Aberrant RNA splicing of the phytic acid synthesis gene inositol-1,3,4 trisphosphate 5/6-kinase in a low phytic acid soybean line

References

• Aggarwal, S., A. Kumar, K. K. Bhati, G. Kaur, V. Shukla, S. Tiwari, and A. K. Pandey. 2018. “RNAi-mediated Downregulation of Inositol Pentakisphosphate Kinase (IPK1) in Wheat Grains Decreases Phytic Acid Levels and Increases Fe and Zn Accumulation.” Frontiers in Plant Science 9: 259. doi:10.3389/fpls.2018.00259.
   PubMed Web of Science ®Google Scholar
• Cordell, D., J.-O. Drangert, and S. White. 2009. “The Story of Phosphorus: Global Food Security and Food for Thought.” Global Environmental Change 19 (2): 292–305. doi:10.1016/j.gloenvcha.2008.10.009.
   Web of Science ®Google Scholar
• Demers, L. C., V. Raboy, S. Li, and M. A. Saghai Maroof. 2021. “Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds.” Frontiers in Plant Science 12: 708286. doi:10.3389/fpls.2021.708286.
   PubMed Web of Science ®Google Scholar
• Dong, Q., K. Echigo, V. Raboy, and H. Saneoka. 2020. “Seedling Growth, Physiological Characteristics, Nitrogen Fixation, and Root and Nodule Phytase and Phosphatase Activity of a low-phytate Soybean Line.” Plant Physiology and Biochemistry 149: 225–232. doi:10.1016/j.plaphy.2020.02.015.
   PubMed Web of Science ®Google Scholar
• Dong, Q., and H. Saneoka. 2020. “Physiological Characteristics, Phytase Activity, and Mineral Bioavailability of a low-phytate Soybean Line during Germination.” Plant Foods for Human Nutrition 75 (3): 383–389. doi:10.1007/s11130-020-00827-x.
   PubMed Web of Science ®Google Scholar
• Ertl, D., K. Young, and V. Raboy. 1998. “Plant Genetic Approaches to Phosphorus Management in Agricultural Production.” Journal of Environmental Quality 27 (2): 299–304. doi:10.2134/JEQ1998.00472425002700020008X.
   Web of Science ®Google Scholar
• Gillman, J. D., V. R. Pantalone, and K. Bilyeu. 2009. “The Low Phytic Acid Phenotype in Soybean Line CX1834 Is Due to Mutations in Two Homologs of the Maize Low Phytic Acid Gene.” The Plant Genome 2 (2): 179–190. doi:10.3835/plantgenome2008.03.0013.
   Web of Science ®Google Scholar
• Guttieri, M., D. Bowen, J. A. Dorsch, V. Raboy, and E. Souza. 2004. “Identification and Characterization of a Low Phytic Acid Wheat.” Crop Science 44: 418–424. doi:10.2135/cropsci2004.4180.
   Web of Science ®Google Scholar
• Hambidge, K. M., J. W. Huffer, V. Raboy, G. K. Grunwald, J. L. Westcott, L. Sian, L. V. Miller, J. A. Dorsch, and N. F. Krebs. 2004. “Zinc Absorption from low-phytate Hybrids of Maize and Their wild-type Isohybrids.” The American Journal of Clinical Nutrition 79 (6): 1053–1059. doi:10.1093/ajcn/79.6.1053.
   PubMed Web of Science ®Google Scholar
• Hambidge, K. M., N. F. Krebs, J. L. Westcott, L. Sian, L. V. Miller, K. L. Peterson, and V. Raboy. 2005. “Absorption of Calcium from Tortilla Meals Prepared from low-phytate Maize.” The American Journal of Clinical Nutrition 82 (1): 84–87. doi:10.1093/ajcn.82.1.84.
