RGG_2024v15n4

Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 176 Kou Y., Liao Y., Toivainen T., Lv Y., Tian X., Emerson J., Gaut B., Zhou Y., and Purugganan M., 2020, Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication, Molecular Biology and Evolution, 37(12): 3507-3524. https://doi.org/10.1093/molbev/msaa185 Li Y., Xiao J., Chen L., Huang X., Cheng Z., Han B., Zhang Q., and Wu C., 2018, Rice functional genomics research: past decade and future, Molecular Plant, 11(3): 359-380. https://doi.org/10.1016/j.molp.2018.01.007 Liao Y., Zhang X., Li B., Liu T., Chen J., Bai Z., Wang M., Shi J., Walling J., Wing R., Jiang J., and Chen M., 2018, Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric regions, Plant Cell, 30(8): 1729-1744. https://doi.org/10.1105/tpc.18.00163 Mishra R., Joshi R., and Zhao K., 2018, Genome editing in rice: recent advances challenges and future implications, Frontiers in Plant Science, 9: 1361. https://doi.org/10.3389/fpls.2018.01361 Ren Z., Qi D., Pugh N., Li K., Wen B., Zhou R., Xu S., Liu S., and Jones A., 2019, Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics data sets, Molecular and Cellular Proteomics: MCP, 18(1): 86-98. https://doi.org/10.1074/mcp.RA118.000832 Seong K., and Krasileva K., 2021, Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen Magnaporthe oryzae, Molecular Plant-Microbe Interactions, 34(11): 1267-1280. https://doi.org/10.1094/MPMI-03-21-0071-R Sharma S., Pinson S., Gealy D., and Edwards J., 2021, Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multitrait index and bayesian networks, G3, 11(10): jkab178. https://doi.org/10.1093/g3journal/jkab178 Song J., Xie W., Wang S., Guo Y., Koo D., Kudrna D., Gong C., Huang Y., Feng J., Zhang W., Zhou Y., Zuccolo A., Long E., Lee S., Talag J., Zhou R., Zhu X., Yuan D., Udall J., Xie W., Wing R., Zhang Q., Poland J., Zhang J., and Chen L., 2021, Two gap-free reference genomes and a global view of the centromere architecture in rice, Molecular Plant, 14(10): 1757-1767. https://doi.org/10.1016/j.molp.2021.06.018 Stein J., Yu Y., Copetti D., Zwickl D., Zhang L., Zhang C., Chougule K., Gao D., Iwata A., Goicoechea J., Wei S., Wang J., Liao Y., Wang M., Jacquemin J., Becker C., Kudrna D., Zhang J., Londono C., Song X., Lee S., Sanchez P., Zuccolo A., Ammiraju J., Talag J., Danowitz A., Rivera L., Gschwend A., Noutsos C., Wu C., Kao S., Zeng J., Wei F., Zhao Q., Feng Q., Baidouri M., Carpentier M., Lasserre E., Cooke R., Farias D., Maia L., Santos R., Nyberg K., McNally K., Mauleon R., Alexandrov N., Schmutz J., Flowers D., Fan C., Weigel D., Jena K., Wicker T., Chen M., Han B., Henry R., Hsing Y., Kurata N., Oliveira A., Panaud O., Jackson S., Machado C., Sanderson M., Long M., Ware D., and Wing R., 2018, Genomes of 13 domesticated and wild rice relatives highlight genetic conservation turnover and innovation across the genus Oryza, Nature Genetics, 50(2): 285-296. https://doi.org/10.1038/s41588-018-0040-0 Tabassum J., Raza Q., R漨᧚az A., Ahmad S., Rashid M., Javed M., Ali Z., Kang F., Khan I., Atif R., and Luo J., 2022, Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate, Frontiers in Plant Science, 13: 1004359. https://doi.org/10.3389/fpls.2022.1004359 Usman B., Nawaz G., Zhao N., Liao S., Qin B., Liu F., Liu Y., and Li R., 2020, Programmed editing of rice (Oryza sativa L.) OsSPL16 gene using CRISPR/Cas9 improves grain yield by modulating the expression of pyruvate enzymes and cell cycle proteins, International Journal of Molecular Sciences, 22(1): 249. https://doi.org/10.3390/ijms22010249 Xiang Z., Chen Y., Chen Y., Zhang L., Liu M., Mao D., and Chen L., 2022, Agrobacterium-mediated high-efficiency genetic transformation and genome editing of chaling common wild rice (Oryza rufipogon Griff.) using scutellum tissue of embryos in mature seeds, Frontiers in Plant Science, 13: 849666. https://doi.org/10.3389/fpls.2022.849666 Xu Y., Ma K., Zhao Y., Wang X., Zhou K., Yu G., Li C., Li P., Yang Z., Xu C., and Xu S., 2021, Genomic selection: a breakthrough technology in rice breeding, The Crop Journal, 9(3): 669-677. https://doi.org/10.1016/j.cj.2021.03.008 Yang R., Li J., Zhang H., Yang F., Wu Z., Zhuo X., An X., Cheng Z., Zeng Q., and Luo Q., 2018, Transcriptome analysis and functional identification of Xa13 and Pi-ta orthologs in Oryza granulata, The Plant Genome, 11(3): 170097. https://doi.org/10.3835/plantgenome2017.11.0097 Zanini S., Bayer P., Wells R., Snowdon R., Batley J., Varshney R., Nguyen H., Edwards D., and Golicz A., 2021, Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs, The Plant Genome, 15(1): e20177. https://doi.org/10.1002/tpg2.20177 Zhang Y., Zhou J., Xu P., Li J., Deng X., Deng W., Yang Y., Yu Y., Pu Q., and Tao D., 2022, A Genetic resource for rice improvement: introgression library of agronomic traits for all aa genome Oryza Species, Frontiers in Plant Science, 13: 856514. https://doi.org/10.3389/fpls.2022.856514 Zhao H., Li J., Yang L., Qin G., Xia C., Xu X., Su Y., Liu Y., Ming L., Chen L., Xiong L., and Xie W., 2021, An inferred functional impact map of genetic variants in rice, Molecular Plant, 14(9): 1584-1599. https://doi.org/10.1016/j.molp.2021.06.025

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