Comparative mapping combined with homology-based cloning of the rice genome reveals candidate genes for grain zinc and iron concentration in maize

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• 作者：Tiantian Jin (1)
  Jingtang Chen (1)
  Liying Zhu (1)
  Yongfeng Zhao (1)
  Jinjie Guo (1)
  Yaqun Huang (1)
  
  1. Hebei Branch of Chinese National Maize Improvement Center ; Agricultural University of Hebei ; Baoding ; People鈥檚 Republic of China
  
• 关键词：Maize ; Grain zinc and iron concentration ; Meta ; analysis ; Comparative mapping ; Ortho ; mMQTL
• 刊名：BMC Genetics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：2,900 KB
• 参考文献：1. Broadley, MR, White, PJ, Hammond, JP, Zelko, I, Lux, A (2007) Zinc in plants. New Phytol 173: pp. 677-702
  The World Health Report 2002: Reducing Risks, Promoting Healthy Life. WHO, Geneva
  2. Hotz, C, Brown, KH (2004) Assessment of the risk of zinc deficiency in populations and options for its control. International Nutrition Foundation for UNU, Tokyo
  3. Boccio, J, lyengar, V (2003) Iron deficiency-causes, consequences, and strategies to overcome this nutritional problem. Biol Trace Elem Res 94: pp. 1-31
  4. Rawat, N, Neelam, K, Tiwari, VK, Dhaliwal, HS, Balyan, H (2013) Biofortification of cereals to overcome hidden hunger. Plant Breed 132: pp. 437-445
  5. Bouis, HE (2003) Micronutrient fortification of plants through plant breeding: can it improve nutrition in man at low cost?. Proc Nutr Soci 62: pp. 403-411
  6. Bouis, HE, Welch, RM (2010) Biofortification-a sustainable agricultural strategy for reducing micronutrient malnutrition in the global south. Crop Sci 50: pp. S20-S32
  7. White, PJ, Broadley, MR (2005) Biofortifying crops with essential mineral elements. Trends Plant Sci 10: pp. 586-593
  8. Stangoulis, JCR, Huynh, B-L, Welch, RM, Choi, E-Y, Graham, RD (2007) Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content. Euphytica 154: pp. 289-294
  9. Li, M, Wang, H, Zhang, J, Lee, J, Yang, R, Zhou, Y (2009) QTL mapping and epistasis analysis for phytic acid concentration in rice grain by using the bayesian model selection. Chin J Rice Sci 23: pp. 475-480
  10. Zhang, X, Yang, L, Zhang, T, Jiang, K, Wang, G, Zheng, J (2009) QTL mapping for zinc content in rice grains. Chin Bull Bot 44: pp. 594-600
  11. Du, J, Zeng, D, Wang, B, Qian, Q, Zheng, S, Ling, HQ (2012) Environmental effects on mineral accumulation in rice grains and identification of ecological specific QTLs. Environ Geochem Health 35: pp. 161-170
  12. Huang, Y, Zou, D, Wang, J, Liu, H, Xing, W, Ma, J (2012) QTL mapping for Mn, Fe, Zn and Cu contents in rice grains. Crop 6: pp. 77-81
  13. Sun, MM (2006) Genetic Analysis and QTL Mapping of the Contents for Mineral Elements Such as Fe, Se, Zn, Cu and Anthocyanins in Rice Seed. Crop Genetic and Breeding, Shandong Agricultural University
  14. Zhong, L (2010) QTL Analysis on Mineral Elements Content in Rice. Crop Genetics and Breeding, Sichuan Agricultural University
  15. Hu, X (2011) Dissection of QTLs for Yield and Grain Quality and Genetic Background Effect on Their Expression Using Backcross Intergression Lines of Rice. Crop Genetic & Breeding, Chinese Academy of Agricultural Science
  16. Jin, T, Zhou, J, Chen, J, Zhu, L, Zhao, Y, Huang, Y (2013) The genetic architecture of zinc and iron content in maize grains as revealed by QTL mapping and meta-analysis. Breed Sci 63: pp. 317-324
  17. Lung鈥檃ho, MG, Mwaniki, AM, Szalma, SJ, Hart, JJ, Rutzke, MA, Kochian, LV (2011) Genetic and physiological analysis of iron biofortification in maize kernels. PLoS One 6: pp. e20429
