Molecular Breeding

, Volume 34, Issue 4, pp 1777–1796 | Cite as

Identification of drought-responsive genes in a drought-tolerant cotton (Gossypium hirsutum L.) cultivar under reduced irrigation field conditions and development of candidate gene markers for drought tolerance

  • Laura Rodriguez-Uribe
  • Abdelraheem Abdelraheem
  • Rashmi Tiwari
  • Champa Sengupta-Gopalan
  • S. E. Hughs
  • Jinfa Zhang


Cotton productivity is affected by water deficit, and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was conducted to identify drought-responsive genes in the third topmost leaves of the field-grown drought-tolerant cotton (Gossypium hirsutum L.) cultivar Acala 1517-99 under drought stress conditions. Water stress was imposed by withholding irrigation for 9 days in the early squaring stage, which resulted in 10–15 % reduction in plant growth compared to the well-watered plants. A total of 110 drought-responsive genes (0.5 % of the total genes) were identified, 79 % (88 genes) of which were drought-repressed and 21 % (22 genes) were drought-induced. The drought-induced genes were grouped into six functional categories including stress-related (ten genes, nine of which encode heat shock proteins), metabolism (three genes) and one gene each for transcription factor, proline biosynthesis and cellular transport. The drought-repressed genes were classified into 14 functional categories, comprising metabolism (20 genes), cellular transport (12 genes), stress-related (12 genes), regulation of gene expression (nine genes), transcription factor (four genes), signal transduction (seven genes) and two genes each for biosynthesis of secondary compounds, cell wall, fatty acids/lipids and chlorophyll, and protein degradation. Most of the genes have been reported in other plants as drought-tolerant/responsive. The responsiveness of 19 selected drought-responsive genes was validated by quantitative RT-PCR. Furthermore, primers were developed and assayed for all the drought-responsive genes to develop single-strand conformation polymorphic markers, many of which were found to be correlated with drought tolerance. This report represents the first study on integration of a transcriptome analysis to develop molecular markers that are associated with drought tolerance in cotton.


Gossypium hirsutum Drought stress Microarray analysis Quantitative RT-PCR Candidate gene markers 



The work was supported by USDA-ARS, Cotton Incorporated and New Mexico Agricultural Experiment Station. The authors thank Dr. Jose Ortega-Carranza for reviewing an early version of this manuscript.

Supplementary material

11032_2014_138_MOESM1_ESM.xlsx (31 kb)
Supplementary material 1 (XLSX 31 kb)


