Our research interest:

1. Development of genome assembly methods. Based on the long-read and single-cell sequencing technologies, we devolop methods for haplotype-resolved and Telomere-to-Telomere (T2T) assembly of complex plant genomes such as heterozygous diploids and polyploid genomes, especially autopolyploid genomes such as the tetraploid potato cultivars.  (Jiao et al., Genome Res. 2017; Sun et al., Nat. Genet. 2022; Xiao et a., Horti. Res. 2023）

   
   

2. Development and application of methods for genetic variant identifying and genotyping.

   1) Based on the theory of graph pan genome and/or deep learning models, we develop methods to identify and genotype all types of genetic variation including the structural variation for complex plant genomes such as heterozygous diploids and polyploid genomes, especially autopolyploid genomes such as the tetraploid potato cultivars. （Du et., Genome Biol., 2024）

   2) We apply these methods to solve some problems in poluation genomics or evolutionary genomics (e.g: the evolution of genetic incompatibilities and self-incompatibilies).  (Jiao et al., Nat. Communi. 2021; Jiao et., Mol. Biol. Evol. 2022)

   
   

3. Identification and design of regulatory elements common in horitculral crops based on multi-omics data

Publications:

ORCiD: http://orcid.org/0000-0001-8355-2959

Some papers with our group members as the first author(s) or the corresponding author(s):

9.Du Z-Z, He J-B, Jiao W-B^*: A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25:91 https://doi.org/10.1186/s13059‑024‑03239‑1 

8. Xiao P-X, Li Y, Lu J, Zuo H, Pingcuo G, Ying H, Zhao F, Xu Q, Zeng X, Jiao W-B^*: High-quality assembly and methylome of a Tibetan wild tree peony genome ( Paeonia ludlowii) reveal the evolution of giant genome architecture. Hortic Res 2023, 10.

7. Song L, Huang Y, Zuo H, Tang N, Li Z, Jiao WB^*, Xu F^*, Xu Q^*, Chen Z^*: Chromosome-level assembly of triploid genome of sichuan pepper (Zanthoxylum armatum). Hortic Plant J 2022 doi:10.1016/j.hpj.2022.12.014.

6. Sun H^#, Jiao WB^#, Krause K, Campoy JA, Goel M, Folz-Donahue K, Kukat C, Huettel B, Schneeberger K: Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nature Genetics 2022, 3:342-348

5. Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, et al. :The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Molecular Biology and Evolution 2021, 38:1225-1240

4. Jiao WB, Schneeberger K: Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nature Communications 2020, 11:989.

3. Jiao WB, Schneeberger K: The impact of third generation genomic technologies on plant genome assembly. Current Opinion Plant Biology 2017, 36:64-70.

2. Jiao WB, Garcia Accinelli G, Hartwig B, Kiefer C, Baker D, Severing E, Willing E-M, Piednoel M, Woetzel S, Madrid-Herrero E, et al.: Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research 2017, 27:778–786.

1. Jiao WB, Huang D, Xing F, Hu Y, Deng XX, Xu Q, Chen LL: Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant Journal 2013, 75:954–964.

Other publications:

14. Hu J, Guo F, Du Z, Chen P, Shi C, Zhang J, Ye J, Deng X, Larkin RM, Jiao W, et al.: A rare inter-haplotypic recombination at the S-locus contributed to the loss of self-incompatibility in trifoliate orange. Plant Commun 2024, doi:10.1016/j.xplc.2024.100940.

13. Yuan-yuan LIU, Jian-ke D, Jing-wen Y, Wen-xiang MEI, Gang C, Jing-jing GUO: 利用野生种 Solanum boliviense 创制马铃薯抗寒种质. 作物学报 2024, doi:10.3724/SP.J.1006.2024.34159.

12. 宋波涛, 涂卫, 王海波, 董建科, 袁平平, 景晟林, 刘园园, 焦文标: 马铃薯种质演化与分类研究进展. 中国马铃薯 2023, 3:536–554.

11. Huang Y, He J, Xu Y, Zheng W, Wang S, Chen P, Zeng B, Yang S, Jiang X, Liu Z, et al.: Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat Genet 2023, 55:1964–1975.

10. Madrid E, Severing E, de Ansorena E, Kiefer C, Brand L, Martinez-Gallegos R, Woetzel S, Kemi U, Jiao WB, Schneeberger K, et al.: Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering. Proc. Natl. Acad. Sci.  2021, 118.

9. Campoy, J.A., Sun, H., Goel, M. Jiao WB, et al. Gamete binning: chromosome-level and haplotype- resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 21, 306 (2020). 

8. Goel M, Sun H, Jiao WB, Schneeberger K: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019, 20:277.

7. Dittberner H, Becker C, Jiao WB, Schneeberger K, Hölzel N, Tellier A, Meaux J: Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD‐seq analysis in floodplain Arabis species. Mol. Ecol. 2019, 28:3887–3901.

6. Kiefer C, Willing E-M, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K: Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. Nature Plants 2019, 5:846–855.

5. Zapata L, Ding J, Willing E, Hartwig B, Bezdan D, Jiao WB, Patel V, et al.: Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc. Natl. Acad. Sci. 2016, 113:E4052–E4060.

4. Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, et al.: Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci. Data 2016, 3:160076.

3. Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, et al.:  Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc. Natl. Acad. Sci. 2016, 113:E5163–E5171.

2. Gutjahr C, Gobbato E, Choi J, Riemann M, Johnston MG, Summers W, Carbonnel S, Mansfield C, Yang SY, Nadal M, Acosta I, Takano M, Jiao WB, et al.: Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science 2015, 350:1521–1524.

1. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, et al.: The draft genome of sweet orange (Citrus sinensis). Nature Genetics 2013, 45:59–66.