  18. Qin, H, Cai, Y, Liu, Z, Wang, G, Wang, J, Guo, Y (2012) Identification of QTL for zinc and iron concentration in maize kernel and cob. Euphytica 187: pp. 345-358
  19. Simic, D, Mladenovic Drinic, S, Zdunic, Z, Jambrovic, A, Ledencan, T, Brkic, J (2012) Quantitative trait loci for biofortification traits in maize grain. J Hered 103: pp. 47-54
  20. Goffinet, B, Gerber, S (2000) Quantitative trait loci: a meta-analysis. Genet 155: pp. 463-473
  21. Li, JZ, Zhang, ZW, Li, YL, Wang, QL, Zhou, YG (2011) QTL consistency and meta-analysis for grain yield components in three generations in maize. Theor Appl Genet 122: pp. 771-782
  22. Swamy, BP, Vikram, P, Dixit, S, Ahmed, HU, Kumar, A (2011) Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics 12: pp. 319
  23. Sun, YN, Pan, JB, Shi, XL, Du, XY, Wu, Q, Qi, ZM (2012) Multi-environment mapping and meta-analysis of 100-seed weight in soybean. Mol Biol Rep 39: pp. 9435-9443
  24. Chardon, F, Virlon, B, Moreau, L, Falque, M, Joets, J, Decousset, L (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genet 168: pp. 2169-2185
  25. Xu, J, Liu, Y, Liu, J, Cao, M, Wang, J, Lan, H (2012) The genetic architecture of flowering time and photoperiod sensitivity in maize as revealed by QTL review and meta analysis. J Integr Plant Biol 54: pp. 358-373
  26. Hao, Z, Li, X, Liu, X, Xie, C, Li, M, Zhang, D (2009) Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize. Euphytica 174: pp. 165-177
  27. Courtois, B, Ahmadi, N, Khowaja, F, Price, AH, Rami, J-F, Frouin, J (2009) Rice root genetic architecture: meta-analysis from a drought QTL database. Rice 2: pp. 115-128
  28. Khowaja, FS, Norton, GJ, Courtois, B, Price, AH (2009) Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics 10: pp. 276
  29. L枚ffler, M, Sch枚n, C-C, Miedaner, T (2009) Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Mol Breed 23: pp. 473-488
  30. Rodr铆guez, VM, Butr贸n, A, Rady, MOA, Soengas, P, Revilla, P (2013) Identification of quantitative trait loci involved in the response to cold stress in maize (Zea mays L.). Mol Breed 33: pp. 363-371
  31. Liu, R, Zhang, H, Zhao, P, Zhang, Z, Liang, W, Tian, Z (2011) Mining of candidate maize genes for nitrogen use efficiency by integrating gene expression and QTL data. Plant Mol Biol Rep 30: pp. 297-308
  32. Xiang, K, Reid, LM, Zhang, Z-M, Zhu, X-Y, Pan, G-T (2011) Characterization of correlation between grain moisture and ear rot resistance in maize by QTL meta-analysis. Euphytica 183: pp. 185-195
  33. Sala, RG, Andrade, FH, Cerono, JC (2012) Quantitative trait loci associated with grain moisture at harvest for line per se and testcross performance in maize: a meta-analysis. Euphytica 185: pp. 429-440
  34. Hund, A, Reimer, R, Messmer, R (2011) A consensus map of QTLs controlling the root length of maize. Plant Soil 344: pp. 143-158
  35. Ku, LX, Zhang, J, Guo, SL, Liu, HY, Zhao, RF, Chen, YH (2012) Integrated multiple population analysis of leaf architecture traits in maize (Zea mays L.). J Exp Bot 63: pp. 261-274
  36. Lacape, J-M, Llewellyn, D, Jacobs, J, Arioli, T, Becker, D, Calhoun, S (2010) Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population. BMC Plant Biol 10: pp. 132
  37. Z-m, Q (2011) Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica 179: pp. 499-514
  38. Danan, S, Veyrieras, J-B, Lefebvre, V (2011) Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 11: pp. 16
  39. Ahn, S, Tanksley, S (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A 90: pp. 7980-7984
