2025

Abdelrahman, M., Jogaiaha, S., Abdelmoteleb, M., Foker, M., Nguyen, H.T. and Tran, L.S.P. 2025. Deciphering crop-specific rhizobacteriome assembly in cotton, sorghum, and soybean under hot semi-arid field conditions in Texas. Journal Environmental Microbiome. In review.

Nguyen, Phuong Thao, Xuan Lan Thi Hoang, Nguyen Nguyen Chuong, Nguyen Cao Nguyen, Nguyen Ngoc Hai, Dung Tien Le; Yasuko Watanabe, Keiichi Mochida, Tien-Dung Nguyen, Henry T Nguyen, Lam-Son Phan Tran. 2025. Enhancing soybean tolerance to drought by homologous expression of cytokinin synthase gene GmIPT10. BB. In review.

Lakhssassi, N., Chhapekar, S.S., Devkar, V. et al. Discovery of two tightly linked soybean genes at the qSCN10 (O) locus conferring broad-spectrum resistance to soybean cyst nematode. Commun Biol 8, 259 (2025). https://doi.org/10.1038/s42003-025-07633-8

Lee, D., Vuong, T.D., Shannon, J.G., Song, Q., Lin, F. and Nguyen, H.T. 2025. QTL mapping and whole-genome sequencing analysis for novel genetic resources associated with sucrose content in soybean [Glycine max (L.) Merr.]. Theoretical and Applied Genetics, 138(2), p.43 DOI: 10.1007/s00122-024-04808-5

Wood, T.D., Tiede, E.R., Izydorczak, A.M., Zemaitis, K.J., Ye, H. and Nguyen, H.T. 2025. Chemical Informatics Combined with Kendrick Mass Analysis to Enhance Annotation and Identify Pathways in Soybean Metabolomics. Metabolites, 15(2), p.73.

Wu, C., Florez‐Palacios, L., Acuna, A., Harrison, D., Rogers, D., Carlin, J., Mozzoni, L., Nguyen, H.T., Shannon, G. and Vieira, C.C. 2025. Impact of flooding at the early reproductive growth stage on soybean yield and seed composition. Crop Science, 65(1), p.e21397.

2024

Abdelrahman, M., Gorafi, Y.S.A., Sulieman, S., Jogaiah, S., Gupta, A., Tsujimoto, H., Nguyen, H.T., Herrera‐Estrella, L. and Tran, L.S.P. 2024. Wild grass‐derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. The Plant Journal, 119(4), pp.1685-1702.

Mishra S, Srivastava AK, Khan AW, Phan Tran LS, Nguyen HT. The era of panomics-driven gene discovery in plants. Trends Plant Sci. 29, 995-1005 (2024). DOI: 10.1016/j.tplants.2024.03.007

Varshney, R.K., Barmukh, R., Bentley, A. and Nguyen, H.T., 2024. Exploring the genomics of abiotic stress tolerance and crop resilience to climate change. The Plant Genome, 17(1), p.e20445.

Mohamedikbal, S., Al‐Mamun, H.A., Marsh, J.I., Upadhyaya, S., Danilevicz, M.F., Nguyen, H.T., Valliyodan, B., Mahan, A., Batley, J. and Edwards, D., 2024. Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean. The Plant Genome, p.e20528.

Lakhssassi, N., El Baze, A., Knizia, D., Salhi, Y., Embaby, M.G., Anil, E., Mallory, C., Lakhssassi, A., Meksem, J., Shi, H., Nguyen, H.T. and Vuong, T.D., 2024. A sucrose-binding protein and β-conglycinins regulate soybean seed protein content and control multiple seed traits. Plant Physiology, p.kiae380.

Song, Q., Quigley, C., He, R., Wang, D., Nguyen, H.T., Miranda, C. and Li, Z., 2024. Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications. The Plant Genome, p.e20491.

Bellaloui, N., Knizia, D., Yuan, J., Song, Q., Betts, F., Register, T., Williams, E., Lakhssassi, N., Mazouz, H., Nguyen, H.T. and Meksem, K., 2024. Genomic Regions and Candidate Genes for Seed Iron and Seed Zinc Accumulation Identified in the Soybean ‘Forrest’by ‘Williams 82’RIL Population. International Journal of Plant Biology, 15(2), pp.452-467.

