Dataset Information

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

ABSTRACT: Plants are exposed to combinations of various biotic and abiotic stresses, but stress responses are usually investigated for single stresses only. Here, we investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions. A set of 214 000 single nucleotide polymorphisms (SNPs) was screened for marker-trait associations in genome-wide association (GWA) analyses using tailored multi-trait mixed models. Stress responses that share phytohormonal signaling pathways also share genetic architecture underlying these responses. After removing the effects of general robustness, for the 30 most significant SNPs, average quantitative trait locus (QTL) effect sizes were larger for dual stresses than for single stresses. Plants appear to deploy broad-spectrum defensive mechanisms influencing multiple traits in response to combined stresses. Association analyses identified QTLs with contrasting and with similar responses to biotic vs abiotic stresses, and below-ground vs above-ground stresses. Our approach allowed for an unprecedented comprehensive genetic analysis of how plants deal with a wide spectrum of stress conditions.

SUBMITTER: Thoen MP

PROVIDER: S-EPMC5248600 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

Thoen Manus P M MP Davila Olivas Nelson H NH Kloth Karen J KJ Coolen Silvia S Huang Ping-Ping PP Aarts Mark G M MG Bac-Molenaar Johanna A JA Bakker Jaap J Bouwmeester Harro J HJ Broekgaarden Colette C Bucher Johan J Busscher-Lange Jacqueline J Cheng Xi X Fradin Emilie F EF Jongsma Maarten A MA Julkowska Magdalena M MM Keurentjes Joost J B JJ Ligterink Wilco W Pieterse Corné M J CM Ruyter-Spira Carolien C Smant Geert G Testerink Christa C Usadel Björn B van Loon Joop J A JJ van Pelt Johan A JA van Schaik Casper C CC van Wees Saskia C M SC Visser Richard G F RG Voorrips Roeland R Vosman Ben B Vreugdenhil Dick D Warmerdam Sonja S Wiegers Gerrie L GL van Heerwaarden Joost J Kruijer Willem W van Eeuwijk Fred A FA Dicke Marcel M

The New phytologist 20161004 3

Plants are exposed to combinations of various biotic and abiotic stresses, but stress responses are usually investigated for single stresses only. Here, we investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions. A set of 214 000 single nucleotide polymorphisms (SNPs) was screened for marker-trait associations in genome-wide association (GWA) analyses using tailored multi-trait mix ...[more]

PMID: 27699793

Similar Datasets

Project description:Background & aimsIn contrast to most other common diseases, few genetic variants have been identified that impact risk of cirrhosis. We aimed to identify new genetic variants that predispose to cirrhosis, to test whether such variants, aggregated into a polygenic score, enable genomic risk stratification, and to test whether alcohol intake or body mass index interacts with polygenic predisposition.MethodsWe conducted a multi-trait genome-wide association study combining cirrhosis and alanine aminotransferase levels performed in 5 discovery studies (UK Biobank, Vanderbilt BioVU, Atherosclerosis Risk in Communities study, and 2 case-control studies including 4829 individuals with cirrhosis and 72,705 controls and 362,539 individuals with alanine aminotransferase levels). Identified variants were replicated in 3 studies (Partners HealthCare Biobank, FinnGen, and Biobank Japan including 3554 individuals with cirrhosis and 343,826 controls). A polygenic score was tested in Partners HealthCare Biobank.ResultsFive previously reported and 7 newly identified genetic variants were associated with cirrhosis in both the discovery studies multi-trait genome-wide association study (P < 5 × 10-8) and the replication studies (P < .05), including a missense variant in the APOE gene and a noncoding variant near EFN1A. These 12 variants were used to generate a polygenic score. Among Partners HealthCare Biobank individuals, high polygenic score-defined as the top quintile of the distribution-was associated with significantly increased risk of cirrhosis (odds ratio, 2.26; P < .001) and related comorbidities compared with the lowest quintile. Risk was even more pronounced among those with extreme polygenic risk (top 1% of the distribution, odds ratio, 3.16; P < .001). The impact of extreme polygenic risk was substantially more pronounced in those with elevated alcohol consumption or body mass index. Modeled as risk by age 75 years, probability of cirrhosis with extreme polygenic risk was 13.7%, 20.1%, and 48.2% among individuals with no or modest, moderate, and increased alcohol consumption, respectively (Pinteraction < .001). Similarly, probability among those with extreme polygenic risk was 6.5%, 10.3%, and 19.5% among individuals with normal weight, overweight, and obesity, respectively (Pinteraction < .001).ConclusionsTwelve independent genetic variants, 7 of which are newly identified in this study, conferred risk for cirrhosis. Aggregated into a polygenic score, these variants identified a subset of the population at substantially increased risk who are most susceptible to the hepatotoxic effects of excess alcohol consumption or obesity.

Dataset Information

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

Publications

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets