A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number

A genome-wide scan to detect evidence of selection was conducted in the Golden Glow maize long-term selection population. The population had been subjected to selection for increased number of ears per plant for 30 generations, with an empirically estimated effective population size ranging from 384...

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Bibliographic Details
Published in:Genetics (Austin) 2014-03, Vol.196 (3), p.829-840
Main Authors: Beissinger, Timothy M, Hirsch, Candice N, Vaillancourt, Brieanne, Deshpande, Shweta, Barry, Kerrie, Buell, C Robin, Kaeppler, Shawn M, Gianola, Daniel, de Leon, Natalia
Format: Article
Language:English
Subjects:
Chromosomes, Plant
Corn
Gene Frequency
Genetic Heterogeneity
Genetic Variation
Genetics
Genome, Plant
Genomes
Investigations
Phenotype
Plant populations
Polymorphism
Polymorphism, Single Nucleotide
Selection, Genetic
Zea mays
Zea mays - genetics
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Summary:A genome-wide scan to detect evidence of selection was conducted in the Golden Glow maize long-term selection population. The population had been subjected to selection for increased number of ears per plant for 30 generations, with an empirically estimated effective population size ranging from 384 to 667 individuals and an increase of more than threefold in the number of ears per plant. Allele frequencies at >1.2 million single-nucleotide polymorphism loci were estimated from pooled whole-genome resequencing data, and FST values across sliding windows were employed to assess divergence between the population preselection and the population postselection. Twenty-eight highly divergent regions were identified, with half of these regions providing gene-level resolution on potentially selected variants. Approximately 93% of the divergent regions do not demonstrate a significant decrease in heterozygosity, which suggests that they are not approaching fixation. Also, most regions display a pattern consistent with a soft-sweep model as opposed to a hard-sweep model, suggesting that selection mostly operated on standing genetic variation. For at least 25% of the regions, results suggest that selection operated on variants located outside of currently annotated coding regions. These results provide insights into the underlying genetic effects of long-term artificial selection and identification of putative genetic elements underlying number of ears per plant in maize.
ISSN:1943-2631
0016-6731
1943-2631
DOI:10.1534/genetics.113.160655