Khan AW , Garg V, Gupta S , Sun S , Dudchenko O , Roorkiwal M, Chitikineni A, Bayer PE , Shi C, Upadhyaya HD , Bohra A, Bharadwaj C, Mir RR , Baruch K , Yang B , Coyne C, Bansal KC, Nguyen HT, Ronen G , Aiden E, Veneklaas E, Siddique KHM, Liu X, Edwards E, Varshney RK. 2024. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea (Cicer arietinum) – Nature Genetics, pp.1-10.

Li, Y., Ye, H., Vuong, T.D., Zhou, L., Do, T.D., Satish Chhapekar, S., Zhao, W., Li, B., Jin, T., Gu, J., Li, C. and Nguyen, HT. 2024., A novel natural variation in the promoter of GmCHX1 regulates conditional gene expression to improve salt tolerance in soybean. Journal of Experimental Botany, 75(3), pp.1051-1062.

Dhingra, A., Shinde, S., D’Agostino, L., Devkar, V., Shinde, H., Rajurkar, A.B., Sonah, H., Vuong, T.D., Siebecker, M.G., Jiao, Y., Nguyen, H.T. and Hancock, C.N., 2024. Identification of novel germplasm and genetic loci for enhancing mineral element uptake in soybean. Environmental and Experimental Botany, 219, p.105643.

Wu, C., Acuña, A., Florez‐Palacios, L., Harrison, D., Ravelombola, F., Oliveira, M.R., Winter, J., Rogers, D.J., Carlin, J.F., Shannon, J.G. and Nguyen, H., 2024. Registration of R16‐45 as a flood‐tolerant, high‐yielding soybean germplasm line. Journal of Plant Registrations.

2023

Lee, D., Lara, L., Moseley, D., Vuong, T.D., Xu, D. and Nguyen, H.T., 2023. Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.). Frontiers in Plant Science, 14, p.1294659.

Lee, D., Vuong, T.D., Shannon, G.J., Shi, H., Rainey, K.M. and Nguyen, H.T., 2023. Environmental stability and genetic effect of soybeans differing in mutant allele combinations between rs and mips1 genes for soluble carbohydrate profiles. Crop Science, 63(6), pp.3326-3337.

Canella Vieira, C., Zhou, J., Jarquin, D., Zhou, J., Diers, B., Riechers, D.E., Nguyen, H.T. and Shannon, G., 2023. Genetic architecture of soybean tolerance to off-target dicamba. Frontiers in Plant Science, 14, p.1230068.

Bellaloui, N., Knizia, D., Yuan, J., Song, Q., Betts, F., Register, T., Williams, E., Lakhssassi, N., Mazouz, H., Nguyen, H.T. and Meksem, K., 2023. Genetic Mapping for QTL Associated with Seed Nickel and Molybdenum Accumulation in the Soybean ‘Forrest’by ‘Williams 82’RIL Population. Plants, 12(21), p.3709.

Knizia, D., Bellaloui, N., Yuan, J., Lakhssasi, N., Anil, E., Vuong, T., Embaby, M., Nguyen, H.T., Mengistu, A., Meksem, K. and Kassem, M.A., 2023. Quantitative Trait Loci and Candidate Genes That Control Seed Sugars Contents in the Soybean ‘Forrest’by ‘Williams 82’Recombinant Inbred Line Population. Plants, 12(19), p.3498.

Guo, B., Zhang, J., Yang, C., Dong, L., Ye, H., Valliyodan, B., Nguyen, H.T. and Song, L., 2023. The Late Embryogenesis Abundant Proteins in Soybean: Identification, Expression Analysis, and the Roles of GmLEA4_19 in Drought Stress. International Journal of Molecular Sciences, 24(19), p.14834.

Garg, V., Khan, A.W., Fengler, K., Llaca, V., Yuan, Y., Vuong, T.D., Harris, C., Chan, T.F., Lam, H.M., Varshney, R.K. and Nguyen, H.T., 2023. Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research. The Plant Genome, 16(4), p.e20382.

Singer, W.M., Lee, Y.C., Shea, Z., Vieira, C.C., Lee, D., Li, X., Cunicelli, M., Kadam, S.S., Khan, M.A.W., Shannon, G., Nguyen, HT. and Mian, M.R., 2023. Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed. The Plant Genome, 16(4), p.e20415.

