Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean
详细信息 查看全文
- 作者：Yung-Tsi Bolon (1)
Bindu Joseph (2)
Steven B Cannon (3)
Michelle A Graham (3)
Brian W Diers (4)
Andrew D Farmer (5)
Gregory D May (5)
Gary J Muehlbauer (6)
James E Specht (7)
Zheng Jin Tu (8)
Nathan Weeks (3)
Wayne W Xu (8)
Randy C Shoemaker (3)
Carroll P Vance (1) (6) - 刊名：BMC Plant Biology
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：10
- 期：1
- 全文大小：2758KB
- 参考文献：1. Hobbs DH, Flintham JE, Hills MJ: Genetic control of storage oil synthesis in seeds of Arabidopsis. / Plant Physiol 2004,136(2):3341-349. CrossRef
2. Weber H, Borisjuk L, Wobus U: Molecular physiology of legume seed development. / Annu Rev Plant Biol 2005, 56:253-79. CrossRef
3. Hajduch M, Ganapathy A, Stein JW, Thelen JJ: A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. / Plant Physiol 2005,137(4):1397-419. CrossRef
4. Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuster H, Thompson R: A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues. / Mol Cell Proteomics 2007,6(12):2165-179. CrossRef
5. Jukanti AK, Heidlebaugh NM, Parrott DL, Fisher IA, McInnerney K, Fischer AM: Comparative transcriptome profiling of near-isogenic barley ( Hordeum vulgare ) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation. / New Phytol 2008, 177:333-49.
6. Dam S, Laursen BS, Ornfelt JH, Jochimsen B, Staerfeldt HH, Friis C, Nielsen K, Goffard N, Besenbacher S, Krusell L, Sato S, Tabata S, Thogersen IB, Enghild JJ, Stougaard J: The proteome of seed development in the model legume Lotus japonicus. / Plant Physiol 2009,149(3):1325-340. CrossRef
7. Liu K: / Soybeans: Chemistry, Technology, and Utilization. New York: Chapman & Hall; 1997.
8. Hill JE, Breidenbach RW: Proteins of soybean seeds. I. Isolation and characterization of the major components. / Plant Physiology 1974, 53:742-46. CrossRef
9. Rubel A, Rinne RW, Canvin DT: Protein, oil and fatty acid in developing soybean seeds. / Crop Sci 1972, 12:739-41. CrossRef
10. Herman EM, Larkins BA: Protein storage bodies and vacuoles. / Plant Cell 1999,11(4):601-14. CrossRef
11. Thanh VH, Shibasaki K: Major proteins of soybean seeds. A straightforward fractionation and their characterization. / J Agric Food Chem 1976, 24:1118.
12. Roberts RC, Briggs DR: Isolation and characterization of the 7S component of soybean globulins. / Cereal Chem 1965, 42:71.
13. Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C: Combined networks regulating seed maturation. / Trends Plant Sci 2007,12(7):294-00. j.tplants.2007.06.003">CrossRef
14. Domoney C, Duc G, Ellis TH, Ferrandiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Kuster H, Madueno F, Munier-Jolain NG, Mayer K, Thompson R, Udvardi M, Salon C: Genetic and genomic analysis of legume flowers and seeds. / Curr Opin Plant Biol 2006,9(2):133-41. j.pbi.2006.01.014">CrossRef
15. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J: A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat. / Science 2006,314(5803):1298-301. CrossRef
16. Ohto MA, Fischer RL, Goldberg RB, Nakamura K, Harada JJ: Control of seed mass by APETALA2. / Proc Natl Acad Sci USA 2005,102(8):3123-128. CrossRef
17. Zhang W, Bi J, Chen L, Zheng L, Ji S, Xia Y, Xie K, Zhao Z, Wang Y, Liu L, Jiang L, Wan J: QTL mapping for crude protein and protein fraction contents in rice ( Oryza sativa L.). / J Cereal Sci 2008, 48:539-47. j.jcs.2007.11.010">CrossRef
18. Timmerman-Vaughan G, Mills A, Whitfield C, Frew T, Butler R, Murray S, Lakeman M, McCallum J, Russell A, Wilson D: Linkage mapping of QTL for seed yield, yield components, and developmental traits in pea. / Crop Sci 2005, 45:1336-344. CrossRef
19. Mansur LM, Lark KG, Kross H, Oliveira A: Interval mapping of quantitative trait loci for reproductive, morphological, and seed traits of soybean ( Glycine max L.). / Theoret Appl Genet 1993,86(8):1432-242.
