eQTL networks reveal complex genetic architecture in the immature soybean seed

Plant Genome

Volumn 7, Issue 1, 2014, Pages

  Bolon, Yung Tsi ^a   Hyten, David L ^b   Orf, James H ^a   Vance, Carroll P ^a   Muehlbauer, Gary J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b PIONEER HI BRED INTERNATIONAL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84897458492     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2013.08.0027     Document Type: Article

References (86)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 494-498.
2. Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29. doi: 10. 1038/75556.
3. Barker, G. C., T. R. Larson, I. A. Graham, J. R. Lynn, and G. J. King. 2007. Novel insights into seed fatty acid synthesis and modification pathways from genetic diversity and quantitative trait loci analysis of the Brassica C genome. Plant Physiol. 144: 1827-1842. doi: 10. 1104/pp. 107. 096172.
4. Benjamini, Y., and D. Yekutieli. 2005. False discovery rate-adjusted multiple confidence intervals for selected parameters. J. Am. Stat. Assoc. 100: 71-81. doi: 10. 1198/016214504000001907.
5. Bolon, Y. T., B. Joseph, S. B. Cannon, M. A. Graham, B. W. Diers, A. D. Farmer, G. D. May, G. J. Muehlbauer, J. E. Specht, Z. J. Tu, N. Weeks, W. W. Xu, R. C. Shoemaker, and C. P. Vance. 2010. Complementary genetic and genomic approaches help characterize the Linkage Group I seed protein QTL in soybean. BMC Plant Biol. 10: 41-66. doi: 10. 1186/1471-2229-10-41.
6. Bonaventure, G., and J. B. Ohlrogge. 2002. Differential regulation of mRNA levels of acyl carrier protein isoforms in Arabidopsis. Plant Physiol. 128: 223-235. doi: 10. 1104/pp. 010397.
7. Brem, R. B., and L. Kruglyak. 2005. The landscape of genetic complexity across 5700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102: 1572-1577. doi: 10. 1073/pnas. 0408709102.
8. Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755. doi: 10. 1126/science. 1069516.
9. Brim, C. A., and J. W. Burton. 1979. Recurrent selection in soybeans. II. Selection for increased percent protein in seeds. Crop Sci. 19: 494-498. doi: 10. 2135/cropsci1979. 0011183X001900040016x.
10. Brummer, E. C., G. L. Graef, J. H. Orf, J. R. Wilcox, and R. C. Shoemaker. 1997. Mapping QTL for seed protein and oil content in eight soybean populations. Crop Sci. 37: 370-378. doi: 10. 2135/cropsci1997. 0011183X00 3700020011x.
11. Bystrykh, L., E. Weersing, B. Dontje, S. Sutton, M. T. Pletcher, T. Wiltshire, A. I. Su, E. Vellenga, J. Wang, K. F. Manly, L. Lu, E. J. Chesler, R. Alberts, R. C. Jansen, R. W. Williams, M. P. Cooke, and G. de Haan. 2005. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat. Genet. 37: 225-232. doi: 10. 1038/ng1497.
12. Chen, X., W. Guo, B. Liu, Y. Zhang, X. Song, Y. Cheng, L. Zhang, and T. Zhang. 2012. Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics. PLoS ONE 7: e30056. doi: 10. 1371/journal. pone. 0030056.
13. Chen, X., C. A. Hackett, R. E. Niks, P. E. Hedley, C. Booth, A. Druka, T. C. Marcel, A. Vels, M. Bayer, I. Milne, J. Morris, L. Ramsay, D. Marshall, L. Cardle, and R. Waugh. 2010. An eQTL analysis of partial resistance to Puccinia hordei. in barley. PLoS ONE 5: e8598. doi: 10. 1371/journal. pone. 0008598.
14. Chesler, E. J., L. Lu, S. Shou, Y. Qu, J. Gu, J. Wang, H. C. Hsu, J. D. Mountz, N. E. Baldwin, M. A. Langston, D. W. Threadgill, K. F. Manly, and R. W. Williams. 2005. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet. 37: 233-242. doi: 10. 1038/ng1518.