Chandnani, Rahul, Tongfei Qin, Heng Ye, Haifei Hu, Karim Panjvani, Mutsutomo Tokizawa, Javier Mora Macias, Alma Armenta Madina, Karine Bernardino, Pankaj Banik, Ashlyn Mooney, Jurandir Magalhaes, Henry T. Nguyen, and Leon V Kochian. 2023. Application of 2-dimensional high-throughput soybean root phenotyping to identify novel putative genetic variants regulating root architecture traits possibly underlying improved water and nutrient acquisition. The Plant Phenomics 5, p.0097.

Lokya, V., Parmar, S., Pandey, A.K., Sudini, H.K., Huai, D., Ozias‐Akins, P., Foyer, C.H., Nwosu, C.V., Karpinska, B., Baker, A., Nguyen, HT. and Xu, P., 2023. Prospects for developing allergen‐depleted food crops. The Plant Genome, 16(4), p.e20375.

Vuong, T.D., Florez‐Palacios, L., Mozzoni, L., Clubb, M., Quigley, C., Song, Q., Kadam, S., Yuan, Y., Chan, T.F., Mian, M.A.R. and Nguyen, H.T., 2023. Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans. The Plant Genome, 16(4), p.e20400.

Razzaq, Muhammad Khuram, Reena Rani, Guangnan Xing, Yufei Xu, Ghulam Raza, Muqadas Aleem, Shahid Iqbal, Muhammad Arif, Zahid Mukhtar, Henry T. Nguyen, and et al. 2023. “Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development.” Genes 14, no. 6: 1254. https://doi.org/10.3390/genes14061254

Derbyshire, M.C., Marsh, J., Tirnaz, S., Nguyen, H.T., Batley, J., Bayer, P.E. and Edwards, D., 2023. Diversity of fatty acid biosynthesis genes across the soybean pangenome. The Plant Genome, p.e20334.

Escamilla, D.M., Xavier, A., Vuong, T.D., Nguyen, H.T. and Rainey, K.M., 2023. An assessment of the interaction between sucrose content and seed quality traits in soybeans. Crop Science, 63(5), pp.2650-2664.

Chen, P., Ali, M.L., Shannon, G., Vieira, C.C., Lee, Y.C., Nascimento, E.F., Granja, M.O., Lee, D., Crisel, M., Smothers, S. and Clubb, M., S. Selves, A. Scaboo, M. Usovsky, H. T. Nguyen, Z. Li, M. G. Mitchum, B. Averitt, J. Bond, C. Meinhardt, S. Li, A. M. Gillen, A.

Mengistu, R. T. Robbins, L. A. Mozzoni, B. Zhang, J. R. Smith, D. Moseley. 2023. Registration of ‘S16‐5503GT’soybean cultivar with high yield, broad adaptation, and glyphosate tolerance. Journal of Plant Registrations, 17(2), pp.304-317.

Chen, Pengyin, J. Grover Shannon, Dongho Lee, Matheus Ogando do Granja, Caio Canella Vieira, Yi‐Chen Lee, Md Liakat Ali. Emanuel Ferrari do Nascimento, Andrew Scaboo, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Henry T. Nguyen, Zenglu Li, Melissa Goellner Mitchum, Ben Averitt, Jason P. Bond, Clinton G. Meinhardt, Mariola Usovsky, Shuxian Li, James R. Smith, Anne M. Gillen, Alemu Mengistu, Bo Zhang, Leandro Angel Mozzoni, David Moseley. 2023. “Registration of ‘S17‐2243C’: A non‐genetically modified maturity group IV soybean cultivar with high yield and elevated oil concentration.” Journal of Plant Registrations, https://doi.org/10.1002/plr2.20276

Shannon G, Chen P, Lee YC, Vieira CC, Nascimento EF, Granja MO, Lee D, Ali ML, Scaboo A, Crisel M, Smothers S., H. T. Nguyen, Z. Li, M. G. Mitchum, J. Bond, C. Meinhardt, M. Usovsky, R. T. Robbins, A. M. Gillen. 2023. Registration of ‘S11‐17025C’soybean: A high‐yielding and high‐oil conventional cultivar with broad resistance to diseases and nematodes. Journal of Plant Registrations, 16(2), pp.234-245.

Chen, Pengyin, J. Grover Shannon, Dongho Lee, Matheus Ogando do Granja, Md Liakat Ali, Caio Canella Vieira, Yi‐Chen Lee Emanuel Ferrari do Nascimento, Andrew Scaboo, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Henry T. Nguyen, Zenglu Li, Melissa Goellner Mitchum, Ben Averitt, Jason P. Bond, Clinton G. Meinhardt, Mariola Usovsky, Shuxian Li, James R. Smith, Anne M. Gillen, Alemu Mengistu, Bo Zhang, Leandro Angel Mozzoni, Robert T. Robbins, David Moseley.2023 “Registration of ‘S16‐11644C’: A maturity group IV soybean cultivar with high‐yielding performance and broad disease resistance.” Journal of Plant Registrations, 17(1): 67-79.

