Novel genomic tools and modern genetic and breeding approaches for crop improvement

Journal of Plant Biochemistry and Biotechnology

Volumn 18, Issue 2, 2009, Pages 127-138

  Varshney, Rajeev K ^a,b   Dubey, Anuja ^a,c  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b Generation Challenge Programme   (Mexico)

^c BARKATULLAH UNIVERSITY   (India)

Author keywords

Breeding methodologies; Crop improvement; Genetic approaches; Genomic tools

Indexed keywords

EID: 70350423199     PISSN: 09717811     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03263311     Document Type: Review

References (126)

1. Varshney RK & Tuberosa R, Edited, Genomics-assisted crop improvement: Genomics approaches and platforms, vol 1, Springer (2007) p 386.
2. Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C & Salse J, Curr Opin Plant Biol, 12 (2009) 119.
3. King GJ, In Model plants and crop improvement (RK Varshney, RMD Koebner, Editors), Taylor and Francis (2006) pp 33-70.
4. Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst E V, Keyder ER, Menda N, Zamir D & Tanksley SD, Plant Physiol, 138 (2005) 1310.
5. Varshney RK, Graner A & Sorrells ME, Trends Plant Sci, 10 (2005) 621.
6. Stein N & Graner A, In Cereal genomics (PK Gupta, RK Varshney, Editors), Kluwer Academic Publishers, Dordrecht, The Netherlands (2004) pp 331-360.
7. Salvi S & Tuberosa R, Trends Plant Sci, 10 (2005) 297.
8. Varshney RK & Tuberosa R, Edited, Genomics-assisted crop improvement: Genomics applications in crops, vol 2, Springer (2007) p 509.
9. Varshney RK, Nayak SN, May GD & Jackson SA, Trends Biotechnol (2009) (in press).
10. Varshney RK. In Molecular techniques in crop improvement, vol 2, (SM Jain, DS Brar, Editors). Springer, The Netherlands (2009) (in press).
11. Service RF, Science, 311 (2006) 1544.
12. Hudson M, Mol Ecol Resour, 8 (2008) 3.
13. Mardis ER, Annu Rev Genomics Hum Genet, 9 (2008) 387.
14. Shendure J & Ji H, Nat Biotechnol, 26 (2008) 1135.
15. Lister R, Gregory BD & Ecker J R, Curr Opin Plant Biol, 12 (2008) 1.
16. Gupta PK, Trends Biotechnol, 26 (2008) 602.
17. Varshney RK, Hoisington DA, Nayak SN & Graner A, In Plant genomics: Methods and protocols (DJ Somers, P Langridge, JP Gustafson, Editors), Humana Press (2009) pp 283-304.
18. Andersen JR & Lubberstedt T, Trends Plant Sci, 8 (2003) 554.
19. Gupta PK & Rustgi S, Funct Integr Genomics, 4 (2004) 139.
20. Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD & Hoisington DA, Jour of SAT Agriculture, 3 (2007) 1 (http://www.icrisat.org/Journal/chickpea_pigeonpea3.htm).
21. Barbazuk WB, Emrich SJ, Chen HD, Li L & Schnable PS, Plant J, 51 (2007) 910.
22. Hyten, DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND & Cregan PB, Theor Appl Genet, 116 (2008) 945.
23. May GD, Lekha PT, Kashiwagi J, Huntley JJ, Farmer AD, Cook DR & Varshney RK, In Plant and animal genome XVI Conf, San Diego, USA (2008) P385 (http://www.intl-pag.org/16/abstracts/PAG16_P05f_385.html).
24. Rostocks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ & Waugh R, Proc Natl Acad Sci, USA, 103 (2006) 18656.
25. Akhunov E, Nicolet C & Dvorak J, Theor Appl Genet, (2009) DOI 10.1007/s00122-009-1059-5.
