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Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (09): 1457-1467.doi: 10.3724/SP.J.1006.2010.01457

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Detection of Consensus Genomic Region of QTLs Relevant to Drought-Tolerance in Maize by QTL Meta-Analysis and Bioinformatics Approach

 LI Wen-Juan1,2,LIU Zhi-Zhai2,3,SHI Yun-Su2,SONG Yan-Chun2,WANG Tian-Yu2*,XU Chen-Wu1*,LI Yu2   

  1. 1 Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 3Southwest University, Chongqing 400716, China
  • Received:2010-01-15 Revised:2010-04-20 Online:2010-09-12 Published:2010-07-05
  • Contact: WANG Tian-Yu,E-mail:wangtianyu@263.net; 徐辰武, E-mail: qtls@yzu.edu.cn E-mail:liwenjuan526@gmail.com

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Abstract: Mapping consensus genomic regions for drought-tolerance is of great importance in the molecular breeding of maize. The present research integrated informations of the published QTLs relevant to drought-tolerance mapped in the environment of water stress. On the basis of the high-density linkage map of IBM2 2008 Neighbors, a total of 79 Meta-QTLs (MQTLs) were screened out through the methods of “overview” and meta-analysis, and the bioinformatic analysis indicated that 43 of these MQTLs (54.43%) contained the information of genes conferring drought tolerance. By integrating the genetic map and the physical map of maize via Genome Brower in maize genome database (http://www.maizegdb.org/), we estimated the physical map distance of MQTLs and analyzed the function of these candidate drought tolerance-related genomic regions based on the maize genome sequence information from the maize sequence database (http://www.maizesequence.org/). The results showed that these regions contained abundant sequences of transcription factors of MYB, bZIP and DREB, and a number of functional genes of LEA family.

Key words: Maize(Zea mays L.), Drought tolerance, Meta-QTL, Meta-analysis, Bioinformatics approach