Shannon, G., Chen, P., Lee, Y.C., Canella Vieira, C., Ali, M.L., Lee, D., Scaboo, A., Crisel, M., Smothers, S., Clubb, M. and Nguyen, H.T., 2023. Registration of ‘S11‐16653C’soybean: A high‐yielding conventional cultivar with broad resistance to diseases and nematodes. Journal of Plant Registrations, 17(1), pp.56-6

2022

Vanika Garg, Olga Dudchenko, Jinpeng Wang, Aamir W. Khan, Saurabh Gupta, Parwinder Kaur, Kai Han, Rachit K. Saxena, Sandip M. Kale, Melanie Pham, Jigao Yu, Annapurna Chitikineni, Zhikang Zhang, Guangyi Fan, Christopher Lui, Vinodkumar Valluri, Fanbo Meng, Aditi Bhandari, Xiaochuan Liu, Tao Yang, Hua Chen, Babu Valliyodan, Manish Roorkiwal, Chengcheng Shi, Hong Bin Yang, Neva C. Durand, Manish K. Pandey, Guowei Li, Rutwik Barmukh, Xingjun Wang, Xiaoping Chen, Hon-Ming Lam, Huifang Jiang, Xuxiao Zong, Xuanqiang Liang, Xin Liu, Boshou Liao, Baozhu Guo, Scott Jackson, Henry T. Nguyen, Weijian Zhuang, Wan Shubo, Xiyin Wang, Erez Lieberman Aiden, Jeffrey L. Bennetzen, Rajeev K. Varshney. 2022. Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. Journal of Advanced Research, 42, pp.315-329.

Wang, R., Chen, Y., Kaur, G., Wu, X., Nguyen, H.T., Shen, R., Pandey, A.K. and Lan, P., 2022. Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency. Physiologia Plantarum, 174(5), p.e13767.

Ayalew, H., Schapaugh, W., Vuong, T. and Nguyen, H.T., 2022. Genome‐wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments. The Plant Genome, p.e20268.

Xiao, Z., Wang, Q., Li, M.W., Huang, M., Wang, Z., Xie, M., Varshney, R.K., Nguyen, H.T., Chan, T.F. and Lam, H.M., 2022. Wildsoydb DataHub: a platform for accessing soybean multiomic datasets across multiple reference genomes. Plant Physiology, 190(4), pp.2099-2102.

Lian, Y., Koch, G., Bo, D., Wang, J., Nguyen, H. T., Li, C., & Lu, W. (2022). The Spatial Distribution and Genetic Diversity of the Soybean Cyst Nematode, Heterodera glycines, in China: It Is Time to Take Measures to Control Soybean Cyst Nematode. Frontiers in Plant Science, 13, 927773.

Qu, C., Boubin, J., Gafurov, D., Zhou, J., Aloysius, N., Nguyen, H. and Calyam, P. 2022. UAV Swarms in Smart Agriculture: Experiences and Opportunities. In 2022 IEEE 18th International Conference on e-Science (e-Science) (pp. 148-158). IEEE.

Zanini, S.F., Bayer, P.E., Wells, R., Snowdon, R.J., Batley, J., Varshney, R.K., Nguyen, H.T., Edwards, D. and Golicz, A.A., 2022. Pangenomics in crop improvement—From coding structural variations to finding regulatory variants with pangenome graphs. The Plant Genome, 15(1), p.e20177.

De Oliveira, M.R., Wu, C., Harrison, D., Florez‐Palacios, L., Acuna, A., Da Silva, M.P., Ravelombola, S.F., Winter, J., Rupe, J., Shakiba, E., Wood, L.S., Chen, P., Nguyen, H.T., Mozzoni, L.A. 2022. Response to selection to different breeding methods for soybean flood tolerance. Crop Science, 62(2), pp.648-660.

Vieira, C.C., Jarquin, D., do Nascimento, E.F., Lee, D., Zhou, J., Smothers, S., Zhou, J., Diers, B., Riechers, D.E., Xu, D., Shannon, G., Nguyen, H.T., Chen, P. 2022. Identification of genomic regions associated with soybean responses to off-target dicamba exposure. Frontiers in Plant Science, 13.

