature Communications, shown at https://www.nature.com/ncomms/editorshighlights)
  • Zhang H&., Mittal et al&#., Finding solutions in the wild – elevated phenolic acids contribute to broad-spectrum resistance to soybean cyst nematode in wild soybean. Communications Biology. minor revision
  • Yates PS#, Roberson J, Ramsue, L and Song, B-H*. 2021: Bridging the gaps between plant and human health- A systematic review of Soyasaponins. 2021. Journal of Agricultural and Food Chemistry. 2021 Dec 8;69(48):14387-14401. doi: 10.1021/acs.jafc.1c04819. Epub 2021 Nov 29. PMID: 34843230.
  • Zhang, H., Hu, Z., Yang, Y., Liu X, Lv H, Song B-H, An Y, Li Z, and Zhang D.,2021. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 22, 453 (2021). https://doi.org/10.1186/s12864-021-07783-z
  • Stiller, A^; Garrison, K#; Gurdyumov, K#; Kenner, J#; Yasmin#, F; Yates#, P  and Song B-H*. 2021. From Fighting Critters to Saving Lives: Polyphenols in Plant Defense and Human Health. Int. J. Mol. Sci. 2021, 22 (in print)
  • Kofsky J#, Zhang H, Song B-H*. 2021. Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean. Scientific Reports. 2021. 11, 7967 https://doi.org/10.1038/s41598-021-86793-z
  • Plant Cell Atlas Consortium, Ghosh Jha S, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodr√≠guez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY (2021) Vision, challenges and opportunities for a Plant Cell Atlas. eLife DOI: 10.7554/eLife.66877
  • Kofsky J#, Zhang H, Song B-H*. 2020. Genetic Architecture of Early Vigor Traits in Wild Soybean. International Journal of Molecular Science. 2020. 21, 3105. https://doi.org/10.3390/ijms21093105 
  • Zhang H, Mujacic I#, Mitchell-Olds T, Song B-H*. 2020. De novo genome assembly and polymorphism identification in an endangered rockcress, Boechera fecunda. Frontiers in Ecology and Evolution. 2020. 8  https://doi.org/10.3389/fevo.2020.55093
  • Xiang, Q.‐Y., Chen, Z.‐D., Song, B.‐H. and Boufford, D.E. 2020. In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology. Journal of Systematics and Evolution., 2020. 58: 527-532. doi:10.1111/jse.12677
  • Anderson J and Song B-H*. 2020. Plant Climate Change Adaptation-where are we? Journal of Systematics and Evolution. 2020. 58: 533-545. doi:10.1111/jse.12649
  • (Selected as one of the Outstanding Papers of the year)
  • Zhang H, Yasmin F#,  Song B-H*. 2019. Neglected treasure in the wild – Legume wild relatives in food security and human health. Current Opinion in Plant Biology. 2019. 49: 17-26. https://doi.org/10.1016/j.pbi.2019.04.004..
  • Zhang H, Zuelsdorf C#, Penneys D, Fan S, Kofsky J#, Song B-H*. 2018. Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance.  Scientific Data. 2018. In print. 
  • Kofsky J#, Zhang H, Song B-H*. 2018. The untapped genetic reservoir: The past, current, and future applications of the wild soybean (Glycine soja).  Frontiers in Plant Science. 2018. 9, 949. https://doi.org/10.3389/fpls.2018.00949 
  • Zhang H, Kjemtrup-Lovelace S, Li C, Luo Y, Chen LP#, Song B-H*. 2017. Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja). Scientific reports. 2017 Aug 29;7(1):9699. doi: 10.1038/s41598-017-09945-0. PubMed PMID: 28852059; PubMed Central PMCID: PMC5575055.
  • Luo Y, Reid R, Freese D#, Li C, Watkins J, Shi H, Zhang H, Loraine A*, Song B-H*. 2017. Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato. Scientific Reports. 2017 Aug 29;7(1):9624. doi: 10.1038/s41598-017-09241-x. PubMed PMID: 28852001; PubMed Central PMCID: PMC5575116.