   PubMed Web of Science ®Google Scholar
• Hill, B. E., A. L. Sutton, and B. T. Richert. 2009. “Effects of low-phytic Acid Corn, low-phytic Acid Soybean Meal, and Phytase on Nutrient Digestibility and Excretion in Growing Pigs.” Journal of Animal Science 87 (4): 1518–1527. doi:10.2527/jas.2008-1219.
   PubMed Web of Science ®Google Scholar
• Hitz, W. D., T. J. Carlson, P. S. Kerr, and S. A. Sebastian. 2002. “Biochemical and Molecular Characterization of a Mutation that Confers a Decreased Raffinosaccharide and Phytic Acid Phenotype on Soybean Seeds.” Plant Physiology 128 (2): 650–660. doi:10.1104/pp.010585.
   PubMed Web of Science ®Google Scholar
• Karmakar, A., S. Bhattacharya, S. Sengupta, N. Ali, S. N. Sarkar, K. Datta, and S. K. Datta. 2020. “RNAi-mediated Silencing of ITPK Gene Reduces Phytic Acid Content, Alters Transcripts of Phytic Acid Biosynthetic Genes, and Modulates Mineral Distribution in Rice Seeds.” Rice Science 27 (4): 315–328. doi:10.1016/j.rsci.2020.05.007.
   Web of Science ®Google Scholar
• Kim, D., G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S. L. Salzberg. 2013. “TopHat2: Accurate Alignment of Transcriptomes in the Presence of Insertions, Deletions and Gene Fusions.” Genome Biology 14 (4): 1–13. doi:10.1186/gb-2013-14-4-r36.
   Web of Science ®Google Scholar
• Krishnan, V., A. Hada, A. Marathe, B. K. Palaka, D. R. Ampasala, S. Praveen, M. Manickavasagam, and A. Sachdev. 2019. “Functional Characterization of Gm ITPK (myo-inositol: 1, 3, 4 Tris Phosphate 5/6 Kinase) Isoforms—‘so Different yet so Similar.’” Journal of Plant Biochemistry and Biotechnology 28 (4): 389–396. doi:10.1007/s13205-017-1076-z.
   Web of Science ®Google Scholar
• Larson, S. R., J. N. Rutger, K. A. Young, and V. Raboy. 2000. “Isolation and Genetic Mapping of a non-lethal Rice (Oryza Sativa L.) Low Phytic Acid 1 Mutation.” Crop Science 40 (5): 1397–1405. doi:10.2135/cropsci2000.4051397x.
   Web of Science ®Google Scholar
• Larson, S. R., K. A. Young, A. Cook, T. K. Blake, and V. Raboy. 1998. “Linkage Mapping of Two Mutations that Reduce Phytic Acid Content of Barley Grain.” Theoretical and Applied Genetic 97 (1): 141–146. doi:10.1007/s001220050878.
   Web of Science ®Google Scholar
• Liu, Q.-L., X.-H. Xu, X.-L. Ren, H.-W. Fu, D.-X. Wu, and Q.-Y. Shu. 2007. “Generation and Characterization of Low Phytic Acid Germplasm in Rice (Oryza Sativa L.).” Theoretical and Applied Geneti 114 (5): 803–814. doi:10.1007/s00122-006-0478-9.
   PubMed Web of Science ®Google Scholar
• Lott, J. N., I. Ockenden, V. Raboy, and G. D. Batten. 2000. “Phytic Acid and Phosphorus in Crop Seeds and Fruits: A Global Estimate.” Seed Science Research 10: 11–33. doi:10.1017/S0960258500000039.
   Web of Science ®Google Scholar
• Lu, H. P., W. Q. Pang, W. X. Li, Y. Y. Tan, Q. Wang, H. J. Zhao, and Q. Y. Shu. 2016. “Tissue-specific Expression, Developmentally and Spatially Regulated Alternative Splicing, and Protein Subcellular Localization of OsLpa Rice.” Journal of Zhejiang University-SCIENCE B 17 (2): 100–109. doi:10.1631/jzus.B1500205.
