The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.

/pdf/whole-genome-sequencing-of-multiple-arabidopsis-thaliana-18cuzjmkr6.pdf

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.

/pdf/molecular-spandrels-tests-of-adaptation-at-the-genetic-level-44f21m18fi.pdf

Molecular spandrels: tests of adaptation at the genetic level.

In all natural habitats, plants are surrounded by an enormous number of potential enemies (biotic) and various kinds of abiotic environmental stress. Nearly all ecosystems contain a wide variety of bacteria, viruses, fungi, nematodes, mites, insects, mammals and other herbivorous animals, greatly responsible for heavy reduction in crop productivity. By their nature, plants protect themselves by producing some compounds called as secondary metabolites. Secondary metabolites, including terpenes, phenolics and nitrogen (N) and sulphur (S) containing compounds, defend plants against a variety of herbivores and pathogenic microorganisms as well as various kinds of abiotic stresses. This review presents an overview about some of the mechanisms by which plants protect themselves against herbivory, pathogenic microbes and various abiotic stresses as well as specific plant responses to pathogen attack, the genetic control of host-pathogen interactions.

/pdf/role-of-secondary-metabolites-in-defense-mechanisms-of-4sphoch7sg.pdf

Role of secondary metabolites in defense mechanisms of plants

Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.

/pdf/genome-wide-association-studies-in-plants-the-missing-3515uakb1m.pdf

Genome-wide association studies in plants: the missing heritability is in the field

Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive. Recent studies in hybrids and allopolyploids using transcriptomic, proteomic, metabolomic, epigenomic and systems biology approaches have provided new insights. Emerging genomic 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. For example, epigenetic modifications of key regulatory genes in hybrids and allopolyploids can alter complex regulatory networks of physiology and metabolism, thus modulating biomass and leading to heterosis. The conceptual advances could help to improve plant and animal productivity through the manipulation of heterosis.

Genomic and epigenetic insights into the molecular bases of heterosis

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.

/pdf/natural-allelic-variation-underlying-a-major-fitness-trade-4dwbsvr5vv.pdf

Christine Kuhns

Papers

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

Live and let die – Arabidopsis nonhost resistance to powdery mildews