Transposable elements (TEs) are mobile genetic elements with very high mutation rates that play important roles in shaping genome architecture and regulating phenotypic variation. However, the extent to which TEs influence the adaptation of organisms in their natural habitats is largely unknown. Here, we scanned 201 representative resequenced genomes from the model plant Arabidopsis thaliana and identified 2,311 polymorphic TEs from noncentromeric regions. We found expansion and contraction of different types of TEs in different A. thaliana populations. More importantly, we identified two TE insertions that are likely candidates to play a role in adaptive evolution. Our results highlight the importance of variations in TEs for the adaptation of plants in general in the context of rapid global climate change.

Background In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. Results To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. Conclusions This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.

Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5′ untranslated region (UTR) of C. rubella FLC, which are associated with local changes in chromatin conformation and histone modifications, reduce its expression levels and promote flowering. We further show that these two pervasive variants originated independently in natural C. rubella populations after speciation and spread to an intermediate frequency, suggesting a role of this parallel cis-regulatory change in adaptive evolution. Our results provide an example of how parallel mutations in the same 5′ UTR region can shape phenotypic evolution in plants.

Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.

Background and Aims Plant elemental composition is of fundamental importance for plant growth and metabolic functions. However, knowledge of how multi-elemental stoichiometry responds to varying nitrogen (N) and phosphorus (P) availabilities remains limited. Methods We conducted experimental manipulations with nine repeat experiments to investigate the effects of N and P supply on the concentrations and variability of six elements, carbon (C), N, P, potassium (K), calcium (Ca) and magnesium (Mg), in leaves of Arabidopsis thaliana. Key Results N supply increased the concentrations of N, K and Mg, decreased the concentration of P, but exerted little influence on the concentrations of C and Ca in green leaves. P supply increased the concentrations of P and Ca, decreased the concentration of C, initially increased and then decreased the concentration of K, but showed little influence on the concentrations of N and Mg in green leaves. Multivariate patterns among the concentrations of these six elements in green leaves was influenced by the type of nutrient supply (i.e. N or P). Elemental variability decreased with increasing elemental concentrations in green leaves at the intraspecific level, supporting the Stability of Limiting Elements Hypothesis that was originally proposed from a meta-analysis of pooled data across species or communities. Compared with green leaves, the senesced leaves showed greater variability in C, N, P, K and Mg concentrations but lower variability in Ca concentration. Conclusions N and P supplies exerted differential influences on the concentrations of C, N, P, K, Ca and Mg in green leaves. The specific C content should be considered when assessing C cycling under global nutrient changes. Stage-dependent patterns of leaf stoichiometric homeostasis differed among elements with various chemical characteristics. These findings can help to improve our understanding of plant eco-physiological responses and acclimation under global nutrient changes from the stoichiometric perspective of multiple elements.