[1] Li Y(黎裕), Wang T-Y(王天宇), Shi Y-S(石云素), Song Y-C(宋艳春). Advances and prospects on QTL analysis of drought tolerance of maize (Zea mays L.). Agric Res Arid Areas (干旱地区农业研究), 2004, 22(1): 32-39 (in Chinese with English abstract)
[2] Li X-H(李雪华), Li X-H(李新海), Hao Z-F(郝转芳), Tian Q-Z(田清震), Zhang S-H(张世煌). Consensus map of the QTL relevant to drought tolerance of maize under drought conditions. Sci Agric Sin (中国农业科学), 2005, 38(5): 882-890 (in Chinese with English abstract)
[3] Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics, 2004, 168: 2169-2185
[4] Hanocq E, Laperche A, Jaminon O, Laine AL, Le Gouis J. Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis. Theor Appl Genet, 2007, 114: 569-584
[5] Ji H-L(吉海莲), Li X-H(李新海), Xie C-X(谢传晓), Hao Z-F(郝转芳), Lü X-L(吕香玲), Shi L-Y(史利玉), Zhang S-H(张世煌). Comparative QTL mapping of resistance to sporisorium reiliana in maize based on meta-analysis of QTL locations. J Plant Genet Resour (植物遗传资源学报), 2007, 8(2): 132-139 (in Chinese with English abstract)
[6] Wang Y(王毅), Yao J(姚骥), Zhang Z-F(张征锋), Zheng Y-L(郑用琏). Comparative analysis of QTL integrated mapping and statistical analysis of QTLs affecting plant height in maize. Chin Sci Bull (科学通报), 2006, 51(15): 1776-1786 (in Chinese)
[7] Xu D P, Duan X L, Wang B Y, Hong B M, David Ho T H, Wu R. Expression of a late embryogenesis abundant protein gene, HVA1, from Barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiol, 1996, 110: 249-257
[8] Liang Z(梁峥), Ma D-Q(马德钦), Tang L(汤岚), Hang Y-G(洪益国), Luo A-L(骆爱玲), Dai X-Y(戴秀玉). Expression of the Spinach Betaine Aldehyde Dehydrogenase (BADH) gene in transgenic tobacco plants. Chin J Biotech (生物工程学报), 1997, 13(3): 236-240 (in Chinese with English abstract)
[9] Schnable P S, Ware D, Fulton R S, Stein J C, Wei F S, Pasternak S, Liang C Z, Zhang J W, Fulton L, Graves T A, Minx P, Reily A D, Courtney,L, Kruchowski S S, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock S M, Belter E, Du F Y, Kim K, Abbott R M, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson S M, Gillam B, Chen W Z, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R F, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H R, Lee S, Lin J, ujmic Z, Kim W, Talag J, Zuccolo A, Fan C Z, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy M J, McMahan L, Buren P V, Vaughn M W, Ying K, Yeh C T, Emrich S J, Jia Y, Kalyanaraman A, Hsia A P, Barbazuk W B, Baucom R S, Brutnell T P, Carpita N C, Chaparro C, Chia J M, Deragon J M, Estill J C, Fu Yan, Jeddeloh J A, Han Y J, Lee H, Li P H, Lisch D R, Liu S Z, Liu Z J, Nagel D H, McCann M C, SanMiguel P, Myers A M, Nettleton D, Nguyen J, Penning B W, Ponnala L, Schneider K L, Schwartz D C, Sharma A, Soderlund C, Springer N M, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber T K, Yang LX, Yu Y, Zhang L F, Zhou S G, Zhu Q H, Bennetzen J L, Dawe R K, Jiang J M, Jiang N, Presting G G, Wessler S R, Aluru S, Martienssen R A, Clifton S W, McCombie W R, Wing R A, Wilson R K. The B73 maize genome: complexity, diversity, and dynamics. Science, 2009, 326: 1112-1115
[10] Darvasi A, Soller M. A simple method to calculate resolving power and confidence interval of QTL map location. Behav Genet, 1997, 27(2): 125-132
[11] Lee M, Beavis W D, Grant D, Katt M, Blair D, Hallauer A. Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol Biol, 2002. 48: 453-461
[12] Sharopova N, McMullen M D, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Hancock S M, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register J C, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long M J, Liscum E, Cone K, Davis G, Coe E H. Development and mapping of SSR markers for maize. Plant Mol Biol, 2002, 48: 463-481
[13] Veyrieras J B, Goffinet B, Charcosset A. MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics, 2007, 8: 49
[14] Goffinet B, G.erber S. Quantitative Trait Loci: A Meta-analysis. Genetics, 2000, 155: 463-473
[15] Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J. BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics, 2004, 20: 2324-2326
[16] Sen T Z, Andorf C M, Schaeffer M L, Harper L C, Sparks M E, Duvick J, Brendel V P, Cannon E, Campbell D A, Lawrence C J. MaizeGDB becomes ‘sequence-centric’. Database, 2009: bap020
[17] Beavis WD, Smith OS, Grant D, Fincher R. Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci, 1994, 34: 882-896
[18] Veldboom L R, Lee M, Woodman W L. Molecular marker-facilitated studies in an elite maize population: I. Linkage analysis and determination of QTL for morphological traits. Theor Appl Genet, 1994, 88: 7-16
[19] Ajmone-Marsan P, Monfredini G, Ludwig W F, Melchinger A E, Franceschini P, Pagnotto G, Motto M. In an elite cross of maize a major quantitative trait locus contols one-fourth of the genetic variation for grain yield. Theor Appl Genet, 1995, 90: 415-424
[20] Agrama H A S, Moussa M E. Mapping QTLs in breeding for drought tolerance in maize (Zea mays L.). Euphytica, 1996, 91: 89-97
[21] Ajmone-Marsan P, Monfredini G, Brandolini A, Melchinger A E, Garay G, Motto M. Identification of QTL of grain yield in an elite hybrid of maize: repeatability of map position and effects in independent samples derived from the same population. Maydica, 1996, 41: 49-57
[22] Ribaut J M, Hoisington D A, Deutsch J A, Jiang C, Gonzalez-de-Leo D. Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interva. Theor Appl Genet, 1996, 92: 905-914
[23] Veldboom LR, Lee M. Genetic mapping of quantitative trait loci in maize in stress and nonstress environments: I. grain yield components. Crop Sci, 1996, 36: 1310-1319
[24] Ribaut J M, Jiang C, Gonzalez-de-Leon D, Edmeades G O, Hoisington D A. Identification of quantitative trait loci under drought conditions in tropical maize. 2. Yield components and marker-assisted selection strategies. Theor Appl Genet, 1997, 94: 887-896
[25] Austin D, Lee M. Detection of quantitative trait loci for grain yield components in maize across generations in stress and nonstress environments. Crop Sci, 1998, 38: 1296-1308
[26] Khairallah M, Bohn M, Jiang C Z, Deutsh J A, Jewell D C, Mihm J A, Melchinger A E, Gonzalez de Leon D, Hoisington D. Molecular mapping of QTL for southwestern corn borer resistance, plant height and flowering in tropical maize. Plant Breed, 1998, 117: 309-318
[27] Frova C, Krajewski P, di Fonzo N, Villa M, Sari-Gorla M. Genetic analysis of drought tolerance in maize by molecular markers I. Yield components. Theor Appl Genet, 1999, 99: 280-288
[28] Sari-Gorla M, Krajewski P, di Fonzo N, Villa M, Frova C. Genetic analysis of drought tolerance in maize by molecular markers.II. Plant height and flowering. Theor Appl Genet, 1999, 99: 289-295
[29] Li X H, Liu X D, Li M S, Zhang S H. Identification of quantitative trait loci for anthesis-silking interval and yield components under drought stress in maize. Acta Bot Sin, 2003, 45(7): 852-857
[30] Gao S-B(高世斌), Feng Z-L(冯质雷), Li W-C(李晚忱), Rong T-Z(荣廷昭). Mapping QTLs for root and yield under drought stress in maize. Acta Agron Sin (作物学报), 2005, 31(6): 718-722 (in Chinese with English abstract)
[31] Gao S-B(高世斌), Zhao M-J(赵茂俊), Pan G-T(潘光堂), Li W-C(李晚忱), Rong T-Z(荣廷昭). Identification of QTLs controlling flowering parameters of maize under drought stress and non-stress environment. Southwest China J Agric Sci (西南农业学报), 2005, 18(5): 593-597 (in Chinese with English abstract)
[32] Lu G H, Tang J H, Yan J B, Ma X Q, Li J S, Chen S J, Ma J C, E L Z, Zhang Y R, Dai J R. Quantitative trait loci mapping of maize yield and its components under different water treatments at flowering time. J Integr Plant Biol, 2006, 48(10): 1233-1243
[33] Wu J-W(吴建伟), Liu C(刘成), Shi Y-S(石云素), Song Y-C(宋燕春), Chi S-M(池书敏), Ma S-Y(马峙英), Wang T-Y(王天宇), Li Y(黎裕). QTL analysis of flowering related traits in maize under different water regions. J Maize Sci (玉米科学), 2008, 16(5): 61-65 (in Chinese with English abstract)
[34] Wei F S, Zhang J W, Zhou S G, He R F, Schaeffer M, Collura K, Kudrna D, Faga B P, Wissotski M, Rock S M, Graves T A, Fulton R S, Coe E, Schnable P S, Schwartz D C, Ware D, Clifton S W, Wilson R K, Wing R A. The physical and genetic framework of the maize B73 genome. PLos Genet, 2009, 5(11): e1000715
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