title: Insights into the effects of long-term artificial selection on seed size in maize.
abstract: Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using FST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211 Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
authors.forename: Sherry A
authors.initials: SA
authors.lastname: Flint-Garcia
authors.affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706 Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Beissinger
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Eichten
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598.
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211 Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
authors.forename: Michael D
authors.initials: MD
authors.lastname: McMullen
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211 Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695.
authors.forename: James B
authors.initials: JB
authors.lastname: Holland
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211 Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853 Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Nathan
authors.initials: N
authors.lastname: Springer
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706 Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Natalia
authors.initials: N
authors.lastname: de Leon
authors.affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706 Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 smkaeppl@wisc.edu.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
mesh_terms: D056915:DNA Copy Number Variations; D005787:Gene Frequency; D018745:Genome, Plant; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D012639:Seeds / Q000033:anatomy & histology / Q000235:genetics*; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development
keywords: copy-number variation; maize; natural variation; seed size; selection signatures