Applications of Molecular Markers to Develop Resistance Against Abiotic Stresses in Wheat

  • Ali Raza
  • Sundas Saher Mehmood
  • Tariq Shah
  • Xiling Zou
  • Lv Yan
  • Xuekun Zhang
  • Rao Sohail Ahmad Khan


Innovations had come into being in the field of plant breeding with the development and advancement of molecular marker techniques by the end of the twentieth century. Advancement in molecular markers for sequencing techniques has led to improvements in crop production. Amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism, random amplified polymorphic DNA, and microsatellite markers are being used in the fields of molecular characterization, describing hybrid vigor, marker-assisted selection, abiotic stress tolerance, and genetic distance range. Numerous troubles that a user can face throughout marker application gametogenesis have also been discussed. Germplasm characterization and marker-mediated varietal fingerprinting seemed very ordinary and have many prevalent applications with AFLPs and simple sequence repeats (SSRs). SSR markers are known to be applicable and suitable techniques for molecular characterization owing to their low price, simplicity, and the lack of radio-isotope demand. Preventing hybrid vigor seemed very problematic, with a slight victory because of the absence of a simplistic marker technique that may categorically classify the hybrids, community, and offspring. A marker-assisted selection of valuable characters is very effective after molecular characterization, whereas for measurable traits, mainly disease-tolerant genes and quantitative trait loci for abiotic stress resistance, the success is inadequate. It is estimated that the implementation of molecular markers will remain limited in such fields until gene-specific markers exist and the price of the markers study is decreased markedly. This chapter discusses the possible responsibility of molecular markers in developing abiotic stress-resistant wheat.


Abiotic stresses Molecular markers PCR Resistance Wheat 


  1. Agarwal P, Jha B (2010) Transcription factors in plants and ABA dependent and independent abiotic stress signalling. Biol Plant 54:201–212CrossRefGoogle Scholar
  2. Agarwal PK, Agarwal P, Reddy M, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263–1274PubMedCrossRefGoogle Scholar
  3. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631PubMedCrossRefGoogle Scholar
  4. Akram M (2011) Growth and yield components of wheat under water stress of different growth stages. Bangladesh J Agric Res 36:455–468CrossRefGoogle Scholar
  5. Alam M, Rabbani MG (2007) Vulnerabilities and responses to climate change for Dhaka. Environ Urban 19:81–97CrossRefGoogle Scholar
  6. Araki H, Hamada A, Hossain MA, Takahashi T (2012) Waterlogging at jointing and/or after anthesis in wheat induces early leaf senescence and impairs grain filling. Field Crop Res 137:27–36CrossRefGoogle Scholar
  7. Araus J, Slafer G, Reynolds M, Royo C (2002) Plant breeding and drought in C3 cereals: what should we breed for? Ann Bot 89:925–940PubMedPubMedCentralCrossRefGoogle Scholar
  8. Asseng S, Ewert F, Martre P, Rötter RP, Lobell D, Cammarano D, Kimball B, Ottman M, Wall G, White JW (2015) Rising temperatures reduce global wheat production. Nat Clim Chang 5:143CrossRefGoogle Scholar
  9. Atkin OK, Tjoelker MG (2003) Thermal acclimation and the dynamic response of plant respiration to temperature. Trends Plant Sci 8:343–351PubMedCrossRefGoogle Scholar
  10. Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543CrossRefGoogle Scholar
  11. Bagge M, Xia X, Lübberstedt T (2007) Functional markers in wheat. Curr Opin Plant Biol 10:211–216PubMedCrossRefGoogle Scholar
  12. Bailey-Serres J, Lee SC, Brinton E (2012) Waterproofing crops: effective flooding survival strategies. Plant Physiol 160:1698–1709PubMedPubMedCentralCrossRefGoogle Scholar
  13. Bates B, Kundzewicz Z, Wu S (2008) Climate change and water. Intergovernmental Panel on Climate Change Secretariat, GenevaGoogle Scholar
  14. Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631CrossRefGoogle Scholar