Lin, Feng, Sushil Satish Chhapekar, Caio Canella Vieira, Marcos Paulo Da Silva, Alejandro Rojas, Dongho Lee, Nianxi Liu, Esteban Mariano Pardo, Yi-Chen Lee, Zhimin Dong, Jose Baldin Pinheiro, Leonardo Daniel Ploper, John Rupe, Pengyin Chen, Dechun Wang, Henry T. Nguyen. 2022. Breeding for disease resistance in soybean: a global perspective. Theoretical and Applied Genetics, pp.1-100.

Chen, Y., Wang, Z., Ye, H., Liu, S., Nguyen, H.T., Lam, H.M. and Siddique, K.H., 2022. Root physiology and morphology of soybean in relation to stress tolerance. Soybean Physiology and Genetics, 102, pp.77-103.

Vieira, C.C., Sarkar, S., Tian, F., Zhou, J., Jarquin, D., Nguyen, H.T., Zhou, J. and Chen, P., 2022. Differentiate soybean response to off-target dicamba damage based on UAV imagery and machine learning. Remote Sensing, 14(7), p.1618.

Gill, M., Anderson, R., Hu, H., Bennamoun, M., Petereit, J., Valliyodan, B., Nguyen, H.T., Batley, J., Bayer, P.E. and Edwards, D., 2022. Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction. BMC Plant Biology, 22(1), pp.1-8.

Marsh, J.I., Hu, H., Petereit, J., Bayer, P.E., Valliyodan, B., Batley, J., Nguyen, H.T. and Edwards, D., 2022. Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003. Theoretical and Applied Genetics, 135(4), pp.1443-1455.

Vieira, C.C., Zhou, J., Usovsky, M., Vuong, T., Howland, A.D., Lee, D., Li, Z., Zhou, J., Shannon, G., Nguyen, H.T. and Chen, P., 2022. Exploring machine learning algorithms to unveil genomic regions associated with resistance to southern root-knot nematode in soybeans. Frontiers in Plant Science, 13.

Canella Vieira, C., Zhou, J., Cross, C., Heiser, J.W., Diers, B., Riechers, D.E., Zhou, J., Hernandez Jarquin, D., Nguyen, H., Shannon, J.G. and Chen, P., 2022. Differential responses of soybean genotypes to off‐target dicamba damage. Crop Science, 62(4), pp.1472-1483.

Chen, P., Shannon, G., Vieira, C.C., Nascimento, E.F., Ali, M.L., Lee, D., Scaboo, A., Crisel, M., Smothers, S., Clubb, M. and Nguyen, H.T., 2022. Registration of ‘S16‐14801C’: A high‐yielding determinate maturity group V soybean cultivar with multiple disease resistance, salt tolerance, and broad adaptation. Journal of Plant Registrations, 16(3), pp.564-575.

Chen, P., Md Liakat Ali, J. Grover Shannon, Caio Canella Vieira, Dongho Lee, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Andrew Scaboo, Mariola Usovsky, Henry Nguyen, Melissa Mitchum, Zenglu Li, Jason P. Bond, Clinton G. Meinhardt, Shuxian Li, Anne M. Gillen, Alemu Mengistu, Robert T. Robbins, Leandro Angel Mozzoni, Bo Zhang, James Rusty Smith, J. Blair Buckley, David Moseley. 2022. Registration of ‘S16-11651C’, a conventional soybean cultivar with high yield, resistance to multiple diseases, and broad adaptation. J Plant Registrations. https://doi.org/10.1002/plr2.20224

Pengyin Chen, J. Grover Shannon, Caio Canella Vieira, Emanuel Ferrari do Nascimento, M. Liakat Ali, Dongho Lee, Andrew Scaboo, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Henry Nguyen, Zenglu Li, Melissa Goellner Mitchum, Jason P. Bond, Clinton G. Meinhardt, Mariola Usovsky, Shuxian Li, Anne M. Gillen, James R. Smith, Alemu Mengistu, Bo Zhang, Leandro Angel Mozzoni, Robert T. Robbins, David Moseley. 2022. Registration of ‘S16‐3747GT’: A high‐yielding determinate maturity group V soybean cultivar with broad biotic and abiotic stressors tolerance. Journal of Plant Registrations, 16(3), pp.550-563.

