Genetical genomics for evolutionary studies

Methods in Molecular Biology

Volumn 856, Issue , 2012, Pages 469-485

  Prins, Pjotr ^a   Smant, Geert ^a   Jansen, Ritsert C ^b  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

eQTL; Evolution; Genetical genomics; Genomics; Metabolomics; Network inference; NGS; QTL; R genes; R qtl; xQTL

Indexed keywords

ANIMAL; ARTICLE; GENETIC SELECTION; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; QUANTITATIVE TRAIT LOCUS;

ANIMALS; EVOLUTION, MOLECULAR; GENOMICS; HUMANS; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC;

EID: 84860208466     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-585-5_19     Document Type: Article

References (63)

1. Nandi S, Subudhi P K, Senadhira D et al. (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet. 255:1-8
2. Meaburn E, Butcher L M, Schalkwyk L C & Plomin R (2006) Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucleic Acids Res. 34:e27p
3. Kim S, Plagnol V, Hu T T et al. (2007) Recombination and linkage disequilibriumin Arabidopsis thaliana. Nat Genet. 39:1151-1155. http://www.ncbi.nlm.nih.gov/pubmed/17676040
4. Dixon A L, Liang L, Moffatt M F et al. (2007) A genome-wide association study of global gene expression. Nat Genet. 39:1202-1207
5. Jansen R C & Nap J P (2001) Genetical genomics: The added value from segregation. Trends Genet. 17:388-391
6. Gibson G & Weir B (2005) The quantitative genetics of transcription. Trends Genet. 21:616-623
7. Li Y, Alvarez O A, Gutteling E Wet al. (2006) Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2:e222p
8. Jansen R C, Tesson B M, Fu J, Yang Y & Mcintyre L M (2009) Defining gene and QTL networks. Curr Opin Plant Biol. 12:241-246
9. Brem R B & Kruglyak L (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci USA. 102:1572-1577
10. Fraser H B, Moses A M & Schadt E E (2010) Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci U S A. 107:2977-2982
11. Zou Y, Su Z, Yang J, Zeng Y & Gu X (2009) Uncovering genetic regulatory network divergence between duplicate genes using yeast eqtl landscape. J Exp Zool B Mol Dev Evol. 312:722-733
12. Li Y, Breitling R&Jansen R C (2008) Generalizing genetical genomics: getting added value from environmental perturbation. Trends Genet. 24:518-524. http://www.ncbi.nlm. nih.gov/pubmed/18774198
13. Kliebenstein D J, West M A, Van Leeuwen H et al. (2006) Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics. 7:308p
14. Gilad Y, Rifkin S A & Pritchard J K (2008) Revealing the architecture of gene regulation: The promise of eQTL studies. Trends Genet. 24:408-415
15. Alberts R, Terpstra P, Li Y et al. (2007) Sequence polymorphisms cause many false cis eqtls. PLoS One. 2:e622p
16. Franke L, Bakel H v, Fokkens L et al. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet. 78:1011-1025
17. Chen X, Hackett C A, Niks R E et al. (2010) An eqtl analysis of partial resistance to puccinia hordei in barley. PLoS One. 5:e8598p
18. Qin L, Kudla U, Roze E H et al. (2004) Plant degradation: A nematode expansin acting on plants.Nature. 427:30p.doi:10.1038/427030a
19. Saijo Y & Schulze-lefert P (2008) Manipulation of the eukaryotic transcriptional machinery by bacterial pathogens. Cell Host Microbe. 4:96-99
20. Chen L Q, Hou B H, Lalonde S et al. (2010) Sugar transporters for intercellular exchange and nutrition of pathogens. Nature. 468:527-532
21. Hewitson J P, Grainger J R & Maizels R M (2009) Helminth immunoregulation: The role of parasite secreted proteins in modulating host immunity. Mol Biochem Parasitol. 167:1-11
22. Bird P I, Trapani J A & Villadangos J A (2009) Endolysosomal proteases and their inhibitors in immunity. Nat Rev Immunol. 9:871-882. doi:10.1038/nri2671
23. BeVan M, Bancroft I, Bent E et al. (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature. 391:485-488. doi:10.1038/35140
24. Bishop J G, Dean A M & Mitchell-olds T (2000) Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci USA. 97:5322-5327
25. Dangl J L & Jones J D (2001) Plant pathogens and integrated defence responses to infection. Nature. 411:826-833. doi:10.1038/35081161
26. Flor H (1956) The complementary genic systems in flax and flax rust. *. AdVances in Genetics. 8:29-54. doi:10.1016/S0065-2660(08) 60498-8
27. Bakker E G, Toomajian C, Kreitman M & Bergelson J (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell. 18:1803-1818. doi:10.1105/tpc.106.042614
28. Mackey D, Belkhadir Y, Alonso J M, Ecker J R & Dangl J L (2003) Arabidopsis rin4 is a target of the type iii virulence effector avrrpt2 and modulates rps2-mediated resistance. Cell. 112:379-389
29. Richly E, Kurth J & Leister D (2002) Mode of amplification and reorganization of resistance genes during recent arabidopsis thaliana evolution. Mol Biol Evol. 19:76-84
30. Medzhitov R & Janeway C A J (1997) Innate immunity: impact on the adaptive immune response. Curr Opin Immunol. 9:4-9
