DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel

Abstract

Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity. A key question concerns the spatial scale at which genetic differentiation occurs and to what extent it is driven by natural selection. The Levant region exhibits a strong ecological gradient along the North-South axis, with numerous small canyons in an East-West direction and with small-scale environmental gradients on the opposing North-and South-facing slopes. We sequenced 34 short genomic regions in 54 accessions of wild barley collected throughout Israel and from the opposing slopes of two canyons. The nucleotide diversity of the total sample is 0.0042, which is about two-thirds of a sample from the whole species range (0.0060). Thirty accessions collected at 'Evolution Canyon' (EC) at Nahal Oren, close to Haifa, have a nucleotide diversity of 0.0036, and therefore harbor a large proportion of the genetic diversity. There is a high level of genetic clustering throughout Israel and within EC, which roughly differentiates the slopes. Accessions from the hot and dry South-facing slope have significantly reduced genetic diversity and are genetically more distinct from accessions from the North-facing slope, which are more similar to accessions from other regions in Northern Israel. Statistical population models indicate that wild barley within the EC consist of three separate genetic clusters with substantial gene flow. The data indicate a high level of population structure at large and small geographic scales that shows isolation-by-distance, and is also consistent with ongoing natural selection contributing to genetic differentiation at a small geographic scale.

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel

“…Although we find no evidence that microsatellites contribute to local adaptations in Evolution Canyon, mobile elements emerge as potential surrogates of adaptive divergence along the sharp microclimate gradient. A similar conclusion has been reached in a study of wild barley (Hordeum spontaneum) from Evolution Canyon (49,50), showing that more BARE-1 retrotransposon copies and proportionally fewer solo LTRs were found in the upper, drier sites of the canyon, particularly at the top of the SFS, than at lower sites. Interestingly, the pattern seems to be roughly opposite to D. melanogaster whose NFS genomes carry a heavier TE load.…”

Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

“…We identified over one thousand SNPs in wild barley, resulting in 4.4 SNPs per kb at high coverage. This is similar to a recent survey of wild barley collected across Israel (one SNP per 239 bp, θ w =0.00418) [ 10 ]. We also identified over one thousand SNPs by mapping against the cultivated barley sequences (Hv.…”

“…Throughout its geographical distribution, wild barley is exposed to multiple environmental stresses such as drought, high temperatures, and high soil salinity. The correlation of genetic and environmental variation within its distribution range suggests the action of local adaptation along macro- and micro-environmental gradients [ 8 – 10 ]. It is therefore an excellent model system for studying plant adaptation and holds a high potential as a genetic resource for the breeding of stress tolerant varieties of cultivated barley [ 11 , 12 ].…”

Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers

“…The level of genetic variation in H. spontaneum has been studied and estimated using phenotypic characters, isozymes and different PCR-based molecular markers (Turpeinen et al 2003;Jana and Pietrzak 1988;Dreiseitl and Dinoor 2004;Jaradat 1991;Baum et al 2004;and Bedada et al 2014). These studies concluded that the genetic variation in wild barley is substantial.…”