Multiparent intercross populations in analysis of quantitative traits

Journal of Genetics

Volumn 91, Issue 1, 2012, Pages 111-117

  Rakshit, Sujay ^a   Rakshit, Arunita ^b   Patil, J V ^a  

^a ICAR INDIAN INSTITUTE OF MILLETS RESEARCH   (India)

^b CENTRAL RESEARCH INSTITUTE FOR DRYLAND AGRICULTURE   (India)

Author keywords

AMPRIL; association mapping; gene mapping; MAGIC; multiparent intercross population; QTL analysis

Indexed keywords

CHROMOSOME MAP; CROSS BREEDING; GENETIC LINKAGE; METHODOLOGY; POPULATION GENETICS; QUANTITATIVE TRAIT; REVIEW;

CHROMOSOME MAPPING; CROSSES, GENETIC; GENETIC LINKAGE; GENETICS, POPULATION; QUANTITATIVE TRAIT, HERITABLE;

ANIMALIA;

EID: 84862499256     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-012-0144-8     Document Type: Review

References (42)

1. Atwell S., Huang Y. S., Vilhjálmsson B. J., Willems G., Horton M., Li Y. et al. 2010 Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature465, 627-631.
2. Bandillo N., Muyco P. A., Caspillo C., Laza M., Sajise A. G., Singh R. K. et al. 2010 Development of multiparent advanced generation intercross (magic) populations for gene discovery in rice (Oryza sativa L.). Philipp. J. Crop Sci. 35, suppl 1, 96.
3. Bentsink L., Hanson J., Hanhart C. J., Blankestijn-de Vries H., Coltrane C., Keizer P. et al. 2010 Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proc. Natl. Acad. Sci. USA107, 4264-4269.
4. Brachi B., Faure N., Horton M., Flahauw E., Vazquez A., Nordborg M. et al. 2010 Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 6, 1-17.
5. Broman K. W. 2005 The genomes of recombinant inbred lines. Genetics169, 1133-1146.
6. Broman K. W., Wu H., Sen S. and Churchill G. A. 2003 R/qtl: QTL mapping in experimental crosses. Bioinformatics19, 889-890.
7. Buckler E. S., Holland J. B., Bradbury P. J., Acharya C. B., Brown P. J., Browne C. et al. 2009 The genetic architecture of maize flowering time. Science325, 714-718.
8. Cavanagh C., Morell M., Mackay I. and 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. Churchill G. A., Airey D. C., Allayee H., Angel J. M., Attie A. D., Beatty J. et al. 2004 The collaborative cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36, 1133-1137.
10. Collard B. C. Y., Jahufer M. Z. Z., Brouwer J. B. and Pang E. C. K. 2005 An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica142, 169-196.
11. Darvasi A. and Soller M. 1995 Advanced intercross lines, an experimental population for fine genetic mapping. Genetics141, 199-1207.
12. Darvasi A. and Soller M. 1997 A simple method to calculate resolving power and confidence interval of QTL map location. Behav. Genet. 27, 125-132.
13. Davey J. W., Hohenlohe P. A., Etter P. D., Boone J. Q., Catchen J. M. and Blaxter M. L. 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499-510.
14. Ehrenreich I. M., Hanzawa Y., Chou L., Roe J. L., Kover P. X. and Purugganan M. D. 2009 Candidate gene association mapping of Arabidopsis flowering time. Genetics183, 325-335.
15. Flint J., Valder W., Shifman S. and Mott R. 2005 Strategies for mapping and cloning quantitative trait genes in rodents. Nat. Rev. Genet. 6, 271-286.
16. Gelderman H. 1975 Investigations on inheritance of quantitative characters in animals by gene markers. Theor. Appl. Genet. 46, 319-330.
17. Goffinet B. and Gerber S. 2000 Quantitative trait loci: A meta analysis. Genetics155, 463-473.
18. Gupta P. K. 2002 Molecular markers and QTL analysis in crop plants. Curr. Sci. 83, 113-114.
19. Gupta P. K., Rustgi S. and Kulwal P. L. 2005 Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57, 461-485.
