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United States Department of Agriculture

Agricultural Research Service

Research Project: REDESIGNING FORAGE GERMPLASM AND PRODUCTION SYSTEMS FOR EFFICIENCY, PROFIT, AND SUSTAINABILITY OF DAIRY FARMS Title: Marker assisted selection made cheap and easy

Author
item Riday, Heathcliffe

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: April 2, 2012
Publication Date: N/A

Interpretive Summary: Although DNA markers are being used in animal breeding programs and in some plant breeding programs, they have not been widely utilized in forage plant breeding. A primary reason for this may be that growing a single forage plant for genetic evaluation is relatively inexpensive compared to growing an animal for genetic evaluation, so there’s no real reason to use DNA markers to eliminate forage plants from breeding programs; it’s cheaper to grow thousands of plants and evaluate them with traditional methods than to use DNA markers. This paper explores the reasons that forage plant breeders are not using DNA markers and presents DNA marker-based plant breeding strategies that are cheap enough to allow easy incorporation into even resource limited forage plant breeding programs. It also points out the limits of DNA markers in forage plant breeding and the need to consider size and genetic diversity of the forage plant breeding program.

Technical Abstract: Molecular markers in perennial forages are becoming ubiquitous for marker assisted selection (MAS). Nevertheless, widespread implementation of MAS in perennial forage breeding programs for highly quantitative traits has not yet occurred. A primary reason is likely the cost associated with genotyping plants using molecular markers. Compared to animal breeding, as well as plant breeding systems involving inbred line development, phenotyping costs in outbred forage species are comparatively much lower. Therefore, many MAS schemes are usually not cost competitive, especially in cases where many molecular markers are required. Presented are cost-effective MAS strategies that are immediately implementable in most diploid or polyploidy perennial forage breeding programs. Breeding methods developed during the pre-MAS era maximize the ratio between additive variance and the square root of the phenotypic variance (i.e. hsA). With the advent of molecular markers, many new breeding methods based primarily on correlated selection responses between molecular markers and quantitative traits have been proposed (i.e. rsA). The MAS strategies presented here use molecular markers to improve hsA by enhancing traditional breeding methods. A selection strategy pyramid is envisioned with traditional maternal halfsib selection serving as the base followed by marker assisted paternity selection. With no additional cost within maternal and paternal maximum linkage, disequilibrium based MAS strategies can be added. Finally, as the total cost to genotype one individual decreases, residual linkage disequilibrium based MAS strategies can be added to the above mentioned strategies or at some price point supplant these strategies. Using this strategy, the greatest amount of information per molecular marker will be obtained from an initial set of markers. However, as the number of markers utilized is increased, the amount of information per marker at some point will decrease. Furthermore, it is unnecessary to have an unlimited number of molecular markers for selection among a smaller number of genotypes since only a certain amount of molecular marker information will be necessary to rank selection units, with less information needed for accurate ranking among fewer genotypes. Therefore, the number of markers utilized in a selection strategy should be optimized so the maximum amount of resources can be applied to increase the number of selection units under evaluation. Even under the perfect correlated selection response scheme (i.e. ksA), selection intensity and the amount of additive variance present are still paramount drivers of selection gain.

Last Modified: 7/31/2014
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