PGT_2026v17n3

Plant Gene and Trait 2026, Vol.17, No.3, 156-172 http://genbreedpublisher.com/index.php/pgt 171 Hendelman A., Zebell S., Rodriguez-Leal D., Dukler N., Robitaille G., Wu X., Kostyun J., Tal L., Wang P., Bartlett M.E., Eshed Y., Efroni I., and Lippman Z.B., 2021, Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection, Cell, 184(7): 1724-1739. https://doi.org/10.1016/j.cell.2021.02.001 Hormozdiari F., Van De Bunt M., Segre A.V., Li X., Joo J.W.J., Bilow M., Sul J.H., Sankararaman S., Pasaniuc B., and Eskin E., 2016, Colocalization of GWAS and eQTL signals detects target genes, The American Journal of Human Genetics, 99(6): 1245-1260. https://doi.org/10.1016/j.ajhg.2016.10.003 Hu X., Zhao J., Lin Z., Wang Y., Peng H., Zhao H., Wang X., and Yang C., 2022, Mendelian randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics, Proceedings of the National Academy of Sciences, 119(28): e2106858119. https://doi.org/10.1073/pnas.2106858119 Hu Y., An Q., Sheu K., Trejo B., Fan S., and Guo Y., 2018, Single cell multi-omics technology: methodology and application, Frontiers in Cell and Developmental Biology, 6: 28. https://doi.org/10.3389/fcell.2018.00028 Jiang L., Miao L., Yi G., Li X., Xue C., Li M. J., Huang H., and Li M., 2022, Powerful and robust inference of complex phenotypes' causal genes with dependent expression quantitative loci by a median-based Mendelian randomization, The American Journal of Human Genetics, 109(5): 838-856. https://doi.org/10.1016/j.ajhg.2022.04.004 Khan M., Ludl A.A., Bankier S., Björkegren J.L., and Michoel T., 2024, Prediction of causal genes at GWAS loci with pleiotropic gene regulatory effects using sets of correlated instrumental variables, PLoS Genetics, 20(11): e1011473. https://doi.org/10.1371/journal.pgen.1011473 Kirsten H., Al-Hasani H., Holdt L., Gross A., Beutner F., Krohn K., Horn K., Ahnert P., Burkhardt R., Reiche K., Hackermüller J., Löffler M., Teupser D., Thiery J., and Scholz M., 2015, Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci, Human Molecular Genetics, 24(16): 4746-4763. https://doi.org/10.1093/hmg/ddv194 Kvamme J., Badsha M.B., Martin E.A., Wu J., Wang X., and Fu A.Q., 2025, Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues, Genetics, 230(2): iyaf064. https://doi.org/10.1093/genetics/iyaf064 Lessard S., Chao M., Reis K., FinnGen and Estonian Biobank Research Team, Beauvais M., Rajpal D.K., Sloane J., Palta P., Klinger K., de Rinaldis E., Shameer K., and Chatelain C., 2024, Leveraging large-scale multi-omics evidences to identify therapeutic targets from genome-wide association studies, BMC Genomics, 25(1): 1111. https://doi.org/10.1186/s12864-024-10971-2 Li B., and Ritchie M.D., 2021, From GWAS to gene: transcriptome-wide association studies and other methods to functionally understand GWAS discoveries, Frontiers in Genetics, 12: 713230. https://doi.org/10.3389/fgene.2021.713230 Liang Y., Wang H., and Zhang Y.D., 2025, A-TWAS: an aggregated transcriptome-wide association study model incorporating multiple Bayesian priors, bioRxiv, 2025-01. https://doi.org/10.1101/2025.01.27.635054 Liu B., Gloudemans M.J., Rao A.S., Ingelsson E., and Montgomery S.B., 2019, Abundant associations with gene expression complicate GWAS follow-up, Nature Genetics, 51(5): 768-769. https://doi.org/10.1038/s41588-019-0404-0 Lu Y., Xu K., Maydanchik N., Kang B., Pierce B.L., Yang F., and Chen L.S., 2024, An integrative multi-context Mendelian randomization method for identifying risk genes across human tissues, The American Journal of Human Genetics, 111(8): 1736-1749. https://doi.org/10.1016/j.ajhg.2024.06.012 Mai J., Lu M., Gao Q., Zeng J., and Xiao J., 2023, Transcriptome-wide association studies: recent advances in methods, applications and available databases, Communications Biology, 6(1): 899. https://doi.org/10.1038/s42003-023-05279-y Mostafavi H., Spence J.P., Naqvi S., and Pritchard J.K., 2023, Systematic differences in discovery of genetic effects on gene expression and complex traits, Nature Genetics, 55(11): 1866-1875. https://doi.org/10.1038/s41588-023-01529-1 Parrish R.L., Gibson G.C., Epstein M.P., and Yang J., 2022, TIGAR-V2: efficient TWAS tool with nonparametric Bayesian eQTL weights of 49 tissue types from GTEx V8, Human Genetics and Genomics Advances, 3(1): 100078. https://doi.org/10.1016/j.xhgg.2021.100068 Porcu E., Rüeger S., Lepik K., Santoni F.A., Reymond A., and Kutalik Z., 2019, Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits, Nature Communications, 10(1): 3300. https://doi.org/10.1101/377267 Rasooly D., Peloso G.M., and Giambartolomei C., 2022, Bayesian genetic colocalization test of two traits using coloc, Current Protocols, 2(12): e627. https://doi.org/10.1002/cpz1.627 Shikov A.E., Skitchenko R.K., Predeus A.V., and Barbitoff Y.A., 2020, Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits, Scientific Reports, 10(1): 1037. https://doi.org/10.1038/s41598-020-58040-4

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