1 Rose, T. J., Liu, L. & Wissuwa, M. Improving phosphorus efficiency in cereal crops: Is breeding for reduced grain phosphorus concentration part of the solution? Frontiers in plant science4, 444 (2013).
2 Raboy, V. Approaches and challenges to engineering seed phytate and total phosphorus. Plant Science177, 281-296 (2009).
3 Singh, S. K., Barnaby, J. Y., Reddy, V. R. & Sicher, R. C. Varying Response of the Concentration and Yield of Soybean Seed Mineral Elements, Carbohydrates, Organic Acids, Amino Acids, Protein, and Oil to Phosphorus Starvation and CO2 Enrichment. Frontiers in plant science7, 1967, doi:10.3389/fpls.2016.01967 (2016).
4 Pilu, R. et al. Phenotypic, genetic and molecular characterization of a maize low phytic acid mutant (lpa241). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik107, 980-987, doi:10.1007/s00122-003-1316-y (2003).
5 Bhati, K. K. et al. Differential expression of structural genes for the late phase of phytic acid biosynthesis in developing seeds of wheat (Triticum aestivum L.). Plant science : an international journal of experimental plant biology224, 74-85, doi:10.1016/j.plantsci.2014.04.009 (2014).
6 Aluru, M. R., Rodermel, S. R. & Reddy, M. B. Genetic modification of low phytic acid 1-1 maize to enhance iron content and bioavailability. Journal of agricultural and food chemistry59, 12954-12962, doi:10.1021/jf203485a (2011).
7 Thavarajah, P., Thavarajah, D. & Vandenberg, A. Low phytic acid lentils (Lens culinaris L.): a potential solution for increased micronutrient bioavailability. Journal of agricultural and food chemistry57, 9044-9049, doi:10.1021/jf901636p (2009).
8 Frank, T., Norenberg, S. & Engel, K. H. Metabolite profiling of two novel low phytic acid (lpa) soybean mutants. Journal of agricultural and food chemistry57, 6408-6416, doi:10.1021/jf901019y (2009).
9 Zhao, N. C. et al. Characteristics of Grain Starch Synthesis at Filling Stage and Translocation of Carbohydrates in Leaves and Sheaths for Low Phytic Acid Mutant Rice. Acta Agronomica Sinica34, 1977-1984 (2008).
10 Suzuki, M., Tanaka, K., Kuwano, M. & Yoshida, K. T. Expression pattern of inositol phosphate-related enzymes in rice (Oryza sativa L.): implications for the phytic acid biosynthetic pathway. Gene405, 55-64, doi:10.1016/j.gene.2007.09.006 (2007).
11 Vincent, J. A., Stacey, M., Stacey, G. & Bilyeu, K. D. Phytic Acid and Inorganic Phosphate Composition in Soybean Lines with Independent IPK1 Mutations. Plant Genome8 (2015).
12 Yuan, F. J. et al. Generation and characterization of two novel low phytate mutations in soybean (Glycine max L. Merr.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik115, 945-957, doi:10.1007/s00122-007-0621-2 (2007).
13 Yuan, F. et al. Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants. BMC plant biology17, 16, doi:10.1186/s12870-016-0953-7 (2017).
14 Shunmugam, A. S. et al. Accumulation of Phosphorus-Containing Compounds in Developing Seeds of Low-Phytate Pea (Pisum sativum L.) Mutants. Plants4, 1-26, doi:10.3390/plants4010001 (2014).
15 Yuan, F. J. et al. Identification and characterization of the soybean IPK1 ortholog of a low phytic acid mutant reveals an exon-excluding splice-site mutation. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik125, 1413-1423, doi:10.1007/s00122-012-1922-7 (2012).
16 Goßner, S. et al. Impact of Cross-Breeding of Low Phytic Acid MIPS1 and IPK1 Soybean (Glycine max L. Merr.) Mutants on Their Contents of Inositol Phosphate Isomers. Journal of agricultural and food chemistry67, 247-257, doi:10.1021/acs.jafc.8b06117 (2019).
17 Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic acids research32, D277 (2003).
18 Ho-Seok, L. et al. InsP6-Sensitive Variants of the Gle1 mRNA Export Factor Rescue Growth and Fertility Defects of the ipk1 Low-Phytic-Acid Mutation in Arabidopsis. The Plant cell27, 417-431 (2015).
19 Chaouch, S. & Noctor, G. Myo-inositol Abolishes Salicylic Acid-dependent Cell Death and Pathogen Defence Responses Triggered by Peroxisomal Hydrogen Peroxide. New Phytologist188, 711-718 (2010).
20 Ali, N. et al. Development of low phytate rice by RNAi mediated seed-specific silencing of inositol 1,3,4,5,6-pentakisphosphate 2-kinase gene (IPK1). PloS one8, e68161 (2013).
21 Zhang, J. et al. Overexpression of PeMIPS1 confers tolerance to salt and copper stresses by scavenging reactive oxygen species in transgenic poplar. Tree physiology, doi:10.1093/treephys/tpy028 (2018).