15. Churchill, G. A., and R. W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
16. Clough, S. J., J. H. Tuteja, M. Li, L. F. Marek, R. C. Shoemaker, and L. O. Vodkin. 2004. Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus. Genome 47: 819-831. doi: 10. 1139/g04-049.
17. Cubillos, F. A., J. Yansouni, H. Khalili, S. Balzergue, S. Elftieh, M. L. Martin-Magniette, Y. Serrand, L. Lepiniec, S. Baud, B. Dubreucq, J. P. Renou, C. Camilleri, and O. Loudet. 2012. Expression variation in connected recombinant populations of Arabidopsis thaliana. highlights distinct transcriptome architectures. BMC Genomics 13: 117. doi: 10. 1186/1471-2164-13-117.
18. Dash, S., J. Van Hemert, L. Hong, R. P. Wise, and J. A. Dickerson. 2012. PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Res. 40: D1194-D1201. doi: 10. 1093/nar/gkr938.
19. Delourme, R., C. Falentin, V. Huteau, V. Clouet, R. Horvais, B. Gandon, S. Specel, L. Hanneton, J. E. Dheu, M. Deschamps, E. Margale, P. Vincourt, and M. Renard. 2006. Genetic control of oil content in oilseed rape (Brassica napus. L.). Theor. Appl. Genet. 113: 1331-1345. doi: 10. 1007/s00122-006-0386-z.
20. Diers, B. W., P. Keim, W. R. Fehr, and R. C. Shoemaker. 1992. RFLP analysis of soybean seed protein and oil content. Theor. Appl. Genet. 83: 608-612. doi: 10. 1007/BF00226905.
21. Drost, D. R., C. I. Benedict, A. Berg, E. Novaes, C. R. Novaes, Q. Yu, C. Dervinis, J. M. Maia, J. Yap, B. Miles, and M. Kirst. 2010. Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc. Natl. Acad. Sci. USA 107: 8492-8497. doi: 10. 1073/pnas. 0914709107.
22. Druka, A., E. Potokina, Z. Luo, N. Bonar, I. Druka, L. Zhang, D. F. Marshall, B. J. Steffenson, T. J. Close, R. P. Wise, A. Kleinhofs, R. W. Williams, M. J. Kearsey, and R. Waugh. 2008. Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis. f. sp. tritici. in barley. Theor. Appl. Genet. 117: 261-272. doi: 10. 1007/s00122-008-0771-x.
23. Fasoula, V. A., D. K. Harris, and H. R. Boerma. 2004. Validation and designation of quantitative trait loci for seed protein, seed oil, and seed weight from two soybean populations. Crop Sci. 44: 1218-1225. doi: 10. 2135/cropsci2004. 1218.
24. Fisher, R. A. 1925. Statistical methods for research workers. Oliver and Boyd, Edinburgh, UK.
25. Footitt, S., S. P. Slocombe, V. Larner, S. Kurup, Y. Wu, T. Larson, I. Graham, A. Baker, and M. Holdsworth. 2002. Control of germination and lipid mobilization by COMATOSE, the Arabidopsis homologue of human ALDP. EMBO J. 21: 2912-2922. doi: 10. 1093/emboj/cdf300.
26. Grupe, A., S. Germer, J. Usuka, D. Aud, J. K. Belknap, R. F. Klein, M. K. Ahluwalia, R. Higuchi, and G. Peltz. 2001. In silico mapping of complex disease-related traits in mice. Science 292: 1915-1918. doi: 10. 1126/science. 1058889.
27. Hammond, J. P., S. Mayes, H. C. Bowen, N. S. Graham, R. M. Hayden, C. G. Love, W. P. Spracklen, J. Wang, S. J. Welham, P. J. White, G. J. King, and M. R. Broadley. 2011. Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa. Plant Physiol. 156: 1230-1241. doi: 10. 1104/pp. 111. 175612.
28. Hobbs, D. H., J. E. Flintham, and M. J. Hills. 2004. Genetic control of storage oil synthesis in seeds of Arabidopsis. Plant Physiol. 136: 3341-3349. doi: 10. 1104/pp. 104. 049486.