20. Lee SH, Bailey MA, Mian MAR, Carter TE Jr, Shipe ER, Ashley DA, Parrot WA, Hussey RS, Boerma HR: RFLP loci associated with soybean seed protein and oil content across populations and locations. / Theoret Appl Genet 1996, 93:649-57. CrossRef
21. Fasoula VA, Harris DK, Boerma HR: Validation and designation of quantitative trait loci for seed protein, seed oil, and seed weight from two soybean populations. / Crop Sci 2004, 44:1218-225. CrossRef
22. Csanádi G, Vollman J, Stift G, Lelly T: Seed quality QTLs identified in a molecular map of early maturing soybean. / Theor Appl Genet 2001, 103:912-19. CrossRef
23. Panthee DR, Pantalone VR, West DR, Saxton AM, Sams CE: Quantitative trait loci for seed protein and oil concentration and seed size in soybean. / Crop Sci 2005, 45:2015-022. CrossRef
24. Diers BW, Keim P, Fehr WR, Shoemaker RC: RFLP analysis of soybean seed protein and oil content. / Theoret Appl Genet 1992, 83:608-12. CrossRef
25. Seboldt AM, Shoemaker RC, Diers BW: Analysis of a quantitative trait locus allele from wild soybean that increases seed protein concentration in soybean. / Crop Sci 2000, 40:1438-444. CrossRef
26. Brummer EC, Graef GL, Orf JH, Wilcox JR, Shoemaker RC: Mapping QTL for seed protein and oil content in eight soybean populations. / Crop Sci 1997, 37:370-78. CrossRef
27. Chung J, Babka HL, Graef GL, Staswick PE, Lee DJ, Cregan PB, Shoemaker RC, Specht JE: The seed protein, oil, and yield QTL on soybean linkage group I. / Crop Sci 2003, 43:1053-067. CrossRef
28. Brim CA, Burton JW: Recurrent selection in soybeans. II. Selection for increased percent protein in seeds. / Crop Sci 1979, 19:494-98. CrossRef
29. Burton JW: Quantitative genetics: results relevant to soybean breeding. In / Soybeans: Improvement, Production, and Uses. / Volume 16. 2nd edition. Edited by: Wilcox JR. Madison, WI: ASA, CSSA, and SSSA; 1987:211-47.
30. Wilcox JR, Cavins JF: Backcrossing high seed protein to a soybean cultivar. / Crop Sci 1995, 35:1036-041. CrossRef
31. Cober ER, Voldeng HD: Developing high-protein, high-yield soybean populations and lines. / Crop Sci 2000, 40:39-2. CrossRef
32. Nichols DM, Glover KD, Carlson SR, Specht JE, Diers BW: Fine mapping of a seed protein QTL on soybean linkage group I and its correlated effects on agronomic traits. / Crop Sci 2006, 46:834-39. CrossRef
33. Ruuska SA, Girke T, Benning C, Ohlrogge JB: Contrapuntal networks of gene expression during Arabidopsis seed filling. / Plant Cell 2002,14(6):1191-206. CrossRef
34. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU: A gene expression map of Arabidopsis thaliana development. / Nat Genet 2005,37(5):501-06. CrossRef
35. Goldberg RB, Barker SJ, Perez-Grau L: Regulation of gene expression during plant embryogenesis. / Cell 1989, 56:149-60. CrossRef
36. Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB: Using genomics to study legume seed development. / Plant Physiol 2007,144(2):562-74. CrossRef
37. Vodkin L, Jones S, Gonzalez DO, Thibaud-Nissen F, Zabala G, Tuteja J: Genomics of soybean seed development. In / Genetics and Genomics of Soybean. / Volume 2. Edited by: Stacey G. New York: Springer; 2008:163-84. CrossRef
38. Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK: A gene expression atlas of the model legume Medicago truncatula . / Plant J 2008,55(3):504-13. j.1365-313X.2008.03519.x">CrossRef
39. Verdier J, Thompson RD: Transcriptional regulation of storage protein synthesis during dicotyledon seed filling. / Plant Cell Physiol 2008,49(9):1263-271. CrossRef
40. Wan Y, Poole RL, Huttly AK, Toscano-Underwood C, Feeney K, Welham S, Gooding MJ, Mills C, Edwards KJ, Shewry PR, Mitchell RA: Transcriptome analysis of grain development in hexaploid wheat. / BMC Genomics 2008, 9:121. CrossRef
41. Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U: Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. / Plant Physiol 2008,146(4):1738-758. CrossRef
42. Wei G, Tao Y, Liu G, Chen C, Luo R, Xia H, Gan Q, Zeng H, Lu Z, Han Y, Li X, Song G, Zhai H, Peng Y, Li D, Xu H, Wei X, Cao M, Deng H, Xin Y, Fu X, Yuan L, Yu J, Zhu Z, Zhu L: A transcriptomic analysis of superhybrid rice LYP9 and its parents. / Proc Natl Acad Sci USA 2009,106(19):7695-701. CrossRef
43. Wang CS, Todd JJ, Vodkin LO: Chalcone synthase mRNA and activity are reduced in yellow soybean seed coats with dominant I alleles. / Plant Physiol 1994,105(2):739-48. CrossRef
44. He G, Luo X, Tian F, Li K, Zhu Z, Su W, Qian X, Fu Y, Wang X, Sun C, Yang J: Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. / Genome Res 2006,16(5):618-26. CrossRef
45. Li R-J, Wang H-Z, Mao H, Lu Y-T, Hua W: Identification of differentially expressed genes in seeds of two near-isogenic Brassica napus lines with different oil content. / Planta 2006, 224:952-62. CrossRef
46. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA: Genome sequence of the palaeopolyploid soybean. / Nature 2010,463(7278):178-83. CrossRef
47. Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE: An integrated genetic linkage map of the soybean genome. / Crop Sci 2006,39(5):1464-490. CrossRef
48. Storey JD, Tibshirani R: Statistical significance for genomewide studies. / Proc Natl Acad Sci USA 2003,100(16):9440-445. CrossRef
49. Weber H, Golombek S, Heim U, Borisjuk L, Panitz R, Manteuffel R, Wobus U: Integration of carbohydrate and nitrogen metabolism during legume seed development: implications for storage product synthesis. / J Plant Physiol 1998, 152:641-48.
50. Asada T, Collings D: Molecular motors in higher plants. / Trends Plant Sci 1997, 2:29-7. CrossRef
51. Hashimoto T: Dynamics and regulation of plant interphase microtubules: a comparative view. / Curr Opin Plant Biol 2003, 6:568-76. j.pbi.2003.09.011">CrossRef
52. Borisjuk L, Walenta S, Weber H, Muehller-Klieser W, Wobus U: High-resolution histographical mapping of glucose concentrations in developing cotyledons of Vicia faba in relation to mitotic activity and storage processes: glucose as a possible developmental trigger. / Plant J 1998,15(4):583-91. j.1365-313X.1998.00214.x">CrossRef
53. Koch KE: Sucrose metabolism: regulatory mechanisms and pivotal roles in sugar sensing and plant development. / Curr Opin Plant Biol 2004, 7:235-46. j.pbi.2004.03.014">CrossRef
54. Koch KE: Carbohydrate-modulated gene expression in plants. / Annu Rev Plant Physiol Plant Mol Biol 1996, 47:509-40. CrossRef
55. Smeekens S: Sugar-induced signal transduction in plants. / Annu Rev Plant Physiol Plant Mol Biol 2000, 51:49-1. CrossRef
56. Wang HW, Zhang B, Hao YJ, Huang J, Tian AG, Liao Y, Zhang JS, Chen SY: The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. / Plant J 2007, 52:716-29. j.1365-313X.2007.03268.x">CrossRef
57. Xu WW, Cho S, Yang SS, Bolon YT, Bilgic H, Jia H, Xiong Y, Muehlbauer GJ: Single-feature polymorphism discovery by computing probe affinity shape powers. / BMC Genet 2009, 10:48. CrossRef
58. Cui X, Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, Close TJ: Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. / Bioinformatics 2005, 21:3852-858. CrossRef
59. Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R: Single-feature polymorphism discovery in the barley transcriptome. / Genome Biology 2005,6(6):R54. CrossRef
60. Gill KS, Gill BS, Endo TR: A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat. / Chromosoma 1993, 102:374-81. CrossRef
61. Wilcox JR: Increasing seed protein in soybean with eight cycles of recurrent selection. / Crop Sci 1998, 38:1536-540. CrossRef
