PI: Prof. Xiao-Qin XIA, PhD   

Group Members: Yaping Wang, Professor 

Phone: 027-68780119; 68780916 

Email: ljliao@ihb.ac.cn; xqxia@ihb.ac.cn 

Website: http://bioinfo.ihb.ac.cn   

Research Overview:   

This research group focuses on unraveling the genetic mechanisms of economically important traits in aquatic animals like fish and crustaceans, including disease resistance, growth, and sex control. We aim to discover key molecular markers, analyze the functions of important genes, and contribute to the breeding of new germplasm and varieties. Our research encompasses three key areas:   

(1) Integration of Genetic Breeding-related Basic Data and Platform Innovation. This involves collecting genetic diversity germplasm, conducting genome sequencing, assembly, and annotation. We also develop omics databases and bioinformatics analysis platforms, innovate high-throughput low-cost gene typing techniques for germplasm identification, and develop rapid phenotypic identification techniques based on machine vision.   

(2) Precise Localization of Trait-related Molecular Targets and Efficient Breeding of New Varieties (Lines). Targeting economic traits such as disease resistance, growth, and sex control, we utilize artificial intelligence-based platforms for genotype-phenotype association analysis. This helps us pinpoint trait-related molecular markers and functional genes, facilitating the efficient breeding of high-quality fish and crustacean germplasm or varieties.   

(3) Precise Analysis of Network Regulation Mechanisms for Economic Traits and Drug Development. Focusing on aquatic viral infection and immune escape, along with host mucosal immune responses and mechanisms, we accurately analyze the molecular mechanisms of network regulation for economic traits. We also develop alternative antibiotic herbal additive formulations and promote green control measures for aquatic diseases. 

Funding and Output: 

The research group receives funding from national key research and development projects, "Science and Technology Innovation - 2030 Major Science and Technology Projects," the National Natural Science Foundation of China, and the Chinese Academy of Sciences Strategic Priority Research Program. Over the past 5 years, the group has published over 80 SCI papers and obtained over 10 invention patents.   

Representative Publications ( # - Co-first authors, * - Corresponding authors): 

1. Fundamental Research in Genomics and Transcriptomics 

[1]     Wang YP*, Lu Y, Zhang Y, Ning ZM, Li Y, Zhao Q, Lu HY, Huang R, Xia XQ, Feng Q, Liang XF, Liu KY, Zhang L, Lu TT, Huang T, Fan DL, Weng QJ, Zhu CR, Lu YQ, Li WJ, Wen ZR, Zhou CC, Tian QL, Kang XJ, Shi MJ, Zhang WT, Jang SH, Du FK, He S, Liao LJ, Li YM, Gui B, He HH, Ning Z, Yang C, He LB, Luo LF, Yang R, Luo Q, Liu XC, Li SS, Huang W, Xiao L, Lin HR*, Han B*, Zhu ZY*. The draft genome of the grass carp (Ctenopharyngodon idellus) provides genomic insights into its evolution and vegetarian diet adaptation. Nature Genetics, 2015, 47: 625-631. 

[2]     He W#, Shi M#, Xia X-Q, Zhang W, Yao W, Gao T. The chromosome-level genome assembly of goldstripe ponyfish (Karalla daura) reveals its similarity to Chinese sillago on contracted immune gene families. Frontiers in Marine Science, 2022, 9: 1049138. 

[3]     Duan Y, Zhang Q, Jiang Y, Zhang W, Cheng Y, Shi M*, Xia X-Q*. Dynamic transcriptional landscape of grass carp (Ctenopharyngodon idella) reveals key transcriptional features involved in fish development. International Journal of Molecular Sciences, 2022, 23: 11547. 

[4]     Yang C#, Chen L#, Huang R*, Gui B, Li YYu, Li YY, Li YM, Liao L, Zhu Z, Wang Y. Screening of genes related to sex determination and differentiation in mandarin fish (Siniperca chuatsi). International Journal of Molecular Sciences, 2022, 23(14): 7692. 

[5]     He L#, Zhu D, Liang X, Li Y, Liao L, Yang C, Huang R, Zhu Z, Wang Y*. Multi-omics sequencing provides insights into age-dependent susceptibility of grass carp (Ctenopharyngodon idellus) to Reovirus. Frontiers in Immunology. 2021, 12: 694965. 