29. Huang, A. H. 1996. Oleosins and oil bodies in seeds and other organs. Plant Physiol. 110: 1055-1061. doi: 10. 1104/pp. 110. 4. 1055.
30. Hyten, D. L., S. B. Cannon, Q. Song, N. Weeks, E. W. Fickus, R. C. Shoemaker, J. E. Specht, A. D. Farmer, G. D. May, and P. B. Cregan. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38. doi: 10. 1186/1471-2164-11-38.
31. Hyten, D. L., V. R. Pantalone, C. E. Sams, A. M. Saxton, D. Landau-Ellis, T. R. Stefaniak, and M. E. Schmidt. 2004. Seed quality QTL in a prominent soybean population. Theor. Appl. Genet. 109: 552-561. doi: 10. 1007/s00122-004-1661-5.
32. Jansen, R. C., and J. P. Nap. 2001. Genetical genomics: The added value from segregation. Trends Genet. 17: 388-391. doi: 10. 1016/S0168-9525(01)02310-1.
33. Kabelka, E. A., B. W. Diers, W. R. Fehr, A. R. LeRoy, I. C. Baianu, T. You, D. J. Neece, and R. L. Nelson. 2004. Putative alleles for increased yield from soybean plant introductions. Crop Sci. 44: 784-791. doi: 10. 2135/cropsci2004. 0784.
34. Keurentjes, J. J., J. Fu, I. R. Terpstra, J. M. Garcia, G. van den Ackerveken, L. B. Snoek, A. J. Peeters, D. Vreugdenhil, M. Koornneef, and R. C. Jansen. 2007. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc. Natl. Acad. Sci. U. S. A. 104: 1708-1713. doi: 10. 1073/pnas. 0610429104.
35. Kirst, M., C. J. Basten, A. A. Myburg, Z. B. Zeng, and R. R. Sederoff. 2005. Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics 169: 2295-2303. doi: 10. 1534/genetics. 104. 039198.
36. Kliebenstein, D. J., M. A. West, H. van Leeuwen, K. Kim, R. W. Doerge, R. W. Michelmore, and D. A. St. Clair. 2006. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 172: 1179-1189. doi: 10. 1534/genetics. 105. 049353.
37. Lark, K. G., K. Chase, F. Adler, L. M. Mansur, and J. H. Orf. 1995. Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc. Natl. Acad. Sci. USA 92: 4656-4660. doi: 10. 1073/pnas. 92. 10. 4656.
38. Lark, K. G., J. H. Orf, and L. M. Mansur. 1994. Epistatic expression of quantitative trait loci (QTL) in soybean [Glycine max. (L.) Merr.] determined by QTL association with RFLP alleles. Theor. Appl. Genet. 88: 486-489.
39. Leach, L. J., Z. Zhang, C. Lu, M. J. Kearsey, and Z. Luo. 2007. The role of cisregulatory motifs and genetical control of expression in the divergence of yeast duplicate genes. Mol. Biol. Evol. 24: 2556-2565. doi: 10. 1093/molbev/msm188.
40. Lee, S. H., M. A. Bailey, M. A. R. Mian, T. E. Carter, Jr., E. R. Shipe, D. A. Ashley, W. A. Parrot, R. S. Hussey, and H. R. Boerma. 1996. RFLP loci associated with soybean seed protein and oil content across populations and locations. Theor. Appl. Genet. 93: 649-657. doi: 10. 1007/BF00224058.
41. Li, L., K. Petsch, R. Shimizu, S. Liu, W. W. Xu, K. Ying, J. Yu, M. J. Scanlon, P. S. Schnable, M. C. Timmermans, N. M. Springer, and G. J. Muehlbauer. 2013. Mendelian and non-Mendelian regulation of gene expression in maize. PLoS Genet. 9: e1003202. doi: 10. 1371/journal. pgen. 1003202.
42. Lin, J. Y., R. M. Stupar, C. Hans, D. L. Hyten, and S. A. Jackson. 2011. Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell 22: 2545-2561.
43. Liu, P. P., N. Koizuka, R. C. Martin, and H. Nonogaki. 2005. The BME3. (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. Plant J. 44: 960-971. doi: 10. 1111/j. 1365-313X. 2005. 02588. x.
