Principal Investigator

Dr. Hang He

Contact Address: No. 699 Binhu Road, Fangzi District, Weifang, Shandong, China

Email: hang.he@pku-iaas.edu.cn

Education

2004 - 2009, PhD. in Bioinformatics, Chinese Academy of Sciences, China

2000 - 2004, B.S. in Mathematics, Peking University, China

Working Experience

Nov 2020 – now, Principal Investigator, Peking University Institute of Advanced Agricultural Sciences, China

Aug 2020 – now, Research Fellow, Peking University,China

Aug 2011 – Jul 2020, Associate Research Fellow, Peking University, China

Jul 2009 – Jul 2011, Postdoctoral research, Peking University, China

Research Interests

l Multi-omics studies in crops

When a huge amount of data is generated every day in biological research, how to understand and mining valuable information is critical. We developed software and algorithms on genome, transcriptome, epigenome and 3D genome, and studied genetic basis and gene regulatory mechanism in crops, including rice, wheat, pepper and kiwifruit.

l Molecular mechanism of heterosis in crops

To understand the molecular mechanism of heterosis in crops, our team constructed several big populations in rice. By collecting the genotyping and phenotyping data of hybrids, we applied GWAS on heterotic performance and identified QTLs. Combined with other information including RNA-seq data and mutations, we analyzed molecular regulatory network of heterosis.

l Molecular design breeding

By applying molecular techniques, breeders are able to perform fast and accurate molecular design breeding. To facilitate molecular design breeding, our team developed a series of SNP arrays in rice, maize and wheat, which were widely applied in China these years. We analyzed the genetic basis of elite rice, maize and wheat varieties, and built mathematic models for breeding. We applied these models in the field and obtained high accuracies to predict the performance of hundreds of cultivars.

Selected Publications

Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H^*, Deng XW^*. 2023. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings.Nat Plants. doi: 10.1038/s41477-023-01544-4.

Sun L^#, Cao Y^#, Li Z^#, Liu Y, Yin X, Deng XW^*, He H^*, Qian W^*. 2023. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. J Integr Plant Biol. 65(8):1966-1982.

Song J^#, Sun B^#, Chen C, Ning Z, Zhang S, Cai Y, Zheng X, Cao B, Chen G, Jin D, Li B, Bian J, Lei J^*, He H^*, Zhu Z^*. 2023. An R-R-type MYB transcription factor promotes non-climacteric pepper fruit carotenoid pigment biosynthesis. Plant J. 115(3):724-741.

Han X^#, Zhang Y^#, Zhang Q^#, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng XW^*, Li D^*, He H^*. 2023.Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol Plant. 16(2):452-470.

Zhang Y^#, Fu J^#, Wang K^#, Han X^#, Yan T, Su Y, Li Y, Lin Z, Qin P, Fu C, Deng XW, Zhou D^*, Yang Y^*, He H^*. 2022. The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnol J. 20(9):1642-1644.

Deng Y^#, Liu S^#, Zhang Y^#, Tan J, Li X, Chu X, Xu B, Tian Y, Sun Y, Li B, Xu Y, Deng XW, He H^*, Zhang X^*. 2022. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol Plant. 2022 16(2):452-470.

Cui D^#, Zhou H^#, Ma X^#, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H^*, Han L^*. 2022. Genomic insights on the contribution of introgressions from Xian/indica to the genetic improvement of Geng/japonica rice cultivars. Plant Comm. 3(3):100325.

Li G^#, Wang L^#, Yang J^#*, He H^#, Jin H^#, Li X^#, Ren T^#, Ren Z, Li F, Han X, Zhao X, Dong L, Li Y, Song Z, Yan Z, Zheng N, Shi C, Wang Z, Yang S, Xiong Z, Zhang M, Sun G, Zheng X, Gou M, Ji C, Du J, Zheng H, Dolezel J, Deng XW, Stein N, Yang Q^*, Zhang K^*, Wang D^*. 2021. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nat Genet. 53(4):574-584.

Lin Z, Qin P, Zhang X, Fu C, Deng H, Fu X, Huang Z, Jiang S, Li C, Tang X, Wang X, He G, Yang Y^*, He H^*, Deng XW^*. 2020. Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. Proc Natl Acad Sci U S A. 117(9):4623-4631.

Sun L^#, Jing Y^#, Liu X, Li Q, Xue Z, Cheng Z, Wang D, He H^*, Qian W^*. 2020. Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nat Commun. 11(1):1886.

Wang B^#, Lin Z^#, Li X^#, Zhao Y^#, Zhao B, Wu G, Ma X, Wang H, Xie Y, Li Q, Song G, Kong D, Zheng Z, Wei H, Shen R, Wu H, Chen C, Meng Z, Wang T, Li Y, Li X, Chen Y, Lai J, Hufford MB, Ross-Ibarra J, He H^*, Wang H^*. 2020. Genome-wide selection and genetic improvement during modern maize breeding. Nat Genet. 52(6):565-571.

Han X, Chang X, Zhang Z, Chen H, He H^*, Zhong B^*, Deng XW^*. 2019. Origin and evolution of core components responsible for monitoring light environment changes during plant terrestrialization. Mol Plant. 12(6):847-862.

Wang Z^#, Li J^#, Chen S^#, Heng Y^#, Chen Z, Yang J, Zhou K, Pei J, He H^*, Deng XW^*, Ma L^*. 2017. Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat. Proc Natl Acad Sci U S A. 114(47):12614-12619.

Zhou D^#, Chen W^#, Lin Z, Chen H, Wang C, Li H, Yu R, Zhang F, Zhen G, Yi J, Li K, Liu Y, Terzaghi W, Tang X, He H^*, Zhou S^*, Deng XW^*. 2016. Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding. Plant Biotechnol J.14(2):638-48.

The IC4R Project Consortium (as Co-corresponding author). Information Commons for Rice (IC4R). 2015. Nucl. Acids Res. doi: 10.1093/nar/gkv1141.

Chen H^#, Xie W^#, He H^#, Yu H^#, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F^*, Deng XW^*, Zhang Q^*. 2013. A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant.7(3):541-53.

Shen H^#, He H^#, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW. 2012. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell. 24(3):875-92.

Charron JB^#, He H^#, Ellinga AA, Deng XW. 2009. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell. 21(12):3732-48.

Li L^#, He H^#, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW. 2008. Transcriptional analysis of highly syntenic regions between Medicago truncatulaand Glycine max using tiling microarrays. Genome Biol. 9(3):R57.

Zhang H^#, He H^#, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW. 2008. A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant. 1(5):720-31.

Honorables and Awards

National Top Young Talents Program, 2021