  15. Bencze S, Veisz O (2011) Quality of winter wheat in relation to heat and drought shock after anthesis. Czech J Food Sci 29:117–128CrossRefGoogle Scholar
  16. Bhatnagar-Mathur P, Vadez V, Sharma KK (2008) Transgenic approaches for abiotic stress tolerance in plants: retrospect and prospects. Plant Cell Rep 27:411–424PubMedCrossRefGoogle Scholar
  17. Bilal M, Rashid R, Rehman S, Iqbal F, Ahmed J, Abid M, Ahmed Z, Hayat A (2015) Evaluation of wheat genotypes for drought tolerance. J Green Physiol Genet Genomics 1:11–21Google Scholar
  18. Bita C, Gerats T (2013) Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops. Front Plant Sci 4:273PubMedPubMedCentralCrossRefGoogle Scholar
  19. Blears M, De Grandis S, Lee H, Trevors J (1998) Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. J Ind Microbiol Biotechnol 21:99–114CrossRefGoogle Scholar
  20. Bogeat-Triboulot M-B, Brosché M, Renaut J, Jouve L, Le Thiec D, Fayyaz P, Vinocur B, Witters E, Laukens K, Teichmann T (2007) Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. Plant Physiol 143:876–892PubMedPubMedCentralCrossRefGoogle Scholar
  21. Boyer J, Byrne P, Cassman K, Cooper M, Delmer D, Greene T, Gruis F, Habben J, Hausmann N, Kenny N (2013) The US drought of 2012 in perspective: a call to action. Glob Food Sec 2:139–143CrossRefGoogle Scholar
  22. Casierra-Posada F, Cutler J (2017) Photosystem II fluorescence and growth in cabbage plants (Brassica oleracea var. capitate) grown under waterlogging stress. Revista UDCA Actualidad & Divulgación Científica 20:321–328CrossRefGoogle Scholar
  23. Chandler PM, Robertson M (1994) Gene expression regulated by abscisic acid and its relation to stress tolerance. Annu Rev Plant Biol 45:113–141CrossRefGoogle Scholar
  24. Chen R-D, Yu L-X, Greer AF, Cheriti H, Tabaeizadeh Z (1994) Isolation of an osmotic stress- and abscisic acid-induced gene encoding an acidic endochitinase from Lycopersicon chilense. Mol Gen Genet MGG 245:195–202PubMedCrossRefGoogle Scholar
  25. Chinnusamy V, Zhu J, Zhu J-K (2007) Cold stress regulation of gene expression in plants. Trends Plant Sci 12:444–451PubMedCrossRefGoogle Scholar
  26. Choi H-K, Mun J-H, Kim D-J, Zhu H, Baek J-M, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci U S A 101:15289–15294PubMedPubMedCentralCrossRefGoogle Scholar
  27. Cole CT (2003) Genetic variation in rare and common plants. Annu Rev Ecol Evol Syst 34:213–237CrossRefGoogle Scholar
  28. Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196CrossRefGoogle Scholar
  29. Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124PubMedCrossRefPubMedCentralGoogle Scholar
  30. de Oliveira ED, Bramley H, Siddique KH, Henty S, Berger J, Palta JA (2013) Can elevated CO2 combined with high temperature ameliorate the effect of terminal drought in wheat? Funct Plant Biol 40:160–171CrossRefGoogle Scholar
  31. Deinlein U, Stephan AB, Horie T, Luo W, Xu G, Schroeder JI (2014) Plant salt-tolerance mechanisms. Trends Plant Sci 19:371–379PubMedPubMedCentralCrossRefGoogle Scholar
  32. Dhanda S, Sethi G (2002) Tolerance to drought stress among selected Indian wheat cultivars. J Agric Sci 139:319–326CrossRefGoogle Scholar
  33. Dhanda S, Toky O (2010) Interaction of provenance (seed source), fertilizers and salinities in Eucalyptus tereticornis and E. camaldulensis grown in north-west India. Range Manag Agrofor 31:120–124Google Scholar
  34. Dhillon T, Pearce S, Stockinger E, Distelfeld A, Li C, Knox AK, Vashegyi I, Vágújfalvi A, Galiba G, Dubcovsky J (2010) Regulation of freezing tolerance and flowering in temperate cereals: the VRN-1 connection. Plant Physiol 153(4):1846–1858. CrossRefPubMedPubMedCentralGoogle Scholar
  35. Dubcovsky J, Santa Maria G, Epstein E, Luo M-C, Dvořák J (1996) Mapping of the K+/Na+ discrimination locus Kna1 in wheat. Theor Appl Genet 92:448–454PubMedPubMedCentralCrossRefGoogle Scholar
  36. Eagles HA, Bariana HS, Ogbonnaya FC, Rebetzke GJ, Hollamby G, Henry RJ, Henschke P, Carter M (2001) Implementation of markers in Australian wheat breeding. Aust J Agric Res 52:1349–1356CrossRefGoogle Scholar
