Title : Selection for silage yield and composition did not affect genomic diversity within 1 the Wisconsin Quality

Maize silage is a forage of high quality and yield, and represents the second 30 most important use of maize in the U.S. The Wisconsin Quality Synthetic (WQS) maize 31 population has undergone five cycles of recurrent selection for silage yield and 32 composition resulting in a genetically improved population. The application of high-33 density molecular markers allows breeders and geneticists to identify important loci 34 through association analysis and selection mapping, as well as monitor changes in the 35 distribution of genetic diversity across the genome. The objectives of this study were: 1) 36 Identify loci controlling variation for maize silage traits through association analysis and 37 the assessment of selection signatures. 2) Describe changes in the genomic distribution of 38 gene diversity through selection and genetic drift in the WQS recurrent selection 39 program. We failed to find any significant marker-trait associations using the historical 40 phenotypic data from WQS breeding trials combined with 17,719 high-quality, 41 informative single nucleotide polymorphisms. Likewise, no strong genomic signatures 42 were left by selection on silage yield and quality in the WQS despite genetic gain for 43 these traits. These results could be due to the genetic complexity underlying these traits, 44 or the role of selection on standing genetic variation. Variation in loss of diversity 45 through drift was observed across the genome. Some large regions experienced much 46 greater loss in diversity than what is expected, suggesting limited recombination 47 combined with small populations in recurrent selection programs could easily lead to 48 fixation of large swaths of the genome.