Soybean Molecular Biology and Molecular Design Breeding
Team name
Soybean Molecular Biology and Molecular Design Breeding
Principal Investigator
Research Objectives
Soybeans are an important food crop all around the world, and are also a major source of oil and protein. Soybeans are the typical short-day crops and are highly sensitive to day length.In photoperiod-sensitive short-day crops, long-day conditions hinder the initiation of flowering. Photoperiod regulation of soybean flowering time not only affects its regional adaptability, but also affects yield. Therefore, mastering the molecular regulation mechanism of photoperiod-induced soybean flowering has important guiding significance for cultivating high-yield soybeans. In addition, soybeans are susceptible to stress during their growth and development (saline-alkali, drought, and high temperature, etc.). Therefore, discovering and utilizing key stress-tolerant genes are crucial to developing new stress-tolerant soybean varieties. This research group will comprehensively use molecular genetics, genomics, cell biology, biochemistry and other methods to create and collect chromatin modification-related mutants in soybean, reveal the chromatin modification regulationmechanism in soybean growth and development by external environmental factors (photoperiod, stress, etc.), and explore the genetic network of the interaction between external environmental factors and soybean. Our research will provide a theoretical basis for soybean molecular design breeding.
The main research directions are as follows:
l The role and mechanism of chromatin modification in soybean flowering
l The mechanism and genetic network of soybean chromatin modification factors in soybean response to environmental stress
l Germplasm enhancement and genetic improvement of soybean
Selected Publications
*Corresponding author; #Co-first author
1.Xiulin Liu#, Chengyang Song#, Yuanyuan Cui, Yu Sun, Xiaofei Ma, Qianyi Luo, Xuan Rong, Zhaohan Zhang, Xing Wang Deng, Xiao Luo*. The Jumonji C domain-containing proteins GmJMJ19 and GmJMJ20 link florigen signaling with epigenetic regulation of photoperiodic flowering and post-flowering plant height in soybean. Plant Communications 2026, doi: https://doi.org/10.1016/j.xplc.2026.102094 (Corresponding author).
2. Shu Tian#, Xiao Luo#, Bowen Cui, Yuehui He*. Auto-downregulation of the florigen FT production prevents precocious flowering in plants. Advanced Science 2026, e22307 (First equal author).
3. Na Zheng#, Can Huang#, Chengyang Song#, Xiaofei Ma, Wenwen Ren, Xiulin Liu, Zhaohan Zhang, Lingyang Feng, Shangwei Zhong, Xing Wang Deng, Xiao Luo*. Antagonistic chromatin regulation of LHY homologs by GmASH2R and GmNF-YC4 fine-tunes flowering time for latitudinal adaptation in soybean. Plant Communications 2026, 101917 (Corresponding author).
4. Leili Wang#, Chengyang Song, Zhu Yan, Tianqi Wang, Yisheng Fang, Xiulin Liu, Junlong Bao, Dan Zhu, Xiao Luo*. Comprehensive analysis of m6A-regulatory genes in soybean uncovers GmMTBa as a critical determinant of salt stress tolerance. aBIOTECH 2026, 7:100046 (Corresponding author).
