Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat

Plant Genome

Volumn 6, Issue 2, 2013, Pages

  Edae, Erena A ^a   Byrne, Patrick F ^a   Manmathan, Harish ^a   Haley, Scott D ^a   Moragues, Marc ^a   Lopes, Marta S ^b   Reynolds, Matthew P ^b  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84883745780     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2013.04.0010     Document Type: Article

References (54)

1. Akbari, M., P. Wenzl, V. Caig, J. Carling, L. Xia, S.Y. Yang, G. Uszynski, V. Mohler, A. Lehmensiek, H. Kuchel, M. J. Hayden, N. Howes, P. Sharp, P. Vaughan, B. Rathmell, E. Huttner, and A. Kilian. 2006. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet. 113:1409-1420. doi:10.1007/s00122-006-0365-4
2. Akhunov, E.D., A.R. Akhunova, O.D. Anderson, J.A. Anderson, N. Blak, M.T. Clegg, D. Coleman-Derr, E.J. Conley, C.C. Crossman, K.R. Deal, J. Dubcovsky, B.S. Gill, Y.Q. Gu, J. Hadam, H. Heo, N. Huo, G.R. Lazo, M. Luo, Y.Q. Ma, D.E. Matthews, P.E. McGuire, P.L. Morrel, C.O. Qualset, J. Renfro, D. Tabanao, L.E. Talbert, C. Tian, D.M. Toleno, M.L. Warburton, F.M. You, W. Zhang, and J. Dvorak. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 11:702. doi:10.1186/1471-2164-11-702
3. Andersen, J., and T. Lubberstedt. 2003. Functional markers in plants. Trends Plant Sci. 18:554-560. doi:10.1016/j.tplants.2003.09.010
4. Bagge, M., and T. Lubberstedt. 2008. Functional markers in wheat: Technical and economic aspects. Mol. Breed. 22:319-328. doi:10.1007/s11032-008-9190-6
5. Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57:289-300.
6. Berloo, V.R. 2008. GGT2.0: Versatile software for visualization and analysis of genetic data. J. Hered. 99(2):232-236.
7. Bernardo, R. 1993. Estimation of coefficient of co-ancestry using molecular markers in maize. Theor. Appl. Genet. 85:1055-1062. doi:10.1007/BF00215047
8. Bhatnagar-Mathur, P., J.M. Devi, M. Lavanya, D.S. Reddy, V. Vadez, R. Serraj, K. Yamaguchi-Shinozaki, and K.K. Sharma. 2007. Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water limiting conditions. Plant Cell Rep. 26:2071-2082. doi:10.1007/s00299-007-0406-8
9. Bradbury, P.J., Z. Zhang, D.E. Kroon, T.M. Casstevens, Y. Ramdoss, and E.S. Buckler. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635. doi:10.1093/bioinformatics/btm308
10. Casadesus, J., Y. Kaya, J. Bort, M.M. Nachit, J.L. Araus, S. Amor, G. Ferrazzano, F. Maalouf, M. Maccaferri, V. Martos, H. Ouabbou, and D. Villegas. 2007. Using vegetation indices derived from conventional digital cameras as selection criteria for wheat breeding in water-limited environments. Ann. Appl. Biol. 150:227-236. doi:10.1111/j.1744-7348.2007.00116.x
11. Cattivelli, L., F. Rizza, F.W. Badeck, E. Mazzucotelli, A.M. Mastrangelo, E. Francia, C. Mare, A. Tondelli, and A.M. Stanca. 2008. Drought tolerance improvement in crop plants: An integrated view from breeding to genomics. Field Crops Res. 105:1-14. doi:10.1016/j. fcr.2007.07.004
12. Chao, S.M., J. Dubcovsky, J. Dvorak, M.C. Luo, P.S. Baenziger, R. Matnyazov, D.R. Clark, L.E. Talbert, J.A. Anderson, S. Dreisigacker, K. Glover, J.L. Chen, K. Campbell, P.L. Bruckner, J.C. Rudd, S. Haley, B.F. Carver, S. Perry, M.E. Sorrells, and E.D. Akhunov. 2010. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 11:727. doi:10.1186/1471-2164-11-727
13. Cutler, S., M. Ghassemian, D. Bonetta, S. Cooney, and P. McCourt. 1996. A protein farnesyl transferase involved in abscisic acid signal transduction in Arabidopsis. Science 273:1239-1241. doi:10.1126/ science.273.5279.1239
14. DNASTAR. 2008. Seqman genome assembler. DNASTAR Inc., Madison, WI.
15. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14:2611-2620. doi:10.1111/j.1365- 294X.2005.02553.x
16. Figueiredo, A.F., B. Sine, J. Chantereau, C. Mestres, G. Fliedel, J.F. Rami, J.C. Glaszmann, M. Deu, and B. Courtois. 2010. Variability of grain quality in sorghum: Association with polymorphism in Sh2, Bt2, SssI, Ae1, Wx and O2. Theor. Appl. Genet. 121:1171-1185. doi:10.1007/s00122-010-1380-z
