Akhtar S, Das JK, Ismail T, Wahid M, Saeed W, Bhutta ZA (2021) Nutritional perspectives for
the prevention and mitigation of COVID-19. Nutr Rev 79(3):289-300
https://doi.org/10.1093/nutrit/nuaa063
Alloway BJ (2008) Zinc in soils and crop nutrition.
http://www.topsoils.co.nz/wp-content/uploads/2014/09/Zinc-in-Soils-and-Crop-Nutrition-Brian-J.-Alloway.pdf .Accessed 15 Apr 2021
Anders S, Pyl PT, Huber W(2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2):166-169
https://doi.org/10.1093/bioinformatics/btu638
Ariel FD, Manavella PA, Dezar, CA, Chan RL (2007) The true story of the HD-Zip family. Trends in plant science (12)9:419-426 https://doi.org/10.1016/j.tplants.2007.08.003
Banakar R, Alvarez FA, Díaz-Benito P, Abadia J, Capell T, Christou P (2017) Phytosiderophores determine thresholds for iron and zinc accumulation in biofortified rice endosperm while inhibiting the accumulation of cadmium. Journal of Experimental Botany 68(17):4983-4995 https://doi.org/10.1093/jxb/erx304
Bandyopadhyay T, Mehra P, Hairat S, Giri J (2017) Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice. Fun & Int Gen (17):565-581 https://doi.org/10.1007/s10142-017-0556-x
Banerjee S, Chandel G (2011a) Understanding the role of metal homeostasis related candidate genes in Fe/Zn uptake, transport and redistribution in rice using semi-quantitative RT-PCR. Plant Mol Biol Biotechnol 2:33–46
Black MM (1998) Zinc deficiency and child development. The American journal of clinical nutrition (68):464S-469S https://dx.doi.org/10.1093%2Fajcn%2F68.2.464S
Bokor B, Bokorová S, Ondoš S, Švubová R, Lukačová Z, Hýblová M, Szemes T, Lux A (2015) Ionome and expression level of Si transporter genes (Lsi1, Lsi2, and Lsi6) affected by Zn and Si interaction in maize. Environmental Science, Research Pollution 22(9):6800-6811 https://doi.org/10.1007/s11356-014-3876-6
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120 https://doi.org/10.1093/bioinformatics/btu170
Cai H, Huang S, Che J, Yamaji N, Ma JF (2019) The tonoplast-localized transporter OsHMA3 plays an important role in maintaining Zn homeostasis in rice. Journal of experimental botany 70(10):2717-2725 https://doi.org/10.1093/jxb/erl054
Chen F, Wang F, Wu F, Mao W, Zhang G, Zhou M (2010) Modulation of exogenous glutathione in antioxidant defense system against Cd stress in the two barley genotypes differing in Cd tolerance. Plant Physiology, Biochemistry 48(8):663-672 https://doi.org/10.1016/j.plaphy.2010.05.001
Cheng S, Zhou DX, Zhao Y (2016) WUSCHEL-related homeobox gene WOX11 increases rice drought resistance by controlling root hair formation and root system development. Plant Sign & Beh11(2):e1130198. https://doi.org/10.1080/15592324.2015.1130198
Childs KL, Davidson RM, Buell CR (2011) Gene coexpression network analysis as a source of functional annotation for rice genes. PloS one 6(7):e22196 https://doi.org/10.1371/journal.pone.0022196
Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY (2014) cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC systems biology 8 Suppl 4(Suppl 4):S11-S11https://doi.org/10.1186/1752-0509-8-S4-S11
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B (2007) Integration of biological networks and gene expression datausing Cytoscape. Nat Protoc (2):2366–2382
https://doi.org/10.1038/nprot.2007.324
Dardenne M (2002) Zinc and immune function. European Journal of Clinical Nutrition (56):S20-S23 https://doi.org/10.1038/sj.ejcn.1601479
Debi BR, Taketa S, Ichii M (2005) Cytokinin inhibits lateral root initiation but stimulates lateral Root elongation in rice (Oryza sativa). Journal of plant physiology 162(5):507-515 https://doi.org/10.1016/j.jplph.2004.08.007
El-Shabrawi H, Kumar B, Kaul T, Reddy MK, Singla-Pareek SL, Sopory SK (2010) Redox homeostasis, antioxidant defense, and methylglyoxal detoxification as markers for salt tolerance in Pokkali rice. Protoplasma 245(1):85-96
https://doi.org/10.1007/s00709-0100144-6
Fan X, Feng H, Tan Y, Xu Y, Miao Q, Xu G (2016) A putative 6-transmembrane nitrate transporter OsNRT1.1b plays a key role in rice under low nitrogen. Integr Plant Biol 58(6):590-599. https://doi.org/10.1111/jipb.12382
Hartwell LH, Hopfield JJ, Leibler S, Murray AW (199) From molecular to modular cell biology. Nature 402(6761):C47-52 https://doi.org/10.1038/35011540
Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, Liang C, Liu L, Piao Z, Deng Q, Deng K, Xu C, Liang Y, Zhang L, Li L, Chu C (2015) Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet 47(7): 834-838 https://doi.org/10.1038/ng.3337