  40. Gale, MD, Devos, KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci U S A 95: pp. 1971-1974
  41. Yan, J-B, Tang, H, Huang, Y-Q, Zheng, Y-L, Li, J-S (2004) Comparative analyses of QTL for important agronomic traits between maize and rice. Acta Genet Sin 31: pp. 1401-1407
  42. Wang, Y, Yao, J, Zhang, Z, Zheng, Y (2006) The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs. Chin Sci Bull 51: pp. 2219-2230
  43. Zhou, X, Li, S, Zhao, Q, Liu, X, Zhang, S, Sun, C (2013) Genome-wide identification, classification and expression profiling of nicotianamine synthase (NAS) gene family in maize. BMC Genomics 14: pp. 238
  44. Li, S, Zhou, X, Huang, Y, Zhu, L, Zhang, S, Zhao, Y (2013) Identification and characterization of the zinc-regulated transporters, iron-regulated transporter-like protein (ZIP) gene family in maize. BMC Plant Biol 13: pp. 114
  45. Zheng, L, Cheng, Z, Ai, C, Jiang, X, Bei, X, Zheng, Y (2010) Nicotianamine, a novel enhancer of rice iron bioavailability to humans. PLoS One 5: pp. e10190
  46. Lee, S, Kim, YS, Jeon, US, Kim, YK, Schjoerring, JK, An, G (2012) Activation of Rice nicotianamine synthase 2 (OsNAS2) enhances iron availability for biofortification. Mol Cells 33: pp. 269-275
  47. Lee, S, Jeon, US, Lee, SJ, Kim, YK, Persson, DP, Husted, S (2009) Iron fortification of rice seeds through activation of the nicotianamine synthase gene. Proc Natl Acad Sci U S A 106: pp. 22014-22019
  48. Inoue, H, Takahashi, M, Kobayashi, T, Suzuki, M, Nakanishi, H, Mori, S (2008) Identification and localisation of the rice nicotianamine aminotransferase gene OsNAAT1 expression suggests the site of phytosiderophore synthesis in rice. Plant Mol Biol 66: pp. 193-203
  49. Cheng, L, Wang, F, Shou, H, Huang, F, Zheng, L, He, F (2007) Mutation in nicotianamine aminotransferase stimulated the Fe(II) acquisition system and led to iron accumulation in rice. Plant Physiol 145: pp. 1647-1657
  50. Bashir, K, Inoue, H, Nagasaka, S, Takahashi, M, Nakanishi, H, Mori, S (2006) Cloning and characterization of deoxymugineic acid synthase genes from graminaceous plants. J Biol Chem 281: pp. 32395-32402
  51. Nozoye, T, Nagasaka, S, Kobayashi, T, Takahashi, M, Sato, Y, Uozumi, N (2011) Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants. J Biol Chem 286: pp. 5446-5454
  52. Koike, S, Inoue, H, Mizuno, D, Takahashi, M, Nakanishi, H, Mori, S (2004) OsYSL2 is a rice metal-nicotianamine transporter that is regulated by iron and expressed in the phloem. Plant J 39: pp. 415-424
  53. Ishimaru, Y, Masuda, H, Bashir, K, Inoue, H, Tsukamoto, T, Takahashi, M (2010) Rice metal-nicotianamine transporter, OsYSL2, is required for the long-distance transport of iron and manganese. Plant J 62: pp. 379-390
  54. Sasaki, A, Yamaji, N, Xia, J, Ma, JF (2011) OsYSL6 is involved in the detoxification of excess manganese in rice. Plant Physiol 157: pp. 1832-1840
  55. Inoue, H, Kobayashi, T, Nozoye, T, Takahashi, M, Kakei, Y, Suzuki, K (2009) Rice OsYSL15 is an iron-regulated iron(III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings. J Biol Chem 284: pp. 3470-3479
  56. Lee, S, Chiecko, JC, Kim, SA, Walker, EL, Lee, Y, Guerinot, ML (2009) Disruption of OsYSL15 leads to iron inefficiency in rice plants. Plant Physiol 150: pp. 786-800
  57. Kakei, Y, Ishimaru, Y, Kobayashi, T, Yamakawa, T, Nakanishi, H, Nishizawa, NK (2012) OsYSL16 plays a role in the allocation of iron. Plant Mol Biol 79: pp. 583-594
  58. Lee, S, Ryoo, N, Jeon, JS, Guerinot, ML, An, G (2012) Activation of rice Yellow Stripe1-Like 16 (OsYSL16) enhances iron efficiency. Mol Cells 33: pp. 117-126
