Jansen RC, Nap JP: Genetical genomics: the added value from segregation. Trends Genet. 2001, 17 (7): 388-391. 10.1016/S0168-9525(01)02310-1.
Article
PubMed
CAS
Google Scholar
West MA, Kim K, Kliebenstein DJ, van Leeuwen H, Michelmore RW, Doerge RW, St Clair DA: Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics. 2007, 175 (3): 1441-1450.
Article
PubMed
CAS
PubMed Central
Google Scholar
Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M: Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant J. 2008, 53 (1): 90-101. 10.1111/j.1365-313X.2007.03315.x.
Article
PubMed
CAS
Google Scholar
Keurentjes JJ, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJ, Vreugdenhil D, Koornneef M, Jansen RC: Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci USA. 2007, 104 (5): 1708-1713. 10.1073/pnas.0610429104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Drost DR, Benedict CI, Berg A, Novaes E, Novaes CR, Yu Q, Dervinis C, Maia JM, Yap J, Miles B, et al: Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc Natl Acad Sci USA. 2010, 107 (18): 8492-8497. 10.1073/pnas.0914709107.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jordan MC, Somers DJ, Banks TW: Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci. Plant Biotechnol J. 2007, 5 (3): 442-453. 10.1111/j.1467-7652.2007.00253.x.
Article
PubMed
CAS
Google Scholar
Kirst M, Basten CJ, Myburg AA, Zeng ZB, Sederoff RR: Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics. 2005, 169 (4): 2295-2303. 10.1534/genetics.104.039198.
Article
PubMed
CAS
PubMed Central
Google Scholar
DeCook R, Lall S, Nettleton D, Howell SH: Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics. 2006, 172 (2): 1155-1164.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fu J, Swertz MA, Keurentjes JJ, Jansen RC: MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nat Protoc. 2007, 2 (3): 685-694. 10.1038/nprot.2007.96.
Article
PubMed
CAS
Google Scholar
Keurentjes JJ: Genetical metabolomics: closing in on phenotypes. Curr Opin Plant Biol. 2009, 12 (2): 223-230. 10.1016/j.pbi.2008.12.003.
Article
PubMed
CAS
Google Scholar
Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, Coppieters W, Breyne P, Steenackers M, Georges M, Messens E, et al: Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J. 2006, 47 (2): 224-237. 10.1111/j.1365-313X.2006.02786.x.
Article
PubMed
CAS
Google Scholar
Acharjee A, Kloosterman B, de Vos RCH, Werij JS, Bachem CWB, Visser RGF, Maliepaard C: Data integration and network reconstruction with ~ omics data using Random Forest regression in potato. Analytica Chimica Acta. corrected proof.
Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, et al: Genetical genomics: spotlight on QTL hotspots. PLoS Genet. 2008, 4 (10): e1000232-10.1371/journal.pgen.1000232.
Article
PubMed
PubMed Central
Google Scholar
Terpstra IR, Snoek LB, Keurentjes JJ, Peeters AJ, van den Ackerveken G: Regulatory network identification by genetical genomics: signaling downstream of the Arabidopsis receptor-like kinase ERECTA. Plant Physiol. 2010, 154 (3): 1067-1078. 10.1104/pp.110.159996.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, et al: Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 2008, 4 (5): e1000070-10.1371/journal.pgen.1000070.
Article
PubMed
PubMed Central
Google Scholar
Kliebenstein DJ, West MA, van Leeuwen H, Loudet O, Doerge RW, St Clair DA: Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics. 2006, 7: 308-10.1186/1471-2105-7-308.
Article
PubMed
PubMed Central
Google Scholar
Druka A, Druka I, Centeno AG, Li H, Sun Z, Thomas WT, Bonar N, Steffenson BJ, Ullrich SE, Kleinhofs A, et al: Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genet. 2008, 9: 73-
Article
PubMed
PubMed Central
Google Scholar
Kliebenstein D: Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. Annu Rev Plant Biol. 2009, 60: 93-114. 10.1146/annurev.arplant.043008.092114.
Article
PubMed
CAS
Google Scholar
Gerrits A, Li Y, Tesson BM, Bystrykh LV, Weersing E, Ausema A, Dontje B, Wang X, Breitling R, Jansen RC, et al: Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genet. 2009, 5 (10): e1000692-10.1371/journal.pgen.1000692.
