Location: Dairy Forage ResearchTitle: Genomic selection in forage breeding: accuracy and methods Author
Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/7/2013
Publication Date: 9/1/2013
Publication URL: http://handle.nal.usda.gov/10113/62400
Citation: Resende, R., Resende, M., Casler, M.D. 2013. Genomic selection in forage breeding: accuracy and methods. Crop Science. 54:143-156. Interpretive Summary: Recent reductions in the cost of large-scale DNA sequencing creates numerous possibilities to increase the efficiency and effectiveness of forage breeding. Use of DNA markers would increase the rate of gain per unit time by decreasing generation time and increasing selection pressure for traits that have traditionally been difficult to measure, such as forage yield. Six distinct approaches to "genomic selection", combining field data with DNA-based laboratory data, were evaluated for their accuracy and expected effectiveness. A selection index, combining field data with laboratory data, was the clear winner, with the potential to triple the rate of gain for complex traits such as forage yield. These methods have the potential to revolutionize forage breeding for many economically important species, providing important options to forage breeders for increasing efficiency and effectiveness of forage breeding.
Technical Abstract: The main benefits expected from genomic selection in forage grasses and legumes are to increase selection accuracy, reduce evaluation costs per genotype, and reduce cycle time. Aiming at designing a training population and first generations of selection, deterministic equations were used to compare the gain and accuracy of various genomic selection methods implemented within the context of traditional experimental plot designs used in forage breeding. The impact of effective population size (Ne), number of markers per centimorgan (Ls per cM) and trait heritability on selection accuracy were evaluated considering one species with genome size of 1,600 Mb as a model. Genomic selection accuracy is high (>0.7) when Ne is low (=50), marker density is high (>10 markers per cM), and heritability >0.3. Genomic selection of individual plants results in higher selection gain than any phenotypic-genotypic based methods when marker density is high, mostly because of significant reductions in cycle time. For low marker densities (~3 per cM), a combination of information from genotype and phenotype results in more gain for heritability <0.3 than genomic selection alone. We propose a selection index method to increase accuracy in early generations of genomic selection, aiming to guarantee higher long-term gain for advanced breeding generations. Considering a recent decline in genotyping costs and an expected reduction in breeding cycle by one-half, genomic selection in forage breeding is worthy of serious consideration for economically important species.