  59. Aoyama, T, Kobayashi, T, Takahashi, M, Nagasaka, S, Usuda, K, Kakei, Y (2009) OsYSL18 is a rice iron(III)-deoxymugineic acid transporter specifically expressed in reproductive organs and phloem of lamina joints. Plant Mol Biol 70: pp. 681-692
  60. Bughio, N, Yamaguchi, H, Nishizawa, NK, Nakanishi, H, Mori, S (2002) Cloning an iron鈥恟egulated metal transporter from rice. J Exp Bot 53: pp. 1677-1682
  61. Lee, S, An, G (2009) Over-expression of OsIRT1 leads to increased iron and zinc accumulations in rice. Plant Cell Environ 32: pp. 408-416
  62. Ishimaru, Y, Suzuki, M, Tsukamoto, T, Suzuki, K, Nakazono, M, Kobayashi, T (2006) Rice plants take up iron as an Fe3+-phytosiderophore and as Fe2+. Plant J 45: pp. 335-346
  63. Ramesh, SA (2003) Differential metal selectivity and gene expression of two zinc transporters from rice. Plant Physiol 133: pp. 126-134
  64. Ishimaru, Y, Suzuki, M, Kobayashi, T, Takahashi, M, Nakanishi, H, Mori, S (2005) OsZIP4, a novel zinc-regulated zinc transporter in rice. J Exp Bot 56: pp. 3207-3214
  65. Ishimaru, Y, Masuda, H, Suzuki, M, Bashir, K, Takahashi, M, Nakanishi, H (2007) Overexpression of the OsZIP4 zinc transporter confers disarrangement of zinc distribution in rice plants. J Exp Bot 58: pp. 2909-2915
  66. Lee, S, Jeong, HJ, Kim, SA, Lee, J, Guerinot, ML, An, G (2010) OsZIP5 is a plasma membrane zinc transporter in rice. Plant Mol Biol 73: pp. 507-517
  67. Yang, X, Huang, J, Jiang, Y, Zhang, HS (2009) Cloning and functional identification of two members of the ZIP (Zrt, Irt-like protein) gene family in rice (Oryza sativa L.). Mol Biol Rep 36: pp. 281-287
  68. Lee, S, Kim, SA, Lee, J, Guerinot, ML, An, G (2010) Zinc deficiency-inducible OsZIP8 encodes a plasma membrane-localized zinc transporter in rice. Mol Cells 29: pp. 551-558
  69. Takahashi, R, Ishimaru, Y, Senoura, T, Shimo, H, Ishikawa, S, Arao, T (2011) The OsNRAMP1 iron transporter is involved in Cd accumulation in rice. J Exp Bot 62: pp. 4843-4850
  70. Xia, J, Yamaji, N, Kasai, T, Ma, JF (2010) Plasma membrane-localized transporter for aluminum in rice. Proc Natl Acad Sci U S A 107: pp. 18381-18385
  71. Yang, M, Zhang, W, Dong, H, Zhang, Y, Lv, K, Wang, D (2013) OsNRAMP3 is a vascular bundles-specific manganese transporter that is responsible for manganese distribution in rice. PLoS One 8: pp. e83990
  72. Ishimaru, Y, Takahashi, R, Bashir, K, Shimo, H, Senoura, T, Sugimoto, K (2012) Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport. Sci Rep 2: pp. 286
  73. Sasaki, A, Yamaji, N, Yokosho, K, Ma, JF (2012) Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice. Plant Cell 24: pp. 2155-2167
  74. Satoh-Nagasawa, N, Mori, M, Nakazawa, N, Kawamoto, T, Nagato, Y, Sakurai, K (2012) Mutations in rice (Oryza sativa) heavy metal ATPase 2 (OsHMA2) restrict the translocation of zinc and cadmium. Plant Cell Physiol 53: pp. 213-224
  75. Takahashi, R, Ishimaru, Y, Shimo, H, Ogo, Y, Senoura, T, Nishizawa, NK (2012) The OsHMA2 transporter is involved in root-to-shoot translocation of Zn and Cd in rice. Plant Cell Environ 35: pp. 1948-1957
  76. Yamaji, N, Xia, J, Mitani-Ueno, N, Yokosho, K, Feng Ma, J (2013) Preferential delivery of zinc to developing tissues in rice is mediated by P-type heavy metal ATPase OsHMA2. Plant Physiol 162: pp. 927-939
  77. Ueno, D, Yamaji, N, Kono, I, Huang, CF, Ando, T, Yano, M (2010) Gene limiting cadmium accumulation in rice. Proc Natl Acad Sci U S A 107: pp. 16500-16505