5. Xiao Luo# * , Xueqin Li*, Zhijuan Chen*, Shu Tian*, Yajie Liu, Zhiyun Shang, Lixian Chen, Yu Sun, Jiamu Du#, Yuehui He#. A pair of readers of histone H3K4 methylation recruit Polycomb repressive complex 2 to regulate photoperiodic flowering. Nature Communications 2025, 16:9376 (Corresponding author and First author)
6. Wanying Zhang#, Chengyang Song#, Tianqi Wang#, Xiulin Liu, Yisheng Fang, Zhu Yan, Yaxi Zhu, Na zheng, Xiaofei Ma, Guochen Qin, Dan Zhu, Junchuan Xiao, Xing Wang Deng, Xiao Luo*. Reprogramming of gene transcripts and metabolites by the wild soybean endophyte Pseudomonas sp. 77S3 improves soybean salt tolerance.Plant Biotechnology Journal 2025, DOI: 10.1111/pbi.70514 (Corresponding author)
7. Qing Yang#, Zhi-Yang Hou#, Linxia Li#, Leili Wang#, Shang-Tong Li, Yaping Li, …Xiaofeng Gu, Zhe Yan, Faming Wang, Xiao Luo*, Long Yan*, and Zhe Liang*. Landscape and m6A post-transcriptional regulation of soybean proteome. Cell Genomics 2025, 5(9):100926 (Co-Corresponding author, Cover article)
8. Xiao Luo# *, Xiulin Liu#, Na Zheng#, Chengyang Song, Yuehui He. Molecular mechanisms of temperature-mediated flowering regulation: From Arabidopsis to Short-Day Crops. Plant, Cell & Environment 2025, 48(9), 7020-7037 (Corresponding author and First author)
9. Yan Xue*, Xiaofeng Cao*, Xiangsong Chen*, Xian Deng*, Xing Wang Deng*, Yong Ding*, Aiwu Dong*, Cheng-Guo Duan*, Xiaofeng Fang*, Lei Gong*, Zhizhong Gong*, Xiaofeng Gu*, Chongsheng He*, Hang He*, Shengbo He*, Xin-Jian He*, Yan He*, Yuehui He*, Guifang Jia*, Danhua Jiang*, Jianjun Jiang*, Jinsheng Lai*, Zhaobo Lang*, Chenlong Li*, Qing Li*, Xingwang Li*, Bao Liu*, Bing Liu*, Xiao Luo*., et al. Epigenetics in the modern era of crop improvements. Science China-Life Sciences 2025, 68(6):1570-1609 (Corresponding author)
10. Fei Huang#, Xiao Luo#, Yang Ou#, & Zhaoxu Gao#, Qiming Tang, Zhenzhen Chu, Xinguang Zhu, Yuehui He*. Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science 2023, 381 (6654): eadf8822. 10.1126/science.adf8822 (First equal author)
11. Zhicheng Zhang#, Xiao Luo#, Yupeng Yang, Yuehui He*. Cold induction of nuclear FRIGIDA condensation in Arabidopsis. Nature 2023, 619, E27–E32 (First equal author)
12. Myeongjune Jeon#, Goowon Jeong, Yupeng Yang, Xiao Luo, Daesong Jeong, Jinseul Kyung, Youbong Hyun, Yuehui He*, Ilha Lee*. Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes. eLife 2023,12:e84594 (co-author)
13. Hong Zhai#, Zhao Wan, Shuang Jiao, Jingwen Zhou, …Tian Pang, Xiao Luo, Hongyan Wu, Guang Yang, Xi Bai, Fanjiang Kong, Zhengjun Xia*. GmMDE genes bridge the maturity gene E1 and florigens in photoperiodic regulation of flowering in soybean. Plant Physiology 2022, 189(2), 1021–1036 (co-author)
14. Zicong Li#, Xiao Luo#, Yang Ou#, Huijun Jiao, Li Peng, Xing Fu, Alberto P Macho, Renyi Liu&Yuehui He*. JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis. Molecular Plant 2021, 14(5):732-747 (First equal author)
15. Xiao Luo#, Yang Ou#, Renjie Li# & Yuehui He*. Maternal transmission of the epigenetic 'memory of winter cold' in Arabidopsis. Nature Plants 2020, 6(10):1211-1218. (First author)
16. Xiao Luo#, Yuehui He*.Experiencing winter for spring flowering – a molecular epigenetic perspective on vernalization.Journal of Integrative Plant Biology 2020, 62(1): 104-117 (First author, ESI Highly Cited Paper)
17. Ying Zhu#, Xiao Luo#, Xuxin Liu#, Wenjuan Wu, Xiaofeng Cui, Yuehui He*& Jirong Huang*. Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth. Journal of Integrative Plant Biology, 2020, 62 (6): 812-831. (First equal author)