  1. Abdelraheem A, Taiwri R, Zhang JF (2012) Genetic analysis and QTL mapping of drought tolerance in cotton under PEG conditions. In: Proceedings of Beltwide cotton conference, pp 719–728Google Scholar
  2. Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 54:911–929PubMedCrossRefGoogle Scholar
  3. Bartel D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58Google Scholar
  4. Basal H, Smith CW, Thaxton PS, Hemphill JK (2005) Seedling drought tolerance in upland cotton. Crop Sci 45:766–771Google Scholar
  5. Beell E, Creelman RA (1995) A chloroplast lipoxygenase is required for wound-induced jasmonic acid accumulation in Arabidopsis. Proc Natl Acad Sci USA 92:8675–8679Google Scholar
  6. Bell E, Mullet JE (1993) Characterization of an Arabidopsis lipoxygenase gene responsive to methyl jasmonate and wounding. Plant Physiol 103:1133–1137PubMedCentralPubMedGoogle Scholar
  7. Berger B, Parent B, Tester M (2010) High-throughput shoot imaging to study drought responses. J Exp Bot 61:3519–3528PubMedGoogle Scholar
  8. Boston RS, Viitanen PV, Vierling E (1996) Molecular chaperones and protein folding in plants. Plant Mol Biol 32:191–222PubMedGoogle Scholar
  9. Bowman DT, Wells R (2005) Breeding for abiotic stress tolerance in cotton. In: Ashraf M, Harris PJC (eds) Abiotic stresses: plant resistance through breeding and molecular approaches. Food Products Press, Binghamton, pp 595–613Google Scholar
  10. Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT (2013) RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS ONE 8:e82634PubMedCentralPubMedGoogle Scholar
  11. Bray EM (2007) Molecular and physiological responses to water-deficit stress. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Berlin, pp 121–140Google Scholar
  12. Burke JJ (2007) Evaluation of source leaf responses to water-deficit stresses in cotton using a novel stress bioassay. Plant Physiol 143:108–121PubMedCentralPubMedGoogle Scholar
  13. Burke JJ, Hatfield LJ, Klein RR, Mullet JE (1985) Accumulation of heat shock proteins in field-grown cotton. Plant Physiol 78:394–398PubMedCentralPubMedGoogle Scholar
  14. Cantrell RG, Roberts CL, Waddell C (2000) Registration of ‘Acala 1517-99’ cotton. Crop Sci 40:1200–1201Google Scholar
  15. Cattivelli L, Rizza F, Badeck F, Mazzucotelli E, Mastrangelo AM, Francia E, Mare C, Tondelli A, Stanca AM (2008) Drought tolerance improvement in crop plants: an integrated view from breeding to genomics. Field Crops Res 105:1–14Google Scholar
  16. Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF (2009) Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genom 10:378Google Scholar
  17. Chen Y, Liu ZH, Feng L, Zheng Y, Li DD, Li XB (2013) Genome-wide functional analysis of cotton (Gossypium hirsutum) in response to drought. PLoS ONE 8:e80879PubMedCentralPubMedGoogle Scholar
  18. Chou IT, Gasser CS (1997) Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins. Plant Mol Biol 35:873–892PubMedGoogle Scholar
  19. Christensen CA, Feldmann KA (2007) Biotechnology approaches to engineering drought tolerant crops. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Berlin, pp 333–357Google Scholar
  20. Claeys H, Inze D (2013) The agony of choice: how plants balance growth and survival under water-limiting conditions. Plant Physiol 162:1768–1779PubMedCentralPubMedGoogle Scholar
  21. Conde A, Chaves MM, Geros H (2011) Membrane transport, sensing and signaling in plant adaptation to environmental stress. Plant Cell Physiol 52:1583–1602PubMedGoogle Scholar
  22. DeRidder BP, Salvucci ME (2007) Modulation of Rubisco activase gene expression during heat stress in cotton (Gossypium hirsutum L.) involves post-transcriptional mechanisms. Plant Sci 172:246–254Google Scholar
  23. Dwivedi RS, Breiman A, Herman EM (2003) Differential distribution of the cognate and heat-stress-induced isoforms of high Mr cis–trans prolyl peptidyl isomerase (FKBP) in the cytoplasm and nucleoplasm. J Exp Bot 54:2679–2689PubMedGoogle Scholar
  24. Fender SE, O’Connell MA (1989) Heat shock protein expression in thermotolerant and thermosensitive lines of cotton. Plant Cell Rep 8:37–40PubMedGoogle Scholar
  25. Feussner I, Wasternack C (2002) The lipoxygenase pathway. Annu Rev Plant Biol 53:275–297PubMedGoogle Scholar