26. Hyten DL, Smith JR, Frederick RD, Tucker ML, Song Q & Cregan PB, Crop Sci, 49 (2009) 265.
27. Sreenivasulu N, Kavikishor PB, Varshney RK & Altschmied L, Curr Sci, 83 (2002) 965.
28. Sreenivasulu N, Varshney RK, Kavikishor PB & Weschke W, In Cereal genomics (PK Gupta, RK Varshney, Editors), Kluwer Academic Publishers, Dordrecht, The Netherlands (2004) pp 483-514.
29. Jansen RC & Nap JP, Trends Genet, 17 (2001) 388.
30. de Koning D-J & Haley CS, Trends Genet, 21 (2005) 377
31. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Canet G, Linsley PS, Mao M, Stoughton RB & Friend SH, Nature, 422 (2003) 297.
32. Jansen RC, Jannink JL & Beavis WD, Crop Sci, 43 (2003) 829.
33. Kirst M & Yu Q, In Genomics assisted crop improvement: Genomics approaches and platforms, vol 1 (RK Varshney and R Tuberosa, Editors), Springer (2007) pp 245-266.
34. Keurentjes JJ, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G & Snoek B, Proc Natl Acad Sci, USA, 104 (2007) 1708.
35. Kazuki S, Cell Technol, 25 (2006) 1399.
36. Taylor J, King RD, Altmann T & Fiehn O, Bioinformatics, 18 (2002) 214.
37. Maloney V, BioTeach J, 2 (2004) 92.
38. Saghatelian A, Trauger SA, Siuzdak G & Cravatt BF, Biochemistry, 16 (2004) 14332.
39. Jacobs DI, van der Heijden R & Verpoorte R, Phytochem Analysis, 11 (2000) 277.
40. van Wijk KJ, Plant Physiol, 126 (2001) 501.
41. Hirano H, Islam N & Kawasaki H, J Phytochem, 16 (2004) 1487.
42. Tsugita A, Kamo M, Kawakami T & Ohki Y, Electrophoresis, 17 (1996) 855.
43. Chang WW, Huang L, Shen M, Webster C, Burlingame AL & Roberts JK, Plant Physiol, 122 (2000) 295.
44. Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S & Chakraborty N, Mol Cell Proteomics, 6 (2007) 1868.
45. Pandey A, Chakraborty S, Datta A & Chakraborty N, Mol Cell Proteomics, 7 (2008) 88.
46. Tanksley S & McCouch S, Science, 277 (1997) 1063.
47. Swamy BP & Sarla N, Biotechnol Adv, 26 (2008) 106.
48. Alisdair R F, Tadmor Y & Zamir D, Curr Opin Plant Biol, 9 (2006) 196.
49. Hajjar R & Hodkkgkin T, Euphytica, 156 (2007) 1.
50. Ashikari M, Sakakibara H, Lin SY, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H & Matsuoka M, Science, 309 (2005) 741.
51. Maxted N, Scholten MA, Codd R & Ford-Lloyd BV, Biol Cons, 140 (2007) 142.
52. Fernie AR & Willmitzer L, In Handbook of plant biotechnology (P Christou, HK Klee, Editors), Wiley, Chichester, UK (2004).
53. Grandillo S, Tanksley SD & Zamir D, In Genomics assisted crop improvement: Genomics approaches and platforms, vol 1 (RK Varshney and R Tuberosa, Editors), Springer (2007) pp 121-150.
54. Monforte AJ & Tanksley SD, Genome, 43 (2000) 803.
55. Matus I, Corey A, Filchkin T, Hayes PM, Vales MI, Kling J, Riera-Lizarazu O, Sato K, Powell W & Waugh R, Genome, 46 (2003) 1010.
56. Wan XY, Wan JM, Su CC, Wang CM, Shen WB, Li JM, Wang HL, Jiang L, Liu SJ, Chen LM, Yasui H & Yoshimura A, Theor Appl Genet, 110 (2004) 71.
57. Koumproglou R, Wilkes TM, Towson P, Wang XY, Beyon J, Pooni HS, Newbury HJ & Kearsey MJ, Plant J, 31 (2002) 355.
58. Eshed Y & Zamir D, Genetics, 141 (1995) 1147.
59. Eshed Y & Zamir D, Genetics, 143 (1996) 1807.
60. Canady MA, Meglic V & Chetelat RT, Genome, 48 (2005) 685.