22 Zhai, H. et al. A myo-inositol-1-phosphate synthase gene, IbMIPS1, enhances salt and drought tolerance and stem nematode resistance in transgenic sweet potato. Plant biotechnology journal14, 592-602, doi:10.1111/pbi.12402 (2016).
23 Raboy, V. Forward genetics studies of seed phytic acid. Israel Journal of Plant Sciences55, 171-181 (2007).
24 Yuan, F. J. Characterization of D-myo-inositol 3-phosphate Synthase Gene Expression in Two Soybean Low Phytate Mutants. Journal of Nuclear Agricultural Sciences (2013).
25 Zhao, H. et al. Disruption of OsSULTR3;3 reduces phytate and phosphorus concentrations and alters the metabolite profile in rice grains. The New phytologist211, 926-939, doi:10.1111/nph.13969 (2016).
26 Zhang, S. et al. Analysis of weighted co-regulatory networks in maize provides insights into new genes and regulatory mechanisms related to inositol phosphate metabolism. BMC genomics17, 129, doi:10.1186/s12864-016-2476-x (2016).
27 Luo, Y. et al. D-myo-inositol-3-phosphate affects phosphatidylinositol-mediated endomembrane function in Arabidopsis and is essential for auxin-regulated embryogenesis. The Plant cell23, 1352-1372 (2011).
28 Donahue, J. L. et al. The Arabidopsis thaliana Myo-inositol 1-phosphate synthase1 gene is required for Myo-inositol synthesis and suppression of cell death. The Plant cell22, 888-903 (2010).
29 Chen, H. & Xiong, L. M. Myo-inositol-1-phosphate synthase is required for polar auxin transport and organ development. Journal of Biological Chemistry285, 24238-24247 (2010).
30 Yuan, F. J. et al. Effects of two low phytic acid mutations on seed quality and nutritional traits in soybean (Glycine max L. Merr). Journal of agricultural and food chemistry57, 3632-3638, doi:10.1021/jf803862a (2009).
31 Marathe, A. et al. Exploring the role of Inositol 1,3,4-trisphosphate 5/6 kinase-2 (GmITPK2) as a dehydration and salinity stress regulator in Glycine max (L.) Merr. through heterologous expression in E. coli. Plant physiology and biochemistry : PPB / Societe francaise de physiologie vegetale123, 331-341, doi:10.1016/j.plaphy.2017.12.026 (2017).
32 Zhao, H. J. et al. Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik126, 3009-3020, doi:10.1007/s00122-013-2189-3 (2013).
33 Nunes, A. C. et al. RNAi-mediated silencing of the myo-inositol-1-phosphate synthase gene (GmMIPS1) in transgenic soybean inhibited seed development and reduced phytate content. Planta224, 125-132, doi:10.1007/s00425-005-0201-0 (2006).
34 Denstadli, V., Vestre, R., Svihus, B., Skrede, A. & Storebakken, T. Phytate degradation in a mixture of ground wheat and ground defatted soybeans during feed processing: effects of temperature, moisture level, and retention time in small- and medium-scale incubation systems. Journal of agricultural and food chemistry54, 5887-5893, doi:10.1021/jf0605906 (2006).
35 Redekar, N. R. et al. Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. BMC genomics16, 1074, doi:10.1186/s12864-015-2283-9 (2015).
36 Nelson, D. E., Rammesmayer, G. & Bohnert, H. J. Regulation of cell-specific inositol metabolism and transport in plant salinity tolerance. The Plant cell10, 753-764 (1998).
37 Kumar, V. et al. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System. Applied biochemistry and biotechnology177, 689-699, doi:10.1007/s12010-015-1773-1 (2015).
38 Xia, Y. et al. Allelic variations of a light harvesting chlorophyll a/b-binding protein gene (Lhcb1) associated with agronomic traits in barley. PloS one7, e37573, doi:10.1371/journal.pone.0037573 (2012).
39 Ma, L. et al. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. Molecular plant9, 541-557, doi:10.1016/j.molp.2015.12.013 (2016).
40 Tognetti, J. A., Pontis, H. G. & Martinez-Noel, G. M. Sucrose signaling in plants: a world yet to be explored. Plant signaling & behavior8, e23316, doi:10.4161/psb.23316 (2013).
41 Karner, U. et al. myo-Inositol and sucrose concentrations affect the accumulation of raffinose family oligosaccharides in seeds. Journal of experimental botany55, 1981-1987, doi:10.1093/jxb/erh216 (2004).
42 Minic, Z. Physiological roles of plant glycoside hydrolases. Planta227, 723-740 (2008).
43 Lee, E. J., Matsumura, Y., Soga, K., Hoson, T. & Koizumi, N. Glycosyl hydrolases of cell wall are induced by sugar starvation in Arabidopsis. Plant & cell physiology48, 405-413, doi:10.1093/pcp/pcm009 (2007).
44 Mohapatra, P. K. et al. Senescence-induced loss in photosynthesis enhances cell wall beta-glucosidase activity. Physiologia plantarum138, 346-355 (2010).