  26. Fleury D, Jefferies S, Kuchel H, Langridge P (2010) Genetic and genomic tools to improve drought tolerance in wheat. J Exp Bot 61:3211–3222PubMedGoogle Scholar
  27. Gao SQ, Chen M, Xia LQ, Xiu HJ, Xu ZS, Li LC, Zhao CP, Cheng XG, Ma YZ (2009) A cotton (Gossypium hirsutum) DRE-binding transcription factor gene, GhDREB, confers enhanced tolerance to drought, high salt, and freezing stresses in transgenic wheat. Plant Cell Rep 28:301–311PubMedGoogle Scholar
  28. Genty B, Briantais JM, Vieira Da Silva JB (1987) Effects of drought on primary photosynthetic process of cotton leaves. Plant Physiol 83:360–364PubMedCentralPubMedGoogle Scholar
  29. Gilbert MK, Turley RB, Kim HJ, Li P, Thyssen G, Tang Y, Delhom CD, Naoumkina M, Fang DD (2013) Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintlesss-1 (Li1). BMC Genom 14:403Google Scholar
  30. Gomi K, Yamamoto H, Akimistu K (2002) Characterization of a lipoxygenase gene in rough lemon induced by Alternaria alternata. J Gen Plant Pathol 68:21–30Google Scholar
  31. Grimes DW, Yamada H (1982) Relation of cotton growth and yield to minimum leaf water potential. Crop Sci 22:134–139Google Scholar
  32. Guo P, Baum M, Grando S, Ceccarelli S, Bai G, Li R, von Korff M, Varshney RK, Graner A, Valkoun J (2009a) Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. J Exp Bot 60:3531–3544PubMedCentralPubMedGoogle Scholar
  33. Guo YH, Yu YP, Wang D, Wu CA, Yang GD, Huang JG, Zheng CC (2009b) GhZFP1, a novel CCCH-type zinc finger protein from cotton, enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5. New Phytol 183:62–75PubMedGoogle Scholar
  34. Hinchliffe D, Wilkins TA, Cantrell RG, Zhang JF (2005) Comparative microarray analysis of genes differentially expressed during fiber development of upland and pima cotton. In: Proceedings of Beltwide cotton conferences, National Cotton Council of America, Memphis, TN, p 883Google Scholar
  35. Hinchliffe DJ, Meredith WR, Yeater KM, Kim HJ, Woodward AW, Chen ZJ, Triplett BA (2009) Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling. Theor Appl Genet 120:1347–1366Google Scholar
  36. Hmida-Sayari A, Gargouri-Bouzid R, Bidani A, Jaoua L, Savouré A, Jaoua S (2005) Overexpression of Δ-pyrroline-5-carboxylate synthetase increases proline production and confers salt tolerance in transgenic potato plants. Plant Sci 169:746–752Google Scholar
  37. Kathiresan A, Lafittea HR, Chen JX, Mansueto L, Bruskiewich R, Bennett J (2006) Gene expression microarrays and their application in drought stress research. Field Crops Res 97:101–110Google Scholar
  38. Kim ES, Choi E, Kim Y, Cho K, Lee A, Shim J, Rakwal R, Agrawal GK, Han O (2003) Dual positional specificity and expression of non-traditional lipoxygenase induced by wounding and methyljasmonate in maize seedlings. Plant Mol Biol 52:1203–1213PubMedGoogle Scholar
  39. Kiribuchi K, Jikumaru Y, Kaku H, Minami E, Hasegawa M, Kodama O, Seto H, Okada H, Nojiri H, Yamane H (2005) Involvement of the basic helix-loop-helix transcription factor RERJ1 in wounding and drought stress responses in rice plants. Biosci Biotechnol Biochem 69:1042–1044PubMedGoogle Scholar
  40. Kosmas SA, Argyrokastritis A, Loukas MG, Eliopoulos E, Taskas S, Kaltsikes P (2006) Isolation and characterization of drought-related trehalose 6-phosphate-synthase gene from cultivated cotton (Gossypium hirsutum L.). Planta 223:329–339PubMedGoogle Scholar
  41. Kuppu S, Mishra N, Hu R, Sun L, Zhu X, Shen G, Blumwald E, Payton P, Zhang H (2013) Water-deficit inducible expression of a cytokinin biosynthetic gene IPT improves drought tolerance in cotton.). PLoS ONE 8:e64190PubMedCentralPubMedGoogle Scholar
  42. Logenberger PS, Smith CW, Thaxton PS, Michael BL (2006) Development of a screening method for drought tolerance in cotton seedlings. Crop Sci 46:2104–2110Google Scholar
  43. Lu Y, Curtiss J, Percy RG, Cantrell RG, Yu S, Hughs SE, Zhang JF (2009) DNA polymorphisms of genes involved in fiber development in a selected set of cultivated tetraploid cotton. Crop Sci 49:1695–1704Google Scholar
  44. Lubbers EL, Chee PW, Saranga Y, Paterson AH (2007) Recent advances and future prospective in molecular breeding of cotton for drought and salinity stress tolerance. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Berlin, pp 775–796Google Scholar