62. Helms TC, Orf JH: Protein, oil and yield of soybean lines selected for increased protein. / Crop Sci 1998, 38:707-11. CrossRef
63. Focks N, Benning C: wrinkled1: A novel, low-seed-oil mutant of Arabidopsis with a deficiency in the seed-specific regulation of carbohydrate metabolism. / Plant Physiol 1998,118(1):91-01. CrossRef
64. Cernac A, Benning C: WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. / Plant J 2004,40(4):575-85. j.1365-313X.2004.02235.x">CrossRef
65. Verdier J, Kakar K, Gallardo K, Le Signor C, Aubert G, Schlereth A, Town CD, Udvardi MK, Thompson RD: Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. / Plant Mol Biol 2008,67(6):567-80. CrossRef
66. Walling L, Drews GN, Goldberg RB: Transcriptional and post-transcriptional regulation of soybean seed protein mRNA levels. / Proc Natl Acad Sci USA 1986,83(7):2123-127. CrossRef
67. Harada JJ, Barker SJ, Goldberg RB: Soybean beta-conglycinin genes are clustered in several DNA regions and are regulated by transcriptional and posttranscriptional processes. / Plant Cell 1989,1(4):415-25. CrossRef
68. Meinke DW, Chen J, Beachy RN: Expression of storage-protein genes during soybean seed development. / Planta 1981, 153:130-39. CrossRef
69. Ohlrogge JB, Jaworski JG: Regulation of Fatty Acid Synthesis. / Annu Rev Plant Physiol Plant Mol Biol 1997, 48:109-36. CrossRef
70. Roesler K, Shintani D, Savage L, Boddupalli S, Ohlrogge J: Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds. / Plant Physiol 1997,113(1):75-1. CrossRef
71. Turnham E, Northcote DH: Changes in the activity of acetyl-CoA carboxylase during rape-seed formation. / Biochem J 1983,212(1):223-29.
72. Macnicol PK, Jacobsen JV: Endosperm acidification and related metabolic changes in the developing barley grain. / Plant Physiol 1992,98(3):1098-104. CrossRef
73. Gonzalez MC, Osuna L, Echevarria C, Vidal J, Cejudo FJ: Expression and localization of phosphoenolpyruvate carboxylase in developing and germinating wheat grains. / Plant Physiol 1998,116(4):1249-258. CrossRef
74. Golombek S, Heim U, Horstmann C, Wobus U, Weber H: Phosphoenolpyruvate carboxylase in developing seeds of Vicia faba L.: gene expression and metabolic regulation. / Planta 1999,208(1):66-2. CrossRef
75. Smith AJ, Rinne RW, Seif RD: Phosphoenolpyruvate carboxylase and pyruvate kinase involvement in protein and oil biosynthesis during soybean seed development. / Crop Sci 1989, 29:349-53. CrossRef
76. Agrawal GK, Hajduch M, Graham K, Thelen JJ: In-depth investigation of the soybean seed-filling proteome and comparison with a parallel study of rapeseed. / Plant Physiol 2008,148(1):504-18. CrossRef
77. Klaus D, Ohlrogge JB, Neuhaus HE, Dormann P: Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase. / Planta 2004,219(3):389-96. CrossRef
78. Kianian SF, Egli MA, Phillilps RL, Rines HW, Somers DA, Gengenbach BG, Webster FH, Livingston SM, Groh S, O'Donoughue LS, Sorrells ME, Wesenberg DM, Stuthman DD, Fulcher RG: Association of a major groat oil content QTL and an acetyl-CoA carboxylase gene in oat. / Theor Appl Genet 1999, 98:884-94. CrossRef
79. Thelen JJ, Ohlrogge JB: Both antisense and sense expression of biotin carboxyl carrier protein isoform 2 inactivates the plastid acetyl-coenzyme A carboxylase in Arabidopsis thaliana . / Plant J 2002,32(4):419-31. j.1365-313X.2002.01435.x">CrossRef
80. Rolletschek H, Borisjuk L, Radchuk R, Miranda M, Heim U, Wobus U, Weber H: Seed-specific expression of a bacterial phosphoenolpyruvate carboxylase in Vicia narbonensis increases protein content and improves carbon economy. / Plant Biotechnol J 2004,2(3):211-19. j.1467-7652.2004.00064.x">CrossRef
81. Huber SC, Hardin SC: Numerous posttranslational modifications provide opportunities for the intricate regulation of metabolic enzymes at multiple levels. / Curr Opin Plant Biol 2004, 7:318-22. j.pbi.2004.03.002">CrossRef
