Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance

Plant Cell Reports

Volumn 34, Issue 6, 2015, Pages 993-1004

  Singh, Bikram Pratap ^a,b   Jayaswal, Pawan Kumar ^a   Singh, Balwant ^a   Singh, Pankaj Kumar ^a   Kumar, Vinod ^a   Mishra, Shefali ^a   Singh, Nisha ^a   Panda, Kabita ^a   Singh, Nagendra Kumar ^a  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b BANASTHALI UNIVERSITY   (India)

Author keywords

Drought tolerance; Haplotypes; Nucleotide diversity; SNP; Wild rice

Indexed keywords

VEGETABLE PROTEIN;

ALLELE; AMINO ACID SEQUENCE; CHEMISTRY; DROUGHT; GENETIC VARIATION; GENETICS; HAPLOTYPE; MOLECULAR GENETICS; ORYZA; PHENOTYPE; PHYSIOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; AMINO ACID SEQUENCE; DROUGHTS; GENETIC VARIATION; HAPLOTYPES; MOLECULAR SEQUENCE DATA; ORYZA; PHENOTYPE; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84939949841     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-015-1760-6     Document Type: Article

References (51)

1. Allah AA (2009) Genetic studies on leaf rolling and some root traits under drought conditions in rice (Oryza sativa L.). African J Biotechnol 8:6241–6248
2. Alizade A (2002) Soil, water and plants relationship, 3rd edn. Emam Reza University Press, Mashhad
3. Blum A (1988) Plant breeding for stress environments. CRC INC, Florida
4. Boyer J (1982) Plant productivity and environment. Science 218:443–448
5. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TN, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
6. Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ (2003) SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 31:3692–3697
7. Garrity DP, O’Toole JC (1995) Selection for reproductive stage drought avoidance in rice, using infrared thermometry. Agron J 87:773–779
8. Cattivelli L, Rizza F, Badeck FW, Mazzucotelli E, Mastrangelo AM, Francia E, Mare C, Tondelli A, Stanca AM (2008) Drought tolerance improvement in crop plants: an integrative view from breeding to genomics. Field Crop Res 105:1–14
9. Chang TT, Loresto GC, Tagum PO (1974) Screening rice germplasm for drought resistance. SABRAO J 6(1):9–16
10. Chelah MKB, Nordin MNB, Musliania MI, Khanif YM, Jahan MS (2011) Composting increases BRIS soil health and sustains rice production on bris soil. ScienceAsia 37:291–295
11. Delauney AJ, Verma DPS (1993) Proline biosynthesis and osmoregulation in plants. Plant J 4:215–223
12. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought- high-salt- and cold-responsive gene expression. Plant J 33:751–763
13. Edae EA, Byrne PF, Manmathan H, Haley SD, Moragues M, Lopes MS, Reynolds MP (2013) Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat. plant Genome. doi:10.3835/plantgenome2013.04.0010
14. Ehrenreich IM, Hanzawa Y, Chou L, Roe JL, Kover XP, Purugganan MD (2009) Candidate gene association mapping of Arabidopsis flowering time. Genetics 183:325–335
15. Fadeev EA et al (2009) NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove. J Mol Biol 388:682–690
16. Fotovat R, Valizadeh M, Toorehi M (2007) Association between water-use-efficiency components and total chlorophyll content (SPAD) in wheat (Triticum aestivum L.) under well-watered and drought stress conditions. J Food Agric Environ 5:225–227
17. Foyer CH, Descourvieres P, Kunert KJ (1994) Photo oxidative stress in plants. Plant Physiol 92:696–717
18. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709
19. Arjenaki FG, Jabbari R, Morshedi A (2012) Evaluation of drought stress on relative water content, chlorophyll content and mineral elements of wheat (Triticum aestivum L.) varieties. Intl J Agri Crop Sci 4(11):726–729
20. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291
21. Khush GS, Ling KC, Aquino RC, Aguiero VM (1977) Breeding for resistance to grassy stunt in rice. In: Proceedings of the 3rd international congress of the society for the advancement of breeding researchers in Asia and Oceania (SABRAO). Canberra, 12–13 Feb 1977
22. Ladizinsky G (1985) Founder effect in crop-plant evolution. Econ Bot 39:191–199
23. Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Bio mol NMR 8:477–496
24. Lata C, Prasad M (2013) Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions. Plant Breed 132:496–499
25. Lata C, Prasad M (2014) Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL. J Plant Biochem Biotechno. 23:119–122
26. Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62:3387–3401
27. Latha R, Rubia L, Bennett J, Swaminathan MS (2004) Allele mining for stress tolerance genes in Oryza species and related germplasm. Mol Biotechnol 27:101–108
28. Martinez-Gonzalez SC, Huber D, Ersoz E, Davis JM, Neale DB (2008) Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101:19–26
29. Mirnoff N (1993) The role of active oxygen in the response of plants to water deficit and desiccation. New Phytol 125:27–58
30. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
31. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
32. 2 concentrations and other environmental stresses within the ESPACE—wheat project. Eur J Agron 10:197–203
33. Rizhsky L, Hongjian L, Mittler R (2002) The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol 130:1143–1151
34. Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R (2004) When defense pathways collide: the response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 134:1683–1696
35. Rozas J, Sánchez Del Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497
36. Rushton PJ, Bokowiec MT, Han S, Zhang H, Brannock JF, Chen X, Laudeman TW, Timko MP (2008) Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae. Plant Physiol 147:280–295
37. Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227
38. Simmonds NW (1976) Evolution of Crop Plants. Longman, London
39. Singh NK, Dalal V, Batra K, Singh BK, Chitra G, Singh A, Ghazi IA, Yadav M, Pandit A, Dixit R, Singh PK, Singh H, Koundal KR, Gaikwad K, Mohapatra T, Sharma TR (2007) Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 7(1):17–35
40. Singh N, Choudhury DR, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Singh NK, Singh R (2013) Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLoS One 8(12):e84136
41. Szabados L, Savoure A (2009) Proline: a multifunctional amino acid. Trends Plant Sci 15:89–97
42. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595
43. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
44. Vikram P, Mallikarjuna Swamy BP, Dixit S, Ahmed HU, Sta Cruz MT, Singh AK, Kumar A (2011) qDTY1.1 a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 12:89
45. Wang Q, Guan Y, Wu Y, Chen H, Chen F, Chu C (2008) Over expression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice. Plant Mol Bio 67:589–602
46. Watterson GA (1975) On the number of segregation sites. Theoret Popul Biol 7:256–276
47. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407–410
48. Yamanaka S, Nakamura I, Nakai H, Sato YI (2003) Dual origin of the cultivated rice based on molecular markers of newly collected annual and perennial strains of wild rice species, Oryza nivara and O. rufipogon. Genet Resour Crop Evol 50:529–538
49. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
50. Yu X, Bai G, Liu S, Luo N, Wang Y, Richmond DS, Pijut PM, Jackson SA, Yu J, Jiang Y (2013) Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions. J Exp Bot 64:1537–1551
51. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40