  45. Lv SL, Yang AF, Zhang KW, Wang L, Zhang JR (2007) Increase of glycinebetaine synthesis improves drought tolerance in cotton. Mol Breed 20:233–248Google Scholar
  46. Maqbool A, Abbas W, Rao AQ, Irfan M, Zahur M, Bakhsh A, Riazuddin S, Husnain T (2010) Gossypium arboreum GHSP26 enhances drought tolerance in Gossypium hirsutum. Biotechnol Prog 26:21–25PubMedGoogle Scholar
  47. Marino R, Ponnaiah M, Krajewski P, Frova C, Gianfranceschi L, Enrico Pe M, Sari-Gorla M (2009) Addressing drought tolerance in maize by transcriptional profiling and mapping. Mol Genet Genomics 281:163–179PubMedGoogle Scholar
  48. Micheletto S, Rodriguez-Uribe L, Hernandez R, Richins RD, Curry J, O’Connell MA (2007) Comparative transcript profiling in roots of Phaseolus acutifolius and P. vulgaris under water deficit stress. Plant Sci 173:510–520Google Scholar
  49. Miller G, Suzuki N, Ciftci-Yilmaz S, Mittler R (2010) Reactive oxygen species homeostasis and singalling during drought and salinity stresses. Plant, Cell Environ 33:453–467Google Scholar
  50. Negi J, Hashimoto-Sugimoto M, Kusumi K, Iba K (2014) New approaches to the biology of stomatal guard cells. Plant Cell Physiol 55:241–250PubMedCentralPubMedGoogle Scholar
  51. Nepomuceno AL, Oosterhuis DM, Stewart JM (1998) Physiological response of cotton leaves and roots to water deficit induced by polyethylene glycol. Environ Exp Bot 40:29–41Google Scholar
  52. Neumann PM (2008) Copping mechanisms for crop plants in drought-prone environments. Ann Bot 101:901–907PubMedCentralPubMedGoogle Scholar
  53. Park W, Scheffler BE, Bauer PJ, Campbell BT (2012) Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 12:90PubMedCentralPubMedGoogle Scholar
  54. Pasapula V, Shen G, Kuppu S, Paez-Valencia J, Mendoza M, Hou P, Chen J, Qui X, Zhu L, Zhang X, Auld D, Blumwald E, Zhang H, Gaxiola R, Payton PR (2010) Expression of an arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) in cotton improves drought- and salt tolerance and increases fibre yield in the field conditions. Plant Biotech J 8:1–12Google Scholar
  55. Payton P, Kottapalli KR, Kebede H, Mahan JR, Wright RJ, Allen RD (2011) Examining the drought stress transcriptome in cotton leaf and root tissue. Biotechnol Lett 33:821–828PubMedGoogle Scholar
  56. Penna JCV, Verhalen LM, Kirkham MB, McNew RW (1998) Screening cotton genotypes for seedling drought tolerance. Genet Mol Biol 21:545–549Google Scholar
  57. Qiao ZX, Huang B, Liu JY (2008) Molecular cloning and functional analysis of an ERF gene from cotton (Gossypium hirsutum). Biochem Biophys Acta 1779:122–127PubMedGoogle Scholar
  58. Quisenberry JE, Roark B, McMichael BL (1982) Use of transpiration decline curves to identify drought-tolerant cotton germplasm. Crop Sci 22:918–922Google Scholar
  59. Rajendrakumar CS, Reddy BV, Reddy AR (1994) Proline–protein interactions: protection of structural and functional integrity of M4 lactatedehydrogenase. Biochem Biophys Res Commun 201:957–963PubMedGoogle Scholar
  60. Ranjan A, Pandey N, Lakhwani D, Dubey NK, Pathre UV, Sawant SV (2012) Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought. BMC Genom 13:680Google Scholar
  61. Ray LL, Wendt CW, Roark B, Quisenberry JE (1974) Genetic modification of cotton plants for more efficient water use. Agric Meteorol 14:31–38Google Scholar
  62. Roark B, Quisenberry JE, Fest G (1973) Behavior, distribution, and frequency of stomates on leaves of selected varieties of Gossypium hirsutum L. In: Beltwide cotton production and research conference, National Cotton Council of America, Memphis, TN, USA, p 51Google Scholar
  63. Royo J, Vanvanneyt G, Perez AG, Sanz C, Stormann K, Rosahl S, Sanchez-Serrano JJ (1996) Characterization of three potato lipoxygenases with distinct enzymatic activities and different organ-specific and wound regulated expression patterns. J Biol Chem 271:21012–21019PubMedGoogle Scholar
  64. Ruan YL, Jin Y, Yang YJ, Li GJ, Boyer JS (2010) Sugar input, metabolism, and signaling mediated by invertase: roles in development, yield potential, and response to drought and heat. Mol Plant 3:942–955PubMedGoogle Scholar
  65. Saradhi A, Saradhi PP (1991) Proline accumulation under heavy metal stress. J Plant Physiol 138:5454–5458Google Scholar
  66. Seki M, Umezawa T, Kim JM, Matsui A, To TK, Shinozaki K (2007) Transcriptome analysis of plant drought and salt stress response. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Berlin, pp 261–283Google Scholar
