Whole‑genome QTL analysis for MAGIC

Theoretical and Applied Genetics

Volumn 127, Issue 8, 2014, Pages 1753-1770

  Verbyla, Arūnas P ^a,b   George, Andrew W ^a   Cavanagh, Colin R ^a   Verbyla, Klara L ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; MAMMALS;

COMPLEX TRAITS; FALSE POSITIVE; GENETIC DISSECTION; METHOD OF ANALYSIS; PLANT SPECIES; QUANTITATIVE TRAIT LOCUS; SIMULATION STUDIES; WHOLE-GENOME APPROACHES;

HIDDEN MARKOV MODELS;

MUS; TRITICUM AESTIVUM;

ANIMAL; CHROMOSOME MAP; COMPUTER SIMULATION; CROSS BREEDING; GENE LOCUS; GENETIC LINKAGE; GENETICS; MOUSE; PLANT CHROMOSOME; PLANT GENOME; PROBABILITY; PROCEDURES; QUANTITATIVE TRAIT LOCUS; WHEAT;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; COMPUTER SIMULATION; CROSSES, GENETIC; GENETIC LINKAGE; GENETIC LOCI; GENOME, PLANT; MARKOV CHAINS; MICE; PROBABILITY; QUANTITATIVE TRAIT LOCI; TRITICUM;

EID: 84925884751     PISSN: 00405752     EISSN: 14322242     Source Type: Journal    
DOI: 10.1007/s00122-014-2337-4     Document Type: Article

References (45)

1. Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoa E, Leung H (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6: 11
2. Broman K (2005) The genomes of recombinant inbred lines. Genetics 169: 1133-1146
3. Broman KW (2006) Use of hidden Markov models for QTL mapping. Technical report. John Hopkins University, Department of Biostatistics, working paper 125
4. Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses. J R Stat Soc Ser B 64: 641-656
5. Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889-890
6. Broman KW, Wu H, Churchill G, Sen S, Yandell B, et al (2012) qtl: Tools for analyzing QTL experiments. http://CRAN. Rprogram. org/package=qtl R package version 1. 23-16
7. Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2011) Mixed models for S language environments: ASReml-R reference manual. Technical report. Queensland Department of Primary Industries, http://www.vsni. co. uk/software/asreml/
8. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11: 215-221
9. Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci 110: 8057-8062. doi: 10. 1073/pnas. 1217133110
10. Cox DR, Hinkley DV (1974) Theoretical statistics. Chapman and Hall, London
11. Cullis BR, Smith AB, Coombes NE (2006) On the design of early generation variety trials with correlated data. J Agric Biol Environ Stat 11: 381-393
12. Gilmour AR, Cullis BR, Verbyla AP (1997) Accounting for natural and extraneous variation in the analysis of field experiments. J Agric Biol Environ Stat 2: 269-293
13. Haldane JBS, Waddington CH (1931) Inbreeding and linkage. Genetics 16: 357-374
14. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324
15. Huang BE, George AW (2011) R/mpmap: A computational platform for the genetic analysis of multi-parent recombinant inbred lines. Bioinformatics 27: 727-729
16. Huang BE, George AW, Forrest KL, Kilian A, Hayden M, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10: 826-839
17. Jansen RC (1994) Controlling the Type I and Type II errors in mapping quantitative trait loci. Genetics 138: 871-881
18. Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216
19. Keller M, Karutz C, Schmid JE, Stamp P, Winzeler M, Keller B, Messmer MM (1999) Quantitative trait loci for lodging resistance in a segregating wheat x spelt population. Theor Appl Genet 98: 1171-1182
20. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5 (e1000): 551
21. Malosetti M, van Eewijk FA, Boer MP, Casas MAM, Elia M, Moralejo M, Bhat PR, Ramsey L, Molina-Cano JL (2011) Gene and QTL detection in a three-way barley cross under selection ny a mixed model with kinship information using SNPs. Theor Appl Genet 122: 1605-1616
22. Martinez O, Curnow RN (1992) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85: 480-488
23. Marza F, Bai GH, Carver BF, Zhou WC (2006) Quantitative trait loci for yield and related traits in the wheat population Ning7840 x Clark. Theor Appl Genet 112: 688-698
24. McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, Cloutier S, McCallum BD (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross rl4452 x ‘ac domain’. Genome 48: 870-883
25. Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci USA 97: 12, 649-12, 654
26. Oakey H, Verbyla A, Pitchford W, Cullis B, Kuchel H (2006) Joint modelling of additive and non-additive genetic line effects in single field trials. Theor Appl Genet 113: 809-819
27. Piessens R, de Doncker-Kapenga E, Uberhuber CW, Kahaner DK (1983) QUADPACK: a subroutine package for automatic integration. Springer, Berlin
28. R Development Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project. org, ISBN 3-900051-07-0
29. Rakshit S, Rakshit A, Patil JV (2012) Multiparent intercross populations in analysis of quantitative traits. J Genet 91: 111-117
30. Smith A, Cullis B, Thompson R (2005) The analysis of crop cultivar breeding and evaluation trials: an overview of current mixed model approaches. J Agric Sci (Cambridge) 143: 449-462
31. Smith AB, Lim P, Cullis BR (2006) The design and analysis of multi-phase quality trait experiments. J Agric Sci (Cambridge) 144: 393-409
32. Stram DO, Lee JW (1994) Variance components testing in the longitudinal mixed effects model. Biometrics 50: 1171-1177
33. Taylor JD, Diffey S, Verbyla AP, Cullis BR (2011) wgaim: Whole genome average interval mapping for QTL detection using mixed models. http://CRAN. R-program. org/package=wgaim R package version 1.1
34. Threadgill DW, Hunter KW, Williams RW (2002) Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm Genome 13: 175-178
35. Trebbi D, Maccaferri M, Giuliani S, Sorensen A, Sanquineti MC, Massi A, Tuberosa R (2008) Development of a multi-parental (four-way cross) mapping population for multi-allelic QTL analysis in durum wheat. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L (eds) The 11th International Wheat Genetics Symposium proceedings. University of Sydney
36. Trow A (1913) Forms of reproduction: primary and secondary. J Genet 2: 313-324
37. Valdar W, Flint J, Mott R (2006a) Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172: 1783-1797
38. Valdar W, Solberg LC, Gauguier D, Burnett S, Klenerman P, Cookson WO, Taylor MS, Rawlins JNP, Mott R, Flint J (2006b) Genomewide genetic association of complex traits in heterogeneous stock mice. Nat Genet 38: 879-887
39. Verbyla AP (1990) A conditional derivation of residual maximum likelihood. Aust J Stat 32: 227-230
40. Verbyla AP, Cullis BR (2012) Multivariate whole genome average interval mapping: QTL analysis for multiple traits and/or environments. Theor Appl Genet 125: 933-953
41. Verbyla AP, Cullis BR, Thompson R (2007) The analysis of QTL by simultaneous use of the full linkage map. Theor Appl Genet 116: 95-111
42. Verbyla AP, Taylor JD, Verbyla KL (2012) RWGAIM: An efficient high dimensional random whole genome average (QTL) interval mapping approach. Genet Res 94: 291-306
43. Verma V, Worland AJ, Sayers EJ, Fish L, Caligari PDS, Snape JW (2005) Identification and characterization of quantitative trait loci related to lodging resistance and associated traits in bread wheat. Plant Breed 124: 234-241
44. Xu S (1996) Mapping quantitative trait loci using four-way crosses. Genet Res 68: 175-181
45. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468