A genome-wide survey of maize lipid-related genes: Candidate genes mining, digital gene expression profiling and co-location with QTL for maize kernel oil

Science China Life Sciences

Volumn 53, Issue 6, 2010, Pages 690-700

  Li, Lin ^a   Li, Hui ^a   Li, Ji Ying ^a   Xu, Shu Tu ^a   Yang, Xiao Hong ^a   Li, Jian Sheng ^a   Yan, Jian Bing ^a,b  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

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

Author keywords

In silico gene cloning; In silico gene expression profiling; Lipid metabolism; Maize; Quantative trait locus(QTL)

Indexed keywords

COMPLEMENTARY DNA; LIPID; VEGETABLE OIL;

ARTICLE; CHEMISTRY; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENETICS; MAIZE; MOLECULAR CLONING; PLANT GENE; QUANTITATIVE TRAIT LOCUS;

CLONING, MOLECULAR; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENES, PLANT; GENOME-WIDE ASSOCIATION STUDY; LIPIDS; PLANT OILS; QUANTITATIVE TRAIT LOCI; ZEA MAYS;

ARABIDOPSIS; ZEA MAYS;

EID: 77954252174     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-4007-3     Document Type: Article

References (69)

1. Sprong H, van der Sluijs P, van Meer G. How proteins move lipids and lipids move proteins. Nat Rev Mol Cell Biol, 2001, 2: 504-513.
2. Wallis J G, Browse J. Mutants of Arabidopsis reveal many roles for membrane lipids. Prog Lipid Res, 2002, 41: 254-278.
3. Broun P, Gettner S, Somerville C. Genetic engineering of plant lipids. Annu Rev Nutr, 1999, 19: 197-216.
4. Schneider K, Kienow L, Schmelzer E, et al. A new type of peroxisomal acyl-coenzyme a synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid. J Biol Chem, 2005, 280: 13962-13972.
5. Li C, Schilmiller A L, Liu G, et al. Role of β-oxidation in jasmonate biosynthesis and systemic wound signaling in tomato. Plant Cell, 2005, 17: 971-986.
6. Angelo A J S, Altschul A M. Lipolysis and the free fatty acid pool in seedlings. Plant Physiol, 1964, 39: 880-883.
7. Gueguen V, Macherel D, Jaquinod M, et al. Fatty acid and lipoic acid biosynthesis in higher plant mitochondria. J Biol Chem, 2000, 275: 5016-5025.
8. Thelen J J, Ohlrogge J B. Metabolic engineering of fatty acid biosynthesis in plants. Metab Eng, 2002, 4: 12-21.
9. Beaudoin F, Napier J A. Biosynthesis and compartmentation of triacylglycerol in higher plants. In Daum G. ed. Lipid Metabolism and Membrane Bioiogenesis. Berlin: Springer, 2004. 267-287.
10. Kunst L, Samuels A L. Biosynthesis and secretion of plant cuticular wax. Prog Lipid Res, 2003, 42: 51-80.
11. Reina-Pinto J J, Yephremov A. Surface lipids and plant defenses. Plant Physiol Biochem, 2009, 47: 540-549.
12. Hynes M J, Murray S L, Duncan A, et al. Regulatory genes controlling fatty acid catabolism and peroxisomal functions in the filamentous fungus aspergillus nidulans. Eukaryot Cell, 2006, 5: 794-805.
13. Graham I A, Eastmond P J. Pathways of straight and branched chain fatty acid catabolism in higher plants. Prog Lipid Res, 2002, 41: 156-181.
14. Goepfert S, Poirier Y. β-Oxidation in fatty acid degradation and beyond. Curr Opin Plant Biol, 2007, 10: 245-251.
15. Bessoule J J, Moreau P. Lipid Metabolism and Membrane Biogenesis. Berlin: Springer. 2003. 1610-2096.
16. Mueller-Roeber B, Pical C. Inositol phospholipid metabolism in arabidopsis characterized and putative isoforms of inositol phospholipid kinase and phosphoinositide-specific phospholipase C. Plant Physiol, 2002, 130: 22-46.
17. Chapman K D. Emerging physiological roles for N-acylphosphatidylethanolamine metabolism in plants: signal transduction and membrane protection. Chem Phys Lipids, 2000, 108: 221-230.
18. Munnik T. Phosphatidic acid: an emerging plant lipid second messenger. Trends Plant Sci, 2001, 6: 227-233.