18. Xiao Luo#, Tao Chen#, Xiaolin Zeng, Dingwei He & Yuehui He*. Feedback regulation of FLC by FLOWERING LOCUS T (FT) and FD through a 5'FLC promoter region in Arabidopsis. Molecular Plant 2019, 12(3): 285~288 (First author)
19. Zeng Tao#, Hongmiao Hu#, Xiao Luo#, Bei Jia, Jiamu Du* & Yuehui He* Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis. Nature Plants 2019, 5(4): 424–435 (First equal author)
20. Xiao Luo#, Zheng Gao#, Yizhong Wang, Zhijuan Chen, Wenju Zhang, Jirong Huang, Hao Yu, Yuehui He*. The NUCLEAR FACTOR-CONSTANS complex antagonizes Polycomb repression to de-repress FLOWERING LOCUS T expression in response to inductive long days in Arabidopsis. Plant Journal 2018, 95(1): 17~29 (First author)
21. Wenya Yuan#, Xiao Luo, Zicong Li, Wannian Yang, Yizhong Wang, Rui Liu, Jiamu Du*& Yuehui He*. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nature Genetics 2016, 48(12): 1527~1534 (co-author)
22. Zicong Li#, Danhua Jiang#, Xing Fu, Xiao Luo, Renyi Liu, Yuehui He*. Coupling of histone methylation and RNA processing by the nuclear mRNA cap-binding complex. Nature Plants 2016, 2(3):1-10 (co-author)
Honors and Awards
1. The National Youth Talent Support Program, 2024
2. The Young Taishan Scholars Program of Shandong Province, 2022
3. "Most Outstanding Science and Technology Worker of Weifang City" Award (2023)
4.The Yuan du Scholars Program of Weifang City (2021)
5. Excellent Young Scholars of Natural Science Foundation of Shandong Province, 2021
patents
1. Xiao Luo, Wanying Zhang, Jianwei Tian, Yisheng Fang; Wild soybean endophyte Pseudomonas sp. 77S3, bacterial agent, and applications in improving soybean salt tolerance; ZL 2023 1 0918701.2; 11-02-2025; CN 118086092 B; China;
2. Xiao Luo, Yaxi Zhu; Method and applications for controlling soybean plant height and/or delaying flowering time; ZL 2024 1 1724789.5; 07-03-2025; CN 119220592 B; China;
3. Xiao Luo, Yu Sun, Yuehui He, Xunde Zheng, Xiulin Liu; Method and applications for simultaneously regulating soybean plant height and flowering time; ZL 2025 1 0233658.5; 22-07-2025; CN 119709855 B; China;
4. Xiao Luo, Xiulin Liu, Yuehui He, Yuanyuan Cui, Yu Sun; Method and applications for regulating soybean plant height; ZL 2025 1 0382487.2; 22-07-2025; CN 119876255 B; China;
5. Xiao Luo, Xiulin Liu, Yuanyuan Cui; Application of histone demethylase GmJD5L in regulating soybean flowering time and plant height; ZL 2025 1 1749165.3; China.
6. Xiao Luo, Zhaohan Zhang, Mingyue Jiang, Wenya Yuan, Yanan Wang; Application of GmRCP1 gene in regulating soybean plant height and flowering time; ZL 2026 1 0399094.7; China.
7. Xiao Luo, Tianqi Wang, Xiulin Liu, Zhu Yan, Xingwang Deng; Method and applications for increasing flavonoid compound content in soybean seeds; ZL 2025 1 1323436.9; China.
8. Xiao Luo, Yu Sun, Yisheng Fang; Protein for synergistically improving soybean yield and protein content, and biological materials and applications thereof; 202611014612.5; China.
9. Xiao Luo, Chengyang Song; Plant data acquisition device; ZL 2023 2 0835779.3; 02-06-2024; CN 220455175 U; China
10. Wenxiu Ye, Linling Guo, Jiao Jiao, Xiao Luo, Jizong Wang, Yaqian Zhu, Yan Wang; Application of a flavonoid compound and derivatives; ZL 2023 1 0767316.2; 19-11-2024; CN 116803268 B; China.
Research Projects
1. PI, 2026-2029, Elucidating the molecular mechanisms of photoperiodic flowering time regulation in soybean coordinated by metabolism and chromatin modifications; National Natural Science Foundation of China; 32570416; ¥0.50 million.
2. PI, 2025-2027, Elucidating the chromatin modification mechanisms of flowering regulation in Arabidopsis and Soybean; National youth talent support program; SQ2024QB02503; ¥1.8 million.
