Predicting genotype environmental range from genome-environment associations

Molecular Ecology
Stéphanie ManelPierre Devaux

Abstract

Genome-environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single-locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals. We illustrate this approach to predict aridity in a database constituted of 950 individuals of wild beets and 299 individuals of cultivated beets genotyped at 14,409 random single nucleotide polymorphisms (SNPs). We detected 66 alleles associated with aridity and used them to calculate the fraction (I) of aridity-associated alleles in each individual. The fraction I correctly predicted the values of aridity in an independent validation set of wild individuals and was then used to predict aridity in the 299 cultivated individuals. Wild individuals had higher ...Continue Reading

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Citations

Feb 8, 2020·Molecular Ecology·Jason M JacksonJeffrey D Lozier
Jul 14, 2019·Nature Reviews. Genetics·Martin F BreedJakki J Mohr
Sep 16, 2020·Molecular Ecology·Steve SmithLuciano B Beheregaray
Aug 14, 2020·Conservation Biology : the Journal of the Society for Conservation Biology·Amanda XuerebMarie-Josée Fortin
Oct 25, 2020·Molecular Ecology Resources·José Luis Blanco-PastorJean-Paul Sampoux
Nov 8, 2019·Current Opinion in Insect Science·Michael E Dillon, Jeffrey D Lozier
Mar 25, 2019·Trends in Ecology & Evolution·Jared A GrummerEric B Taylor
Jun 3, 2021·Biology·Pierre Sourdille, Pierre Devaux

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