Article
PubMed
PubMed Central
Google Scholar
Potokina E, Druka A, Luo Z, Moscou M, Wise R, Waugh R, Kearsey M: Tissue-dependent limited pleiotropy affects gene expression in barley. Plant J. 2008, 56 (2): 287-296. 10.1111/j.1365-313X.2008.03601.x.
Article
PubMed
CAS
Google Scholar
Sergeeva LI, Vonk J, Keurentjes JJ, van der Plas LH, Koornneef M, Vreugdenhil D: Histochemical analysis reveals organ-specific quantitative trait loci for enzyme activities in Arabidopsis. Plant Physiol. 2004, 134 (1): 237-245. 10.1104/pp.103.027615.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, de Pamphilis CW, Becker A, Theissen G, Ma H: Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evol Dev. 2006, 8 (1): 30-45. 10.1111/j.1525-142X.2006.05073.x.
Article
PubMed
CAS
Google Scholar
Lynch M, Force A: The probability of duplicate gene preservation by subfunctionalization. Genetics. 2000, 154 (1): 459-473.
PubMed
CAS
PubMed Central
Google Scholar
Li L, Paulo MJ, Strahwald J, Lubeck J, Hofferbert HR, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, et al: Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet. 2008, 116 (8): 1167-1181. 10.1007/s00122-008-0746-y.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, et al: Genome sequence and analysis of the tuber crop potato. Nature. 2011, 475 (7355): 189-195. 10.1038/nature10158.
Article
PubMed
CAS
Google Scholar
Keiner R, Kaiser H, Nakajima K, Hashimoto T, Drager B: Molecular cloning, expression and characterization of tropinone reductase II, an enzyme of the SDR family in Solanum tuberosum (L.). Plant Mol Biol. 2002, 48 (3): 299-308. 10.1023/A:1013315110746.
Article
PubMed
CAS
Google Scholar
Wang P, Dawson JA, Keller MP, Yandell BS, Thornberry NA, Zhang BB, Wang IM, Schadt EE, Attie AD, Kendziorski C: A model selection approach for expression quantitative trait loci (eQTL) mapping. Genetics. 2011, 187 (2): 611-621. 10.1534/genetics.110.122796.
Article
PubMed
CAS
PubMed Central
Google Scholar
Grieve IC, Dickens NJ, Pravenec M, Kren V, Hubner N, Cook SA, Aitman TJ, Petretto E, Mangion J: Genome-wide co-expression analysis in multiple tissues. PLoS One. 2008, 3 (12): e4033-10.1371/journal.pone.0004033.
Article
PubMed
PubMed Central
Google Scholar
Hughes KA, Ayroles JF, Reedy MM, Drnevich JM, Rowe KC, Ruedi EA, Caceres CE, Paige KN: Segregating variation in the transcriptome: cis regulation and additivity of effects. Genetics. 2006, 173 (3): 1347-1355. 10.1534/genetics.105.051474.
Article
PubMed
CAS
PubMed Central
Google Scholar
Brem RB, Kruglyak L: The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci USA. 2005, 102 (5): 1572-1577. 10.1073/pnas.0408709102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Petretto E, Mangion J, Dickens NJ, Cook SA, Kumaran MK, Lu H, Fischer J, Maatz H, Kren V, Pravenec M, et al: Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet. 2006, 2 (10): e172-10.1371/journal.pgen.0020172.
Article
PubMed
PubMed Central
Google Scholar
Celis-Gamboa C, Struik PC, Jacobsen E, Visser RGF: Temporal dynamics of tuber formation and related processes in a crossing population of potato (Solanum tuberosum). Ann Appl Biol. 2003, 143 (2): 175-186. 10.1111/j.1744-7348.2003.tb00284.x.
Article
Google Scholar
Edwards EJ, Saint RE, Cobb AH: Is there a link between greening and light-enhanced glycoalkaloid accumulation in potato (Solanum tuberosumL) tubers?. J Sci Food Agric. 1998, 76 (3): 327-333. 10.1002/(SICI)1097-0010(199803)76:3<327::AID-JSFA934>3.0.CO;2-G.
Article
CAS
Google Scholar
Griffiths DW, Dale MFB, Bain H: The effect of cultivar, maturity and storage on photo-induced changes in the total glycoalkaloid and chlorophyll contents of potato (Solanum tuberosum). Plant Science. 1994, 98 (1): 103-109. 10.1016/0168-9452(94)90153-8.
