Publications

Preprint

● Liu H-J^*, Swarts K, Xu S, Yan J, Nordborg M. On the contribution of genetic heterogeneity to complex traits. bioRxiv, 2024, 586967.

● Igolkina A^#, Vorbrugg S^#, Rabanal F^#, Liu H-J^#, Ashkenazy H^#, Kornienko A^#, Fitz J, Collenberg M, Kubica C, Morales M. A, Jaegle B, Wrightsman T, Voloshin V, Llaca V, Nizhynska V, Reichardt I, Lanz C, Bemm F, Flood J. P, Nemomissa S, Hancock A, Guo Y-L, Kersey P, Weigel D^*, Nordborg M^*. Towards an unbiased characterization of genetic polymorphism. bioRxiv, 2024, 596703.

● Wenjie Wei^#, Songtao Gui^#, Jian Yang, Erik Garrison, Jianbing Yan, Liu H-J^*. wgatools: an ultrafast toolkit for manipulating whole genome alignments. arXiv, 2024; 2409.08569.

☆ Reviews & Comments ☆

○ Clauw P, Ellis TJ, Liu H-J, Sasaki E^*. Beyond the Standard GWAS—A Guide for Plant Biologists. Plant Cell Physiol, 2024, pcae079.

● Liang Y^#, Liu H-J^#, Yan J^*, Tian F^*. Natural Variation in Crops: Realized Understanding, Continuing Promise. Annu Rev Plant Biol, 2021, 72:357-385.

● Xiao Y^#, Liu H^#, Wu L^#, Warburton M, Yan J^*. Genome-wide Association Studies in Maize: Praise and Stargaze. Mol Plant, 2017, 10(3):359-374.

● Liu H-J^*, Yan J^*. Crop genome-wide association study: A harvest of biological relevance. Plant J, 2019, 97: 8-18.

● Liu H^*, Yan J^*. Rice domestication: An imperfect African solution. Nat Plants, 2017, 3:17083. [Comment]

☆ Functional genomics/Gene cloning ☆

● Liu H-J^#, Wang X^#, Xiao Y^#, Luo J^#, Qiao F^#, Yang W^#, Zhang R^#, Meng Y, Sun J, Yan S, Peng Y, Niu L, Jian L, Song W, Yan J, Li C, Zhao Y, Liu Y, Warburton ML, Zhao J^*, Yan J^*. CUBIC: an atlas of genetic architecture promises directed maize improvement. Genome Biol. 2020, 21(1):20.

○ Jin M, Liu H, Liu X, Guo T, Guo J, Yin Y, Ji Y, Li Z, Zhang J, Wang X, Qiao F, Xiao Y, Zan Y^*, Yan J^*. Complex genetic architecture underlying the plasticity of maize agronomic traits. Plant Commun, 2023, 4(3):100473.

○ Xiao Y^#, Tong H^#, Yang X, Xu S, Pan Q, Qiao F, Raihan MS, Luo Y, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Liu J, Zhan W, Liu N, Wang H, Chen G, Cai Y, Xu G, Wang W, Zheng D, Yan J^*. Genome-wide dissection of the maize ear genetic architecture using multiple populations. New Phytol, 2016, 210(3):1095-106.

○ Jin M, Liu X^*, Jia W, Liu H, Li W, Peng Y, Du Y, Wang Y, Yin Y, Zhang X, Liu Q, Deng M, Li N, Cui X, Hao D, Yan J^*. ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT. J Integr Plant Biol, 2018, 60(6):465-480.

○ Wang H, Xu S, Fan Y, Liu N, Zhan W, Liu H, Xiao Y, Li K, Pan Q, Li W, Deng M, Liu J, Jin M, Yang X, Li J, Li Q, Yan J^*. Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses. Plant Biotechnol J, 2018, 16(8):1464-1475.

○ Liu J, Huang J, Guo H, Lan L, Wang H, Xu Y, Yang X, Li W, Tong H, Xiao Y, Pan Q, Qiao F, Raihan MS, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Zhan W, Liu N, Wang H, Chen G, Li Q^, Yan J^. The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice. Plant Physiol, 2017, 175(2):774-785.

○ Yan W^#, Liu H^#, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y^*. Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res, 2013, 23(7):969-71.

○ Zuo W^#, Chao Q^#, Zhang N^#, Ye J, Tan G, Li B, Xing Y, Zhang B, Liu H, Fengler KA, Zhao J, Zhao X, Chen Y, Lai J, Yan J, Xu M^*. A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet, 2015, 47(2):151-7.

☆ Gene editing ☆

● Liu H-J^#, Jian L^#, Xu J^#, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, Yang X, Li Z, Zhang M, Sun J, Bai M, Song W, Chen H, Sun X, Li W, Lu Y, Liu Y, Zhao J, Qian Y, Jackson D, Fernie AR, Yan J^*. High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize. Plant Cell, 2020, 32(5):1397-1413.

