Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant

Abstract

Determining the extent of genetic variation that reflects local adaptation in crop-wild relatives is of interest for the purpose of identifying useful genetic diversity for plant breeding. We investigated the association of genomic variation with geographical and environmental factors in wild barley (Hordeum vulgare L. ssp. spontaneum) populations of the Southern Levant using genotyping by sequencing (GBS) of 244 accessions in the Barley 1K+ collection. The inference of population structure resulted in four genetic clusters that corresponded to eco-geographical habitats and a significant association between lower gene flow rates and geographical barriers, e.g. the Judaean Mountains and the Sea of Galilee. Redundancy analysis (RDA) revealed that spatial autocorrelation explained 45% and environmental variables explained 15% of total genomic variation. Only 4.5% of genomic variation was solely attributed to environmental variation if the component confounded with spatial autocorrelation was excluded. A synthetic environmental variable combining latitude, solar radiation, and accumulated precipitation explained the highest proportion of genomic variation (3.9%). When conditioned on population structure, soil water capacity was the most important environmental variable explaining 1.18% of genomic variation. Genome scans with outlier analysis and genome-environment association studies were conducted to identify adaptation signatures. RDA and outlier methods jointly detected selection signatures in the pericentromeric regions, which have reduced recombination, of the chromosomes 3H, 4H, and 5H. However, selection signatures mostly disappeared after correction for population structure. In conclusion, adaptation to the highly diverse environments of the Southern Levant over short geographical ranges had a limited effect on the genomic diversity of wild barley. This highlighted the importance of nonselective forces in genetic differentiation.

Host Tree and Geography Induce Metabolic Shifts in the Epiphytic Liverwort Radula complanata

“…At the geographic level, we found that the majority of the detected metabolites involved primary metabolites, specifically amino acids or peptides. This finding is in line with previous studies that found geography and climatic conditions to significantly shape plant populations by genetic variations [ 25 , 26 ]. These genetic variations can cause changes in gene expression, protein synthesis, and, ultimately, the production of metabolic compounds.…”

Rapid lineage diversification of gray mangroves (Avicennia marina) driven by isolation in cryptic glacial refugia and extreme environmental conditions in the Arabian Peninsula

“…The amount of variance explained by environmental variables was comparable to the values reported in studies applying RDA to genotype-environment analysis in plants, typically ranging from 15% to 40% (e.g. Leamy et al, 2016;Garot et al, 2019;Capblancq et al, 2020;Faske et al, 2021;Chang et al, 2022). We also identified 31 functionally annotated genes associated with one or more RDA outliers.…”

Altitudinal Patterns in Adaptive Evolution of Genome Size and Inter-Genome Hybridization Between Three Elymus Species From the Qinghai–Tibetan Plateau

“…However, based on FCM and genome sequencing, all three wild Elymus species can be recognized easily. In addition, Hordeum vulgare L. was considered an ideal internal standard due to its very few secondary compounds and approximate genome size to Elymus as well as strong genetic stability (Tuna et al, 2006;Chang et al, 2022). The most plausible reason for interspecific and intraspecific genome size variation was suggested to be one or the other kind of repetitive sequences along with complex genetic mechanisms, karyotypic, environmental, and phylogenetic factors (Du et al, 2017).…”