  • Zhang H, Song Q, Griffin J, and Song B-H*. 2017. Genetic Architecture of Wild Soybean (Glycine soja) Response to Soybean Cyst Nematode (Heterodera glycines). Molecular Genetics and Genomics. 2017 Jul 14. doi: 10.1007/s00438-017-1345-x
  • Yan L, Hofmann N, Li S, Ferreira ME, Song B-H, Jiang G, Ren S, Quigley C, Fickus E, Cregan P, Song Q. 2017. Identification of QTL with a large effect on soybean (Glycine max) seed weight in a selective population from Maturity Groups II, III and IV. 2017, BMC Genomics. 18:529. doi.org/10.1186/s12864-017-3922-0 .
  • Leamy JL, Zhang H, Li C, Chen CY,  and Song B-H*. 2017. A genome-wide association study of seed composition traits in wild soybean (Glycine soja). 2017 BMC Genomics. 18:18. DOI: 10.1186/s12864-016-3397-4
  • Zhang H, Song B-H*. 2017. RNA-seq data comparisons of wild soybean genotypes in response to soybean cyst nematode (Heterodera glycines). Genomics Data. 2017 Aug 9;14:36-39. doi: 10.1016/j.gdata.2017.08.001. eCollection 2017 Dec. PubMed PMID: 28856099; PubMed Central PMCID: PMC5565783.
  • Song Q, Yan L, Quigley C, Jordan BD, Fickus E, Schroeder S, Song B-H, Charles An YQ, Hyten D, Nelson R, Rainey K, Beavis WD, Specht J, Diers B, Cregan P. 2017. Genetic Characterization of the Soybean Nested Association Mapping Population. Plant Genome. 2017 Jul;10(2). doi: 10.3835/plantgenome2016.10.0109. PubMed PMID: 28724064.
  • Yu Y, Xiang Q, Manos PS, Soltis DE, Chen S, Song B-H, Liu X, and Wong G. 2017. Whole-genome duplication and accelerated molecular evolution in the angiosperm genus Cornus L. 2017. PLoS One. 12: e0171361.
  • Zhang H, Mittal N#, Leamy JL, Barazani O, and Song B-H*. 2017. Back into the Wild – Apply untapped genetic diversity of wild relatives for crop improvement. 2017 Evolutionary Applications. 1752-4571. DOI: 10.1111/eva.12434 . 
  • Zhang H, Li C, Davis EL, Wang J, Griffin JD. kofsky J#, and Song B-H*.  2016. Genome-Wide Association Analysis of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja). 2016 Frontiers in Plant Science. 7: 1214.doi:  10.3389/fpls.2016.01214 
  • Reid RW, Luo Y, Yan S, Miller T, Song B-H*. 2016. Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato. 2016 Frontiers in Plant Science. 7: 1267. http://dx.doi.org/10.3389/fpls.2016.01267.
  • Leamy JL, Lee C-R, Song Q, Mujacic I#, Luo Y, Chen CY, Li C, Kjemtrup S, and Song B-H*. 2016. Environmental versus geographical effects on genomic variation in a wild soybean (Glycine soja) across its native range in Northeast Asia. 2016. Ecology and Evolution. DOI: 10.1002/ece3.2351 
  • Luo Y*, Hu J-Y, Li L, Luo Y-L, Wang P-F and Song B-H*. 2016. Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae). 2016. BMC Genomics 17: 382.  DOI: 10.1186/s12864-016-2732-0
  • Mittal N#, Varshney VK, Song B-H*, 2015. Ginwal HS. High Levels of Diversity in the Phytochemistry, Ploidy and Genetics of the Medicinal Plant Acorus calamus L. 2015. Medicinal and Aromatic Plants S1:002. doi:10.4172/2167-0412.S1-002
  • Leamy LJ, Lee C-R, Cousins V#, Mujacic I#, Manzaneda AJ, Prasad K, Mitchell-Olds T and Song B-H*. 2014. Large-scale adaptive divergence in Boechera fecunda, an endangered wild relative of Arabidopsis. Ecology and Evolution 2014, doi: 10.1002/ece3.1148.