  37. Eskandari H, Kazemi KK (2010) Response of different bread wheat (Triticum aestivum L.) genotypes to post-anthesis water deficit. Not Sci Biol 2:49CrossRefGoogle Scholar
  38. Farooq M, Bramley H, Palta JA, Siddique KH (2011) Heat stress in wheat during reproductive and grain-filling phases. Crit Rev Plant Sci 30:491–507CrossRefGoogle Scholar
  39. Farooq M, Hussain M, Siddique KH (2014) Drought stress in wheat during flowering and grain-filling periods. Crit Rev Plant Sci 33:331–349CrossRefGoogle Scholar
  40. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690PubMedPubMedCentralCrossRefGoogle Scholar
  41. Fracasso A, Trindade LM, Amaducci S (2016) Drought stress tolerance strategies revealed by RNA-Seq in two sorghum genotypes with contrasting WUE. BMC Plant Biol 16:115PubMedPubMedCentralCrossRefGoogle Scholar
  42. Fukao T, Bailey-Serres J (2008) Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc Natl Acad Sci 105:16814–16819PubMedCrossRefGoogle Scholar
  43. Fukao T, Xu K, Ronald PC, Bailey-Serres J (2006) A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18:2021–2034PubMedPubMedCentralCrossRefGoogle Scholar
  44. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467PubMedPubMedCentralCrossRefGoogle Scholar
  45. Gajghate R, Sharma R, Jain N, Singh AM, Kumar M, Kala Y, Singh A (2015) Validation of known molecular markers associated with QTLs for terminal heat tolerance traits in bread wheat. In: Compendium of abstracts of the 2nd international conference on bio-resource and stress management, ANGRAU & PJTSAU, Hyderabad, India, pp 7–10Google Scholar
  46. Gale M, Devos K (1998) Plant comparative genetics after 10 years. Science 282:656–659PubMedCrossRefGoogle Scholar
  47. Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488:535PubMedCrossRefGoogle Scholar
  48. Gómez J, Sánchez-Martínez D, Stiefel V, Rigau J, Puigdomènech P, Pagès M (1988) A gene induced by the plant hormone abscisic acid in response to water stress encodes a glycine-rich protein. Nature 334:262PubMedCrossRefGoogle Scholar
  49. Gómez-Cadenas A, Verhey SD, Holappa LD, Shen Q, Ho T-HD, Walker-Simmons M (1999) An abscisic acid-induced protein kinase, PKABA1, mediates abscisic acid-suppressed gene expression in barley aleurone layers. Proc Natl Acad Sci 96:1767–1772PubMedCrossRefGoogle Scholar
  50. Gonzali S, Loreti E, Novi G, Poggi A, Alpi A, Perata P (2005) The use of microarrays to study the anaerobic response in Arabidopsis. Ann Bot 96:661–668PubMedPubMedCentralCrossRefGoogle Scholar
  51. Gourdji SM, Sibley AM, Lobell DB (2013) Global crop exposure to critical high temperatures in the reproductive period: historical trends and future projections. Environ Res Lett 8:024041CrossRefGoogle Scholar
  52. Guóth A, Tari I, Gallé Á, Csiszár J, Pécsváradi A, Cseuz L, Erdei L (2009) Comparison of the drought stress responses of tolerant and sensitive wheat cultivars during grain filling: changes in flag leaf photosynthetic activity, ABA levels, and grain yield. J Plant Growth Regul 28:167–176CrossRefGoogle Scholar
  53. Gupta N, Gupta S, Kumar A (2001) Effect of water stress on physiological attributes and their relationship with growth and yield of wheat cultivars at different stages. J Agron Crop Sci 186:55–62CrossRefGoogle Scholar
  54. Gupta P, Mir R, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genomics 2008:896451PubMedPubMedCentralGoogle Scholar
  55. Hamrick J (1989) Isozymes and the analysis of genetic structure in plant populations. In: Isozymes in plant biology. Springer, Dordrecht, pp 87–105CrossRefGoogle Scholar
  56. Hao C, Wang Y, Chao S, Li T, Liu H, Wang L, Zhang X (2017) The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat. Sci Rep 7:41247PubMedPubMedCentralCrossRefGoogle Scholar
  57. Hasanuzzaman M, Hossain MA, da Silva JAT, Fujita M (2012) Plant response and tolerance to abiotic oxidative stress: antioxidant defense is a key factor. In: Crop stress and its management: perspectives and strategies. Springer, Dordrecht, pp 261–315CrossRefGoogle Scholar
  58. Hattori Y, Nagai K, Furukawa S, Song X-J, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026PubMedCrossRefGoogle Scholar
