Insights into the effects of long-term artificial selection on seed size in maize

Authors: HIRSCH, CANDICE - University Of Minnesota; Flint-Garcia, Sherry; BEISSINGER, TIMOTHY - University Of Wisconsin; EICHTEN, STEVEN - University Of Minnesota; DESHPANDE, SHWETA - Department Of Energy Joint Genome; BARRY, KERRIE - Department Of Energy Joint Genome; McMullen, Michael; Holland, Jim - Jim; Buckler, Edward - Ed; SPRINGER, NATHAN - University Of Minnesota; BUELL, ROBIN - Michigan State University; DELEON, NATALIA - University Of Wisconsin; KAEPPLER, SHAWN - University Of Wisconsin

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2014
Publication Date: 9/18/2014
Publication URL: http://handle.nal.usda.gov/10113/59622
Citation: Hirsch, C.N., Flint Garcia, S.A., Beissinger, T.M., Eichten, S.R., Deshpande, S., Barry, K., Mcmullen, M.D., Holland, J.B., Buckler IV, E.S., Springer, N., Buell, R.C., de Leon, N., Kaeppler, S.M. 2014. Insights into the effects of long-term artificial selection on seed size in maize. Genetics. 198(1):409-421.

Interpretive Summary: Grain produced by cereal crops, including corn (maize), is a staple food source in many regions of the world in terms of direct human consumption and as an animal feed source. Seed size and weight are important traits in determining overall grain yield. An understanding of the genes controlling these traits will provide valuable information on how to improve grain yield in cereal crops. In this study we identified regions of the genome that vary between two maize populations that were divergently selected for small and large seed size. In total, 94 highly divergent regions were identified that provide candidate genes controlling seed size. These results were compared to regions controlling seed weight in the genetically diverse maize nested association mapping (NAM) population. Nearly half of the regions identified in the NAM population showed overlap with the candidate regions from the divergently selected populations. The results presented in this study can be used by cereal breeders and geneticists to facilitate increases in grain yield.

Technical Abstract: Grain produced from cereal crops is a major source of human and animal feed worldwide. To understand the genetic basis of seed size variation, a component trait of grain yield, we conducted a genome-wide scan to detect evidence of selection in the Krug Yellow Dent long-term selection experiment for small and large seed size. The empirically estimated effective population size of the selected populations was 369 individuals, and previous reports demonstrated significant phenotypic divergence between the populations. Allele frequency estimates for 3,090,214 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 highly divergent regions were identified with a median of six genes per region. Additionally, 2,729 SNPs were identified that reached fixation in both selected populations with opposing fixed alleles, many of which clustered in two large regions of the genome. Copy number variation was also highly prevalent between the selected populations, with 532 total regions identified from coverage variation and comparative genome hybridization. Overlap between regions identified in the long-term selection experiment and nearly half of the regions identified from natural genetic variation for seed weight were observed. The results of this study provide insights into the genetic elements underlying seed size variation in maize and other cereal crops. In particular, genes underlying regions identified in this study support previous reports on the importance of rate of developmental and seed composition to seed size variation.