Adnan M, Hussain M, Anjum MZ, Rehman FU, Bilal HB, Toor MD et al. (2020) Role of phosphorous in wheat production: A review. Int J Agric Sci 8(2):10–15
Ahmed W, Xia Y, Li R, Bai G, Siddique KH, Guo P (2020) Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 112(2):1419–1424
Google Scholar
Ariel F, Brault-Hernandez M, Laffont C, Huault E, Brault M, Plet J et al. (2012) Two direct targets of cytokinin signaling regulate symbiotic nodulation in Medicago truncatula. Plant Cell 24:3838–3852
Google Scholar
Balyan HS, Gahlaut V, Kumar A, Jaiswal V, Dhariwal R, Tyagi S et al. (2016) Nitrogen and phosphorus use efficiencies in wheat: Physiology, phenotyping, genetics and breeding. Plant Breed Rev 40:167–234
Bogard M, Allard V, Brancourt-Hulmel M, Heumez E, Machet JM, Jeuffroy MH et al. (2010) Deviation from the grain protein concentration–grain yield negative relationship is highly correlated to post-anthesis N uptake in winter wheat. J Exp Bot 61:4303–4312
Google Scholar
Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. Plant Bioinformatics 1374:115–140
Google Scholar
Borrill P, Harrington SA, Uauy C (2017) Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat. G3: Genes Genomes Genet 7:3019–3029
Google Scholar
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314
Google Scholar
Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL (2006) Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 18:412–421
Google Scholar
Correll DL (1998) The role of phosphorus in the eutrophication of receiving waters: A review. J Environ Qual 27:261–266
Google Scholar
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Elser JJ, Sterner RW, Galford AE, Chrzanowski TH, Findlay DL, Mills KH et al. (2000) Pelagic C: N: P stoichiometry in a eutrophied lake: responses to a whole-lake food-web manipulation. Ecosystems 3:293–307
Fischer JJ, Beatty PH, Good AG, Muench DG (2013) Manipulation of microRNA expression to improve nitrogen use efficiency. Plant Sci 210:70–81
Google Scholar
Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685–695
Google Scholar
Grennan AK (2006) Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiol 141:1164–1166
Google Scholar
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185
Google Scholar
Gupta PK, Rustugi S, Mir RR (2013a) Array-based high-throughput DNA markers and genotyping platforms for cereal genetics and genomics. In: Gupta PK, Varshney RK (eds.) Cereal Genomics II. Springer, The Netherlands, 10.1007/978-94-007-6401-92
Gupta PK, Kulwal PL, Mir RR (2013b) QTL mapping: Methodology and applications in cereal breeding. In: Gupta PK, Varshney RK (eds.) Cereal Genomics II. Springer, The Netherlands, 10.1007/978-94-007-6401-9_11
Gupta PK, Varshney RK, Sharma PC, Ramesh B (1999) Molecular markers and their applications in wheat breeding. Plant Breed 118:369–390
Google Scholar
Hasan MM, Hasan MM, da Silva JAT, Li X (2016) Regulation of phosphorus uptake and utilization: transitioning from current knowledge to practical strategies. Cell Mol Biol 21:1–19
Hawkesford MJ (2012) The diversity of nitrogen use efficiency for wheat varieties and the potential for crop improvement. Better Crops 96:10–12
Hawkesford MJ (2014) Reducing the reliance on nitrogen fertilizer for wheat production. J Cereal Sci 59:276–283
Google Scholar
Hirel B, Tétu T, Lea PJ, Dubois F (2011) Improving nitrogen use efficiency in crops for sustainable agriculture. Sustainability 3:1452–1485
Google Scholar
Hoagland DR, & Arnon DI. (1950) The water-culture method for growing plants without soil. Circular. California agricultural experiment station, 347(2nd ed)
Hou G, Du C, Gao H, Liu S, Sun W, Lu H et al. (2020) Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC Plant Biol 20:1–21
Google Scholar
Jagadhesan B, Sathee L, Meena HS, Jha SK, Chinnusamy V, Kumar A et al. (2020) Genome wide analysis of NLP transcription factors reveals their role in nitrogen stress tolerance of rice. Sci Rep 10:1–16
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376–385
Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47:155–162
Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R (2015) NPK macronutrients and microRNA homeostasis. Front Plant Sci 6:451
Google Scholar
Kumar A, Kumar S, Kumar U, Suravajhala P, Gajula MP (2016) Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach. Comput Biol Chem 64:217–226
Google Scholar
Kumar A, Chauhan A, Sharma M, Kompelli SK, Gahlaut V, Ijaq J et al. (2017a) Genome-wide mining, characterization and development of miRNA-SSRs in Arabidopsis thaliana. bioRxiv 203851