3. PI, 2025-2029, Matching Funds from Shandong Province for the National youth talent support program; ¥1.25 million.
4. PI, 2024-2027, Identification of chromatin regulatory factors mediating photoperiod regulation of flowering time and protein-oil content in soybean; National Key Research and Development Program of China; 2024YFF1000303; ¥1.2 million.
5. PI, 2023-2026, Construction of soybean saturation mutant library and mining of key agronomic trait regulatory genes; Major research program of Shandong Laboratory of Advanced Agricultural Sciences in Weifang, ¥2.25 million.
6. PI, 2022-2025, Young Taishan Scholars Program of Shandong Province, ¥0.75 million, Rated Excellent in Final Evaluation
7. PI, 2022-2025, Yuandu Scholars Program of Weifang, ¥0.4 million.
8. PI, 2022-2025, Matching Funds from Weifang City for the Taishan Scholars Program, ¥0.6 million.
9. PI, 2022-2024, Elucidating the role and molecular mechanism of soybean histone reader protein INGs in photoperiodic regulation of flowering; Excellent Young Scholars fund of Natural Science Foundation of Shandong Province; ZR2021YQ16; ¥0.4 million, Rated Excellent in Final Evaluation
10. PI, 2022-2024, Screening, functional characterization, and molecular mechanism study of endophytic bacteria for enhancing soybean saline-alkali tolerance; Director’s research fund from Peking University Institute of Advanced Agricultural Sciences, ¥0.9 million.
11. PI, 2020-2023, Elucidating photoperiodic flowering-time regulation by two homologous histone marker readers in Arabidopsis thaliana; National Natural Science Foundation of China; 31970327; ¥0.58 million.
12.Co-Investigator (Second in contribution), 2019-2023, Molecular epigenetic mechanisms of early embryonic reset of "vernalization memory" in plants, Key Program of the National Natural Science Foundation of China; 31830049; ¥2.82 million.
13. PI, 2022-2023, Screening of salt-alkali tolerant soybean germplasm resources and mining of related epigenetic regulatory genes; Weifang Science and Technology Plan; 2021ZJ1299, ¥50 thousand.
14. PI, 2013-2015, Analysis of the promoter of GmTFL1b, a gene involved in soybean stem growth habit regulation, National Natural Science Funding for Young Scientist; 31201223; ¥0.24 million.
Team members
（姓名，学位，专业，职称，在本团队从事的工作）
（团队核心成员也可以包括与PI相似的CV，可通过点击姓名进入；请根据需要提供团队核心成员的CV，一般应具有副高级职称或博士学位；请提供核心成员最新登记照片或头像比较大的工作照一张）
l Liu Xiulin, Ph.D. in Botany, assistant professor, The function of histone demethylation in soybean adaptation to environment.
l Fang Yisheng, Ph.D. in crop genetics and breeding, assistant professor,, trait discovery for soybean abiotic stress tolerance
l Na Zheng, Ph.D. in plant pathology, assistant professor, histone lysine methylation in soybean.
l Yaxi Zhu，Ph.D in biochemistry and molecular biology, research associate, to explore the mechanism of soybean FT regulation
Research Projects
l Elucidating photoperiodic flowering-time regulation by two homologous histone marker readers in Arabidopsis thaliana, National Natural Science Funding (Grant no.31970327), 2020.01-2023.12; Project objectives: This project will reveal the molecular mechanisms underlying FT regulation by two homologous histone marker readers, and explore the dynamic control of FT expression by chromatin modifications in response to long-day.
l Study on the role and molecular mechanism of soybean histone reading proteins in photoperiodic regulation of flowering. Shandong Provincial Science Foundation for Outstanding Youth (Grant no. ZR2021YQ16), 2022.01-2024.12; Project objectives: This project will reveal the function of histone reading protein homologous in soybean photoperiodic flowering pathway, and analyze the molecular mechanism of soybean FT expression by chromatin modifications under short-day conditions.