19. Wang X M. Plant phsopholipases. Plant Mol Biol, 2001, 52: 211-231.
20. Futerman A H, Riezman H. The ins and outs of sphingolipid synthesis. Tr Cell Biol, 2005, 15: 312-318.
21. Sato N, Moriyama T. Genomic and biochemical analysis of lipid biosynthesis in the unicellular rhodophyte cyanidioschyzon merolae: lack of a plastidic desaturation pathway results in the coupled pathway of galactolipid synthesis. Eukaryot Cell, 2007, 8: 1006-1017.
22. Benning C. Biosynthesis and function of the sulfolipid sulfoquinovosyl diacylglycerol. Plant Mol Biol, 1998, 49: 53-75.
23. Baysal T, Demirdoven A. Lipoxygenase in fruits and vegetables: a review. Enzyme Microb Technol, 2007, 40: 491-496.
24. Feussner I, Wasternack C. The lipoxygenase pathway. Annu Rev Plant Biol, 2002, 53: 275-297.
25. Pollard M, Ohlrogge J. Testing models of fatty acid transfer and lipid synthesis in spinach leaf using in vivo oxygen-18 labeling. Plant Physiol, 1999, 121: 1217-1226.
26. Germain V, Rylott E L, Larson T R, et al. Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. Plant J, 2001, 28: 1-12.
27. Stymne S, Stobart A K, Glad G. The role of the acyl-CoA pool in the synthesis of polyunsaturated 18-carbon fatty acids and triacylglycerol production in the microsomes of developing safflower seeds. Lipids and Lipid Metabolism, 1983, 752: 198-208.
28. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature, 2005, 436: 793-800.
29. Paterson A H, Bowers J E, Bruggmann R, Dubchak I et al. The sorghum bicolor genome and the diversification of grasses. Nature, 2009, 457: 551-556.
30. Borevitz J O, Chory J. Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol, 2004, 7: 132-136.
31. Varshney R K, Hoisington D A, Tyagi A K. Advances in cereal genomics and applications in crop breeding. Trends Biotechnol, 2006, 24: 490-499.
32. Henrissat B, Coutinho P M, Davies G J. A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol, 2001, 47: 55-72.
33. Ward J M. Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics, 2001, 17: 560-563.
34. Beisson F, Koo A J K, Ruuska S, et al. Arabidopsis genes involved in acyl lipid metabolism a 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiol, 2003, 132: 681-697.
35. Altschul S F, Madden T L, Schaffer A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997, 25: 3389-3402.
36. Zdobnov E M, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 2001, 17: 847-849.
37. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res, 1999, 9: 868-877.
38. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol, 1997, 268: 78-94.
39. Salamov A A, Solovyev V V. Ab initio gene finding in Drosophila genomic DNA. Genome Res, 2000, 10: 516-522.
40. Stekel D J, Git Y, Falciani F. The comparison of gene expression from multiple cDNA Libraries. Genome Res, 2000, 10: 2055-2061.
41. Varuzza L, Lauretto M S, Brentani H, et al. Significance index for digital expression. In: Clamp M, ed. Genome Information Meeting, on CSHL. UK: University of Dundee, 2007.
42. Li L, Yan J B, Lei H Z, et al. QTL-Finder: a bioinformatics tool for QTL integration, comparison and discovery of candidate genes across genomes and experiments. In: Zhang Q F, ed. The Abstract of Plant Genomics Conference in China VIII. Plant Genomics Conference in China. Shanghai. 2007. 56-56.
43. Lee M, Sharopova N, Beavis W D, et al. Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol, 2002, 48: 453-461.
44. Song X F, Song T M, Dai J R, et al. QTL mapping of kernel oil concentration with high-oil maize by SSR markers. Maydica, 2004, 49: 41-48.
45. Zhang J, Lu X Q, Song X F, et al. Mapping quantitative trait loci for oil, starch, and protein concentrations in grain with high-oil Maize by SSR Markers. Euphytica, 2008, 162: 335-344.
