Coherent synthesis of genomic associations with phenotypes and home environments

Jesse R. Lasky, Brenna R. Forester, Matthew Reimherr

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade-offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.

Original languageEnglish (US)
Pages (from-to)91-106
Number of pages16
JournalMolecular Ecology Resources
Volume18
Issue number1
DOIs
StatePublished - Jan 2018

Fingerprint

local adaptation
phenotype
genomics
fitness
Genotype
Phenotype
loci
gardens
synthesis
Single Nucleotide Polymorphism
genotype
Alleles
allele
cline
alleles
Geographic Locations
garden
Climate
Arabidopsis
Gene Frequency

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Genetics
  • Medicine(all)

Cite this

@article{f389fcf43e5d4739b2da6628907a3cd0,
title = "Coherent synthesis of genomic associations with phenotypes and home environments",
abstract = "Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade-offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.",
author = "Lasky, {Jesse R.} and Forester, {Brenna R.} and Matthew Reimherr",
year = "2018",
month = "1",
doi = "10.1111/1755-0998.12714",
language = "English (US)",
volume = "18",
pages = "91--106",
journal = "Molecular Ecology Resources",
issn = "1755-098X",
publisher = "Wiley-Blackwell",
number = "1",

}

Coherent synthesis of genomic associations with phenotypes and home environments. / Lasky, Jesse R.; Forester, Brenna R.; Reimherr, Matthew.

In: Molecular Ecology Resources, Vol. 18, No. 1, 01.2018, p. 91-106.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Coherent synthesis of genomic associations with phenotypes and home environments

AU - Lasky, Jesse R.

AU - Forester, Brenna R.

AU - Reimherr, Matthew

PY - 2018/1

Y1 - 2018/1

N2 - Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade-offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.

AB - Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade-offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.

UR - http://www.scopus.com/inward/record.url?scp=85029445138&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85029445138&partnerID=8YFLogxK

U2 - 10.1111/1755-0998.12714

DO - 10.1111/1755-0998.12714

M3 - Article

C2 - 28861950

AN - SCOPUS:85029445138

VL - 18

SP - 91

EP - 106

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

IS - 1

ER -