Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana

The “mustard oil bomb” is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genome-wide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide FST scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe.

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QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana

BMC Plant Biology ◽

10.1186/s12870-019-1996-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Mohamed El-Soda ◽

Charles Neris Moreira ◽

Nakai Goredema-Matongera ◽

Diaan Jamar ◽

Maarten Koornneef ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Candidate Genes ◽

Long Distance ◽

Gene Encoding ◽

Significant Treatment ◽

P Deficiency ◽

Sulphate Concentration ◽

Genome Wide ◽

Pi Starvation ◽

Phosphatase 2A

Abstract Background Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability. Results Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus. Conclusion We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .

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A genome-wide association study reveals a novel regulator of ovule number and fertility in Arabidopsis thaliana

PLoS Genetics ◽

10.1371/journal.pgen.1007934 ◽

2019 ◽

Vol 15 (2) ◽

pp. e1007934 ◽

Cited By ~ 12

Author(s):

Jing Yuan ◽

Sharon A. Kessler

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Ovule Number

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Genome-wide association study of Arabidopsis thaliana leaf microbial community

Nature Communications ◽

10.1038/ncomms6320 ◽

2014 ◽

Vol 5 (1) ◽

Cited By ~ 157

Author(s):

Matthew W. Horton ◽

Natacha Bodenhausen ◽

Kathleen Beilsmith ◽

Dazhe Meng ◽

Brian D. Muegge ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Microbial Community ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

Nature ◽

10.1038/nature08800 ◽

2010 ◽

Vol 465 (7298) ◽

pp. 627-631 ◽

Cited By ~ 1075

Author(s):

Susanna Atwell ◽

Yu S. Huang ◽

Bjarni J. Vilhjálmsson ◽

Glenda Willems ◽

Matthew Horton ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Genome Wide Association Study ◽

Inbred Lines ◽

Genome Wide Association ◽

Genome Wide

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The maternal environment interacts with genetic variation in regulating seed dormancy in Arabidopsis thaliana

10.1101/117879 ◽

2017 ◽

Author(s):

Envel Kerdaffrec ◽

Magnus Nordborg

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Seed Dormancy ◽

Genome Wide Association Study ◽

Seed Maturation ◽

Genome Wide Association ◽

Maternal Environment ◽

Genome Wide ◽

A Genome ◽

Wide Range

AbstractSeed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions.HighlightThe effect of low seed-maturation temperatures on seed dormancy is highly variable in Arabidopsis thaliana accessions from Sweden, denoting strong genotype-environment interactions, and a genome-wide association study identified compelling candidates that could account for this plasticity.

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