Association Genetics Strategies and Resources
Genomic technologies are making it possible to strategically exploit genetic diversity in crops to map complex agronomic and physiological traits and improve these traits for grain and biomass production. Sorghum is well positioned to benefit from these a
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Association Genetics Strategies and Resources Jianming Yu, Martha T. Hamblin, and Mitchell R. Tuinstra
Abstract Genomic technologies are making it possible to strategically exploit genetic diversity in crops to map complex agronomic and physiological traits and improve these traits for grain and biomass production. Sorghum is well positioned to benefit from these association genetics strategies, and essential components of association mapping have been established. Research in sorghum association mapping contributes to a better understanding of genetics of complex traits and improved breeding methods to exploit genetic diversity. Keywords Association mapping • Candidate gene • Complex trait dissection • Genetic diversity • Genome-wide association study • Linkage disequilibrium • Nested association mapping • Single nucleotide polymorphism • Sorghum diversity panel
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Association Genetics
Many genetic mapping studies in plants have been conducted with recombinant inbred line (RIL) populations from a biparental cross because it is easy to maintain these populations for replicated trials (Bernardo 2008; Holland 2007). In contrast, association genetics has been implemented extensively in human genetics studies, J. Yu (*) Department of Agronomy, Kansas State University, 3004 Throckmorton Plant Science Center, Manhattan, KS 66506-5501, USA e-mail: [email protected] M.T. Hamblin Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA e-mail: [email protected] M.R. Tuinstra Department of Agronomy, Purdue University, West Lafayette, IN, USA e-mail: [email protected] A.H. Paterson (ed.), Genomics of the Saccharinae, Plant Genetics and Genomics: Crops and Models 11, DOI 10.1007/978-1-4419-5947-8_9, © Springer Science+Business Media New York 2013
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partly because of the early adoption of large-scale genotyping strategies and the necessity of exploiting population-based samples for studying complex human diseases. However, widespread use of single nucleotide polymorphism (SNP) markers and the reduced cost of sequencing and genotyping have led researchers working with different plant species to adopt association mapping and the underlying linkage disequilibrium (LD) approach (Zhu et al. 2008). Here we briefly introduce the concept of linkage analysis and association mapping. Readers should refer to other detailed reviews for a full explanation (Flint-Garcia et al. 2003; Nordborg and Tavare 2002; Risch and Merikangas 1996; Zhu et al. 2008). In essence, both linkage analysis and association mapping strategies are designed to identify marker–trait association signals that result from co-inheritance of functional polymorphisms and neighboring DNA variants (markers). In linkage analysis in plants, the signals are typically generated by co-inheritance within a segregating population. This segregating population starts with the cross of two homogenous inbred parents and contains one or more generations of recombination. Association mapping is aimed at detection of marker–trait association signals withi
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