Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize
Candice N. Hirsch, Sherry A. Flint-Garcia, Timothy M. Beissinger, Steven R. Eichten, Shweta Deshpande, Kerrie Barry, Michael D. McMullen, James B. Holland, Edward S. Buckler, Nathan M. Springer, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler

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 approximately 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, 2,729 SNPs were identified that reached fixation in both selected populations with opposing fixed alleles, 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 based on 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.

  • Received June 12, 2014.
  • Accepted July 8, 2014.