46. Yang X H, Guo Y Q, Yan J B, et al. Major and minor QTL and epistasis contribute to fatty acid composition and oil content in high-oil maize. Theor Appl Genet, 2010, 120: 665-678.
47. Goldman I, Rocheford T R, Dudley J W. Molecular markers associated with maize kernel oil concentration in an Illinois high protein x Illinois low protein cross. Crop Sci, 1994, 34: 908-915.
48. Alrefai R, Berke T G, Rocheford T R. Quantitative trait locus analysis of fatty acid concentration in maize. Genome, 1995, 38: 894-901.
49. Berke T, Rocheford T R. Quantitative trait loci for flowering, plant and ear height, and kernel traits in maize. Crop Sci, 1995, 35: 1542-1549.
50. Clark D, Dudley J W, Rocheford T R, et al. Genetic analysis of corn kernel chemical composition in the random mated 10 generation of the cross of generation 70 of IHO × ILO. Crop Sci, 2006, 46: 807-819.
51. Dudley J W, Clark D, Rocheford T R, et al. Genetic Analysis of corn kernel chemical composition in the random mated 7 generation of the cross of generations 70 of IHP×ILP. Crop Sci, 2007, 47: 45-57.
52. Dudley J W. Epistatic interactions in crosses of Illinois High Oil × Illinois Low Oil and of Illinois High Protein × Illinois Low Protein corn strains. Crop Sci, 2008, 48: 59-68.
53. Wassom J J, Wong J C, Martinez E, et al. QTL associated with maize kernel oil, protein, and starch concentrations; kernel mass; and grain yield in Illinois High Oil × B73 backcross-derived lines. Crop Sci, 2008, 48: 243-252.
54. Wassom J J, Mikkelineni V, Bohn M O, et al. QTL for fatty acid composition of maize kernel oil in Illinois High Oil × B73 backcross-derived lines. Crop Sci, 2008, 48: 69-78.
55. Mangolin C A, de Souza Jr C L, Garcia A A F, et al. Mapping QTLs for kernel oil content in a tropical maize population. Euphytica, 2004, 137: 251-259.
56. Guigo R, Knudsen S, Drake N, et al. Prediction of gene structure. J Mol Biol, 1992, 226: 141-157.
57. Snyder E E, Stormo G D. Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res, 1993, 21: 607-613.
58. Uberbacher E C, Mural R J. Locating protein-codeing regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl Acad Sci USA, 1991, 88: 11261-11265.
59. Wang Z, Chen Y, Li Y. A brief review of computational gene prediction methods. Geno Prot Bioinfo, 2004, 2: 216-221.
60. Zheng P, Allen W B, Roesler K et al. A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat Genet, 2008, 40: 367-372.
61. Lee K, Huang A H C. Genes encoding oleosins in maize kernel of inbreds Mo17 and B73. Plant Mol Biol, 2004, 26: 1981-1987.
62. Beló A, Zheng P Z, Luck S, et al. Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics, 2008, 279: 1-10.
63. Hill W G. A century of corn selection. Science, 2005, 307: 683-684.
64. Voelker T A, Hayes T R, Cranmer A M, et al. Genetic engineering of a quantitative trait: Metabolic and genetic parameters influencing the accumulation of laurate in rapeseed. Plant J, 1996, 9: 229-241.
65. Domann P, Voelker T A, Ohlrogge J B. Accumulation of palmitate in Arabidopsis mediated by the acyl-acyl carrier protein thioesterase FATB1. Plant Physiol, 2000, 123: 637-643.
66. Liu Q, Singh S, Green A. Genetic modification of cotton seed oil using inverted-repeat gene-silencing techniques. Biochem Soc Trans, 2000, 28: 927-929.
67. Ye X, Al-Babili S, Klöti A, et al. Engineering provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science, 2000, 287: 303-305.
68. Zhu C F, Naqvi S, Breitenbach J, et al. Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in Maize. Proc Natl Acad Sci USA, 2008, 105: 18232-18237.
69. Harjes C E, Rocheford T R, Bai L, et al. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science, 2008, 319: 330-333.