  59. He X, Zhang Y, He Z, Wu Y, Xiao Y, Ma C, Xia X (2008) Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. Theor Appl Genet 116:213–221PubMedCrossRefGoogle Scholar
  60. Hirabayashi Y, Mahendran R, Koirala S, Konoshima L, Yamazaki D, Watanabe S, Kim H, Kanae S (2013) Global flood risk under climate change. Nat Clim Chang 3:816CrossRefGoogle Scholar
  61. Hirschi M, Seneviratne SI, Alexandrov V, Boberg F, Boroneant C, Christensen OB, Formayer H, Orlowsky B, Stepanek P (2011) Observational evidence for soil-moisture impact on hot extremes in southeastern Europe. Nat Geosci 4:17CrossRefGoogle Scholar
  62. Holappa LD, Walker-Simmons M (1995) The wheat abscisic acid-responsive protein kinase mRNA, PKABA1, is up-regulated by dehydration, cold temperature, and osmotic stress. Plant Physiol 108:1203–1210PubMedPubMedCentralCrossRefGoogle Scholar
  63. Hu H, Xiong L (2014) Genetic engineering and breeding of drought-resistant crops. Annu Rev Plant Biol 65:715–741PubMedCrossRefGoogle Scholar
  64. Huang X, Shabala S, Shabala L, Rengel Z, Wu X, Zhang G, Zhou M (2015) Linking waterlogging tolerance with Mn2+ toxicity: a case study for barley. Plant Biol 17:26–33PubMedCrossRefGoogle Scholar
  65. Ibba MI, Kiszonas AM, Guzmán C, Morris CF (2017) Definition of the low molecular weight glutenin subunit gene family members in a set of standard bread wheat (Triticum aestivum L.) varieties. J Cereal Sci 74:263–271CrossRefGoogle Scholar
  66. Ihsan MZ, El-Nakhlawy FS, Ismail SM, Fahad S (2016) Wheat phenological development and growth studies as affected by drought and late season high temperature stress under arid environment. Front Plant Sci 7:795PubMedPubMedCentralCrossRefGoogle Scholar
  67. Iizumi T, Sakuma H, Yokozawa M, Luo J-J, Challinor AJ, Brown ME, Sakurai G, Yamagata T (2013) Prediction of seasonal climate-induced variations in global food production. Nat Clim Chang 3:904CrossRefGoogle Scholar
  68. Jaggard KW, Qi A, Ober ES (2010) Possible changes to arable crop yields by 2050. Philos Trans R Soc Lond B Biol Sci 365:2835–2851PubMedPubMedCentralCrossRefGoogle Scholar
  69. Jatoi W, Baloch M, Kumbhar M, Khan N, Kerio M (2011) Effect of water stress on physiological and yield parameters at anthesis stage in elite spring wheat cultivars. Sarhad J Agric 27:59–65Google Scholar
  70. Jiang G-L (2013) Molecular markers and marker-assisted breeding in plants. In: Andersen SB (ed) Plant breeding from laboratories to fields. InTech, Rijeka. CrossRefGoogle Scholar
  71. Jones DL, Cross P, Withers PJ, DeLuca TH, Robinson DA, Quilliam RS, Harris IM, Chadwick DR, Edwards-Jones G (2013) Nutrient stripping: the global disparity between food security and soil nutrient stocks. J Appl Ecol 50:851–862CrossRefGoogle Scholar
  72. Joshi M, Deshpande J (2010) Polymerase chain reaction: methods, principles and application. Int J Biomed Res 2:81–97Google Scholar
  73. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan A (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334CrossRefGoogle Scholar
  74. Karaköy T, Baloch FS, Toklu F, Özkan H (2014) Variation for selected morphological and quality-related traits among 178 faba bean landraces collected from Turkey. Plant Genet Resour 12:5–13CrossRefGoogle Scholar
  75. Kebriyaee D, Kordrostami M, Rezadoost MH, Lahiji HS (2012) QTL analysis of agronomic traits in rice using SSR and AFLP markers. Not Sci Biol 4:116–123CrossRefGoogle Scholar
  76. Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ (2010) CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121:21–35PubMedCrossRefGoogle Scholar
  77. Komatsu S, Yanagawa Y (2013) Cell wall proteomics of crops. Front Plant Sci 4:17PubMedPubMedCentralGoogle Scholar
  78. Kosová K, Vítámvás P, Planchon S, Renaut J, Vanková R, Prášil IT (2013) Proteome analysis of cold response in spring and winter wheat (Triticum aestivum) crowns reveals similarities in stress adaptation and differences in regulatory processes between the growth habits. J Proteome Res 12:4830–4845PubMedCrossRefGoogle Scholar