44. Liu, S., K. Ying, C. T. Yeh, J. Yang, R. Swanson-Wagner, W. Wu, T. Richmond, D. J. Gerhardt, J. Lai, N. Springer, D. Nettleton, J. A. Jeddeloh, and P. S. Schnable. 2012. Changes in genome content generated via segregation of non-allelic homologs. Plant J. 72: 390-399. doi: 10. 1111/j. 1365-313X. 2012. 05087. x.
45. Mansur, L. M., K. G. Lark, H. Kross, and A. Oliveira. 1993. Interval mapping of quantitative trait loci for reproductive, morphological, and seed traits of soybean (Glycine max. L.). Theor. Appl. Genet. 86: 907-913. doi: 10. 1007/BF00211040.
46. Mehrabian, M., H. Allayee, J. Stockton, P. Y. Lum, T. A. Drake, L. W. Castellani, M. Suh, C. Armour, S. Edwards, J. Lamb, A. J. Lusis, and E. E. Schadt. 2005. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat. Genet. 37: 1224-1233. doi: 10. 1038/ng1619.
47. Morley, M., C. M. Molony, T. M. Weber, J. L. Devlin, K. G. Ewens, R. S. Spielman, and V. G. Cheung. 2004. Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747. doi: 10. 1038/nature02797.
48. Moscou, M. J., N. Lauter, B. Steffenson, and R. P. Wise. 2011. Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genet. 7: e1002208. doi: 10. 1371/journal. pgen. 1002208.
49. Mou, Z., Y. He, Y. Dai, X. Liu, J. Li. 2000. Deficiency in fatty acid synthase leads to premature cell death and dramatic alterations in plant morphology. Plant Cell. 12(3): 494-498.
50. Nyathi, Y., C. De Marcos Lousa, C. W. van Roermund, R. J. Wanders, B. Johnson, S. A. Baldwin, F. L. Theodoulou, and A. Baker. 2010. The Arabidopsis peroxisomal ABC transporter, Comatose, complements the Saccharomyces cerevisiae pxa1 pxa2Δ mutant for metabolism of longchain fatty acids and exhibits fatty acyl-CoA-stimulated ATPase activity. J. Biol. Chem. 285: 29892-29902. doi: 10. 1074/jbc. M110. 151225.
51. Orf, J. H., K. Chase, T. Jarvik, L. M. Mansur, P. B. Cregan, F. R. Adler, and K. G. Lark. 1999. Genetics of soybean agronomic traits I. Comparison of three related recombinant inbred populations. Crop Sci. 39: 1642-1651. doi: 10. 2135/cropsci1999. 3961642x.
52. Panthee, D. R., V. R. Pantalone, D. R. West, A. M. Saxton, and C. E. Sams. 2005. Quantitative trait loci for seed protein and oil concentration and seed size in soybean. Crop Sci. 45: 2015-2022. doi: 10. 2135/cropsci2004. 0720.
53. Parthibane, V., R. Iyappan, A. Vijayakumar, V. Venkateshwari, and R. Rajasekharan. 2012b. Serine/Threonine/Tyrosine protein kinase phosphorylates oleosin, a regulator of lipid metabolic functions. Plant Physiol. 159: 95-104. doi: 10. 1104/pp. 112. 197194.
54. Parthibane, V., S. Rajakumari, V. Venkateshwari, R. Iyappan, and R. Rajasekharan. 2012a. Oleosin is bifunctional enzyme that has both monoacylglycerol acyltransferase and phospholipase activities. J. Biol. Chem. 287: 1946-1954. doi: 10. 1074/jbc. M111. 309955.
55. Potokina, E., A. Druka, Z. Luo, R. Wise, R. Waugh, and M. Kearsey. 2008. Gene expression quantitative trait locus analysis of 16, 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant J. 53: 90-101. doi: 10. 1111/j. 1365-313X. 2007. 03315. x.
56. Quigley, D. A., M. D. To, J. Perez-Losada, F. G. Pelorosso, J. H. Mao, H. Nagase, D. G. Ginzinger, and A. Balmain. 2009. Genetic architecture of mouse skin inflammation and tumour susceptibility. Nature 458: 505-508. doi: 10. 1038/nature07683.
