An application of vGWAS to differences in flowering time in maize across mega-environments

Matthew D. Murphy, Alexander E. Lipka

Research output: Contribution to journalArticlepeer-review


Genomic regions containing loci with effect sizes that interact with environmental factors are desirable targets for selection because of increasingly unpredictable growing seasons. Although selecting upon such gene-by-environment (G × E) loci is vital, identifying significantly associated loci is challenging due to the multiple testing correction. Consequently, G × E loci of small- to moderate effect sizes may never be identified via traditional genome-wide association studies (GWAS). Variance GWAS (vGWAS) have been previously shown to identify G × E loci. Combined with its inherent reduction in the severity of multiple testing, we hypothesized that vGWAS could be successfully used to identify genomic regions likely to contain G × E effects. We used publicly available genotypic and phenotypic data in maize (Zea mays L.) to test the ability of two vGWAS approaches to identify G × E loci controlling two flowering traits. We observed high inflation of (Figure presented.) from both approaches. This suggests that these two vGWAS approaches are not suitable to the task of identifying G × E loci. We advocate that similar future applications of vGWAS use more sophisticated models that can adequately control the inflation of (Figure presented.). Otherwise, the application of vGWAS to search for G × E effects that are critical for combating the effects of climate change will not reach its full potential.

Original languageEnglish (US)
Pages (from-to)2807-2817
Number of pages11
JournalCrop Science
Issue number5
StatePublished - Sep 1 2023

ASJC Scopus subject areas

  • Agronomy and Crop Science


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