  79. Kumar R, Rai R (2014) Can wheat beat the heat: understanding the mechanism of thermotolerance in wheat (Triticum aestivum L.) a review. Cereal Res Commun 42:1–18CrossRefGoogle Scholar
  80. Lata C, Prasad M (2011) Role of DREBs in regulation of abiotic stress responses in plants. J Exp Bot 62:4731–4748PubMedCrossRefGoogle Scholar
  81. Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461CrossRefGoogle Scholar
  82. Li J-Y, Liu J, Dong D, Jia X, McCouch SR, Kochian LV (2014) Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance. Proc Natl Acad Sci U S A 111(17):6503–6508. CrossRefPubMedPubMedCentralGoogle Scholar
  83. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397PubMedPubMedCentralGoogle Scholar
  84. Liu J, Piñeros MA, Kochian LV (2014) The role of aluminum sensing and signaling in plant aluminum resistance. J Integr Plant Biol 56:221–230PubMedCrossRefGoogle Scholar
  85. Lobell DB, Hammer GL, Chenu K, Zheng B, McLean G, Chapman SC (2015) The shifting influence of drought and heat stress for crops in northeast Australia. Glob Chang Biol 21:4115–4127PubMedCrossRefGoogle Scholar
  86. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer, SunderlandGoogle Scholar
  87. Madhumati B (2014) Potential and application of molecular markers techniques for plant genome analysis. Int J Pure Appl Biosci 2:169–188Google Scholar
  88. Magalhaes JV, Liu J, Guimaraes CT, Lana UG, Alves VM, Wang Y-H, Schaffert RE, Hoekenga OA, Pineros MA, Shaff JE (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39:1156PubMedCrossRefGoogle Scholar
  89. Majid SA, Asghar R, Murtaza G (2007) Yield stability analysis conferring adaptation of wheat to pre-and post-anthesis drought conditions. Pak J Bot 39:1623–1637Google Scholar
  90. Mano Y, Oyanagi A (2009) Trends of waterlogging tolerance studies in the Poaceae. Jpn J Crop Sci 78:441–448CrossRefGoogle Scholar
  91. Mao X, Zhang H, Tian S, Chang X, Jing R (2009) TaSnRK2. 4, an SNF1-type serine/threonine protein kinase of wheat (Triticum aestivum L.), confers enhanced multistress tolerance in Arabidopsis. J Exp Bot 61:683–696PubMedPubMedCentralCrossRefGoogle Scholar
  92. Maron LG, Guimarães CT, Kirst M, Albert PS, Birchler JA, Bradbury PJ, Buckler ES, Coluccio AE, Danilova TV, Kudrna D (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A:201220766. CrossRefGoogle Scholar
  93. Mateu-Andres I, De Paco L (2004) Allozymic differentiation of the Antirrhinum majus and A. siculum species groups. Ann Bot 95:465–473PubMedPubMedCentralCrossRefGoogle Scholar
  94. Mickelbart MV, Hasegawa PM, Bailey-Serres J (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 16:237–251CrossRefGoogle Scholar
  95. Mittler R (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci 11:15–19PubMedCrossRefGoogle Scholar
  96. Mittler R, Blumwald E (2010) Genetic engineering for modern agriculture: challenges and perspectives. Annu Rev Plant Biol 61:443–462PubMedCrossRefGoogle Scholar
  97. Mondini L, Noorani A, Pagnotta MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1:19–35CrossRefGoogle Scholar
  98. Moore G, Devos K, Wang Z, Gale M (1995) Cereal genome evolution: grasses, line up and form a circle. Curr Biol 5:737–739PubMedCrossRefGoogle Scholar
  99. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194. CrossRefPubMedGoogle Scholar
  100. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51(Pt 1):263–273PubMedCrossRefGoogle Scholar
  101. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681CrossRefGoogle Scholar
  102. Munns R, James RA, Xu B, Athman A, Conn SJ, Jordans C, Byrt CS, Hare RA, Tyerman SD, Tester M (2012) Wheat grain yield on saline soils is improved by an ancestral Na+ transporter gene. Nat Biotechnol 30:360–364PubMedCrossRefGoogle Scholar
  103. Nable RO, Bañuelos GS, Paull JG (1997) Boron toxicity. Plant Soil 193:181–198CrossRefGoogle Scholar
  104. Nemoto Y, Sasakuma T (2002) Differential stress responses of early salt-stress responding genes in common wheat. Phytochemistry 61:129–133PubMedCrossRefGoogle Scholar
  105. Niwas R, Khichar M (2016) Managing impact of climatic vagaries on the productivity of wheat and mustard in India. Mausam 67:205–222Google Scholar