17. Flint-Garcia, S.A., A.C. Thuillet, J. Yu, G. Pressoir, S.M. Romero, S.E. Mitchell, J. Doebley, S. Kresovich, M.M. Goodman, and E.S. Buckler. 2005. Maize association population: A high-resolution platform for quantitative trait locus dissection. Plant J. 44:1054-1064. doi:10.1111/j.1365-313X.2005.02591.x
18. Fusari, C., V. Lia, E. Hopp, R. Heinz, and N. Paniego. 2008. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC Plant Biol. 8:7. doi:10.1186/1471-2229-8-7
19. Giordani, T., M. Buti, L. Natali, C. Pugliesi, F. Cattonaro, M. Morgante, and A. Cavallini. 2011. An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.). Theor. Appl. Genet. 122:1039-1049. doi:10.1007/s00122-010-1509-0
20. Haseneyer, G., S. Stracke, H.P. Piepho, S. Sauer, H.H. Geiger, and A. Graner. 2010. DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits. BMC Plant Biol. 10:5. doi:10.1186/1471-2229-10-5
21. Haudry, A., A. Cenci, C. Ravel, T. Bataillon, D. Brunel, C. Poncet, I. Hochu, S. Poirier, S. Santoni, S. Glémin, and J. David. 2007. Grinding up wheat: A massive loss of nucleotide diversity since domestication. Mol. Biol. Evol. 24:1506-1517. doi:10.1093/molbev/ msm077
22. Hincha, D.K., E. Zuther, and A.G. Heyer. 2003. The preservation of liposomes by raffinose family oligosaccharides during drying is mediated by effects on fusion and lipid phase transitions. Biochim. Biophys. Acta 1612:172-177. doi:10.1016/S0005-2736(03)00116-0
23. Kobayashi, F., M. Ishibashi, and S. Takumi. 2008. Transcriptional activation of Cor/Lea genes and increase in abiotic stress tolerance through expression of a wheat DREB2 homolog in transgenic tobacco. Transgenic Res. 17:755-767. doi:10.1007/s11248-007-9158-z
24. Langridge, P., and D. Fleury. 2011. Making the most of 'omics' for crop breeding. Trends Biotechnol. 29:33-40. doi:10.1016/j. tibtech.2010.09.006
25. Latini, A., C. Rasi, M. Sperandei, C. Cantale, M. Lannetta, M. Dettori, K. Ammar, and P. Galeffi. 2007. Identification of a DREB-related gene in Triticum durum and its expression under stress conditions. Ann. Appl. Biol. 150:187-195. doi:10.1111/j.1744-7348.2007.00128.x
26. Lopes, M.S., and M.P. Reynolds. 2012. Stay-green in spring wheat can be determined by spectral reflectance measurements (normalized difference vegetation index) independently from phenology. J. Exp. Bot. 63:3789-3798. doi:10.1093/Jxb/Ers071
27. Lopes, M., M.P. Reynolds, M. Jalal-Kamali, M. Mousa, Y. Feltaous, I. Tahir, N. Barma, and M. Vargas. 2012. The yield correlations of selectable physiological traits in a population of advanced spring wheat lines grown in warm and drought environments. Field Crops Res. 128:129-136. doi:10.1016/j.fcr.2011.12.017
28. Lothier, J., B. Lasseur, K. Le Roy, A. Van Laere, M. Prud'homme, P. Barre, W. Van Den Ende, and A. Morvan-Bertrand. 2007. Cloning, gene mapping, and Functional analysis of a fructan 1-exohydrolase (1-FEH) from Lolium perenne implicated in fructan synthesis rather than in fructan mobilization. J. Exp. Bot. 58:1969-1983. doi:10.1093/ jxb/erm053
29. Manmathan, H., D. Shaner, J. Snelling, N. Tisserat, and N. Lapitan. 2013. Virus-induced gene silencing of Arabidopsis thaliana gene homologues in wheat identifies genes conferring improved drought tolerance. J. Exp. Bot. 64:1381-1392. doi:10.1093/jxb/ert003
30. Martinez-Gonzalez, S.C., D. Huber, E. Ersoz, J.M. Davis, and D.B. Neale. 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101:19-26. doi:10.1038/hdy.2008.21
31. McCouch, S., K. Zhao, M. Wright, C. Tung, K. Ebana, M. Thomson, A. Reynolds, D. Wang, G. DeClerck, M. Ali, A. McClung, G. Eizenga, and C. Bustamante. 2010. Development of genome-wide SNP assays for rice. Breed. Sci. 60:524-535. doi:10.1270/jsbbs.60.524
32. Mochida, K., Y. Yamazaki, and Y. Ogihara. 2003. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Genet. Genomics 270:371-377. doi:10.1007/s00438-003-0939-7
33. Nei, M. 1987. Molecular evolutionary genetics. Columbia Univ. Press, New York, NY.