Chen, P., G. Shannon, C.C. Vieira, M.L. Ali, D. Lee, A. Scaboo, M. Crisel, S. Smothers, M. Clubb, S. Selves, H.T. Nguyen, Z. Li, M.G. Mitchum, J. Bond, C. Meinhardt, M. Usovsky, S. Li, A. Gillen, A. Mengistu, B. Zhang, L. Mozzoni, R.T. Robbins, and D. Moseley. 2022. Registration of ‘S16-15170C’ Soybean: A High-yielding Indeterminate Maturity Group V Cultivar with Wide Adaptability and Multiple Disease Resistance. J. Plant Reg. doi:10.1002/plr2.20220.

Ravelombola, F., Chen, P., Vuong, T., Nguyen, H., Mian, R., Acuña, A., Florez-Palacios, L., Wu, C., Harrison, D., De Oliveira, M. and Winter, J., 2022. Genetics of seed protein and oil inherited from “BARC-7” soybean in two F2-derived mapping populations. Journal of Crop Improvement, 36(6), pp.875-891.

Usovsky M, Robbins RT, Fultz Wilkes J, Crippen D, Shankar V, Vuong TD, Agudelo P, Nguyen HT. Classification Methods and Identification of Reniform Nematode Resistance in Known Soybean Cyst Nematode-Resistant Soybean Genotypes. 2022. Plant Dis. 2022 Feb 1:PDIS01210051RE. doi: 10.1094/PDIS-01-21-0051-RE. Epub ahead of print. PMID: 34494868.

Derrick Harrison, Maria Roberta De Oliveira, Chengjun Wu, Liliana Florez-Palacios, Andrea Acuna, Marcos Paulo da Silva, Seconde Francia Ravelombola, Joshua Winter, Kristofor Brye, Ryan Dickson, Alejandro Rojas, Pengyin Chen, Henry T. Nguyen, Leandro Angel Mozzoni. 2022. Developing a high‐throughput method to screen soybean germplasm for hypoxia tolerance in a hydroponic system. Crop Science, 62(2), pp.592-609.

Salim M, Chen Y, Ye H, Nguyen HT, Solaiman ZM, Siddique KHM. Screening of Soybean Genotypes Based on Root Morphology and Shoot Traits Using the Semi-Hydroponic Phenotyping Platform and Rhizobox Technique. Agronomy. 2022; 12(1):56. https://doi.org/10.3390/agronomy12010056.

Chen. P., G. Shannon, D. Lee, C.C. Vieira, M.L. Ali, A. Scaboo, M. Crisel, S. Smothers, M. Clubb, S. Selves, H.T. Nguyen, Z. Li, M.G. Mitchum, J. Bond, C. Meinhardt, M. Usovsky, S. Li, A. Gillen, A. Mengistu, B. Zhang, L. Mozzoni, R.T. Robbins, and D. Moseley. 2022. ‘S16-7922C’: A semi-determinate maturity group IV conventional soybean cultivar with high yield and broad disease resistance. J. Plant Reg. doi: 10.1002/plr2.20211.

Chen, P., G. Shannon, A. Scaboo, M. Crisel, S. Smothers, M. Clubb, S. Selves, C.C. Vieira, M.L. Ali, D. Lee, N. Lord, H.T. Nguyen, Z. Li, M.G. Mitchum, J. Bond, C. Meinhardt, M. Usovsky, S. Li, A. Mengistu, B. Zhang, L. Mozzoni, and R.T. Robbins. 2022. ‘S16-14730C’: A high-yielding maturity group IV conventional soybean variety with indeterminate growth habit and multiple disease resistance adapted to the Mid-South. J. Plant Reg. doi: 10.1002/plr2.20208

2021

Bayer, Philipp E., Babu Valliyodan, Haifei Hu, Jacob Marsh, Yuxuan Yuan, Tri D. Vuong, Gunvant Patil, Qijian Song, Jacqueline Batley, Rajeev K. Varshney, Hon-Ming Lam, David Edwards, Henry T. Nguyen. (2021). Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome. 24 June 2021 https://doi.org/10.1002/tpg2.20109

Mariola Usovsky, Naoufal Lakhssassi, Gunvant B. Patil, Tri D. Vuong, Sarbottam Piya, Tarek Hewezi, Robert T. Robbins, Robert M. Stupar, Khalid Meksem, Henry T. Nguyen. (2021). Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes. Plant Genome. 2021 Mar 16:e20083. doi: 10.1002/tpg2.20083. Epub ahead of print. PMID: 33724721.