  106. Ortiz R, Sayre KD, Govaerts B, Gupta R, Subbarao G, Ban T, Hodson D, Dixon JM, Ortiz-Monasterio JI, Reynolds M (2008) Climate change: can wheat beat the heat? Agric Ecosyst Environ 126:46–58CrossRefGoogle Scholar
  107. Pallotta M, Schnurbusch T, Hayes J, Hay A, Baumann U, Paull J, Langridge P, Sutton T (2014) Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars. Nature 514:88–91PubMedCrossRefGoogle Scholar
  108. Patel R, Prasher S, Bonnell R (2000) Effects of watertable depth, irrigation water salinity, and fertilizer application on root zone salt buildup. Can Agric Eng 42:111–116Google Scholar
  109. Powell N, Ji X, Ravash R, Edlington J, Dolferus R (2012) Yield stability for cereals in a changing climate. Funct Plant Biol 39:539–552CrossRefGoogle Scholar
  110. Pradhan GP, Prasad PV, Fritz AK, Kirkham MB, Gill BS (2012) Effects of drought and high temperature stress on synthetic hexaploid wheat. Funct Plant Biol 39:190–198CrossRefGoogle Scholar
  111. Prasad P, Pisipati S, Momčilović I, Ristic Z (2011) Independent and combined effects of high temperature and drought stress during grain filling on plant yield and chloroplast EF-Tu expression in spring wheat. J Agron Crop Sci 197:430–441CrossRefGoogle Scholar
  112. Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147PubMedCrossRefGoogle Scholar
  113. Pryor S, Barthelmie R, Schoof J (2013) High-resolution projections of climate-related risks for the Midwestern USA. Clim Res 56:61–79CrossRefGoogle Scholar
  114. Qadir M, Quillérou E, Nangia V, Murtaza G, Singh M, Thomas RJ, Drechsel P, Noble AD (2014) Economics of salt-induced land degradation and restoration. Nat Res Forum 38:282–295CrossRefGoogle Scholar
  115. Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K, Sundaram RM (2006) Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 23:1–4PubMedCrossRefGoogle Scholar
  116. Rashed M, Atta A, El-Din TS, Mostafa A (2017) Development of SSR & STS molecular markers associated with stem rust resistance in bread wheat (Triticum aestivum L.). Egypt J Genet Cytol 45:261–278CrossRefGoogle Scholar
  117. Raza A, Shaukat H, Ali Q, Habib M (2018) Assessment of RAPD markers to analyse the genetic diversity among sunflower (Helianthus annuus L.) genotypes. Turkish J Agric Food Sci Technol 6:107–111CrossRefGoogle Scholar
  118. Raza A, Razzaq A, Mehmood SS, Zou X, Zhang X, Lv Y, Xu J (2019a) Impact of climate change on crops adaptation and strategies to tackle its outcome: a review. Plan Theory 8:34Google Scholar
  119. Raza A, Mehmood SS, Ashraf F, Khan RS (2019b) Genetic diversity analysis of brassica species using PCR-based SSR markers. Gesunde Pflanz 71:1–7CrossRefGoogle Scholar
  120. Ren Z-H, Gao J-P, Li L-G, Cai X-L, Huang W, Chao D-Y, Zhu M-Z, Wang Z-Y, Luan S, Lin H-X (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141PubMedCrossRefGoogle Scholar
  121. Rhine MD, Stevens G, Shannon G, Wrather A, Sleper D (2010) Yield and nutritional responses to waterlogging of soybean cultivars. Irrig Sci 28:135–142CrossRefGoogle Scholar
  122. Ridout CJ, Donini P (1999) Use of AFLP in cereals research. Trends Plant Sci 4:76–79PubMedCrossRefGoogle Scholar
  123. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C-Z, Keddie J, Adam L, Pineda O, Ratcliffe O, Samaha R (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110PubMedCrossRefGoogle Scholar
  124. Rizhsky L, Liang H, Mittler R (2002) The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol 130:1143–1151PubMedPubMedCentralCrossRefGoogle Scholar
  125. Röder M, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedPubMedCentralGoogle Scholar
  126. Röder M, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke R (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73PubMedCrossRefGoogle Scholar
  127. Romina P, Abeledo LG, Miralles DJ (2014) Identifying the critical period for waterlogging on yield and its components in wheat and barley. Plant Soil 378:265–277CrossRefGoogle Scholar