57. Rockman, M. V., and L. Kruglyak. 2006. Genetics of global gene expression. Nat. Rev. Genet. 7: 862-872. doi: 10. 1038/nrg1964.
58. Ruuska, S. A., T. Girke, C. Benning, and J. B. Ohlrogge. 2002. Contrapuntal networks of gene expression during Arabidopsis seed filling. Plant Cell 14: 1191-1206. doi: 10. 1105/tpc. 000877.
59. Ruuska, S. A., J. Schwender, and J. B. Ohlrogge. 2004. The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes. Plant Physiol. 136: 2700-2709. doi: 10. 1104/pp. 104. 047977.
60. Schadt, E. E., S. A. Monks, T. A. Drake, A. J. Lusis, N. Che, V. Colinayo, T. G. Ruff, S. B. Milligan, J. R. Lamb, G. Cavet, P. S. Linsley, M. Mao, R. B. Stoughton, and S. H. Friend. 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302. doi: 10. 1038/nature01434.
61. Schmutz, J., S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. L. Hyten, Q. Song, J. J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. D. May, Y. Yu, T. Sakurai, T. Umezawa, M. K. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X. C. Zhang, K. Shinozaki, H. T. Nguyen, R. A. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R. C. Shoemaker, and S. A. Jackson. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183. doi: 10. 1038/nature08670.
62. Severin, A. J., G. A. Peiffer, W. W. Xu, D. L. Hyten, B. Bucciarelli, J. A. O'Rourke, Y. T. Bolon, D. Grant, A. D. Farmer, G. D. May, C. P. Vance, R. C. Shoemaker, and R. M. Stupar. 2010a. An integrative approach to genomic introgression mapping. Plant Physiol. 154: 3-12. doi: 10. 1104/pp. 110. 158949.
63. Severin, A. J., J. L. Woody, Y. T. Bolon, B. Joseph, B. W. Diers, A. D. Farmer, G. J. Muehlbauer, R. T. Nelson, D. Grant, J. E. Specht, M. A. Graham, S. B. Cannon, G. D. May, C. P. Vance, and R. C. Shoemaker. 2010b. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biol. 10: 160. doi: 10. 1186/1471-2229-10-160.
64. Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504. doi: 10. 1101/gr. 1239303.
65. Shoemaker, R. C., J. Schlueter, and J. J. Doyle. 2006. Paleopolyploidy and gene duplication in soybean and other legumes. Curr. Opin. Plant Biol. 9: 104-109. doi: 10. 1016/j. pbi. 2006. 01. 007.
66. Siloto, R. M., K. Findlay, A. Lopez-Villalobos, E. C. Yeung, C. L. Nykiforuk, and M. M. Moloney. 2006. The accumulation of oleosins determines the size of seed oilbodies in Arabidopsis. Plant Cell 18: 1961-1974. doi: 10. 1105/tpc. 106. 041269.
67. Sonderby, I. E., B. G. Hansen, N. Bjarnholt, C. Ticconi, B. A. Halkier, and D. J. Kliebenstein. 2007. A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates. PLoS ONE 2: e1322. doi: 10. 1371/journal. pone. 0001322.
68. Song, H., Z. Yin, M. Chao, L. Ning, D. Zhang, and D. Yu. 2013. Functional properties and expression quantitative trait loci for phosphate transporter GmPT1 in soybean. Plant Cell Environ. (In press) doi: 10. 1111/pce. 12170.
69. Stombaugh, S. K., J. H. Orf, H. G. Jung, K. Chase, K. G. Lark, and D. A. Somers. 2004. Quantitative trait loci associated with cell wall polysaccharides in soybean seed. Crop Sci. 44: 2101-2106. doi: 10. 2135/cropsci2004. 2101.
70. Storey, J. D., and R. Tibshirani. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100: 9440-9445. doi: 10. 1073/pnas. 1530509100.
71. Tajuddin, T., S. Watanabe, N. Yamanaka, and K. Harada. 2003. Analysis of quantitative trait loci for protein and lipid contents in soybean seeds using recombinant inbred lines. Breed. Sci. 53: 133-140. doi: 10. 1270/jsbbs. 53. 133.
