MAGIC populations in crops: current status and future prospects
- 4.8k Downloads
MAGIC populations present novel challenges and opportunities in crops due to their complex pedigree structure. They offer great potential both for dissecting genomic structure and for improving breeding populations.
The past decade has seen the rise of multiparental populations as a study design offering great advantages for genetic studies in plants. The genetic diversity of multiple parents, recombined over several generations, generates a genetic resource population with large phenotypic diversity suitable for high-resolution trait mapping. While there are many variations on the general design, this review focuses on populations where the parents have all been inter-mated, typically termed Multi-parent Advanced Generation Intercrosses (MAGIC). Such populations have already been created in model animals and plants, and are emerging in many crop species. However, there has been little consideration of the full range of factors which create novel challenges for design and analysis in these populations. We will present brief descriptions of large MAGIC crop studies currently in progress to motivate discussion of population construction, efficient experimental design, and genetic analysis in these populations. In addition, we will highlight some recent achievements and discuss the opportunities and advantages to exploit the unique structure of these resources post-QTL analysis for gene discovery.
KeywordsQuantitative Trait Locus Quantitative Trait Locus Analysis Quantitative Trait Locus Mapping Collaborative Cross Marker Score
Many thanks to three anonymous reviewers for their helpful suggestions. Dr. Huang is the recipient of an Australian Research Council Discovery Early Career Researcher Award (Project Number DE120101127).
Conflict of interest
No authors have any conflicts of interest.
- Bardol N, Ventelon M, Mangin B, Jasson S, Loywick V et al (2013) Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism. Theor Appl Genet 126:2717–2736CrossRefPubMedGoogle Scholar
- Buet C, Dubreuil P, Tixier M-H, Durantin K, Praud S et al (2013) The molecular characterization of a MAGIC population reveals high potential for gene discovery. MaizeGDB proceedingsGoogle Scholar
- Butler D (2009) asreml: asreml() fits the linear mixed model. R package version 3.0. http://www.vsni.co.uk
- Goulden CH (1939) Problems in plant selection. In: Proceedings of the Seventh International Genetics Congress. Cambridge University Press, pp 132–133Google Scholar
- Maluszynski M, Kasha KJ, Szareiko I (2003) Published doubled haploid protocols in plant species. In: Doubled haploid production in crop plants, a manual. Kluwer Academic Publishers, Dordecht, pp 309–335Google Scholar
- McClearn GE, Wilson JR, Meredith W (1970) The use of isogenic and heterogenic mouse stocks in behavioral research. In: Lindzey G, Thiessen D (eds) Contributions to behavior-genetic analysis: the mouse as a prototype. Appleton Century Crofts, New York, pp 3–22Google Scholar
- Pascual L, Desplat N, Huang BE, Desgroux A, Bruguier L et al (2015) Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol J (in press)Google Scholar
- Pea G, Dell’Acqua M, Hlaing ALL, Pe ME (2013) From mice to maize: a multiparental population for fine mapping in Zea mays. MAGIC Populations Workshop. http://openwetware.org/images/e/e6/MatteoDellAcqua_MaizePoster.pdf
- Smith AB, Butler DG, Cavanagh CR, Cullis BR (2015) Multi-phase variety trials using both composite and individual replicate samples: a model-based design approach. J Agric Sci Camb (in press)Google Scholar
- Verbyla AP, Cavanagh CR, Verbyla KL (2014b) Whole genome analysis of multi-environment or multi-trait QTL in MAGIC G3(4):1569–1584Google Scholar