● Sun J^#, Liu H^#, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu H-J^*, Chen L-L^*. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics, 2019, 35(14):2501-2503.

☆ Omics ☆

● Wang S^#, Tian L^#, Liu H^#, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J^*, Wu L^*. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. Mol Plant, 2020, 13(7):1078-1093.

● Liu H^#, Luo X^#, Niu L, Xiao Y, Chen L, Liu J, Wang X, Jin M, Li W, Zhang Q, Yan J^*. Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize. Mol Plant, 2017, 10(3):414-426.

● Chen Q^#, Han Y^#, Liu H^#, Wang X, Sun J, Zhao B, Li W, Tian J, Liang Y, Yan J, Yang X^, Tian F^. Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize. Plant Cell, 2018, 30(7):1404-1423.

● Jin M^#, Liu H^#, He C^#, Fu J^*, Xiao Y, Wang Y, Xie W, Wang G, Yan J^*. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep, 2016, 6:18936.

● Liu H^#, Wang X^#, Warburton ML, Wen W, Jin M, Deng M, Liu J, Tong H, Pan Q, Yang X, Yan J^*. Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding. Mol Plant, 2015, 8(6):871-84.

○ Zhu F, Alseekh S, Koper K, Tong H, Nikoloski Z, Naake T, Liu H, Yan J, Brotman Y, Wen W, Maeda H, Cheng Y^*, Fernie AR^*. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. Plant Cell, 2022, 34(1):557-578.

○ Deng M, Zhang X, Luo J, Liu H, Wen W, Luo H, Yan J, Xiao Y^*. Metabolomics analysis reveals differences in evolution between maize and rice. Plant J, 2020, 103(5):1710-1722.

○ Deng M, Li D, Luo J, Xiao Y, Liu H, Pan Q, Zhang X, Jin M, Zhao M, Yan J^*. The genetic architecture of amino acids dissection by association and linkage analysis in maize. Plant Biotechnol J, 2017, 15(10):1250-1263.

○ Wen W^*, Liu H, Zhou Y, Jin M, Yang N, Li D, Luo J, Xiao Y, Pan Q, Tohge T, Fernie AR, Yan J. Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel. Plant Physiol, 2016, 170(1):136-46.

○ Wen W^#, Jin M^#, Li K, Liu H, Xiao Y, Zhao M, Alseekh S, Li W, de Abreu E Lima F, Brotman Y, Willmitzer L, Fernie AR^*, Yan J^*. An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize. Plant J, 2018, 93(6):1116-1128.

○ Wen W, Li K, Alseekh S, Omranian N, Zhao L, Zhou Y, Xiao Y, Jin M, Yang N, Liu H, Florian A, Li W, Pan Q, Nikoloski Z, Yan J^*, Fernie AR^*. Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. Plant Cell, 2015, 27(7):1839-56.

○ Wen W^#, Li D^#, Li X, Gao Y, Li W, Li H, Liu J, Liu H, Chen W, Luo J^*, Yan J^*. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun, 2014, 5:3438.

○ Zhang X, Warburton ML, Setter T, Liu H, Xue Y, Yang N, Yan J, Xiao Y^*. Genome-wide association studies of drought-related metabolic changes in maize using an enlarged SNP panel. Theor Appl Genet, 2016, 129(8):1449-63.

☆ Methodology and Databases ☆

● Liu H, Wang F, Xiao Y, Tian Z, Wen W, Zhang X, Chen X, Liu N, Li W, Liu L, Liu J, Yan J, Liu J^*. MODEM: multi-omics data envelopment and mining in maize. Database (Oxford), 2016, 2016:baw117.

○ Luo J, Wei C, Liu H, Cheng S, Xiao Y, Wang X, Yan J, Liu J^*. MaizeCUBIC: a comprehensive variation database for a maize synthetic population. Database (Oxford), 2020, 2020:baaa044.

○ Liu J^*, Tian Z, Xiao Y, Liu H, Hao S, Zhang X, Wang C, Sun J, Yu H, Yan J^*. Gene Regulatory Relationship Mining Using Improved Three-Phase Dependency Analysis Approach. IEEE/ACM Trans Comput Biol Bioinform, 2020, 17(1):339-346.

★ Agricultural Economics ★

○ Li X^*, Liu N, You L, Ke X, Liu H, Huang M, Waddington SR. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security. PLoS One, 2016, 11(7):e0159061.

★ Patents ★

刘海军, 许洁婷, 严建兵. 一种基因组特定区域的DNA测序方法: 中国, 201811606050.9. 2021-4-2.

金敏亮, 刘海军, 刘相国, 许洁婷, 严建兵. 降低玉米株高或延迟开花的方法: 中国, 202010109172.8. 2022-5-3.

金敏亮, 刘海军, 刘相国, 许洁婷, 严建兵. 控制玉米株高和花期的基因及其应用: 中国, 202010080086.9. 2020-2-4.