  128. Rosenzweig C, Elliott J, Deryng D, Ruane AC, Müller C, Arneth A, Boote KJ, Folberth C, Glotter M, Khabarov N (2014) Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison. Proc Natl Acad Sci 111:3268–3273PubMedCrossRefGoogle Scholar
  129. Sangtarash M (2010) Responses of different wheat genotypes to drought stress applied at different growth stages. Pak J Biol Sci 13:114PubMedCrossRefGoogle Scholar
  130. Sasaki T, Ryan PR, Delhaize E, Hebb DM, Ogihara Y, Kawaura K, Noda K, Kojima T, Toyoda A, Matsumoto H (2006) Sequence upstream of the wheat (Triticum aestivum L.) ALMT1 gene and its relationship to aluminum resistance. Plant Cell Physiol 47:1343–1354PubMedCrossRefGoogle Scholar
  131. Sauter M (2013) Root responses to flooding. Curr Opin Plant Biol 16:282–286PubMedCrossRefGoogle Scholar
  132. Schlotteröer C, Amos B, Tautz D (1991) Conservation of polymorphic simple sequence loci in cetacean species. Nature 354:63CrossRefGoogle Scholar
  133. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279–292PubMedCrossRefGoogle Scholar
  134. Semagn K, Bjørnstad Å, Ndjiondjop M (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568Google Scholar
  135. Semiz GD, Suarez DL, Ünlükara A, Yurtseven E (2014) Interactive effects of salinity and N on pepper (Capsicum annuum L.) yield, water use efficiency and root zone and drainage salinity. J Plant Nutr 37:595–610CrossRefGoogle Scholar
  136. Setter T, Waters I, Sharma S, Singh K, Kulshreshtha N, Yaduvanshi N, Ram P, Singh B, Rane J, McDonald G (2008) Review of wheat improvement for waterlogging tolerance in Australia and India: the importance of anaerobiosis and element toxicities associated with different soils. Ann Bot 103:221–235PubMedPubMedCentralCrossRefGoogle Scholar
  137. Shah SH, Houborg R, McCabe MF (2017) Response of chlorophyll, carotenoid and SPAD-502 measurement to salinity and nutrient stress in wheat (Triticum aestivum L.). Agronomy 7:61CrossRefGoogle Scholar
  138. Shamsi K, Kobraee S (2011) Bread wheat production under drought stress conditions. Ann Biol Res 2:352–358Google Scholar
  139. Shamsi K, Petrosyan M, Noor-Mohammadi G, Haghparast R (2010) The role of water deficit stress and water use efficiency on bread wheat cultivars. J Appl Biosci 35:2325–2331Google Scholar
  140. Sharkey TD (1988) Estimating the rate of photorespiration in leaves. Physiol Plant 73:147–152CrossRefGoogle Scholar
  141. Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227PubMedCrossRefGoogle Scholar
  142. Singh N, Dang TT, Vergara GV, Pandey DM, Sanchez D, Neeraja C, Septiningsih EM, Mendioro M, Tecson-Mendoza EM, Ismail AM (2010) Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A. Theor Appl Genet 121:1441–1453PubMedCrossRefGoogle Scholar
  143. Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194PubMedCrossRefGoogle Scholar
  144. Soliman M, Kostandi S, Van Beusichem M (1992) Influence of sulfur and nitrogen fertilizer on the uptake of iron, manganese, and zinc by corn plants grown in calcareous soil. Commun Soil Sci Plant Anal 23:1289–1300CrossRefGoogle Scholar
  145. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Mahmoud A, Ma X, Gustafson PJ, Qi LL (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827PubMedPubMedCentralGoogle Scholar
  146. Sutton T, Baumann U, Hayes J, Collins NC, Shi B-J, Schnurbusch T, Hay A, Mayo G, Pallotta M, Tester M (2007) Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318:1446–1449PubMedCrossRefGoogle Scholar
  147. Tanksley S, Orton T (1983) Isozymic variation and plant breeders’ rights. Iso Plant Genet Breed 1:425CrossRefGoogle Scholar
  148. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedPubMedCentralCrossRefGoogle Scholar
  149. Thakur P, Nayyar H (2013) Facing the cold stress by plants in the changing environment: sensing, signaling, and defending mechanisms. In: Plant acclimation to environmental stress. Springer, New York, pp 29–69CrossRefGoogle Scholar
  150. Tiryakioğlu M, Karanlik S, Arslan M (2015) Response of bread-wheat seedlings to waterlogging stress. Turk J Agric For 39:807–816CrossRefGoogle Scholar
  151. Tiwari V, Mamrutha H, Sareen S, Sheoran S, Tiwari R, Sharma P, Singh C, Singh G, Rane J (2017) Managing abiotic stresses in wheat. In: Abiotic stress management for resilient agriculture. Springer, Singapore, pp 313–337CrossRefGoogle Scholar