Kumar A, Pandeya A, Malik G, Hima KP, Anil KS, Sharma M et al. (2017b) A web-resource for nutrient use efficiency related Genes, QTLs, and microRNA in important cereals and model plants. bioRxiv 222992
Kumar A, Sharma M, Kumar S, Tyagi P, Wani SH, Gajula MP et al. (2018a) Functional and structural insights into candidate genes associated with nitrogen and phosphorus nutrition in wheat (Triticum aestivum L.). Int J Biol Macromol 118:76–91
Google Scholar
Kumar A, Batra R, Gahlaut V, Gautam T, Kumar S, Sharma M et al. (2018b) Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PLoS One 13:e0208409
Google Scholar
Kumar M, Singh B (2019) Precision nutrient management in wheat using nutrient expert. Int J Curr Microbiol Appl Sci 8(2):2265–2269
Kumar S, Kumar M, Mir RR, Kumar R, Kumar S. (2021) Advances in molecular markers and their use in genetic improvement of wheat. In Physiological, molecular, and genetic perspectives of wheat improvement. Springer Cham 139–174
Ladha JK, Tirol-Padre A, Reddy CK, Cassman KG, Verma S, Powlson DS et al. (2016) Global nitrogen budgets in cereals: A 50-year assessment for maize, rice and wheat production systems. Sci Rep 6:1–9
Lawson MJ, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7(1):11
Li C, Yu X, Bai L, He C, Li Y (2016) Responses of miRNAs and their target genes to nitrogen-or phosphorus-deficiency in grafted cucumber seedlings. Hortic Environ Biotechnol 57:97–112
Google Scholar
Liang G, He H, Yu D (2012) Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS One 7:e48951
Google Scholar
Liu X, Wang H, Zhou J, Hu F, Zhu D, Chen Z et al. (2016) Effect of N fertilization pattern on rice yield, N use efficiency and fertilizer–N fate in the Yangtze River Basin, China. PLoS One 11:e0166002
Google Scholar
Longnecker N, Kirby EJM, Robson A (1993) Leaf emergence, tiller growth, and apical development of nitrogen‐deficient spring wheat. Crop Sci 33:154–160
Maniatis T, Jeffrey A, Van dSH (1975) Chain length determination of small double-and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 14:3787–3794
Google Scholar
Marschner H, Kirkby EA, Cakmak I (1996) Effect of mineral nutritional status on shoot-root partitioning of photoassimilates and cycling of mineral nutrients. J Exp Bot 47:1255–1263
Google Scholar
Mathpal P, Kumar U, Kumar A, Kumar S, Malik S, Kumar N et al. (2018) Identification, expression analysis, and molecular modeling of Iron-deficiency-specific clone 3 (Ids3)-like gene in hexaploid wheat. 3 Biotech 8:1–11
Mehta KM, Puntamkar SS, Kalamkar VG (1963) Study on uptake of nutrients by wheat as influenced by nitrogen and phosphorus fertilization. Soil Sci Plant Nutr 9:29–34
Mehta G, Muthusamy SK, Singh GP, Sharma P (2021) Identification and development of novel salt-responsive candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (mir-SSRs) in bread wheat (Triticum aestivum). Sci Rep 11:1–15
Min X, Zhang Z, Liu Y, Wei X, Liu Z, Wang Y et al. (2017) Genome-wide development of microRNA-based SSR markers in Medicago truncatula with their transferability analysis and utilization in related legume species. Int J Mol Sci 18:2440
Google Scholar
Mir RR, Hiremath PJ, Riera-Lizarazu O, Varshney RK (2013) Evolving molecular marker technologies in plants: from RFLPs to GBS. Diagnostics in Plant Breeding 2013. Springer, Dordrecht, pp 229–247
Mir RR, Varshney RK (2012) Future prospects of molecular markers in plants. In: Henry RobertJ (eds.) Molecular Markers in Plants. Blackwell Publishing Ltd, Oxford, UK, p 169–190. ISBN 9781118473023
Moll RH, Kamprath EJ, Jackson WA (1982) Analysis and interpretation of factors which contribute to efficiency of nitrogen utilization 1. Agronomy 74:562–564
Mondal TK, Ganie SA (2014) Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa). Gene 535:204–209
Google Scholar
Nagy S, Poczai P, Cernak I, Gorgi A, Hegedus G, Taller J (2012) PICcalc: An online programme to calculate polymorphic information content for molecular genetic studies. Bioche. Nguyen G, Rothstein S, Spangenberg G, Kant S (2015) Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. Front Plant Sci 6:629
Olsen SR (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. US Dep Agric 939
Paul S, Datta SK, Datta K (2015) miRNA regulation of nutrient homeostasis in plants. Front Plant Sci 6:232
Google Scholar
Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Perrier X, Jacquemoud-Collet JP (2006) DARwin software http://darwin.cirad.fr/
Plett DC, Holtham LR, Okamoto M, Garnett TP (2018) Nitrate uptake and its regulation in relation to improving nitrogen use efficiency in cereals. Semin Cell Dev Biol 74:97–104.