34. Pei, Z.M., M. Ghassemian, C.M. Kwak, P. McCourt, and J.I. Schroeder. 1998. Role of famesyltransferase in ABA regulation of guard cell anion channels and plant water loss. Science 282:287-290. doi:10.1126/science.282.5387.287
35. Pellegrineschi, A., M. Reynolds, M. Pacheco, R.M. Brito, R. Ameraya, K.Y. Shinozaki, and D. Hoisington. 2004. Stress-induced expression in wheat of the A. thaliana DREB1A gene delays water stress symptoms under greenhouse conditions. Genomics 47:493-500.
36. Pritchard, J., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
37. Rafalski, A. 2002. Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci. 162:329-333. doi:10.1016/S0168- 9452(01)00587-8
38. Ravel, C., S. Praud, A. Canaguier, P. Dufour, S. Giancola, F. Balfourier, B. Chalhoub, D. Brunel, L. Linossier, M. Dardevet, M. Beckert, M. Rousset, A. Murigneux, and G. Charmet. 2007. DNA sequence polymorphisms and their application to bread wheat quality. Euphytica 158:331-336. doi:10.1007/s10681-006-9288-z
39. Reif, J.C., P. Zhang, S. Dreisigacker, M.L. Warburton, M. van Ginkel, D. Hoisington, M. Bohn, and A.E. Melchinger. 2005. Wheat genetic diversity trends during domestication and breeding. Theor. Appl. Genet. 110:859-864. doi:10.1007/s00122-004-1881-8
40. Rozas, J., P. Librado, J.C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. 1999. DnaSP version 5: An integrated program for population genetics and molecular evolution analysis. Bioinformatics 15:174-175. doi:10.1093/bioinformatics/15.2.174
41. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. In: S. Krawetz and S. Misener, editors, Bioinformatics methods and protocols. Humana Press, Totowa, NJ. p. 365-386.
42. Saint Pierre, C., J. Crossa, D. Bonnet, K. Yamaguchi-Shinozaki, and M. Reynolds. 2012. Phenotyping transgenic wheat for drought resistance. J. Exp. Bot. 63:1799-1808. doi:10.1093/jxb/err385
43. SAS Institute. 2006. SAS for mixed models. SAS Inst., Cary, NC.
44. SAS Institute. 2011. The SAS system for Windows. Version 9.3. SAS Inst., Cary, NC.
45. Shinozaki, K., and K. Yamaguchi-Shinozaki. 2007. Gene networks involved in drought stress response and tolerance. J. Exp. Bot. 58:221-227. doi:10.1093/jxb/erl164
46. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
47. Vadez, V., J.S. Rao, P. Bhatnagar-Mathur, and K.K. Sharma. 2013. DREB1A promotes root development in deep soil layers and increases water extraction under water stress in groundnut. Plant Biol. 15:45-52. doi:10.1111/j.1438-8677.2012.00588.x
48. Vadez, V., S. Rao, K.K. Sharma, P. Bhatnagar-Mathur, and M.J. Devi. 2007. DREB1A allows for more water uptake in groundnut by a large modification in the root/shoot ratio under water deficit. Int. Arachis Newsl. 27:27-31.
49. VSN International. 2005. CycDesigN 3.0. VSN International Ltd., Hemel Hempstead, UK.
50. Wei, B., R. Jing, C. Wang, J. Chen, X. Mao, X. Chang, and J. Jia. 2009. Dreb1 genes in wheat (Triticum aestivum L.): Development of functional markers and gene mapping based on SNPs. Mol. Breed. 23:13-22. doi:10.1007/s11032-008-9209-z
51. Yang, D., R. Jing, X. Chang, and W. Li. 2007. Identification of quantitative trait loci and environmental interactions for accumulation and remobilization of water-soluble carbohydrates in wheat (Triticum aestivum L.) stems. Genetics 176:571-584. doi:10.1534/ genetics.106.068361
52. Yu, J.M., G. Pressoir, W.H. Briggs, I.V. Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, D.M. Nielsen, J.B. Holland, S. Kresovich, and E.S. Buckler. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38:203-208. doi:10.1038/Ng1702
53. Zhang, J., S. Huang, J. Fosu-Nyarko, B. Dell, M. McNeil, I. Waters, P. Moolhuijzen, E. Conocono, and R. Appels. 2008. The genome structure of the 1-FEH genes in wheat (Triticum aestivum L.): New markers to track stem carbohydrates and grain filling QTLs in breeding. Mol. Breed. 22:339-351. doi:10.1007/s11032-008-9179-1
54. Ziegelhoffer, E., J. Leonard, and M. Elliot. 2000. Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development. Proc. Natl. Acad. Sci. USA 97:7633-7638. doi:10.1073/pnas.130189397