  152. Turner NC (2004) Sustainable production of crops and pastures under drought in a Mediterranean environment. Ann Appl Biol 144:139–147CrossRefGoogle Scholar
  153. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314:1298–1301PubMedPubMedCentralCrossRefGoogle Scholar
  154. Uga Y, Okuno K, Yano M (2011) Dro1, a major QTL involved in deep rooting of rice under upland field conditions. J Exp Bot 62:2485–2494PubMedCrossRefGoogle Scholar
  155. Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol 17:113–122PubMedCrossRefGoogle Scholar
  156. Vashisht D, Hesselink A, Pierik R, Ammerlaan J, Bailey-Serres J, Visser E, Pedersen O, Van Zanten M, Vreugdenhil D, Jamar D (2011) Natural variation of submergence tolerance among Arabidopsis thaliana accessions. New Phytol 190:299–310PubMedCrossRefGoogle Scholar
  157. Vos P, Hogers R, Bleeker M, Reijans M, van der Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedPubMedCentralCrossRefGoogle Scholar
  158. Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218:1–14PubMedCrossRefGoogle Scholar
  159. Weber JL (1990) Informativeness of human (dC-dA) n·(dG-dT) n polymorphisms. Genomics 7:524–530PubMedPubMedCentralCrossRefGoogle Scholar
  160. Wei T-M, Chang X-P, Min D-H, Jing R-L (2010) Analysis of genetic diversity and trapping elite alleles for plant height in drought-tolerant wheat cultivars. Acta Agron Sin 36:895–904Google Scholar
  161. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218PubMedPubMedCentralCrossRefGoogle Scholar
  162. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedPubMedCentralCrossRefGoogle Scholar
  163. Wolff K, Schoen E, Peters-Van Rijn J (1993) Optimizing the generation of random amplified polymorphic DNAs in chrysanthemum. Theor Appl Genet 86:1033–1037PubMedCrossRefPubMedCentralGoogle Scholar
  164. Wu K, Jones R, Danneberger L, Scolnik PA (1994) Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res 22:3257PubMedPubMedCentralCrossRefGoogle Scholar
  165. Xu Y (2010) Plant genetic resources: management, evaluation and enhancement. Molecular plant breeding, pp 151–194Google Scholar
  166. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708PubMedCrossRefGoogle Scholar
  167. Xu J, Li Y, Sun J, Du L, Zhang Y, Yu Q, Liu X (2013) Comparative physiological and proteomic response to abrupt low temperature stress between two winter wheat cultivars differing in low temperature tolerance. Plant Biol 15:292–303PubMedCrossRefGoogle Scholar
  168. Yamori W, Hikosaka K, Way DA (2014) Temperature response of photosynthesis in C3, C4, and CAM plants: temperature acclimation and temperature adaptation. Photosynth Res 119:101–117PubMedCrossRefGoogle Scholar
  169. Yildiz M, Cuevas HE, Sensoy S, Erdinc C, Baloch FS (2015) Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources. Biochem Syst Ecol 59:45–53CrossRefGoogle Scholar
  170. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16PubMedCrossRefGoogle Scholar
  171. Zhang H, Mao X, Jing R, Chang X, Xie H (2010) Characterization of a common wheat (Triticum aestivum L.) TaSnRK2.7 gene involved in abiotic stress responses. J Exp Bot 62:975–988PubMedPubMedCentralCrossRefGoogle Scholar
  172. Zhang X, Jiang D, Zheng C, Dai T, Cao W (2011) Post-anthesis salt and combination of salt and waterlogging affect distributions of sugars, amino acids, Na+ and K+ in wheat. J Agron Crop Sci 197:31–39CrossRefGoogle Scholar
  173. Zhu J-K (2001) Plant salt tolerance. Trends Plant Sci 6:66–71CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Ali Raza
    • 1
  • Sundas Saher Mehmood
    • 1
  • Tariq Shah
    • 1
  • Xiling Zou
    • 1
  • Lv Yan
    • 1
  • Xuekun Zhang
    • 1
  • Rao Sohail Ahmad Khan
    • 2
  1. 1.Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research InstituteChinese Academy of Agricultural Sciences (CAAS) WuhanPeople’s Republic of China
  2. 2.Centre of Agricultural Biochemistry and Biotechnology (CABB) University of AgricultureFaisalabadPakistan

Personalised recommendations