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Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

TLDR
It is demonstrated that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6), underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains.
Abstract
Plants can defend themselves against a wide array of enemies, from microbes to large animals, yet there is great variability in the effectiveness of such defences, both within and between species. Some of this variation can be explained by conflicting pressures from pathogens with different modes of attack. A second explanation comes from an evolutionary 'tug of war', in which pathogens adapt to evade detection, until the plant has evolved new recognition capabilities for pathogen invasion. If selection is, however, sufficiently strong, susceptible hosts should remain rare. That this is not the case is best explained by costs incurred from constitutive defences in a pest-free environment. Using a combination of forward genetics and genome-wide association analyses, we demonstrate that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6), underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains. A hyperactive ACD6 allele, compared to the reference allele, strongly enhances resistance to a broad range of pathogens from different phyla, but at the same time slows the production of new leaves and greatly reduces the biomass of mature leaves. This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth.

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Whole-genome sequencing of multiple Arabidopsis thaliana populations

TL;DR: The majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome are described, their effects on gene function, and the patterns of local and global linkage among these variants.
Journal ArticleDOI

Molecular spandrels: tests of adaptation at the genetic level.

TL;DR: Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles and may lead to incorrect conclusions about the relationships between gene function and fitness.
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Genome-wide association studies in plants: the missing heritability is in the field

TL;DR: Genome-wide association studies (GWAS) have been even more successful in plants than in humans and mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.
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Genomic and epigenetic insights into the molecular bases of heterosis

TL;DR: Genetic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids.
Journal ArticleDOI

The past, present and future of breeding rust resistant wheat.

TL;DR: Initial indications are that APR genes encode a more heterogeneous range of proteins than R proteins, and a research priority to better inform rust resistance breeding is to characterize further APR genes in wheat.
References
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Journal ArticleDOI

MUSCLE: multiple sequence alignment with high accuracy and high throughput

TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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Clustal W and Clustal X version 2.0

TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
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APE: Analyses of Phylogenetics and Evolution in R language

TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.
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PAML 4: Phylogenetic Analysis by Maximum Likelihood

TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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The plant immune system

TL;DR: A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production and provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms.
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