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Title: Harnessing quantitative genetics and genomics for understanding and improving complex traits in crops

item Holland, Jim - Jim

Submitted to: Drought Frontier Project Planning Workshop
Publication Type: Proceedings
Publication Acceptance Date: 7/1/2008
Publication Date: 12/1/2008
Citation: Holland, J.B., Cardinal, A.J. 2008. Harnessing quantitative genetics and genomics for understanding and improving complex traits in crops. Drought Frontier Project Planning Workshop. p:123-136.

Interpretive Summary: Drought resistance in rice and other crops is a complex trait, controlled by many genes and affected by the environment. This paper outlines two approaches to the genetic dissection of complex traits and the use of genetic information in crop improvement. In one strategy, the basic biology of the trait is studied to understand the physiology and biochemistry of the trait. This information can then be used to identify the underlying genes, and DNA markers targeting these genes can then be used for selection to improve the trait. An alternative strategy employs large-scale evaluation of many plant lines from diverse pedigrees to identify genome regions that are associated with the complex trait (without necessarily unraveling all of the pathways that affect the trait). Markers targeting these regions can be used for selection and trait improvement. Both strategies have distinct advantages and drawbacks, which are reviewed to suggest situations in which the different strategies are most appropriate.

Technical Abstract: Classical quantitative genetics aids crop improvement by providing the means to estimate heritability, genetic correlations, and predicted responses to various selection schemes. Genomics has the potential to aid quantitative genetics and applied crop improvement programs via large-scale, high-throughput DNA sequencing and fingerprinting, gene expression analyses, and reverse genetics methods. To date, these techniques have mainly been useful in the identification of genes with discrete or at least moderate effects on high-value traits. A practical result of this research is the development of allele-specific markers that tend to be useful across many breeding populations. For example, knowledge of the fatty acid biosynthesis pathway in plants and the sequencing of genes in that pathway is being exploited to produce DNA markers to aid selection for specific modified fatty acid traits in soybean. Application of large-scale gene mapping techniques to improvement of highly quantitative traits (controlled by many genes of small effects) is not yet proven, however, and, even if useful, may not be highly-cost effective unless large-scale genomics infrastructure is already in place to aid breeding programs. An example of the application of genomics to large-scale genetic diversity studies is the large-scale maize QTL mapping study underway based on the development of 26 related RIL populations that capture a large portion of the genetic variation available worldwide among public lines. For genomics to be useful for the improvement of drought resistance in rice may require the identification of component traits with relatively simpler architecture or a very large scale investment in genomics-assisted breeding.