[6]     Huang R#, Shi M#, Luo L, Yang C, Ou M, Zhang W, Liao L, Li Y, Xia X, Zhu Z, Wang Y*. De novo screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation. GigaScience, 2021, 10(11):giab075. 

[7]     Ou M#, Huang R#, Yang C, Gui B, Luo Q, Zhao J, Li Y, Liao L, Zhu Z, Wang Y*, Chen K*. Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability. GigaScience, 2021; 10: 1-11. 

2. Development of Bioinformatics Tools and Databases 

[8]     Zhang L#, Li H#, Shi M*, Ren K, Zhang W, Cheng Y, Wang Y, Xia X-Q*. FishSNP: a high quality cross-species SNP database of fishes. Scientific Data, 2024, 11:286. 

[9]     Xia L#, Shi M#, Li H, Zhang W, Cheng Y, Xia X-Q*. PMSeeker: a scheme based on the greedy algorithm and the exhaustive algorithm to screen low-redundancy marker sets for large-scale parentage assignment with full parental genotyping. Biology, 2024, 13(2): 100. 

[10] Guo C#, Ye W#, Cao D, Shi M*, Zhang W, Cheng Y, Wang Y, Xia X-Q*. Unraveling the stereoscopic gene transcriptional landscape of zebrafish using FishSED, a fish spatial expression database with multispecies scalability. Science China Life Sciences, 2023. DOI: 10.1007/s11427-023-2418-2. 

[11] Guo C#, Duan Y#, Ye W, Zhang W, Cheng Y, Shi M*, Xia X-Q*, FishGET: a fish gene expression and transcriptome database with improved accuracy and visualization. iScience, 2023, 26: 106539. 

[12] Guo C#, Ye W#, Shi M*, Duan Y, Zhang W, Cheng Y, Xia X-Q*. FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. Science China Life Sciences, 2023, 66(9): 2185-2188. 

[13] Li H, Shi M*, Ren K, Zhang L, Ye W, Zhang W, Cheng Y, Xia X-Q*. Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. Bioinformatics, 2023, 39(1): btac777. 

[14] Yang C#, Huang R*, Ou M, Gui B, Zhao J, He L, Li Y, Liao L, Chen K, Wang Y*. A rapid method of sex-marker discovery based on NGS and determination of the XX / XY sex-determination type in Channa maculate. Aquaculture, 2020; 528: 735499. 

3. Antiviral, Mucosal Immunity, and Other Disease Research 

[15] Liang X#, Wang Q, Wang H, Wang X, Chu P, Yang C, Li Y, Liao L, Zhu Z, Wang Y, He L*. Grass carp superoxide dismutases exert antioxidant function and inhibit autophagy to promote grass carp reovirus (GCRV) replication. International Journal of Biological Macromolecules, 2024, 256(Pt 2): 128454. 

[16] Liu Y#, Cao D#, Wu N*, Zhao X, Zhu Q, Su L, Altaf F, Zhang Q, Liu H, Li Y, Unger BH, Cheng Y, Zhang W, Li A, Wang Y, Xia X-Q*. Sinomenine improves resistance to foodborne enteritis and anti-bacteria mucosal immunity in grass carp. Aquaculture, 2024, 581: 740364. 

[17] Zhao X#, Zhang L#, Wu N*, Liu Y, Xie J, Su L, Zhu Q, Unger BH, Altaf F, Hu Y, Ye W, Qiao Z, Cheng Y, Zhang W, Wang Y, Xia X-Q*. Gallic acid acts as an anti-inflammatory agent via PPARγ-mediated immunomodulation and antioxidation in fish gut-liver axis. Aquaculture, 2024, 578: 740142. 

[18] Ouyang G, Yuan L, Xia X-Q, Zhang W, Shi M*. Transcriptomes of zebrafish in early stages of multiple viral invasions reveal the role of sterols in innate immune switch-on. International Journal of Molecular Sciences, 2023, 24: 4427. 

