ARS | Publication request: Snapshots of Selection: Changes in SNP Allele Frequencies during Phenotypic, Marker-Assisted, and Genomewide Selection in Maize

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 15, 2009
Publication Date: January 9, 2010
Citation: Massman, J., Jung, H.G., Bernardo, R. 2010. Snapshots of Selection: Changes in SNP Allele Frequencies during Phenotypic, Marker-Assisted, and Genomewide Selection in Maize [abstract]. Plant and Animal Genome XVIII Conference. January 9-13, 2010, San Diego, California. Abstract P370.

Technical Abstract: Changes in allele frequencies underlie improvements in mean performance for quantitative traits. Limited published information is available on how genomewide marker-allele frequencies change during phenotypic and marker-based selection for multiple traits in applied breeding programs. Here we describe how SNP allele frequencies have changed in two selection programs for grain yield, agronomic performance, and stover-quality traits for cellulosic ethanol production in maize (Zea mays L.). Marker-assisted recurrent selection (MARS) involved selection for subsets of 58-59 SNP markers that had significant effects for the target traits. Genomewide selection involved selection based on predicted breeding values across all 288 SNP markers. Testcrosses of the intermated B73 x Mo17 mapping population were phenotyped in multiple field environments. Phenotypic selection was conducted in cycle 0 whereas MARS and genomewide selection were conducted in cycle 1. Mean changes in SNP allele frequencies were 0.14-0.17 in phenotypic selection, 0.18 in genomewide selection, and 0.19-0.20 in MARS. Maximum changes in SNP allele frequencies were 0.53-0.63 in phenotypic selection, 0.53-0.59 in genomewide selection and 0.58-0.63 in MARS. We anticipate that differences in mean performance will reflect differences both in the mean change in SNP allele frequencies and in the specific SNP markers for which shifts in allele frequencies are the largest.