Huizar MI, Arena R, Laddu DR (2021) The global food syndemic: the impact of food insecurity, malnutrition and obesity on the healthspan amid the COVID-19 pandemic. Progress in cardiovascular diseases 64:105–107 https://dx.doi.org/10.1016%2Fj.pcad.2020.07.002
Ishimaru Y, Bashir K, Nishizawa NK (2011) Zn Uptake and Translocation in Rice Plants. Rice 4:21–27 https://doi.org/10.1007/s12284-011-9061-3
Ishimaru Y, Suzuki M, Kobayashi T, Takahashi M, Nakanishi H, Mori S, Nishizawa NK (2005) OsZIP4, a novel zinc-regulated zinc transporter in rice. Journal of Experimental Botany 56(422):3207-3214 https://doi.org/10.1093/jxb/eri317
Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC (2012) Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC genomics (1):1-9 https://doi.org/10.1186/1471-2164-13-544
Keller C, Rizwan M, Davidian JC, Pokrovsky OS, Bovet N, Chaurand P, Meunier JD (2015) Effect of silicon on wheat seedlings (Triticum turgidum L.) grown in hydroponics and exposed to 0 to 30 µM Cu. Planta 241(4):847-860 https://doi.org/10.1007/s00425-014-2220-1
Kitomi Y, Hidemi K, Inukai Y (2011) Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice. Plant signaling, behavior 6(9): 1276-1278 https://doi.org/10.4161/psb.6.9.16787
Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 9(1):1-13 https://doi.org/10.1186/1471-2105-9-559
Lee S, Chiecko JC, Kim SA, Walker EL, LeeY, Guerinot ML, An G (2009) Disruption of OsYSL15 leads to iron inefficiency in rice plants. Plant physiology 150(2):786-800
https://doi.org/10.1104/pp.109.135418
Lee S, Kim SA, Lee J, Guerinot ML, An G (2010) Zinc deficiency-inducible OsZIP8 encodes a plasma membrane-localized zinc transporter in rice. Mol Cells (29):551-558
https://doi.org/10.1007/s10059-010-0069-0
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078-2079 https://doi.org/10.1093/bioinformatics/btp352
Li J, Han Y, Liu L, Chen Y, Du Y, Zhang J, Sun H, Zhao Q (2015) qRT9, a quantitative trait locus controlling root thickness and root length in upland rice. Journal of Experimental Botany 66(9):2723-32 https://doi.org/10.1093/jxb/erv076
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923-930 https://doi.org/10.1093/bioinformatics/btt656
Lu X, Liu S, Zhi S, Chen J, Ye G (2020) Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. Plant Biol 23(2):375-390 https://doi.org/10.1111/plb.13227
Ma JF, Yamaji N, Mitani N, Xu XY, Su YH, McGrath SP, Zhao FJ (2008) Transporters of arsenite in rice and their role in arsenic accumulation in rice grain. Proceedings of the National Academy of Sciences 105(29):9931-5 https://doi.org/10.1073/pnas.0802361105
Masuda H, Ishimaru Y, Aung MS, Kobayashi T, Kakei Y, Takahashi M, Higuchi K, Nakanishi H, Nishizawa NK (2012) Iron biofortification in rice by the introduction of multiple genes involved in iron nutrition. Sci Rep 2, 543 https://doi.org/10.1038/srep00543
Maurya S, Vishwakarma AK, Dubey M, Shrivastava P, Shrivastava R, Chandel G (2018) Developing gene-tagged molecular marker for functional analysis of OsZIP10 metal transporter gene in rice. Indian Journal of Genetics and Plant Breeding (The) 78(2): 180-186. https://doi.org/10.5958/0975-6906.2018.00023.8
Mering VC, Huynen M, Jaeggi, D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Research 31(1):258-261 https://doi.org/10.1093/nar/gkg034
Nanda AK, Pujol V, Wissuwa M (2017) Patterns of stress response and tolerance based on transcriptome profiling of rice crown tissue under zinc deficiency. Journal of Experimental Botany 68(7):1715-1729 https://doi.org/10.1093/jxb/erx039
Nanda AK, Wissuwa M (2016a) Rapid crown root development confers tolerance to zinc deficiency in rice. Frontiers in plant science 7, 428 https://doi.org/10.3389/fpls.2016.00428
Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav S (2019) Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. Plant Cell Physiol 60(10):2343-2355 https://doi.org/10.1093/pcp/pcz132
Noctor G, Mhamdi A, Chaouch S, Han Y, Neukermans J, Marquez-Garcia B, Queval G, Foyer C H (2012) Glutathione in plants: an integrated overview. Plant Cell Environ 35(2):454-84 https://doi.org/10.1111/j.1365-3040.2011.02400.x
Nozoye T, Nagasaka S, Kobayashi T, Takahashi M, Sato Y, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK (2011) Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants. Journal of Biological Chemistry 286(7):5446-54.