72. Thimm, O., O. Blasing, Y. Gibon, A. Nagel, S. Meyer, P. Kruger, J. Selbig, L. A. Muller, S. Y. Rhee, and M. Stitt. 2004. MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939. doi: 10. 1111/j. 1365-313X. 2004. 02016. x.
73. Tuteja, J. H., S. J. Clough, W. C. Chan, and L. O. Vodkin. 2004. Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. Plant Cell 16: 819-835. doi: 10. 1105/tpc. 021352.
74. Tuteja, J. H., G. Zabala, K. Varala, M. Hudson, and L. O. Vodkin. 2009. Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in Glycine max. seed coats. Plant Cell 21: 3063-3077. doi: 10. 1105/tpc. 109. 069856.
75. Van Ooijen, J. W. 1999. LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83: 613-624. doi: 10. 1038/sj. hdy. 6886230.
76. Vuylsteke, M., F. van Eeuwijk, P. Van Hummelen, M. Kuiper, and M. Zabeau. 2005. Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171: 1267-1275. doi: 10. 1534/genetics. 105. 041509.
77. Wang, C.-S., and L. O. Vodkin. 1994. Extraction of RNA from tissues containing high levels of procyanidins that bind RNA. Plant Mol. Biol. Rep. 12: 132-145. doi: 10. 1007/BF02668374.
78. Wentzell, A. M., I. Boeye, Z. Zhang, and D. J. Kliebenstein. 2008. Genetic networks controlling structural outcome of glucosinolate activation across development. PLoS Genet. 4: e1000234. doi: 10. 1371/journal. pgen. 1000234.
79. Wentzell, A. M., H. C. Rowe, B. G. Hansen, C. Ticconi, B. A. Halkier, and D. J. Kliebenstein. 2007. Linking metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways. PLoS Genet. 3: 1687-1701. doi: 10. 1371/journal. pgen. 0030162.
80. West, M. A., K. Kim, D. J. Kliebenstein, H. van Leeuwen, R. W. Michelmore, R. W. Doerge, and D. A. St. Clair. 2007. Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175: 1441-1450. doi: 10. 1534/genetics. 106. 064972.
81. Wu, C., D. L. Delano, N. Mitro, S. V. Su, J. Janes, P. McClurg, S. Batalov, G. L. Welch, J. Zhang, A. P. Orth, J. R. Walker, R. J. Glynne, M. P. Cooke, J. S. Takahashi, K. Shimomura, A. Kohsaka, J. Bass, E. Saez, T. Wiltshire, and A. I. Su. 2008. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 4: e1000070. doi: 10. 1371/journal. pgen. 1000070.
82. Yin, Z., F. Meng, H. Song, X. Wang, M. Chao, G. Zhang, X. Xu, D. Deng, and D. Yu. 2011. GmFtsH9 expression correlates with in vivo Photosystem II function: Chlorophyll a fluorescence transient analysis and eQTL mapping in soybean. Planta 234: 815-827. doi: 10. 1007/s00425-011-1445-5.
83. Yin, Z., F. Meng, H. Song, X. Wang, X. Xu, and D. Yu. 2010. Expression quantitative trait loci analysis of two genes encoding rubisco activase in soybean. Plant Physiol. 152: 1625-1637. doi: 10. 1104/pp. 109. 148312.
84. Zeng, Z. B. 1994. Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
85. Zhao, J., J. Huang, F. Chen, F. Xu, X. Ni, H. Xu, Y. Wang, C. Jiang, H. Wang, A. Xu, R. Huang, D. Li, and J. Meng. 2012. Molecular mapping of Arabidopsis thaliana. lipid-related orthologous genes in Brassica napus. Theor. Appl. Genet. 124: 407-421. doi: 10. 1007/s00122-011-1716-3.
86. Zheng, Q., and X. J. Wang. 2008. GOEAST: A web-based software toolkit for gene ontology enrichment analysis. Nucleic Acids Res. 36: W358-W363. doi: 10. 1093/nar/gkn276.