Overall our Research Contents
Our research centers on cotton as the primary target crop and utilizes synthetic biology as the enabling technology platform. We aim to enhance cotton’s insect resistance, herbicide tolerance, and the comprehensive utilization of cottonseed through the rational design and engineering of genetic circuits, regulatory elements, and metabolic pathways.
Specifically, we develop high-performance synthetic gene modules and tissue-specific or inducible expression systems to precisely control agronomically important traits. By integrating genome editing, multi-omics analysis, and metabolic pathway reconstruction, we optimize key traits and introduce novel functions. We also construct customized chassis vectors and transformation systems tailored for cotton, supporting trait stacking and multi-gene expression. Furthermore, we explore the biosynthesis of high-value compounds in cottonseed to boost its nutritional and industrial value.
The project combines fundamental research with breeding application, aiming to build a standardized and scalable platform that supports green, efficient, and intelligent cotton improvement.
Research Objectives
- Develop cotton germplasm with high insect resistance using synthetic biology-enabled metabolic pathways.
- Construct herbicide-tolerant cotton lines through precise genome editing of target genes.
- Improve cottonseed value by engineering key biosynthetic pathways to increase oil, protein, and functional metabolites.
- Build standardized synthetic biology toolkits, including promoters, regulators, and chassis vectors tailored for cotton.
- Establish a sustainable platform integrating genetic design, transformation, and trait evaluation for industrial application.
Research 1: Big Data Mining and Analytics
This research focuses on mining and analyzing large-scale multi-omics datasets—including genomics, transcriptomics, proteomics, and metabolomics—from diverse cotton germplasm and engineered lines. By integrating data from natural variation, synthetic constructs, and edited traits, we aim to identify key regulatory networks and candidate genes related to insect resistance, herbicide tolerance, and cottonseed quality. Advanced machine learning and statistical modeling will be employed to predict gene functions, prioritize engineering targets, and guide rational design.
The outcomes will provide a data-driven foundation for synthetic biology design, trait optimization, and intelligent decision-making in cotton breeding and metabolic engineering.
Representative Publications:
Research 2: Biotechnology (CRISPR and Synthetic Biology) Development
This research aims to develop advanced biotechnological tools centered on CRISPR-based genome editing and synthetic biology for cotton improvement. We will design efficient editing systems—including base editors, prime editors, and multiplex CRISPR constructs—to precisely modify genes associated with insect resistance, herbicide tolerance, and cottonseed traits.
In parallel, we will construct modular synthetic biology toolkits, such as tissue-specific promoters, inducible switches, and chassis vectors tailored for cotton. These tools will enable the precise control of gene expression and the introduction of novel biosynthetic pathways. Our goal is to establish a versatile, high-efficiency platform for engineering complex traits and accelerating the translation of molecular designs into elite cotton varieties.
Representative Publications:
- Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum)
- The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol-free cotton
- High-efficient and precise base editing of C•G to T•A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system
- Robust CRISPR/Mb2Cas12a genome editing tools in cotton plants
- Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants
- CRISPR/dCas13(Rx) Derived RNA N6-methyladenosine (m6A) Dynamic Modification in Plant
Research 3: Cotton-Insect Interaction
This research focuses on elucidating the molecular mechanisms underlying cotton-insect interactions to support the development of insect-resistant cotton varieties. Using transcriptomic, proteomic, and metabolomic approaches, we will identify key defense-related genes, regulatory networks, and metabolite signatures activated in response to major insect pests. Functional validation through gene editing and transgenic analysis will help uncover critical insect resistance pathways. We will also explore insect feeding behavior, detoxification mechanisms, and potential resistance-breaking adaptations.
These insights will guide the design of synthetic gene circuits and enable the deployment of durable insect resistance traits in cotton. The findings will provide essential targets for both breeding and biotechnological intervention.
Representative Publications:
- A transgenic strategy for controlling plant bugs (Adelphocoris suturalis) through expression of double-stranded RNA homologous to fatty acyl-coenzyme A reductase in cotton
- Utilizing the mutant library to investigate the functional characterization of GhGLR3.4 regulating jasmonic acid to defense pest infestation
- Cotton bollworm (H. armigera) effector PPI5 targets FKBP17-2 to inhibit ER immunity and JA/SA responses, enhancing insect feeding
- CRISPR-Cas9-mediated construction of a cotton CDPK mutant library for identification of insect-resistance genes
- Construction of Host Plant Insect-Resistance Mutant Library by High-Throughput CRISPR/Cas9 System and Identification of A Broad-Spectrum Insect Resistance Gene
- Comprehensive analysis of MAPK gene family in upland cotton (Gossypium hirsutum) and functional characterization of GhMPK31 in regulating defense response to insect infestation
Research 4: Genotype-Independent Efficient Transformation System
This research aims to establish a robust, genotype-independent transformation system to facilitate the application of synthetic biology and genome editing in diverse cotton varieties. We will optimize tissue culture protocols and regeneration systems, including shoot apical meristem (SAM)-based and callus-free regeneration strategies. Multiple delivery methods—such as Agrobacterium-mediated transformation, particle bombardment, electroporation, and viral delivery—will be systematically evaluated and improved.
In particular, we will explore cotton-compatible viral vectors for transient and stable gene delivery, enabling rapid functional validation and trait introduction. The integration of developmental regulators and morphogenic genes will further enhance transformation efficiency. Our goal is to build a universal, high-efficiency platform for cotton genetic improvement across genotypes.
Representative Publications:
Research 5: Cotton Ideotype Breeding
This research focuses on the design and development of cotton ideotypes with optimized plant architecture, stress resilience, and high-value seed traits. Using trait-guided breeding strategies combined with synthetic biology and genome editing, we aim to fine-tune key regulatory genes involved in branching, flowering time, fiber development, and seed composition. Multi-omics analysis and phenotyping platforms will be employed to dissect trait-genotype relationships and identify elite alleles. Molecular modules conferring insect resistance, herbicide tolerance, and enhanced seed oil/protein content will be rationally assembled into elite backgrounds.
Ultimately, we seek to develop next-generation cotton varieties with superior yield, adaptability, and multi-trait integration to meet future agricultural and industrial demands.
Representative Publications:
Research 6: Comprehensive Database Development
This research aims to build an integrated, user-friendly database system to support cotton synthetic biology and precision breeding. The platform will curate and standardize multi-omics datasets, including genome assemblies, gene annotations, regulatory elements, metabolic pathways, and trait-associated variants across diverse cotton germplasm. It will incorporate tools for sgRNA design, gene circuit simulation, pathway reconstruction, and trait prediction. Advanced visualization modules and APIs will facilitate data access and interoperability. The database will also host phenotypic, transformation, and functional validation records linked to specific constructs and genotypes.
Ultimately, this resource will serve as a central hub for data-driven design, trait optimization, and knowledge sharing across cotton research and breeding communities.