Google Scholar
Poli Y, Nallamothu V, Balakrishnan D, Ramesh P, Desiraju S, Mangrauthia SK et al. (2018) Increased catalase activity and maintenance of photosystem II distinguishes high-yield mutants from low-yield mutants of rice var. Nagina22 under low-phosphorus stress. Front Plant Sci 9:1543
Google Scholar
Rouached H, Arpat AB, Poirier Y (2010) Regulation of phosphate starvation responses in plants: signaling players and cross-talks. Mol plant 3:288–299
Google Scholar
Shen Z, Zhang K, Ma L, Duan J, Ao Y (2017) Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data. Electron J Biotechnol 26:33–39
Shewry PR, Hey SJ (2015) The contribution of wheat to human diet and health. Food Energy Secur 4:178–202
Google Scholar
Sihag P, Sagwal V, Kumar A, Balyan P, Mir RR, Dhankher OP et al. (2021) Discovery of miRNAs and development of heat-responsive miRNA-SSR markers for characterization of wheat germplasm for terminal heat tolerance breeding. Front. Genet. 12:699420. https://doi.org/10.3389/fgene.2021.699420
Google Scholar
Singh AK, Chaurasia S, Kumar S, Singh R, Kumari J, Yadav MC et al. (2018) Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat. BMC Plant Biol 18:1–15
Subbiah BV, Asija GL (1956) A rapid procedure for the determination of available nitrogen in soils. Curr Sci 25:259–60
Google Scholar
Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203
Google Scholar
Tyagi S, Sharma S, Ganie SA, Tahir M, Mir RR, Pandey R (2019) Plant microRNAs: Biogenesis, gene silencing, web-based analysis tools and their use as molecular markers. 3 Biotech 9(11):413
Google Scholar
Tyagi S, Kumar A, Gautam T, Pandey R, Rustgi S, Mir RR (2021) Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties. PLoS One 16(2):e0231063
Google Scholar
Vance CP (2010) Quantitative trait loci, epigenetics, sugars, and microRNAs: quaternaries in phosphate acquisition and use. Plant Physiol 154:582–588
Google Scholar
Venske E, Dos Santos RS, Busanello C, Gustafson P, de Oliveira AC (2019) Bread wheat: a role model for plant domestication and breeding. Hereditas 156:1–11
Vinod KK, Heuer S (2012) Approaches towards nitrogen- and phosphorus-efficient rice. AoB Plants 2012:pls028. https://doi.org/10.1093/aobpla/pls028
Google Scholar
Wang M, Guo W, Li J, Pan X, Pan L, Zhao J et al. (2021) The miR528-AO module confers enhanced salt tolerance in rice by modulating the ascorbic acid and abscisic acid metabolism and ROS scavenging. J Agric Food Chem 69(31):8634–8648
Google Scholar
Xu HX, Weng XY, Yang Y (2007) Effect of phosphorus deficiency on the photosynthetic characteristics of rice plants. Russ J Plant Physiol 54:741–748
Google Scholar
Xu Z, Zhong S, Li X, Li W, Rothstein SJ, Zhang S et al. (2011) Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots. PloS One 6:e28009
Google Scholar
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D et al. (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinforma 9:1–13
Zhang M, An P, Li H, Wang X, Zhou J, Dong P et al. (2019) The miRNA-mediated post-transcriptional regulation of maize in response to high temperature. Int J Mol Sci 20(7):1754
Google Scholar
Zeng H, Wang G, Hu X, Wang H, Du L, Zhu Y (2014) Role of microRNAs in plant responses to nutrient stress. Plant Soil 374:1005–1021
Google Scholar
Zhao X, Liu X, Guo C, Gu J, Xiao K (2013) Identification and characterization of microRNAs from wheat (Triticum aestivum L.) under phosphorus deprivation. J Plant Biochem Biotechnol 22:113–123
Google Scholar
Zuluaga DL, Sonnante G (2019) The use of nitrogen and its regulation in cereals: Structural genes, transcription factors, and the role of miRNAs. Plants 8:294
Google Scholar