l The study of soybean histone demethylase JMJ in photoperiodic regulation of flowering time. Shandong Provincial Natural Science Foundation (Grant no. ZR2022QC262). 2023.01-2025.12;Project objectives: This project will reveal the response of soybean histone demethylase to photoperiod and the regulation of flowering time.
l Molecular mechanism of GmFRL3a regulates drought tolerance in soybean, Shandong Provincial Natural Science Foundation (Grant no. ZR2023QC085). 2024.01-2026.12; Project objectives:This project will reveal the GmFRL3a functions in soybean flowering time and drought stress response.
l Screening of Soybean Salt-Alkali Tolerant Germplasm Resources and Mining of Related Genes, Weifang Science and Technology Planning Project (Grant no. 2021ZJ1299), 2021.10-2023.12;Project objectives: This project will focus on soybean salt-tolerant germplasm resources collection, evaluation and gene discovery and allele mining for salt tolerance
Research Achievements
Revealing the molecular mechanism of plant gene expression regulationbyα-ketoglutarate dehydrogenase (Science, 2023: 381. eadf8822. 10.1126, cooperation with Yuehui He Lab).
In eukaryotes, histone methylation modification plays an important role in regulating chromatin structure, gene transcription and other chromatin-related processes. Jumonji C (JmjC) domain-containing demethylases (JMJs) play an important role in dynamically controlling histone methylation levels. However, the universal mechanism underlying the regulation of JMJ activity remains unclear. We reported that the rate-limiting enzyme of the tricarboxylic acid cycle, α-ketoglutarate dehydrogenase (KGDH), enters the nucleus in response to light signals.KGDH interacts with JMJs proteins and inhibits the histone demethylation activity of JMJs by competitively metabolizing α-ketoglutarate, thereby regulating histone methylation modification at the genome-wide level and regulating a series of gene expression.
This research has been published in Science titled as “Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase”, Science also published a review article “Metabolic control of transcription”for our research, indicating that light changes histone methylation in plants through nuclear α-ketoglutarate dehydrogenase.
Selected Publications
Fei Huang #, Xiao Luo#, Yang Ou#, &Zhaoxu Gao#, Qiming Tang, Zhenzhen Chu, Xinguang Zhu, Yuehui He*.2023. Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science. 381. eadf8822. 10.1126/science.adf8822.
Zhicheng Zhang#, Xiao Luo#,Yupeng Yang,Yuehui He*.2023. Cold induction of nuclear FRIGIDA condensation in Arabidopsis.Nature 619, E27–E32. https://doi.org/10.1038/s41586-023-06189-z
Zicong Li#, Xiao Luo#, Yang Ou#, Huijun Jiao, Li Peng, Xing Fu, Alberto P Macho, RenyiLiu&Yuehui He*.2021.JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis. Molecular Plant,14(5):732-747.
Zhaohan Zhang, Wanpeng Wang, Shahid Ali, Xiao Luo*, Linan Xie*.2022. CRISPR/Cas9-mediated multiple knockouts in abscisic acid receptor genes reduced the sensitivity to ABA during soybean seed germination. Int. J. Mol. Sci. 2022,18;23(24):16173.
Myeongjune Jeon, Goowon Jeong, Yupeng Yang, Xiao Luo, Daesong Jeong, Jinseul Kyung, Youbong Hyun, Yuehui H, Ilha Lee.2023. Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes. eLife,12:e84594. doi: 10.7554/eLife.84594.
Hong Zhai, Zhao Wan, Shuang Jiao, Jingwen Zhou, Kun Xu, Haiyang Nan, Yingxiang Liu, Shangshang Xiong, Rong Fan, Jinlong Zhu, Wenting Jiang, Tian Pang, Xiao Luo, Hongyan Wu, Guang Yang, Xi Bai, Fanjiang Kong, Zhengjun Xia.2022.GmMDE genes bridge the maturity gene E1 and florigens in photoperiodic regulation of flowering in soybean. Plant Physiology,189(2), 1021–1036
Honorablesand Awards
Yuandu Scholar from Weifangcity forXiao Luo (2021)
Taishan Scholar-Young Expert from Shandong Province for Xiao Luo (2022)
Outstanding Scientific and Technological Workers of Weifang City for Xiao Luo (2023)