Mahendar Thudi, Ramesh Palakurthi, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Odeny, Vijay K. Tiwari, Hon-Ming Lam, Yan Bin Hong, Vikas K. Singh, Guowei Li, Yunbi Xu, Xiaoping Chen, Sanjay Kaila, Henry Nguyen, Sobhana Sivasankar, Scott A. Jackson, Timothy J. Close, Wan Shubo, Rajeev K. Varshney. (2021). Genomic resources in plant breeding for sustainable agriculture. J. Plant Physiology. 2021 Feb;257:153351. doi: 10.1016/j.jplph.2020.153351. Epub 2020 Dec 17. PMID: 33412425; PMCID: PMC7903322.

Miftahudin, Dewi Indriyani Roslim, Miftahul Huda Fendiyanto, Rizky Dwi Satrio, Ahmad Zulkifli, Eka Indah Umaiyah, Tatik Chikmawati, Henry T. Nguyen, J. Perry Gustafson. OsGERLP, A Novel Gene Encoding a Ribosomal L32-like Protein Isolated from Indonesian Local Rice cv. Hawara Bunar Enhances Aluminum Tolerance in Rice and Transgenic Tobacco. OsGERLP: A novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia.(2021). Plant Physiol Biochem. 2021 May;162:86-99. doi: 10.1016/j.plaphy.2021.02.019. Epub 2021 Feb 21. PMID: 33667970.

Jing Zhou, Jianfeng Zhou, Heng Ye, Md Liakat Ali, Pengyin Chen, Henry T. Nguyen. Yield estimation of soybean breeding lines under drought stress using unmanned aerial vehicle-based imagery and convolutional neural network. (2021). Biosystems Engineering. https://doi.org/10.1016/j.biosystemseng.2021.01.017

Zhou L, Song L, Lian Y, Ye H, Usovsky M, Wan J, Vuong TD, Nguyen HT. Genetic characterization of qSCN10 from an exotic soybean accession PI 567516C reveals a novel source conferring broad-spectrum resistance to soybean cyst nematode. Theor Appl Genet. 2021 Jan 4. doi: 10.1007/s00122-020-03736-4.

Usovsky M, Ye H, Vuong TD, Patil GB, Wan J, Zhou L, Nguyen HT. Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. Theor Appl Genet. 2021 Feb;134(2):621-631. doi: 10.1007/s00122-020-03718-6. Epub 2020 Nov 13.

Torkamaneh D, Laroche J, Valliyodan B, O’Donoughue L, Cober E, Rajcan I, Vilela Abdelnoor R, Sreedasyam A, Schmutz J, Nguyen HT, Belzile F. Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics. Plant Biotechnol J. 2021 Feb;19(2):324-334. doi: 10.1111/pbi.13466. Epub 2020 Sep 14.

Valliyodan B, Brown AV, Wang J, Patil G, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R, Marri P, Reddy S, Sessions A, Wu X, Grant D, Bayer PE, Roorkiwal M, Varshney RK, Liu X, Edwards D, Xu D, Joshi T, Cannon SB, Nguyen HT. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Nature Sci Data. 2021 Feb 8;8(1):50. doi: 10.1038/s41597-021-00834-w.

Caio Canella Vieira, Pengyin Chen, Mariola Usovsky, Tri Vuong, Amanda D. Howland, Henry T. Nguyen, Zenglu Li, Melissa G. Mitchum, Grover Shannon. (2021). A major quantitative trait locus resistant to southern root‐knot nematode sustains soybean yield under nematode pressure. Crop Science https://doi.org/10.1002/csc2.20443

de Ronne M, Santhanam P, Cinget B, Labbé C, Lebreton A, Ye H, Vuong TD, Hu H, Valliyodan B, Edwards D, Nguyen HT, Belzile F, Bélanger R. Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL. Plant Genome. 2021 Dec 28:e20184. doi: 10.1002/tpg2.20184. Epub ahead of print. PMID: 34964282.

Zemaitis K J, Ye H, Nguyen H T, et al. Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max. Metabolites, 2021, 11(12): 843.

Liu, S., Begum, N., An, T., Zhao, T., Xu, B., Zhang, S., Deng, X., Lam, H.M., Nguyen, H.T., Siddique, K.H. and Chen, Y., 2021. Characterization of root system architecture traits in diverse soybean genotypes using a semi-hydroponic system. Plants, 10(12), p.2781.

