Shuxiang Yan

Huazhong University of Science and Technology

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Ke Shao

Mongolian Academy of Sciences

Maoteng Li

Huazhong University of Science and Technology

Huaixin Li

Huazhong University of Science and Technology

Meihua Xiong

China Agricultural University

Jianjie He

Wuhan National Laboratory for Optoelectronics

Nian Xu

Nanjing Medical University

Bin Zhu

China Agricultural University

Yiyi Xiong

Ministry of Education of the People's Republic of China

Hongbo Chao

Zhengzhou University

Weiguo Zhao

Chinese Academy of Agricultural Sciences

Cooperative Institutions

Huazhong University of Science and Technology

Central South University

Second Xiangya Hospital of Central South University

Chinese Academy of Sciences

Ministry of Education of the People's Republic of China

Institute of Hydroecology

Ministry of Water Resources of the People's Republic of China

University of Chinese Academy of Sciences

Zhejiang University

Ministry of Agriculture and Rural Affairs

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Complete mitochondrial genome ofPareuchiloglanis sinensis(Siluriformes: Sisoridae)

Mitochondrial DNA Part A (2014)

Ke Shao Shuxiang Yan Bin Zhu Nian Xu Wei-tao Li

The complete mitochondrial genome of Pareuchiloglanis sinensis, an endemic Chinese sisorid fish, was determined by DNA sequencing based on the PCR fragments. The complete mtDNA genome sequence of P. sinensis is 16,593 bp in length, with a gene content of 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and a typical gene arrangement identical to many other reported fishes. The overall base composition of the heavy strand was 30.6% A, 24.2% T, 16.0% G and 29.2% C, with a relatively high A + T content (54.8%). This will provide a useful tool for understanding the genetic diversity, population structure and conservation status of P. sinensis in future.

Heavy strand

GC-content

10.3109/19401736.2014.913155

Cite

Citations (4)

Genome-scale targeted mutagenesis inBrassica napususing a pooled CRISPR library

Genome Research (2023)

Jianjie He Kai Zhang Shuxiang Yan Mi Tang Weixian Zhou

The recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the genome complexity, it is a big challenge to accomplish large-scale targeted mutagenesis in polyploid plants. Here, we demonstrate the feasibility of using a pooled CRISPR library to achieve genome-scale targeted editing in an allotetraploid crop of Brassica napus . A total of 18,414 sgRNAs were designed to target 10,480 genes of interest, and afterward, 1104 regenerated transgenic plants harboring 1088 sgRNAs were obtained. Editing interrogation results revealed that 93 of the 178 genes were identified as mutated, thus representing an editing efficiency of 52.2%. Furthermore, we have discovered that Cas9-mediated DNA cleavages tend to occur at all the target sites guided by the same individual sgRNA, a novel finding in polyploid plants. Finally, we show the strong capability of reverse genetic screening for various traits with the postgenotyped plants. Several genes, which might dominate the fatty acid profile and seed oil content and have yet to be reported, were unveiled from the forward genetic studies. Our research provides valuable resources for functional genomics, elite crop breeding, and a good reference for high-throughput targeted mutagenesis in other polyploid plants.

Polyploid

Functional Genomics

10.1101/gr.277650.123

Cite

Citations (14)

Refinement of four major QTL for oil content in Brassica napus by integration of genome resequencing and transcriptomics

The Crop Journal (2022)

Shuxiang Yan Huaixin Li Hongbo Chao Jianjie He Yiran Ding

Rapeseed (Brassica napus) supplies about half of the vegetable oil in China. Increasing oil production and searching for genes that control oil content in the crop are research goals. In our previous studies, four major QTL for oil content located on A08, A09, C03 and C06 in the KenC-8 × N53-2 (KN DH) mapping population were detected. The parental lines were resequenced to identify structural variations and candidate genes affecting oil content in these four major QTL regions. Insertion-deletion (InDel) markers were developed and used to narrow the regions. Differentially expressed genes located in the regions were investigated. GO and KEGG analysis showed that several genes were associated with lipid metabolism. Several transcription factors with higher expression in N53-2 than in KenC-8 were identified. These results shed light on the genetic control of oil content and may be helpful for the development of high-oil-content cultivars.