Article
CAS
Google Scholar
Percival GC: The influence of light upon glycoalkaloid and chlorophyll accumulation in potato tubers (Solanum tuberosum L.). Plant Science. 1999, 145 (2): 99-107. 10.1016/S0168-9452(99)00081-3.
Article
CAS
Google Scholar
McClung CR: A modern circadian clock in the common angiosperm ancestor of monocots and eudicots. BMC Biol. 2010, 8: 55-10.1186/1741-7007-8-55.
Article
PubMed
PubMed Central
Google Scholar
Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carre IA, Coupland G: The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell. 1998, 93 (7): 1219-1229. 10.1016/S0092-8674(00)81465-8.
Article
PubMed
CAS
Google Scholar
Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, Sakakibara H: PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell. 2010, 22 (3): 594-605. 10.1105/tpc.109.072892.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nakamichi N, Kita M, Ito S, Yamashino T, Mizuno T: PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Plant Cell Physiol. 2005, 46 (5): 686-698. 10.1093/pcp/pci086.
Article
PubMed
CAS
Google Scholar
Imaizumi T: Arabidopsis circadian clock and photoperiodism: time to think about location. Curr Opin Plant Biol. 2010, 13 (1): 83-89. 10.1016/j.pbi.2009.09.007.
Article
PubMed
CAS
PubMed Central
Google Scholar
Martinez-Garcia JF, Virgos-Soler A, Prat S: Control of photoperiod-regulated tuberization in potato by the Arabidopsis flowering-time gene CONSTANS. Proc Natl Acad Sci USA. 2002, 99 (23): 15211-15216. 10.1073/pnas.222390599.
Article
PubMed
CAS
PubMed Central
Google Scholar
Navarro C, Abelenda JA, Cruz-Oro E, Cuellar CA, Tamaki S, Silva J, Shimamoto K, Prat S: Control of flowering and storage organ formation in potato by FLOWERING LOCUS T. Nature. 2011, 478 (7367): 119-122. 10.1038/nature10431.
Article
PubMed
CAS
Google Scholar
Wang ZY, Tobin EM: Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell. 1998, 93 (7): 1207-1217. 10.1016/S0092-8674(00)81464-6.
Article
PubMed
CAS
Google Scholar
Sawa M, Nusinow DA, Kay SA, Imaizumi T: FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science. 2007, 318 (5848): 261-265. 10.1126/science.1146994.
Article
PubMed
CAS
PubMed Central
Google Scholar
Simko I, Haynes KG, Jones RW: Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics. 2006, 173 (4): 2237-2245. 10.1534/genetics.106.060905.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, Sonnewald S, Sonnewald U, Bryan GJ, Prat S, et al: Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct Integr Genomics. 2008, 8 (4): 329-340. 10.1007/s10142-008-0083-x.
Article
PubMed
CAS
Google Scholar
Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, et al: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001, 19 (4): 342-347. 10.1038/86730.
Article
PubMed
CAS
Google Scholar
Turro E, Su SY, Goncalves A, Coin LJ, Richardson S, Lewin A: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 2011, 12 (2): R13-10.1186/gb-2011-12-2-r13.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bachem CW, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RG: Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 1996, 9 (5): 745-753. 10.1046/j.1365-313X.1996.9050745.x.
Article
PubMed
CAS
Google Scholar
Van Ooijen JW: JoinMap® 4, Software for the Calculation of Genetic Linkage Maps in Experimental Populations. Wageningen: Kyazma B.V.2006.
Google Scholar
Anithakumari AM, Tang J, van Eck HJ, Visser RG, Leunissen JA, Vosman B, van der Linden CG: A pipeline for high throughput detection and mapping of SNPs from EST databases. Mol Breed. 2010, 26 (1): 65-75. 10.1007/s11032-009-9377-5.
Article
PubMed
CAS
PubMed Central
Google Scholar
Broman KW, Wu H, Sen S, Churchill GA: R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003, 19 (7): 889-890. 10.1093/bioinformatics/btg112.
Article
PubMed
CAS
Google Scholar
Li J, Ji L: Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity. 2005, 95 (3): 221-227. 10.1038/sj.hdy.6800717.
Article
PubMed
CAS
Google Scholar