Zhou, Z., Lakhssassi, N., Knizia, D., Cullen, M.A., El Baz, A., Embaby, M.G., Liu, S., Badad, O., Vuong, T.D., AbuGhazaleh, A. and Nguyen, H.T., 2021. Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed. Theoretical and Applied Genetics, 134, pp.3611-3623.

Rajeev K. Varshney, Manish Roorkiwal, Shuai Sun, Prasad Bajaj, Annapurna Chitikineni, Mahendar Thudi, Narendra P. Singh, Xiao Du, Hari D. Upadhyaya, Aamir W. Khan, Yue Wang, Vanika Garg, Guangyi Fan, Wallace A. Cowling, José Crossa, Laurent Gentzbittel, Kai Peter Voss-Fels, Vinod Kumar Valluri, Pallavi Sinha, Vikas K. Singh, Cécile Ben, Abhishek Rathore, Ramu Punna, Muneendra K. Singh, Bunyamin Tar’an, Chellapilla Bharadwaj, Mohammad Yasin, Motisagar S. Pithia, Servejeet Singh, Khela Ram Soren, Himabindu Kudapa, Diego Jarquín, Philippe Cubry, Lee T. Hickey, Girish Prasad Dixit, Anne-Céline Thuillet, Aladdin Hamwieh, Shiv Kumar, Amit A. Deokar, Sushil K. Chaturvedi, Aleena Francis, Réka Howard, Debasis Chattopadhyay, David Edwards, Eric Lyons, Yves Vigouroux, Ben J. Hayes, Eric von Wettberg, Swapan K. Datta, Huanming Yang, Henry T. Nguyen, Jian Wang, Kadambot H. M. Siddique, Trilochan Mohapatra, Jeffrey L. Bennetzen, Xun Xu & Xin Liu. Nature, 2021, 599(7886): 622-627.

Knizia D, Yuan J, Bellaloui N, Vuong T, Usovsky M, Song Q, Betts F, Register T, Williams E, Lakhssassi N, Mazouz H, Nguyen HT, Meksem K, Mengistu A, Kassem MA. The Soybean High Density ‘Forrest’ by ‘Williams 82’SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content. Plants, 2021, 10(10): 2029.

Vuong, T.D., Sonah, H., Patil, G., Meinhardt, C., Usovsky, M., Kim, K.S., Belzile, F., Li, Z., Robbins, R., Shannon, J.G. and Nguyen, H.T., 2021. Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305. Theoretical and Applied Genetics, 134, pp.3379-3395.

Virender Kumar,Sanskriti Vats,Surbhi Kumawat,Ashita Bisht,Vacha Bhatt,S. M. Shivaraj,Gunashri Padalkar,Vinod Goyal,Sajad Zargar,Sanjay Gupta,Giriraj Kumawat,Subhash Chandra,V. Celia Chalam,Milind B. Ratnaparkhe,Balwinder S. Gill,Martine Jean,Gunvant B. Patil,Tri Vuong,Istvan Rajcan,Rupesh Deshmukh,Francois Belzile,Tilak Raj Sharma, Henry T. Nguyen &Humira Sonah. Omics advances and integrative approaches for the simultaneous improvement of seed oil and protein content in soybean (Glycine max L.). Critical Reviews in Plant Sciences, 2021, 40(5): 398-421.

Zhou, J., Mou, H., Zhou, J., Ali, M.L., Ye, H., Chen, P. and Nguyen, H.T., 2021. Qualification of soybean responses to flooding stress using UAV-based imagery and deep learning. Plant Phenomics, 2021.

Li, Y., Ye, H., Song, L., Vuong, T.D., Song, Q., Zhao, L., Shannon, J.G., Li, Y. and Nguyen, H.T., 2021. Identification and characterization of novel QTL conferring internal detoxification of aluminium in soybean. Journal of Experimental Botany, 72(13), pp.4993-5009.

Lakhssassi N, Lopes-Caitar VS, Knizia D, Cullen MA, Badad O, El Baze A, Zhou Z, Embaby MG, Meksem J, Lakhssassi A, Chen P, AbuGhazaleh A, Vuong TD, Nguyen HT, Hewezi T, Meksem K. 2021. TILLING-by-Sequencing+ Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. Cells.10(5):1245..

Deshmukh, R., Rana, N., Liu, Y., Zeng, S., Agarwal, G., Sonah, H., Varshney, R., Joshi, T., Patil, G.B. and Nguyen, H.T., 2021. Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Physiologia Plantarum, 171(4), pp.756-770.