Indel

Candidate gene

KEGG

10.1016/j.cj.2022.01.002

Cite

Citations (9)

Additional file 1 of Lysophosphatidic acid acyltransferase 2 and 5 commonly, but differently, promote seed oil accumulation in Brassica napus

Figshare (2022)

Kai Zhang Jianjie He Yongtai Yin Kang Chen Xiao Deng

Additional file 1: Table S1. Transformation efficiency of different lines. Table S2. Detailed information of RNA-seq samples. Table S3. Summary of read data generated, quality control and mapping on the B. napus genome for different samples. Table S4. Numbers of genes expressed at different expression levels at the different seed development stages. Table S5. Numbers of commonly and specifically expressed DEGs at each stage of seed development in BnLPAT2 and BnLPAT5 transgenic lines. Table S6. Detailed GO enrichments of all DEGs at different transgenic lines during seed development. Table S7. Enriched KEGG pathways involved in metabolism for ten subclusters of all DEGs. Table S8. Enriched KEGG pathways involved in basic metabolism at late seed development of different transgenic lines. Table S9. Primers used in present study.

Acyltransferases

10.6084/m9.figshare.20484694

Cite

Citations (0)

Seventeen microsatellite loci isolated from Rhinogobio cylindricus (Gunther), and their cross-amplification in six Gobioninae species

Conservation Genetics Resources (2012)

Ke Shao Shuxiang Yan Yu Zhao Meihua Xiong Nian Xu

Linkage Disequilibrium

10.1007/s12686-012-9798-z

Cite

Citations (2)

Development and characterization of polymorphic microsatellite markers for Chinese raccoon dog (Nyctereutes procyonoides procyonoides)

Genetics and Molecular Research (2013)

Shuxiang Yan Y.M. Li Chen Bai Xiaodong Ding Wenjing Li

useful tools for population genetic studies, individual

Raccoon Dogs

10.4238/2013.december.6.2

Cite

Citations (10)

A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus

Science Advances (2025)

Huaixin Li Mei Wu Hongbo Chao Ya-Le Yin Yutian Xia

Yellow seed coat color (SCC) is a valuable trait in Brassica napus , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus . In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 ( dominant gene of yellow seed coat color and improved seed oil content 1 ) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus , which has excellent potential for yellow SCC and high SOC rapeseed breeding.

Coat

Doubled haploidy

10.1126/sciadv.ads7620

Cite

Citations (0)

3D genome structural variations play important roles in regulating seed oil content of Brassica napus

Plant Communications (2023)

Libin Zhang Lin Liu Huaixin Li Jianjie He Hongbo Chao

Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Doubled haploidy

Genetic architecture

Candidate gene

10.1016/j.xplc.2023.100666

Cite

Citations (8)

Crosstalk of pyroptosis and cytokine in the tumor microenvironment: from mechanisms to clinical implication

Molecular Cancer (2024)

Hua Wang Tao Wang Shuxiang Yan Jinxin Tang Yibo Zhang

In the realm of cancer research, the tumor microenvironment (TME) plays a crucial role in tumor initiation and progression, shaped by complex interactions between cancer cells and surrounding non-cancerous cells. Cytokines, as essential immunomodulatory agents, are secreted by various cellular constituents within the TME, including immune cells, cancer-associated fibroblasts, and cancer cells themselves. These cytokines facilitate intricate communication networks that significantly influence tumor initiation, progression, metastasis, and immune suppression. Pyroptosis contributes to TME remodeling by promoting the release of pro-inflammatory cytokines and sustaining chronic inflammation, impacting processes such as immune escape and angiogenesis. However, challenges remain due to the complex interplay among cytokines, pyroptosis, and the TME, along with the dual effects of pyroptosis on cancer progression and therapy-related complications like cytokine release syndrome. Unraveling these complexities could facilitate strategies that balance inflammatory responses while minimizing tissue damage during therapy. This review delves into the complex crosstalk between cytokines, pyroptosis, and the TME, elucidating their contribution to tumor progression and metastasis. By synthesizing emerging therapeutic targets and innovative technologies concerning TME, this review aims to provide novel insights that could enhance treatment outcomes for cancer patients.

Pyroptosis

Crosstalk

Tumor progression

Proinflammatory cytokine

10.1186/s12943-024-02183-9

Cite

Citations (5)

The complete mitochondrial genome ofXenophysogobio nudicorpa(Cypriniformes; Cyprinidae)

Mitochondrial DNA Part A (2014)

Wei-tao Li Ke Shao Shuxiang Yan Nian Xu Meihua Xiong

In this study, the complete mitochondrial DNA genome sequence of Xenophysogobio nudicorpa was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of X. nudicorpa is a circular molecule of 16,616 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of X. nudicorpa is 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). The results could provide useful data for studying genetic diversity and phylogenetics in X. nudicorpa and related species.

Cypriniformes

Heavy strand

Nucleotide diversity

10.3109/19401736.2014.971279

Cite

Citations (0)