  78. Miyadate, H, Adachi, S, Hiraizumi, A, Tezuka, K, Nakazawa, N, Kawamoto, T (2011) OsHMA3, a P1B-type of ATPase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles. New Phytol 189: pp. 190-199
  79. Deng, F, Yamaji, N, Xia, J, Ma, JF (2013) A member of the heavy metal P-type ATPase OsHMA5 is involved in xylem loading of copper in rice. Plant Physiol 163: pp. 1353-1362
  80. Lee, S, Kim, YY, Lee, Y, An, G (2007) Rice P1B-type heavy-metal ATPase, OsHMA9, is a metal efflux protein. Plant Physiol 145: pp. 831-842
  81. Yuan, L, Yang, S, Liu, B, Zhang, M, Wu, K (2012) Molecular characterization of a rice metal tolerance protein, OsMTP1. Plant Cell Rep 31: pp. 67-79
  82. Menguer, PK, Farthing, E, Peaston, KA, Ricachenevsky, FK, Fett, JP, Williams, LE (2013) Functional analysis of the rice vacuolar zinc transporter OsMTP1. J Exp Bot 64: pp. 2871-2883
  83. Chen, Z, Fujii, Y, Yamaji, N, Masuda, S, Takemoto, Y, Kamiya, T (2013) Mn tolerance in rice is mediated by MTP8.1, a member of the cation diffusion facilitator family. J Exp Bot 64: pp. 4375-4387
  84. Yokosho, K, Yamaji, N, Ueno, D, Mitani, N, Ma, JF (2009) OsFRDL1 is a citrate transporter required for efficient translocation of iron in rice. Plant Physiol 149: pp. 297-305
  85. Zhang, Y, Xu, YH, Yi, HY, Gong, JM (2012) Vacuolar membrane transporters OsVIT1 and OsVIT2 modulate iron translocation between flag leaves and seeds in rice. Plant J 72: pp. 400-410
  86. Bashir, K, Takahashi, R, Akhtar, S, Ishimaru, Y, Nakanishi, H, Nishizawa, NK (2013) The knockdown of OsVIT2 and MIT affects iron localization in rice seed. Rice 6: pp. 1-7
  87. Ogo, Y, Itai, RN, Nakanishi, H, Inoue, H, Kobayashi, T, Suzuki, M (2006) Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants. J Exp Bot 57: pp. 2867-2878
  88. Ogo, Y, Itai, RN, Nakanishi, H, Kobayashi, T, Takahashi, M, Mori, S (2007) The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Plant J 51: pp. 366-377
  89. Ogo, Y, Itai, RN, Kobayashi, T, Aung, MS, Nakanishi, H, Nishizawa, NK (2011) OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil. Plant Mol Biol 75: pp. 593-605
  90. Zheng, L, Ying, Y, Wang, L, Wang, F, Whelan, J, Shou, H (2010) Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa. BMC Plant Biol 10: pp. 166
  91. Zhang, H, Uddin, MS, Zou, C, Xie, C, Xu, Y, Li, WX (2014) Meta-analysis and candidate gene mining of low-phosphorus tolerance in maize. J Integr Plant Biol 56: pp. 262-270
  92. Truntzler, M, Barriere, Y, Sawkins, MC, Lespinasse, D, Betran, J, Charcosset, A (2010) Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes. Theor Appl Genet 121: pp. 1465-1482
  93. Wang, Y, Huang, Z, Deng, D, Ding, H, Zhang, R, Wang, S (2013) Meta-analysis combined with syntenic metaQTL mining dissects candidate loci for maize yield. Mol Breed 31: pp. 601-614
  94. Vidal, SM, Malo, D, Vogan, K, Skamene, E, Gros, P (1993) Natural resistance to infection with intracellular parasites: Isolation of a candidate for Bcg. Cell 73: pp. 469-485
  95. Cellier, M, Prive, G, Belouchi, A, Kwan, T, Rodrigues, V, Chia, W (1995) Nramp defines a family of membrane proteins. Proc Natl Acad Sci U S A 92: pp. 10089-10093
  96. CURIE, C, Alonso, J, JEAN, M, Ecker, J, Briat, J (2000) Involvement of NRAMP1 from Arabidopsis thaliana in iron transport. Biochem J 347: pp. 749-755
  97. Ishimaru, Y, Bashir, K, Nakanishi, H, Nishizawa, NK (2012) OsNRAMP5, a major player for constitutive iron and manganese uptake in rice. Plant Signal Behav 7: pp. 763-766
