Local-Scale Patterns of Genetic Variability, Outcrossing, and Spatial Structure in Natural Stands of Arabidopsis thaliana

Abstract

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local “outcrossing hotspots” appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing inArabidopsis thalianaF1 epihybrids

“…Further, mutations altering the function of DNA methylation regulators may spontaneously arise in natural populations, generating individuals with partially hypomethylated genomes and even activated TEs (61)(62)(63). Although A. thaliana is a mainly self-fertilizing species, its effective outcrossing rate varies considerably between different stands and can be higher than 10% (64). Thus, it is plausible that epigenomic shocks, although likely less drastic than the one we report here, may occur in the wild and generate novel heritable epigenetic diversity and associated regulatory patterns.…”

Genetic architecture of nonadditive inheritance inArabidopsis thalianahybrids

“…The drawback of highly inbred lines is that the contribution of dominance to phenotype cannot be assessed directly. However, Arabidopsis thaliana outcrossing rates of over 10% have been reported in the field, suggesting that dominance may contribute to phenotypic variation in natural populations (34). Here we explore the magnitude of nonadditive genetic variation in A. thaliana using a half diallel intercrossing scheme.…”

Whole-genome sequencing of multiple Arabidopsis thaliana populations

“…A. thaliana and its close relatives have been at the forefront of investigations of these processes in plants 1,2 . For example, both the local and global population structures of A. thaliana, which reflect the species' migration history since the Ice Age as well as the surprisingly frequent outcrossing events between the inbred strains, have been studied in considerable detail 3,4 . The first genome-wide haplotype map of a plant was produced for this species 5 , and the information from this endeavor has already been successfully used for genome-wide association studies (GWAS) [6][7][8][9] .…”