61. von Korff M, Wang H, Léon J & Pillen K, Theor Appl Genet, 109 (2004) 1736.
62. Schmalenbach I & Pillen K, Theor Appl Genet, 118 (2009) 1411.
63. Tian F, Li de J, Fu Q, Zhu ZF, Fu YC, Wang XK & Sun CQ, Theor Appl Genet, 112 (2006) 570.
64. Tadmor Y, Fridman E, Gur A, Larkov O, Lastochkin E, Ravid U, Zamir D & Lewinsohn E, J Agric Food Chem, 50 (2002) 2005.
65. Rousseaux MC, Jones CM, Adams D, Chetelat R, Bennett A & Powel A, Theor Appl Genet, 111 (2005) 1396.
66. Jie C, Bughio HUR, Da-Zhou C, Guang-Jie L, Kang-Le Z & Jie-Yun Z, Rice Science, 13 (2006) 15.
67. Tanksley SD & Nelson JC, Theor Appl Genet, 92 (1996) 191.
68. Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J & Beck-Bunn T, Theor Appl Genet, 92 (1996) 213.
69. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD & McCouch SR, Genetics, 150 (1998) 899.
70. Moncada P, Martínez CP, Borrero J, Chatel M, Gauch Jr H, Guimaraes E, Tohme J & McCouch SR, Theor Appl Genet, 102 (2001) 41.
71. McCouch SR, Sweeney M, Li JM, Jiang H, Thomson M, Septiningsih E, Edward J, Moncada P, Xiao JH, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yung LP & Ahn SN, Euphytica, 154 (2007) 317.
72. Huang XQ, Cöster H, Ganal MW & Röder MS, Theor Appl Genet, 106 (2003) 1379.
73. Kunert A, Naz AA, Dedeck O, Pillen K & Leon J, Theor Appl Genet, 115 (2007) 683.
74. Ho JC, McCouch SR & Smith ME, Theor Appl Genet, 105 (2002) 440.
75. Mano Y & Omori F, Breed Sci, 58 (2008) 3217.
76. Pillen K, Zacharias A & Léon J, Theor Appl Genet, 107 (2003) 340.
77. Pillen K, Zacharias A & Léon J, Theor Appl Genet, 108 (2004) 591.
78. Talamè V, Sanguineti MC, Chiapparino E, Bahri H, Ben Salem M, Forster BP, Ellis RP, Rhouma S, Zoumarou W, Waugh R & Tuberosa R, Ann Appl Biol, 144 (2004) 309.
79. Li JZ, Huang XQ, Heinrichs F, Ganal MW & Röder MS, Theor Appl Genet, 110 (2005) 356.
80. Li JZ, Huang XQ, Heinrichs F, Ganal MW & MS Röder, Genome, 49 (2006) 454.
81. Yun SJ, Gyenis L, Bossolini E, Hayes PM, Matus I, Smith KP, Steffenson BJ, Tuberosa R & Muehlbauer GJ, Crop Sci, 46 (2006) 1179.
82. Gyenis L, Yun SJ, Smith KP, Steffenson BJ, Bossolini E, Sanguineti MC & Muehlbauer GJ, Genome, 50 (2007) 714.
83. von Korff M, Wang H, Leon J & Pillen K, Theor Appl Genet, 112 (2006) 1221.
84. Scchmalenbach I, Leon J & Pillen K, Theor Appl Genet, 118 (2009) 483.
85. Doerge RW, Nat Rev Genet, 3 (2002) 43.
86. Buckler ES & Thornsberry J, Curr Opin Plant Biol, 5 (2002) 107.
87. Flint-Garcia SA, Thornsberry JM & Buckler ES, Annu Rev Plant Biol, 54 (2003) 357.
88. Yu J & Buckler ES, Curr Opin Biotechnol, 17 (2006) 155.
89. Pritchard JK, Stephens M, Rosenberg NA & Donnelly P, Am J Hum Genet, 67 (2000) 170.
90. Risch N & Merikangas K, Science, 273 (1996) 1516.
91. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D & Buckler, Nat Genet, 28 (2001) 286.
92. Palaisa KA, Morgante M, Williams M & Rafalski A, Plant Cell, 15 (2003) 1795.
93. Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandian CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J & Buckler ES, Science, 18 (2008) 330.
94. Tracy WF, Whitt SR & Buckler ES, Crop Sci, 46 (2006) 1.
95. Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P & Van Eewuijk FA, Genetics, 168 (2004) 435.
96. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Meckay IJ, Powell W & O'Sullivan DM, BMC Genet, 9 (2008) 16.
97. Comadran J, Russell JR, van Eeuwijk FA, Ceccarelli S, Grando S, Baum M, Stanca AM, Pecchioni N, Mastrangelo AM, Akar T, Al-Yassin A, Benbelkacem A, Choumane W, Ouabbou H, Dahan R, Bort J, Araus JL, Pswarayi A, Romagosa I, Hackett CA & Thomas WTB, Euphytica, 161 (2007) 35.
98. Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J & Purugganan MD, Genetics, 167 (2004) 1361.
99. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P & Nordborg M, PLoS Genet, 1 (2005) 60.
100. Olsen KM & Purugganan MD, Genetics, 162 (2002) 941.
101. Paull JG, Chalmers KJ, Karakousis A, Kretschmer JM, Manning S & Langridge P, Theor Appl Genet, 96 (1994) 435.
102. Paull JG, Pallotta MA, Lanngridge P & The TT, Theor Appl Genet, 89 (1998) 1039.
103. Breseghello F & Sorrells ME, Genetics, 172 (2006) 1165.
104. Crossa J, Burgueno J, Drreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowaaan R, Warburton M, Franco J, Reynold M, Crouch JH & Oritz R, Genetics, 177 (2007) 1889.
105. Zhao J, Paul MJ, Jamar D, Ping L, van Eeuwijk F, Guusje B, Vreugdenhil D & Koornneef M, Genome, 50 (2007) 963.
106. Yalcin B, Flint J & Mott R, Genetics, 171 (2005) 673.
107. Cavanagh C, Morell M, Mackay I & Powell W, Curr Opin Plant Biol, 11 (2008) 215.
108. Valdar W, Flint J & Mott R, Genetics, 172 (2006) 1783.
109. Moose S & Mumm RH, Plant Physiol, 147 (2008) 969.
110. Varshney RK, Hoisington DA & Tyagi AK, Trends Biotechnol, 24 (2006) 490.
111. Utomo HS & Linscombe SD, Recent Pat DNA Gene Seq, 3 (2009) 53.
112. Collard BC & Mackill DJ, Philos Trans R Soc Lond B Biol Sci, 12 (2008) 557.
113. Hospital F & Charcosset, Genetics, 147 (1997) 1469.
114. Frisch M, Bohn M & Melchinger AE, Crop Sci, 39 (1999) 967.
115. Varshney RK, Thudi M, May GD & Jackson SA, Plant Breed Rev, (2009) (in press).
116. Hammer G, Cooper M, Tardieu F, Welch S, Walsh B, van Eeuwijk FA, Chapman S & Podlich D, Trends Plant Sci, 11 (2006) 587.
117. Boer MP, Wright D, Feng L, Podlich DW, Luo L, Cooper M & van Eeuwijk FA, Genetics, 177 (2007) 1801.
118. Matthews KL, Malosetti M, Chapman S, McIntyre L, Reynolds M, Shorter R & van Eeuwijk FA, Theor Appl Genet, 117 (2008) 1077.
119. Cooper M, Podlich DW & Luo L, In Genomic assisted crop improvement: Genomics approaches and platforms, vol 1 (RK Varshney, R Tuberosa, Editors), Springer (2007) pp 57-96.
120. Edward M & Johnson L, In Proc Joint Plant Breeding Symp Series of CSSA and ASHA, Corvallis, OR. Am Soc Hort Sci, Alexandria VA, (1994) pp 33-40.
121. Hospital F, Moreau L, Lacoudre F, Charcosset A & Galais A, Theor Appl Genet, 95 (1997) 1181.
122. Bernardo R & Charcosset A, Crop Sci, 46 (2006) 614.
123. Kuchel H, Fox R, Reinheimer J, Mosinoek L, Willey N, Bariana H & Jefferies S, Mol Breed, 20 (2007) 295.
124. Ragot M, Gay G, Muller JP & Durovray J, In Molecular approaches for the genetic improvement of cereals for stable production in water-limited environments (JM Ribaut, D Poland, Editors), Mexico, DF: CIMMYT, (2000) pp 128-130.
125. Ribaut JM & Ragot, M, J Exp Bot, 58 (2006) 351.
126. Meuwissen THE, Hayes BJ & Goddard, Genetics, 157 (2001) 1819.