Genomic and Phenotypic Divergence in Wild Barley Driven by Microgeographic Adaptation

Abstract

Microgeographic adaptation is a fundamental driving force of evolution, but the underlying causes remain undetermined. Here, the phenotypic, genomic and transcriptomic variations of two wild barley populations collected from sharply divergent and adjacent micro-geographic sites to identify candidate genes associated with edaphic local adaptation are investigated. Common garden and reciprocal transplant studies show that large phenotypic differentiation and local adaptation to soils occur between these populations. Genetic, phylogenetic and admixture analyses based on population resequencing show that significant genetic divergences occur between basalt and chalk populations. These divergences are consistent with the phenotypic variations observed in the field. Genome sweep analyses reveal 162.7 Mb of selected regions driven by edaphic local adaptation, in which 445 genes identified, including genes associated with root architecture, metal transport/detoxification, and ABA signaling. When the phenotypic, genomic and transcriptomic data are combined, HvMOR, encoding an LBD transcription factor, is determined to be the vital candidate for regulating the root architecture to adapt to edaphic conditions at the microgeographic scale. This study provides new insights into the genetic basis of edaphic adaptation and demonstrates that edaphic factors may contribute to the evolution and speciation of barley.

Multi‐Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha)

“…[ 18 ] and Bian et al. [ 3 ] revealed that genomic divergence plays a crucial role in edaphic adaptation of wild barley. Both studies identified novel genes and alleles associated with ABA signaling and root architecture, which facilitates the wild barley to adapt to the dry Terra Rossa and Chalk soils.…”

“…The studies on evolutionary microsites in Israel provided excellent examples of the adaptation to micro ecological environment from viruses and bacteria, through fungi, plants, and animals. [38][39][40][41][42][43][44] Recently, Wang et al [18] and Bian et al [3] revealed that genomic divergence plays a crucial role in edaphic adaptation of wild barley. Both studies identified novel genes and alleles associated with ABA signaling and root architecture, which facilitates the wild barley to adapt to the dry Terra Rossa and Chalk soils.…”

“…For instance, poor water retention capacity of sandy soil and frequent drought events tend to drive the evolution and development of deep root plants towards better water use efficiency. [ 3 , 4 ] On the contrary, reduced soil aeration and high moisture in siliceous soil facilitates the spread of pathogenic bacteria and fungi, resulting in root infection and deleterious plant health. [ 5 , 6 ] Therefore, sustainable and efficient utilization of soil resources could be realized by developing the better crop cultivars adapted to the various types of soils.…”

“…[13] Previous studies revealed that the wild barley population inhabiting the Terra Rossa soil are much more tolerant to drought stress than those growing in the Basalt soil. [14,15] Recently, Bian et al [3] reported that the wild barley Chalk population displays better water deficit tolerance than Basalt population when grown in the dry Chalk soil. In another microclimatic ecosystem-the Evolution Canyon at Mount Carmel of Israel, the population of wild emmer wheat from the wet and shady European Slope exhibited high resistance to pathogens.…”

Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis

“…Ca 2+ is the most abundant element in the chalk soil ( Figure 1 D), followed by Si 4+ , Al 3+ , Fe 3+ , and Mg 2+ , and Si 4+ is the most abundant chemical in the abutting contrasting basalt soil, followed by Al 3+ , Fe 3+ , and Ca 2+ . Al 3+ , Fe 3+ , and Ca 2+ contents are significantly different between the two soils [ 35 ]. Thus, basalt is generally acidic, while chalk is slightly alkaline [ 36 ].…”