45 Mohapatra, P. K. et al. Senescence-induced loss in photosynthesis enhances cell wall beta-glucosidase activity. Physiologia plantarum138, 346-355, doi:10.1111/j.1399-3054.2009.01327.x (2010).
46 Bahaji, A. et al. Characterization of multiple SPS knockout mutants reveals redundant functions of the four Arabidopsis sucrose phosphate synthase isoforms in plant viability, and strongly indicates that enhanced respiration and accelerated starch turnover can alleviate the blockage of sucrose biosynthesis. Plant science : an international journal of experimental plant biology238, 135-147, doi:10.1016/j.plantsci.2015.06.009 (2015).
47 But, S. Y., Khmelenina, V. N., Reshetnikov, A. S. & Trotsenko, Y. A. Bifunctional sucrose phosphate synthase/phosphatase is involved in the sucrose biosynthesis by Methylobacillus flagellatus KT. FEMS microbiology letters347, 43-51, doi:10.1111/1574-6968.12219 (2013).
48 Mozzoni, L., Shi, A. & Chen, P. Genetic Analysis of High Sucrose, Low Raffinose, and Low Stachyose Content in V99-5089 Soybean Seeds. Journal of Crop Improvement27, 606-616 (2013).
49 Graf, E. & Eaton, J. W. Antioxidant functions of phytic acid. Free radical biology & medicine8, 61-69 (1990).
50 Lemtiri-Chlieh, F. et al. Inositol hexakisphosphate mobilizes an endomembrane store of calcium in guard cells. Proceedings of the National Academy of Sciences of the United States of America100, 10091-10095 (2003).
51 Alex M, M., Bettina, O., Charles A, B., John P, C. & David E, H. A role for inositol hexakisphosphate in the maintenance of basal resistance to plant pathogens. The Plant Journal56, 638-652 (2010).
52 Cancela, J. M., Gerasimenko, O. V., Gerasimenko, J. V., Tepikin, A. V. & Petersen, O. H. Two different but converging messenger pathways to intracellular Ca(2+) release: the roles of nicotinic acid adenine dinucleotide phosphate, cyclic ADP-ribose and inositol trisphosphate. The EMBO journal19, 2549-2557, doi:10.1093/emboj/19.11.2549 (2000).
53 Wan, H. et al. Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns. BMC genomics13, 502, doi:10.1186/1471-2164-13-502 (2012).
54 Zhang, H. et al. A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature. BMC plant biology11, 160, doi:10.1186/1471-2229-11-160 (2011).
55 Sun, W. et al. Probing the Arabidopsis Flagellin Receptor: FLS2-FLS2 Association and the Contributions of Specific Domains to Signaling Function. The Plant cell24, 1096-1113, doi:10.1105/tpc.112.095919 (2012).
56 Chinchilla, D. et al. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature448, 497-500, doi:10.1038/nature05999 (2007).
57 Heese, A. et al. The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants. Proceedings of the National Academy of Sciences104, 12217-12222, doi:10.1073/pnas.0705306104 (2007).
58 Zhao, H., Jiang, J., Li, K. & Liu, G. Populus simonii x Populus nigra WRKY70 is involved in salt stress and leaf blight disease responses. Tree physiology37, 827-844, doi:10.1093/treephys/tpx020 (2017).
59 Li, J., Zhong, R. & Palva, E. T. WRKY70 and its homolog WRKY54 negatively modulate the cell wall-associated defenses to necrotrophic pathogens in Arabidopsis. PloS one12, e0183731, doi:10.1371/journal.pone.0183731 (2017).
60 Besseau, S., Li, J. & Palva, E. T. WRKY54 and WRKY70 co-operate as negative regulators of leaf senescence in Arabidopsis thaliana. Journal of experimental botany63, 2667-2679, doi:10.1093/jxb/err450 (2012).
61 Pitzschke, A., Schikora, A. & Hirt, H. MAPK cascade signalling networks in plant defence. Current opinion in plant biology12, 421-426 (2009).
62 Abdin, M. Z. et al.Signal Transduction and Regulatory Networks in Plant-Pathogen Interaction: A Proteomics Perspective. (Springer New York, 2013).
63 Tan, Y. Y. et al. Development of an HRM-based, safe and high-throughput genotyping system for two low phytic acid mutations in soybean. Molecular Breeding36, 1-9 (2016).
64 Gu, S., Fang, L. & Xu, X. Using SOAPaligner for Short Reads Alignment. Curr Protoc Bioinformatics44, 11 11 11-17 (2013).
65 Ghosh, S. & Chan, C. K. K. Analysis of RNA-Seq Data Using TopHat and Cufflinks. Methods in molecular biology1374, 339-361 (2016).
66 Thissen, D., Steinberg, L. & Kuang, D. Quick and Easy Implementation of the Benjamini-Hochberg Procedure for Controlling the False Positive Rate in Multiple Comparisons. Journal of Educational & Behavioral Statistics27, 77-83 (2002).
67 Alexa, A., Rahnenführer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics22, 1600 (2006).
68 Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics23, 257-258 (2007).