  67. Shan DP, Huang JG, Yang YT, Guo YH, Wu CA, Yang GD, Gao Z, Zheng CC (2007) Cotton GhDREB1 increases plant tolerance to low temperature and is negatively regulated by gibberellic acid. New Phytol 176:70–81PubMedGoogle Scholar
  68. Sharma AD, Singh P (2003) Comparative studies on drought-induced changes in peptidyl prolyl cis–trans isomerase activity in drought-tolerant and susceptible cultivars of Sorghum bicolor. Curr Sci 84:911–918Google Scholar
  69. Sofo A, Dichio B, Xiloyannis C, Masia A (2004) Lypoxygenase activity and proline accumulation in leaves and roots of olive trees in response to drought stress. Physiol Plant 121:58–65PubMedGoogle Scholar
  70. Spiteller G (2003) The relationship between changes in the wall, lipid peroxidation, proliferation, senescence, and cell death. Physiol Plant 119:5–18Google Scholar
  71. Tiwari R, Picchioni G, Steiner R, Jones D, Hughs SH, Zhang JF (2013a) Genetic variation in salt tolerance during seed germination in a backcross inbred line population and advanced breeding lines derived from Gossypium hirsutum × G. barbadense. Crop Sci 53:1974–1982Google Scholar
  72. Tiwari R, Picchioni G, Steiner R, Jones D, Hughs SH, Zhang JF (2013b) Genetic variation in salt tolerance at the seedling stage in an interspecific backcross inbred line population of cotton. Euphytica 194:1–11Google Scholar
  73. Tuberosa R, Salvi S (2006) Genomics-based approaches to improve drought tolerance of crops. Trends Plant Sci 11:405–412PubMedGoogle Scholar
  74. Turner NC, Hearn AB, Begg JE, Constable GA (1986) Cotton (Gossypium hirsutum L.) physiological and morphological responses to water deficits and their relationship to yield. Field Crops Res 14:153–170Google Scholar
  75. Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp RA, Swanson JM, Lee JJ, Gingle AR, Nettleton D, Town CD, Chen ZJ, Wendel JF (2007) Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genom 8:81Google Scholar
  76. 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 17:113–122PubMedGoogle Scholar
  77. Valliyodan B, Nguyen HT (2006) Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr Opin Plant Biol 9:1–7Google Scholar
  78. Wang XS, Zhu J, Mansueto L, Bruskiewich R (2005) Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map. J Zhejiang Univ Sci 6B:382–388Google Scholar
  79. Wilkins TA, Smart LB (1996) Isolation of RNA from plant tissue. In: Krieg PA (ed) A laboratory guide to RNA: isolation, analysis, and synthesis. Wiley-Liss, New York, pp 21–41Google Scholar
  80. Xue T, Li X, Zhu W, Wu C, Yang G, Zheng C (2009) Cotton metallothionein GhMT3a, a reactive oxygen species scavenger, increased tolerance against abiotic stress in transgenic tobacco and yeast. J Exp Bot 60:339–349PubMedCentralPubMedGoogle Scholar
  81. Yamaguchi M, Sharp RE (2010) Complexity and coordination of root growth at low water potentials: recent advances from transcriptomic and proteomic analyses. Plant, Cell Environ 33:590–603Google Scholar
  82. Yan J, Wang J, He C, Holaday AS, Zhang H (2004) Overexpression of the Arabidopsis 14-3-3 protein GF14I in cotton delays leaf senescence and improves drought tolerance. Plant Cell Physiol 45:1007–1014PubMedGoogle Scholar
  83. Yildiz-Aktas L, Dagnon S, Gurel A, Gesheva E, Edreva A (2009) Drought tolerance in cotton: involvement of non-enzymatic ROS-scavenging compounds. J Agron Crop Sci 195:247–253Google Scholar
  84. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY (2009) Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. BMC Res Notes 2:120PubMedCentralPubMedGoogle Scholar
  85. Zhu L, Zhang X, Auld D, Blumwald E, Zhang H, Gaxiola R, Payton P (2010) Expression of an Arabidopsis vacuolar H(+)-pyrophosphatase gene (AVP1) in cotton improves drought- and salt tolerance and increases fibre yield in the field conditions. Plant Biotechnol J 9:88–99Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Laura Rodriguez-Uribe
    • 1
  • Abdelraheem Abdelraheem
    • 1
  • Rashmi Tiwari
    • 1
  • Champa Sengupta-Gopalan
    • 1
  • S. E. Hughs
    • 2
  • Jinfa Zhang
    • 1
  1. 1.Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesUSA
  2. 2.Southwestern Cotton Ginning Research LaboratoryUSDA-ARSMesilla ParkUSA

Personalised recommendations