AbstractChromosomal inversions are frequently implicated in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this property makes it difficult to identify the genetic mechanisms that underlie an inversion's role in adaption. In this study, we explore how large-scale transcriptomic data can be used to dissect the functional importance of chromosomal inversions. Specifically, we study a 13 Mb inversion

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... us found almost exclusively in highland populations of maize (Zea mays ssp. mays) known as Inv4m. Inv4m is known to have introgressed into domesticated maize from a wild relative also present in the highlands of Mexico and is thought to be important for the adaptation of certain maize landraces to cultivation in highland environments. First, using a large publicly available association mapping panel, we confirmed that Inv4m is associated with locally adaptive agronomic phenotypes, but only in highland fields. Second, we created two Near Isogenic Line populations segregating for alternative alleles of Inv4m, and measured gene expression variation association with Inv4m across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m allele, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m, and speculate that the genetic basis of its effects on adaptive traits is distributed across many separate functional variants.