[19] Zhao X#, Liu Y#, Xie J, Guo C, Li H, Cheng Y, Zhang W, Su L, Wu N*, Xia X-Q*. The manipulation of cell suspensions from zebrafish intestinal mucosa contributes to understanding enteritis. Frontiers in Immunology, 2023, 14: 1193977. 

[20] Shan J#, Wang G#, Li H, Zhao X, Ye W, Su L, Zhu Q, Liu Y, Cheng Y, Zhang W, Wu N*, Xia X-Q*. The immunoregulatory role of fish specific type II SOCS via inhibiting metaflammation in gut-liver axis. Water Biology and Security, 2023, 2(2): 100131. 

[21] He L*, Wang Q, Liang X, Wang H, Chu P, Yang C, Li Y, Liao L, Zhu Z, Wang Y*. Grass carp reovirus induces formation of lipid droplets as sites for its replication and assembly. mBio. 2022, 13(6): e0229722. 

[22] He L*, Liang X, Wang Q, Yang C, Li Y, Liao L, Zhu Z, Wang Y*. Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp. Immunity & Ageing. 2022, 19(1): 28. 

[23] Xie J#, Li M#, Ye W, Shan J, Zhao X, Duan Y, Liu Y, Unger BH, Cheng Y, Zhang W, Wu N*, Xia X-Q*. Sinomenine hydrochloride ameliorates fish foodborne enteritis via α7nAchR mediated anti-inflammatory effect whilst altering microbiota composition. Frontiers in Immunology, 2021, 12: 766845. 

[24] Li M#, Zhao X#, Xie J, Tong X, Shan J, Shi M, Wang G, Ye W, Liu Y, Unger BH, Cheng Y, Zhang W, Wu N*, Xia X-Q*. Dietary inclusion of seabuckthorn (Hippophae rhamnoides) mitigates foodborne enteritis in zebrafish through the gut-liver immune axis. Frontiers in Physiology, 2022, 13:831226. 

[25] Chu P, He L*, Huang R, Liao L, Li Y, Zhu Z, Hu W, Wang Y*. Autophagy inhibits grass carp reovirus (gcrv) replication and protects Ctenopharyngodon idella kidney (CIK) cells from excessive inflammatory responses after gcrv infection. Biomolecules, 2020, 10: 1296-1318. 

[26] Li Y, Huang R*, Chen L, Li Y, Li YM, Liao L, He L, Zhu Z, Wang Y. Characterization of SR-B2a and SR-B2b genes and their ability to promote GCRV infection in grass carp (Ctenopharyngodon idellus). Developmental & Comparative Immunology 2021; 124: 104202. 

[27] Chen L, Huang R*, Li Y, Li YM, Liao L, He L, Zhu Z, Wang Y. Genome-wide identification, evolution of Krüppel-like factors (klfs) and their expressions during GCRV challenge in grass carp (Ctenopharyngodon idella). Developmental & Comparative Immunology 2021; 120: 104062. 

4. Research on Growth and Other Economic Traits 

[28] Ye W, Shi M*, Chen S, Duan Y, Jiang Y, Cheng Y, Zhang W, Chen J, Wang Y, Xia X-Q*. Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp. Genomics, 2023, 115(5): 110706. 

[29] Ye W, Shi M*, Ren K, Liu Y, Duan Y, Cheng Y, Zhang W, Xia X-Q*. Profiling the spatial expression pattern and ceRNA network of lncRNA, miRNA, and mRNA associated with the development of intermuscular bones in zebrafish. Biology, 2023, 12(1): 75. 

[30] Shi M#, Luo H#, Zhang W, Jiang Y, Chen J, Cheng Y, Hu W*, Xia X-Q*. A genome-wide linkage map and QTL mapping for growth traits of Asian rice-field eel (Monopterus albus). Aquaculture, 2021, 536: 736394. 

[31] Huang X#, Jiang Y#, Zhang W, Cheng Y, Wang Y, Ma X, Duan Y, Xia L, Chen Y, Wu N, Shi M*, Xia X-Q*. Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus). BMC Genomics, 2020, 21:313. 

[32] Ye W, Duan Y, Zhang W, Cheng Y, Shi M*, Xia X-Q*. Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits. Genomics, 2021, 113(6): 4004-4014.