  • Lovell, JT, Aliyu W, Mau M, Schranz ME, Koch M, Kiefer C, Song B-H, Mitchell-Olds T and Sharbel TF*. 2013. On the origin and evolution of apomixis in Boechera, Plant Reproduction 2013, 26:309-315
  • Prasad, KVS&, Song B-H&, C Olson-Manning§, JT Anderson, C-R Lee, ME Schranz, AJ Windsor, MJ Clauss, AJ Manzaneda, I Naqvi, M Reichelt, J Gershenzon, SG Rupasinghe, MA Schuler, T Mitchell-Olds*, 2012. A novel gain-of-function polymorphism controlling complex traits and fitness in nature. Science 2012, 337-1081-1084
  • Song B-H and Mitchell-Olds T, Evolutionary and ecological genomics of non-model plants. Journal of Systematics and Evolution 2011, 49: 17-24
  • Rushworth C, Song B-H, Lee C-R and Mitchell-Olds T, Boechera, a model system for ecological genomics. Molecular Ecology 2011, 20: 4843–4857
  • Gossmann TI, Song B-H, Windsor AJ, Mitchell-Olds T and Eyre-Walker, Genome wide analyses reveal little evidence for adaptive evolution in plants. Molecular Biology and Evolution 2010, 27: 1822-1832
  • Song B-H, Windsor A, Ramos-Onsins S, Schmid KJ, Schranz ME, Heidel A, Mitchell-Olds T, Multilocus nucleotide diversity, population structure and linkage disequilibrium of a wild Arabidopsis relative − Boechera stricta. Genetics 2009, 181: 1021–1033
  • Song B-H and Mitchell-Olds T, High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis. Molecular Ecology 2007, 16: 4079-4088
  • Schranz ME, Song B-H, Winsor AJ and Mitchell-Olds T, Comparative genomics in the Brassicaceae: the need for family- a family-wide perspective. Current Opinion in Plant Biology 2007, 10: 168-175
  • Schranz ME, Winsor AJ, Song B-H and Mitchell-Olds T, Comparative genetic mapping in Boechera stricta (Brassicaceae). Plant Physiology 2007, 14: 286-298
  • Song B-H, Clauss M, Pepper A, Mitchell-Olds T, Spatial patterns of microsatellite variation in Boechera stricta, a close relative of Arabidopsis. Molecular Ecology 2006, 15:357–369
  • Song B-H, Wang X-Q, Wang X-R, Ding K-Y, Hong D-Y, Cytoplasmic composition of Pinus densata and population establishment of the diploid hybrid pine. Molecular Ecology 2003, 12: 2995-3001
  • Song B-H, Wang X-Q, Wang X-R, Sun L-J, Hong D-Y, Peng P-H, Maternal Lineage of Pinus densata, a diploid hybrid. Molecular Ecology 2002, 11: 1057-1063
  • Song B-H, Li F-Z, The utility of trnK introns 5’ region in phylogenetic analysis of Ulmaceae s.l. Journal of Systematics and Evolution 2002, 40 (2): 125-132
  • Song B-H, Zhang X-J, Li F-Z, Wan P, Chromosome numbers of 14 species in Amaranthus from China. Journal of Systematics and Evolution 2002, 40: 428-432
  • Li Z-Y, Song B-H, Li F-Z, The identity of Amaranthus taishanensis F. Z. Li et C. K. Ni. Journal of Systematics and Evolution 2002, 40: 383-384
  • Li F-Z, Song B-H, Lu Y-Q, Two new records of plants from China. Guihaia 2002, 22: 7-8
  • Song B-H, Wang X-Q, Li F-Z, Hong D-Y, Further evidence for paraphyly of the Celtidaceae from the chloroplast gene matK. Plant Systematics and Evolution 2001, 228:107-115
  • Song B-H, Chen Z-D, Wang X-Q, Li F-Z. Sequence analysis of the ITS region of nuclear ribosomal DNA (nrDNA) in Chinese Amaranthus and its systematic utility. Journal of Integrative Plant Biology 2000, 42: 1184-1189
  • Song B-H, Li F-Z, He X-Q, Ni C-K, The determination of composition and content of amino acids in leaf protein of 30 species and its nutritive value. Journal of Plant Resources and Environment 2000, 9: 59-60
 

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