   PubMed Web of Science ®Google Scholar
• McCarthy, D. J., Y. Chen, and G. K. Smyth. 2012. “Differential Expression Analysis of Multifactor RNA-Seq Experiments with respect to Biological Variation.” Nucleic Acids Research 40 (10): 4288–4297. doi:10.1093/nar/gks042.
   PubMed Web of Science ®Google Scholar
• Meis, S. J., W. R. Fehr, and S. R. Schnebly. 2003. “Seed Source Effect on Field Emergence of Soybean Lines with Reduced Phytate and Raffinose Saccharides.” Crop Science 43 (4): 1336–1339. doi:10.2135/cropsci2003.1336.
   Web of Science ®Google Scholar
• Mendoza, C., F. E. Viteri, B. Lönnerdal, K. A. Young, V. Raboy, and K. H. Brown. 1998. “Effect of Genetically Modified, low-phytic Acid Maize on Absorption of Iron from Tortillas.” The American Journal of Clinical Nutrition 68 (5): 1123–1127. doi:10.1093/ajcn/68.5.1123.
   PubMed Web of Science ®Google Scholar
• Nishida, S., Y. Kakei, Y. Shimada, and T. Fujiwara. 2017. “Genome‐wide Analysis of Specific Alterations in Transcript Structure and Accumulation Caused by Nutrient Deficiencies in Arabidopsis Thaliana.” The Plant Journal 91 (4): 741–753. doi:10.1111/tpj.13606.
   PubMed Web of Science ®Google Scholar
• Panzeri, D., E. Cassani, E. Doria, G. Tagliabue, L. Forti, B. Campion, R. Bollini, et al. 2011. “A Defective ABC Transporter of the MRP Family, Responsible for the Bean lpa1 Mutation, Affects the Regulation of the Phytic Acid Pathway, Reduces Seed myo-inositol and Alters ABA Sensitivity.” New Phytologist 191 (1): 70–83. doi:10.1111/j.1469-8137.2011.03666.x.
   PubMed Web of Science ®Google Scholar
• Powers, W., E. Fritz, W. Fehr, and R. Angel. 2006. “Total and water-soluble Phosphorus Excretion from Swine Fed low-phytate Soybeans.” Journal of Animal Science 84: 1907–1915. doi:10.2527/jas.2005-656.
   PubMed Web of Science ®Google Scholar
• Qin, D., Y. Hara, V. Raboy, and H. Saneoka. 2020. “Characteristics and Quality of Japanese Traditional Fermented Soybean (Natto) from a low-phytate Line.” Plant Foods for Human Nutrition 75 (4): 651–655. doi:10.1007/s11130-020-00865-5.
   PubMed Web of Science ®Google Scholar
• Raboy, V. 2003. “myo-Inositol-1,2,3,4,5,6-hexakisphosphate.” Phytochemistry 64 (6): 1033–1043. doi:10.1016/s0031-9422(03)00446-1.
   PubMed Web of Science ®Google Scholar
• Raboy, V. 2009. “Approaches and Challenges to Engineering Seed Phytate and Total Phosphorus.” Plant Science 177 (4): 281–296. doi:10.1016/j.plantsci.2009.06.012.
   Web of Science ®Google Scholar
• Raboy, V., P. F. Gerbasi, K. A. Young, S. D. Stoneberg, S. G. Ickett, A. T. Bauman, P. P. Murthy, W. F. Sheridan, and D. S. Ertl. 2000. “Origin and Seed Phenotype of Maize Low Phytic Acid 1-1 and Low Phytic Acid 2-1.” Plant Physiology 124 (1): 355–368. doi:10.1104/pp.124.1.355.
   PubMed Web of Science ®Google Scholar
• Raboy, V., R. S. Gibson, K. B. Bailey, and J. C. King. 2020. “Comparison of Four Methods for Phytate Analysis in plant-based Foods.” Journal of Food Composition and Analysis 90: 103481. doi:10.1016/j.jfca.2020.103481.