31. Holub E B (2001) The arms race is ancient history in Arabidopsis, the wildflower. Nat Rev Genet. 2:516-527. doi:10.1038/35080508
32. Xiao S, Emerson B, Ratanasut K et al. (2004) Origin and maintenance of a broad-spectrum disease resistance locus in Arabidopsis. Mol Biol Evol. 21:1661-1672. doi:10.1093/molbev/msh165
33. Mondragon-Palomino M, Meyers B C, Michelmore R W & Gaut B S (2002) Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 12:1305-1315. doi:10.1101/gr.159402
34. Sun X, Cao Y & Wang S (2006) Point mutations with positive selection were a major force during the evolution of a receptor-kinase resistance gene family of rice. Plant Physiol. 140:998-1008. doi:10.1104/pp.105.073080
35. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556. http://www.ncbi.nlm.nih.gov/ pubmed/9367129
36. Kosiol, C., & Anisimova, M. (2012) Selection on the protein coding genome. In: Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business Media New York
37. Prins, P., Belhachemi, D.,Möller, S. & Smant, G. (2012) Scalable computing in evolutionary genomics. In: Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business Media New York
38. Altschul S F, Madden T L, Schaffer A A et al. (1997) Gapped blast and psi-blast: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402
39. Edgar R C (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. doi:10.1093/nar/gkh340
40. Suyama M, Torrents D & Bork P (2006) Pal2-nal: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:W609-W612. doi:10.1093/nar/gkl315
41. Goto N, Prins P, Nakao M et al. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 26:2617-2619. doi:10.1093/bioinformatics/btq475
42. Altschul S F, Madden T L, Schaffer A A et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402
43. Rhee S Y, Beavis W, Berardini T Z et al. (2003) The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31:224-228. http://www.ncbi.nlm.nih.gov/pubmed/12519987
44. Anisimova M, Nielsen R & Yang Z (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics. 164:1229-1236
45. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408:796-815
46. Michelmore R W & Meyers B C (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8:1113-1130. http://www.ncbi.nlm.nih.gov/pubmed/9847076
47. Salinas J & Sanchez-serrano J (2006) Arabidopsis protocols. Humana Pr Inc, Totowa, NJ 48.
48. Fu J & Jansen R C (2006) Optimal design and analysis of genetic studies on gene expression. Genetics. 172:1993-1999. doi:10.1534/genetics.105. 047001
49. Mortazavi A,Williams B A, Mccue K, Schaeffer L & Wold B (2008) Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods. 5:621-628. doi:10.1038/nmeth.1226
50. Eklund A C, Turner L R, Chen P et al. (2006) Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol. 24:1071-1073. doi:10.1038/nbt0906-1071
51. Hoen P A, Ariyurek Y, Thygesen H H et al. (2008) Deep sequencing-based expression analysis shows major adVances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 36: e141p. doi:10.1093/nar/gkn705
52. Keurentjes J J, Sulpice R, Gibon Y et al. (2008) Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana. Genome Biol. 9: R129p. doi:10.1186/gb-2008-9-8-r129
53. Fu J, Swertz M A, Keurentjes J J & Jansen R C (2007) Metanetwork: A computational protocol for the genetic study of metabolic networks. Nat Protoc. 2:685-694. doi:10.1038/nprot.2007.96
54. Fu J, Keurentjes J J, Bouwmeester H et al. (2009) System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet. 41:166-167. doi:10.1038/ng.308
55. Breitling R, Li Y, Tesson B M et al. (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genet. 4:e1000232p. doi:10.1371/journal.pgen.1000232
56. Development core team R (2010) R: A language and environment for statistical computing. http://www.R-project.org
57. Broman K & Sen (2009) A guide to QTL mapping with R/qtl. Springer Verlag, New York, NY
58. Arends D, Prins P, Jansen R C & Broman K W (2010) R/qtl: high-throughput multiple QTL mapping. Bioinformatics. 26:2990-2992. doi:10.1093/bioinformatics/btq565
59. Tierney L, Rossini A & Li N (2009) SNOW: A parallel computing framework for the R system. International Journal of Parallel Programming. 37:78-90
60. Arends D, Prins P, Broman K W & Jansen R C (2010) Tutorial -Multiple-QTL Mapping (MQM) Analysis. http://www.rqtl.org/tutorials/MQM-tour.pdf
61. Li Y, Tesson B M, Churchill G A & Jansen R C (2010) Critical reasoning on causal inference in genome-wide linkage and association studies. Trends Genet. 26:493-498. doi:10.1016/j.tig.2010.09.002
62. Wayne M L & Mcintyre L M (2002) Combining mapping and arraying: An approach to candidate gene identification. Proc Natl Acad Sci USA. 99:14903-14906. doi:10.1073/pnas.222549199
63. Westra HJ, Jansen RC, Fehrmann RS, te Meerman GJ, Van Heel D, Wijmenga C, Franke L. (2011)MixupMapper: correcting samplemixups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics. Aug 1;27(15):2104-11. Epub 2011 Jun 7. http://www.ncbi.nlm.nih.gov/pubmed/21653519