  98. Belouchi, A, Kwan, T, Gros, P (1997) Cloning and characterization of the OsNramp family from Oryza sativa, a new family of membrane proteins possibly implicated in the transport of metal ions. Plant Mol Biol 33: pp. 1085-1092
  99. Narayanan, NN, Vasconcelos, MW, Grusak, MA (2007) Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray. Plant Physiol Biochem 45: pp. 277-286
  100. Thomine, S, Wang, R, Ward, JM, Crawford, NM, Schroeder, JI (2000) Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proc Natl Acad Sci U S A 97: pp. 4991-4996
  101. Lanquar, V, Ramos, MS, Leli猫vre, F, Barbier-Brygoo, H, Krieger-Liszkay, A, Kr盲mer, U (2010) Export of vacuolar manganese by AtNRAMP3 and AtNRAMP4 is required for optimal photosynthesis and growth under manganese deficiency. Plant Physiol 152: pp. 1986-1999
  102. Thomine, S, Leli猫vre, F, Debarbieux, E, Schroeder, JI, Barbier-Brygoo, H (2003) AtNRAMP3, a multispecific vacuolar metal transporter involved in plant responses to iron deficiency. Plant J 34: pp. 685-695
  103. Temnykh, S, DeClerck, G, Lukashova, A, Lipovich, L, Cartinhour, S, McCouch, S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11: pp. 1441-1452
  104. Arcade, A, Labourdette, A, Falque, M, Mangin, B, Chardon, F, Charcosset, A (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20: pp. 2324-2326
  105. Larkin, MA, Blackshields, G, Brown, N, Chenna, R, McGettigan, PA, McWilliam, H (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: pp. 2947-2948
  106. Tamura, K, Dudley, J, Nei, M, Kumar, S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: pp. 1596-1599
  
• 刊物主题：Life Sciences, general; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics; Genetics and Population Dynamics;
• 出版者：BioMed Central
• ISSN：1471-2156

文摘

Background Grain zinc and iron concentration is a complex trait that is controlled by quantitative trait loci (QTL) and is important for maintaining body health. Despite the substantial effort that has been put into identifying QTL for grain zinc and iron concentration, the integration of independent QTL is useful for understanding the genetic foundation of traits. The number of QTL for grain zinc and iron concentration is relatively low in a single species. Therefore, combined analysis of different genomes may help overcome this challenge. Results As a continuation of our work on maize, meta-analysis of QTL for grain zinc and iron concentration in rice was performed to identify meta-QTL (MQTL). Based on MQTL in rice and maize, comparative mapping combined with homology-based cloning was performed to identify candidate genes for grain zinc and iron concentration in maize. In total, 22 MQTL in rice, 4 syntenic MQTL-related regions, and 3 MQTL-containing candidate genes in maize (ortho-mMQTL) were detected. Two maize orthologs of rice, GRMZM2G366919 and GRMZM2G178190, were characterized as natural resistance-associated macrophage protein (NRAMP) genes and considered to be candidate genes. Phylogenetic analysis of NRAMP genes among maize, rice, and Arabidopsis thaliana further demonstrated that they are likely responsible for the natural variation of maize grain zinc and iron concentration. Conclusions Syntenic MQTL-related regions and ortho-mMQTL are prime areas for future investigation as well as for marker-assisted selection breeding programs. Furthermore, the combined method using the rice genome that was used in this study can shed light on other species and help direct future quantitative trait research. In conclusion, these results help elucidate the molecular mechanism that underlies grain zinc and iron concentration in maize.