   Web of Science ®Google Scholar
• Roche, D. B., M. T. Buenavista, and L. J. McGuffin. 2013. “The FunFOLD2 Server for the Prediction of protein-ligand Interactions.” Nucleic Acids Research 41 (W1): W303–W307. doi:10.1093/nar/gkt498.
   PubMed Web of Science ®Google Scholar
• Seelan, R. S., J. Lakshmanan, M. F. Casanova, and R. N. Parthasarathy. 2009. “Identification of myo-inositol-3-phosphate Synthase Isoforms.” Journal of Biological Chemistry 284 (14): 9443–9457. doi:10.1074/jbc.M900206200.
   PubMed Web of Science ®Google Scholar
• Shi, J., H. Wang, K. Schellin, B. Li, M. Faller, J. M. Stoop, R. B. Meeley, D. S. Ertl, J. P. Ranch, and K. Glassman. 2007. “Embryo-specific Silencing of a Transporter Reduces Phytic Acid Content of Maize and Soybean Seeds.” Nature Biotechnology 25 (8): 930–937. doi:10.1038/nbt1322.
   PubMed Web of Science ®Google Scholar
• Sparvoli, F., and E. Cominelli. 2015. “Seed Biofortification and Phytic Acid Reduction: A Conflict of Interest for the Plant?” Plants 4 (4): 728–755. doi:10.3390/plants4040728.
   Google Scholar
• Stiles, A. R., X. Qian, S. B. Shears, and E. A. Grabau. 2008. “Metabolic and Signaling Properties of an Itpk Gene Family in Glycine Max.” FEBS Letters 582 (13): 1853–1858. doi:10.1016/j.febslet.2008.04.054.
   PubMed Web of Science ®Google Scholar
• Sun, Y., M. Thompson, G. Lin, H. Butler, Z. Gao, S. Thornburgh, K. Yau, D. A. Smith, and V. K. Shukla. 2007. “Inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase from Maize: Molecular and Biochemical Characterization.” Plant Physiology 144 (3): 1278–1291. doi:10.1104/pp.107.095455.
   PubMed Web of Science ®Google Scholar
• Taliman, N. A., Q. Dong, K. Echigo, V. Raboy, and H. Saneoka. 2019. “Effect of Phosphorus Fertilization on the Growth, Photosynthesis, Nitrogen Fixation, Mineral Accumulation, Seed Yield, and Seed Quality of a Soybean low-phytate Line.” Plants (Basel) 8 (5): 119. doi:10.3390/plants8050119.
   PubMedGoogle Scholar
• Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. Van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. 2010. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 2 (5): 511–515. doi:10.1038/nbt.1621.
   Web of Science ®Google Scholar
• Vanichkina, D. P., U. Schmitz, J. J. L. Wong, and J. E. Rasko. 2018. “Challenges in Defining the Role of Intron Retention in Normal Biology and Disease.” Seminars in Cell & Developmental Biology 75: 40–49. doi:10.1016/j.semcdb.2017.07.030.
   PubMed Web of Science ®Google Scholar
• Wilcox, J. R., G. S. Premachandra, K. A. Young, and V. Raboy. 2000. “Isolation of High Seed Inorganic P, low-phytate Soybean Mutants.” Crop Science 40 (6): 1601–1605. doi:10.2135/cropsci2000.4061601x.
   Web of Science ®Google Scholar
• Yuan, F. J., D. H. Zhu, Y. Y. Tan, D. K. Dong, X. J. Fu, S. L. Zhu, B. Q. Li, and Q. Y. Shu. 2012. “Identification and Characterization of the Soybean IPK1 Ortholog of a Low Phytic Acid Mutant Reveals an exon-excluding splice-site Mutation.” Theoretical and Applied Genetics 125 (7): 1413–1423. doi:10.1007/s00122-012-1922-7.
   PubMed Web of Science ®Google Scholar