Work

Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens

Year: 2019

Type: article

Abstract: Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.

Source: Genetics

DOI: 10.1534/genetics.118.301786

Authors: Emily B. Josephs, Jeremy J. Berg, Jeffrey Ross-Ibarra, Graham Coop

Institutions: University of California, Davis, Columbia University

Language: English

Topic: Genetic Mapping and Diversity in Plants and Animals

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Zero hunger

Open Access status: bronze

Funders: National Science Foundation, U.S. Department of Agriculture, National Institutes of Health, National Institute of General Medical Sciences