20. Gupta P. K., Langridge P. and Mir R. R. 2010 Marker-assisted wheat breeding: present status and future possibilities. Mol. Breed. 26, 145-161.
21. Hirschhorn J. N. and Daly M. J. 2005 Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 6, 95-108.
22. Huang B. E. and George A. W. 2011 R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. Bioinformatics27, 727-729.
23. Huang X., Paulo M. J., Boer M., Effgen S., Keizer P., Koornneef M. and Eeuwijk F. V. 2011 Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc. Natl. Acad. Sci. USA108, 4488-4493.
24. Keurentjes J. J., Bentsink L., Alonso-Blanco C., Hanhart C. J., Blankestijn-De Vries H., Effgen S. et al. 2007 Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics175, 891-905.
25. Keurentjes J. J. B., Willems G., van Eeuwijk F., Nordborg M. and Koornneef M. 2011 A comparison of population type used for QTL mapping in Arabidopsis thaliana. Plant Genet. Res. 9, 185-188.
26. Kover P. X., Valder W., Trakalo J., Scarcelli N., Ehrenreich I. M., Purugganan M. D. et al. 2009 A multiparent advanced generation inter-cross to fine map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5, e1000551.
27. Leung H., McNally K., Thomson M., Bandillo N., Muyco P. and Singh R. K. 2011 Expanding and fine-tuning genetic resources for discovery of gene functions in rice. In Plant and animal genome conference, Sandiago (http://www. intl-pag. org/19/abstracts/W80_PAGXIX_500. html).
28. Li H., Hearne S., Banziger K., Li Z. and Wang J. 2010 Statistical properties of QTL linkage mapping in biparental genetic populations. Heredity105, 257-267.
29. Li R., Lyons M. A., Wittenburg H., Paigen B. and Churchill G. A. 2005 Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping. Genetics169, 1699-1709.
30. Mackay T. F. C. 2004 The genetic architecture of quantitative traits: lessons from Drosophila. Curr. Opin. Genet. Dev. 14, 253-257.
31. McMullen M. D., Kresovich S., Villeda H. S., Bradbury P., Li H., Sun Q. et al. 2009 Genetic properties of the maize nested association mapping population. Science325, 737-740.
32. Mott R., Talbot C. J., Turri M. G., Collins A. C. and Flint J. 2000 A method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl. Acad. Sci. USA97, 12649-12654.
33. Nordborg M. and Weigel D. 2008 Next-generation genetics in plants. Nature456, 720-723.
34. Rafalski J. A. 2010 Association genetics in crop improvement. Curr. Opin. Plant. Biol. 13, 174-180.
35. Rakshit S., Zaide P. H. and Mishra S. K. 2002 Molecular markers and tagging of genes in crop plants. In Advances in plant physiology, vol 4 (ed. A. Hemantaranjan), pp. 205-223. Scientific Publications, Jodhpur, India.
36. Sax K. 1923 Association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics8, 552-560.
37. Sturtevant A. H. 1913 The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J. Exp. Zool. 14, 43-59.
38. Valder W., Solberg L. C., Gauguier D., Burnett S., Klenerman P., Cookson W. O. et al. 2006 Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet. 38, 879-887.
39. Varshney R. K., Nayak S. N., May G. D. and Jackson S. A. 2009 Next generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27, 522-530.
40. Watson J. D. and Crick F. H. C. 1953 Genetical implications of the structure of deoxyribonucleic acid. Nature171, 964-967.
41. Yalchin B., Flint J. and Mott R. 2005 Using progenitor strain information to identify quantitative trait nucleotides in out bred mice. Genetics171, 673-681.
42. Yu J., Holland J. B., McMullen M. D. and Buckler E. S. 2008 Genetic design and statistical power of nested association mapping in maize. Genetics178, 539-551.