Multi-Omics Studies in Crops
Team name
Multi-Omics Studies in Crops
Principal Investigator
Research Objectives
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.
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.
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.
Team members
l Xue Han, Ph.D in biotechnology, associate professor, molecular design breeding of kiwifruit
l Jiayue Chen, Ph.D in biotechnology, associate professor, plant science and callus research
l Linhua Sun, Ph.D. in integrated life sciences, associate professor, 3D chromatin structure and function, genetics and NGS sequencing
l Jianxin Bian, Ph.D in crop science, associate professor, crop genomics andmolecular design breeding of peanut and wheat
l Kui Li, Ph.D. in botany, associate professor, Wheat Genetics and Genomics
l Xiuru Dai, Ph.D. in crop science, assistant professor, multi-omics data analysis of wheat and maize
l Jin Congcong, Ph.D. in developmental biology, assistant professor, molecular regulatory mechanism of light signaling pathways
l Shoucheng Liu, M.S. in genomics, assistant professor, genomics and molecular breeding in Triticeae crops
l Zhangsheng Zhu, Ph.D. in horticulture, associate professor. Capsicum germplasm resources collection and characterization. Adopt genetics, omics, physiological and molecular biology approaches to discover and characterize the key genes that control important agronomic traits and metabolites biosynthesis in pepper
l Di Cui, Ph.D. in crop germplasm resources, associate professor, multi-omics of rice
l Yilin Zhang, Ph.D. candidate in bioinformatics, visiting student, genomics and pan-genomics, population genetics and genome selection breeding
l Ni Ma, Ph.D. candidate in epigenomics, visiting student, chromatin organization in plant interphase nuclei
l Haiyue Zeng, Ph.D. candidate in biotechnology, visiting student, origin, evolution and molecular breeding of key traits of plants
l Yijun Chen, Ph.D. candidate in crop omics and bioinformatics, crop multi-omics and bioinformatics of horticultural plants
l Xiao Xu, M.S. in bioengineering, research assistant, genetics and NGS sequencing
l Jingru Zhou, M.S. in crop cultivation and farming system, research assistant, genetics and 3D genomics
l Yutong Liu, M.S. in agronomy and seed industry, research assistant, genetics and 3D genomics
l Shuai Ding, M.S. in engineering, research assistant, genomics research
l Yan Wang, M.S. in animal husbandry, research assistant, responsible for population genetics analysis and multi-omics analysis
l Guoliang Zhou, M.S. in crop science, research assistant, crop population genetics
l Hao Jiang,M.S. in agricultural engineering, research assistant, crop phenotype big data
l Xinlong Hu,M.S. in engineering,research assistant, crop phenotype big data
l Weimin Liu, M.S. in agriculture, research assistant, kiwifruit transformation system and exploring the influence of growth conditions on plant development
l Zhiying Lou, M.S. in plant pathology, research assistant, genetic and breeding research on the cold resistance of kiwifruit
l Zizheng Ren, M.S. in pomology,research assistant,genetic transformation and molecular breeding of kiwifruit
l Yuqi Guo, M.S. in agricultural, research assistant, kiwifruit tissue culture and genetic transformation experiments
l Kai Wu, M.S. in plant nutritional genetics, research assistant, population genetics of kiwifruit
l Zenghui Chen, M.S. in biochemical engineering, research assistant, crop population genetics
l ShiqiaoYan, M.S. in arts, responsible for laboratory administration
l Xiaopeng Li, B.S. in electric engineering, research assistant, plant genomics and cluster operation and maintenance management
l Jingming Chen, B.S. in computer science and technology, network administrator，network security managementand network device management
l Yuan Lv, B.S in computer science, research assistant, crop genomics, genome selection, and population genetics
l Wudi Gai, B.S. in agricultural in horticulture, research assistant, studying on crop genomics, pan-genome studies of melons, plant population genetics
l Junjie Luo, B.S, technician, field management
Research Achievements
l Thefirst T2T genome referenceofwatermelon
Watermelon (Citrullus lanatus) belongs to the genus Cucurbitaceae, which is native to Africa and is the third largest fruit crop in the world, with important economic value. China is the world's largest producer and consumer of watermelon. In 2020, the planting area in China is 1.528 million hectares, with an output of 62 million tons, accounting for more than 60% of the global planting area. The research basis of watermelon is relatively weak. We reported the first high-quality telomere to telomere (T2T) genome of small fruit watermelon inbred line G42, and constructed the EMS saturated mutant library of G42 by using the method of pollen mutation, which provides valuable resources for analyzing the gene function and breeding of watermelon. The total length of G42 reference genome assembled in this study is 369,321,829 bp, 24,205 protein coding genes are predicted, all telomere and centromere sequence information are analyzed, and all 220 gaps in 97103v2 reference genome are filled. This is the first reported T2T reference genome in Cucurbitaceae.
Fig.Watermeloninbred line G42and its T2T genome sequence that fills gaps of former assemblies.
l Two haplotype-resolved T2T kiwifruit genomes shed light on the regulatory mechanisms of vitamin C and sucrose metabolism
Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value, especially because of the high content of vitamin C in its fruit. For the first time, we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var. ‘Donghong’ (DH) and Actinidia latifolia ‘Kuoye’ (KY), with total lengths of 608 327 852 and 640 561 626 bp for 29 chromosomes, respectively. Witha burst of structural variants involving inversion, translocations, and duplications within 8.39 million years,the metabolite content of DH and KY exhibited differences in saccharides, lignans, and vitamins. A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha, both of which haveultra-high vitamin C content. Synchronizedmetabolome and transcriptome changes during DH fruit development revealed the same dynamic patternsin expression levels and metabolite contents; free fatty acids and flavonols accumulated in the early stages,but sugar substances and amino acids accumulated in the late stages. The AcSWEET9b gene that exhibitsallelic dominance was further identified to positively correlate with high sucrose content in fruit. Comparedwith wild varieties and other Actinidia species, AcSWEET9b promoters were selected in red-flesh kiwifruitsthat have increased fruit sucrose content, providing a possible explanation on why red-flesh kiwifruits aresweeter. Collectively, these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.
Fig. Two haplotype-resolved T2T genome assemblies of Actinidia chinensisand Actinidia latifolia
l Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in plant
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specificdifferentiation and the associated transcriptional regulation is still lacking. We obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes.
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.