https://doi.org/10.1074/jbc.M110.18002
Ogo Y, Itai RN, Nakanishi H, Inoue H, Kobayashi T, Suzuki M, Takahashi M, Mori S, Nishizawa NK (2006) Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants. Journal of Experimental Botany 57, 2867-78 https://doi.org/10.1093/jxb/erl054
Ogo Y, Itai RN, Kobayashi T, Nakanishi H, Mori S, Nishizawa NK (2009) Overexpression of OsIRO2 improves both iron uptake and translocation to seeds in rice. UC Davis: Department of Plant Sciences. https://escholarship.org/uc/item/2kd7m133 .Accessed 15 Apr 2021
Ogo Y, Nakanishi IR, Nakanishi H, Kobayashi T, Takahashi M, Mori S, Nishizawa NK (2007) The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe‐deficient conditions. Plant journal 51(3):366-377
https://doi.org/10.1111/j.1365-313X.2007.03149.x
Olsen LI, Palmgren MG (2014) Many rivers to cross: the journey of zinc from soil to seed. Frontiers in Plant Science 5, 30 https://doi.org/10.3389/fpls.2014.00030
Pérez-Rodríguez P, Riano-Pachon DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic acids research 38(suppl_1):D822-7 https://doi.org/10.1093/nar/gkp805
Ptashnyk M, Roose T, Jones DL, Kirk G (2011) Enhanced zinc uptake by rice through phytosiderophore secretion: a modelling study. Plant Cell Environ 34(12):2038-2046
https://doi.org/10.1111/j.1365-3040.2011.02401.x
Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, Van Ex F, Pasha A (2018) The transcriptional landscape of polyploid wheat. Science 361(6403) https://doi.org/10.1126/science.aar6089
Sasaki A, Yamaji N, Ma JF (2014) Overexpression of OsHMA3 enhances Cd tolerance and expression of Zn transporter genes in rice. Journal of experimental botany 65(20):6013-6021 https://doi.org/10.1093/jxb/eru340
Seneviratne G, Jayasinghearachchi HS (2003) Mycelial colonization by bradyrhizobia and azorhizobia. Journal of biosciences 28(2):243-247 https://doi.org/10.1007/BF02706224
Sharma A, Shahzad B, Rehman A, Bhardwaj R, Landi M, Zheng B (2019) Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 24(13):2452 https://doi.org/10.3390/molecules24132452
Sinclair SA, Krämer U (2012) The zinc homeostasis network of land plants. Biochimica et Biophysica Acta -Molecular Cell Research 1823(9):1553-1567
https://doi.org/10.1016/j.bbamcr.2012.05.016
Singh SP, Gruissem W, Bhullar NK (2017) Single genetic locus improvement of iron, zinc and β-carotene content in rice grains. Scientific Reports 7(1):6883
https://doi.org/10.1038/s41598-017-07198-5
Sichul L, Jeff CC, Sun AK, Elsbeth LW, Youngsook L, Mary LG, Gynheung A (2009) Disruption of OsYSL15 leads to iron inefficiency in rice plants. Plant physiology 150(2):786-800 https://doi.org/10.1104/pp.109.135418
Song A, Li P, Fan F, Li Z, Liang Y (2014) The effect of silicon on photosynthesis and expression of its relevant genes in rice (Oryza sativa L.) under high-zinc stress. PLoS One 9(11):e113782 https://doi.org/10.1371/journal.pone.0113782
Suzuki M, Bashir K, Inoue H, Takahashi M, Nakanishi H, Nishizawa NK (2012) Accumulation of starch in Zn-deficient rice. Rice 5(1):1-8 https://doi.org/10.1186/1939-8433-5-9
Takahashi R, Bashir K, Ishimaru Y, Nishizawa NK, Nakanishi H (2012) The role of heavy-metal ATPases, HMAs, in zinc and cadmium transport in rice. Plant signaling & behavior 7(12):1605-1607 https://doi.org/10.4161/psb.22454
Tan M, Cheng D, Yang Y, Zhang G, Qin M, Chen J, Chen Y, Jiang M (2017) Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes. BMC Plant Biology 17(1):194