82. Allen DK, Ohlrogge JB, Shachar-Hill Y: The role of light in soybean seed filling metabolism. / Plant J 2009,58(2):220-34. j.1365-313X.2008.03771.x">CrossRef
83. Borisjuk L, Nguyen TH, Neuberger T, Rutten T, Tschiersch H, Claus B, Feussner I, Webb AG, Jakob P, Weber H, Wobus U, Rolletschek H: Gradients of lipid storage, photosynthesis and plastid differentiation in developing soybean seeds. / New Phytol 2005,167(3):761-76. j.1469-8137.2005.01474.x">CrossRef
84. Rolletschek H, Weber H, Borisjuk L: Energy status and its control on embryogenesis of legumes. Embryo photosynthesis contributes to oxygen supply and is coupled to biosynthetic fluxes. / Plant Physiol 2003,132(3):1196-206. CrossRef
85. Wei W-H, Chen B, Yan X-H, Wang L-J, Zhang H-F, Cheng J-P, Zhou X-A, Sha A-H, Shen H: Identification of differentially expressed genes in soybean seeds differing in oil content. / Plant Sci 2008, 175:663-73. j.plantsci.2008.06.018">CrossRef
86. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: UniProt: the Universal Protein knowledgebase. / Nucleic Acids Res 2004, (32 Database):D115-19.
87. Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. / Genome Res 2009, 19:57-9. CrossRef
88. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK: Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. / Cell 2005,123(7):1279-291. j.cell.2005.11.035">CrossRef
89. zur Nieden U, Neumann D, Bucka A, Nover L: Tissue-specific localization of heat-stress proteins during embryo development. / Planta 1995, 196:530-38. CrossRef
90. DeRocher AE, Vierling E: Developmental control of small heat shock protein experssion during pea seed maturation. / Plant J 1994,5(1):93-02. j.1365-313X.1994.5010093.x">CrossRef
91. Rolletschek H, Radchuk R, Klukas C, Schreiber F, Wobus U, Borisjuk L: Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds. / New Phytol 2005,167(3):777-86. j.1469-8137.2005.01473.x">CrossRef
92. Borisjuk L, Rolletschek H, Walenta S, Panitz R, Wobus U, Weber H: Energy status and its control on embryogenesis of legumes: ATP distribution within Vicia faba embryos is developmentally regulated and correlated with photosynthetic capacity. / Plant J 2003,36(3):318-29. j.1365-313X.2003.01879.x">CrossRef
93. Kawagoe Y, Mura N: A novel basic region/helix-loop-helix protein binds to a G-box motif CACGTG of the bean seed storage protein β-phaseolin gene. / Plant Sci 1996, 116:47-7. CrossRef
94. Pla M, Vilardell J, Guiltinan MJ, Marcotte WR, Niogret MF, Quatrano RS, Pagès M: The cis-regulatory element CCACGTGG is involved in ABA and water-stress responses of the maize gene rab28. / Plant Molecular Biology 1993, 21:259-66. CrossRef
95. Ezcurra I, Wycliffe P, Nehlin L, Ellerstr?m M, Rask L: Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box. / Plant J 2000, 24:57-6. j.1365-313x.2000.00857.x">CrossRef
96. de Pater S, Pham K, Chua NH, Memelink J, Kijne J: A 22-bp fragment of the pea lectin promoter containing essential TGAC-like motifs confers seed-specific gene expression. / Plant Cell 1993, 5:877-86. CrossRef
97. Emrich SJ, Barbazuk WB, Li L, Schnable PS: Gene discovery and annotation using LCM-454 transcriptome sequencing. / Genome Res 2007,17(1):69-3. CrossRef
98. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. / Science 2008,321(5891):956-60. CrossRef
99. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. / Nature 2008,453(7199):1239-243. CrossRef
100. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. / Nature 2008,456(7221):470-76. CrossRef
101. Soderlund C, Longden I, Mott R: FPC: A system for building contigs from restriction fingerprinted clones. / Comput Appl Biosci 1997, 13:523-35.
102. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. / J Mol Biol 1990, 215:494-98.
103. AOAC: / Official Methods of Analysis. Gaithersburg, MD: AOAC International; 2006.
104. Boddu J, Cho S, Muehlbauer G: Transcriptome analysis of trichothecene-induced gene expression in barley. / Mol Plant Microbe Interact 2007,20(11):1364-375. CrossRef
105. Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA: Distinct biphasic mRNA changes in response to Asian soybean rust infection. / Mol Plant Microbe Interact 2007,20(8):887-99. CrossRef
106. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. / Biostatistics 2003,4(2):249-64. CrossRef
107. Hubbell E, Liu WM, Mei R: Robust estimators for expression analysis. / Bioinformatics 2002,18(12):1585-592. CrossRef
108. Wise RP, Caldo RA, Hong L, Shen L, Cannon EK, Dickerson JA: BarleyBase/Plexdb - a unified expression profiling database for plants and plant pathogens. In / Methods in Molecular Biology. / Volume 406. Totowa, NJ, U.S.A.: Humana Press; 2007:347-63.
109. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F: A model based background adjustment for oligonucleotide expression data. / J Am Stat Assoc 2004, 99:909-17. CrossRef
110. Li C, Wong HW: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. / Proc Natl Acad Sci USA 2001, 98:31-6. CrossRef
111. Hubbell E, Liu W-M, Mei R: Robust estimators for expression analysis. / Bioinformatics 2002,18(12):1585-592. CrossRef
112. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. / Nucleic Acids Res 2004, 32:D138-41. CrossRef
113. Berardini TZ, Mundodi S, Resier R, Huala E, Garcia-Hernandez M, Zhang P, Mueller LM, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY: Functional annotation of the Arabidopsis genome using controlled vocabularies. / Plant Physiol 2004,135(2):1-1. CrossRef
114. Gene Ontology Consortium T: Gene ontology: tool for the unification of biology. / Nature Genet 2000, 25:25-9. CrossRef
115. Fisher R: A preliminary linkage test with Agouti and undulated mice; the fifth linkage-group. / Heredity 1949, 3:229-41. CrossRef
116. Bonferroni CE: Ill calcolo delle assicurazioni su gruppi di teste. / Studi in Onore del Professore Salvatore Ortu Carboni 1935, 13-0.
117. Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. / Genome Res 2008,18(11):1851-858. CrossRef - 作者单位：Yung-Tsi Bolon (1)
Bindu Joseph (2)
Steven B Cannon (3)
Michelle A Graham (3)
Brian W Diers (4)
Andrew D Farmer (5)
Gregory D May (5)
Gary J Muehlbauer (6)
James E Specht (7)
Zheng Jin Tu (8)
Nathan Weeks (3)
Wayne W Xu (8)
Randy C Shoemaker (3)
Carroll P Vance (1) (6)
1. United States Department of Agriculture-Agricultural Research Service, Plant Research Unit, St Paul, MN, 55108, USA
2. Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
3. United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
4. Department of Crop Sciences, University of Illinois, 1101 West Peabody Dr, Urbana, IL, 61801, USA
5. National Center for Genome Resources, Santa Fe, NM, 87505, USA
6. Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
7. Department of Agronomy, University of Nebraska, Lincoln, NE, 68583, USA
8. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
文摘
Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix? Soy GeneChip and high-throughput Illumina? whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.