https://doi.org/10.1186/s12870-017-1143-y
Tripathi P, Tripathi RD, Singh RP, Dwivedi S, Goutam D, Shri M, Trivedi PK, Chakrabarty D (2013) Silicon mediates arsenic tolerance in rice (Oryza sativa L.) through lowering of arsenic uptake and improved antioxidant defence system. Ecological engineering 52:96-103 https://doi.org/10.1016/j.ecoleng.2012.12.057
Van DSD, Bhullar NK, De SH, Gruissem W, MacKenzie D, Pfeiffer W, Qaim M, Slamet-Loedin I, Strobbe S, Tohme J, Trijatmiko KR, Vanderschuren H, Van MM, Zhang C, Bouis H (2020) Multiplying the efficiency and impact of biofortification through metabolic engineering. Nature Communications 11(1):5203 https://doi.org/10.1038/s41467-020-19020-4
Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR (2016) Integration of omic networks in a developmental atlas of maize. Science 353(6301):814-818 https://doi.org/10.1126/science.aag1125
Wang W, Ye J, Ma Y, Wang T, Shou H, Zheng L (2020) OsIRO3 Plays an Essential Role in Iron Deficiency Responses and Regulates Iron Homeostasis in Rice. Plants (Basel) 9(9):1095
https://doi.org/10.3390/plants9091095
Widodo B, Broadley MR, Rose T, Frei M, Pariasca-Tanaka J, Yoshihashi T, Thomson M, Hammond JP, Aprile A, Close TJ, Ismail AM, Wissuwa M (2010) Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity. New Phytol 186(2):400-414 https://doi.org/10.1111/j.1469-8137.2009.03177.x
Yamaji N, Sakurai G, Mitani-Ueno N, Ma JF (2015) Orchestration of three transporters and distinct vascular structures in node for intervascular transfer of silicon in rice. Proc Natl Acad Sci 112(36):11401-11406 https://doi.org/10.1073/pnas.1508987112
Yamaji Ni, Xia J, Mitani-Ueno N, Yokosho K, Ma JF (2013) Preferential delivery of zinc to developing tissues in rice is mediated by P-type heavy metal ATPase OsHMA2. Plant physiology 162(2):927-939 https://doi.org/10.1104/pp.113.216564
Yang Z, Wu Y, Li Y, Ling HQ, Chu C (2009) OsMT1a, a type 1 metallothionein, plays the pivotal role in zinc homeostasis and drought tolerance in rice. Plant molecular biology 70(1-2): 219-229 https://doi.org/10.1007/s11103-009-9466-1
Zeng H, Zhang X, Ding M, Zhu Y (2019b) Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings. BMC Plant Biol 19(1):585 https://doi.org/10.1186/s12870-019-2203-2
Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4(1): Article17 https://doi.org/10.2202/1544-6115.1128
Zhang L, Hu B, Deng K, Gao X, Sun G, Zhang Z, Li P, Wang W, Li H, Zhang Z, Fu Z, Yang J, Gao S, Li L, Yu F, Li Y, Ling H, Chu C (NRT1.1B) improves selenium concentrations in rice grains by facilitating selenomethinone translocation. Plant Biotechnol 17(6):1058-1068 https://doi.org/10.1111/pbi.13037
Zhang Y, Yu C, Lin J, Liu J, Liu B, Wang J, Huang A, Li H, Zhao T (2017) OsMPH1 regulates plant height and improves grain yield in rice. PLoS One 12(7): e0180825
https://doi.org/10.1371/journal.pone.0180825
Zhao W, Langfelder P, Fuller T, Dong J, Li A, Hovarth S (2010) Weighted gene coexpression network analysis: state of the art. Journal of biopharmaceutical statistics 20(2):281-300 https://doi.org/10.1080/10543400903572753
Zheng L, Ying Y, Wang L, Wang F, Whelan J, Shou H (2010) Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa. BMC Plant Biol 10:166 https://doi.org/10.1186/1471-2229-10-166
Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni J (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular plant 9(12):1667-1670 https://doi.org/10.1016/j.molp.2016.09.014