Adaptive evolution of α-amylase genes in wild barley (Hordeum spontaneum) on micro and macro scales

Alpha-amylases play essential roles in germination, and the malting and brewing processes, by hydrolyzing starch granules present in the endosperm of barley.Hordeum spontaneum C. Koch, the progenitor of cultivated barley that harbors rich genetic diversity, was collected from seven different environments. To investigate the influence of microclimatic ecological divergence on α-amylase, single nucleotide polymorphisms (SNPs) in amy genes from these populations were determined. A total of 16 and 17 SNPs were detected in the coding sequences of amy1 and amy2, respectively, from the seven wild barley populations. Among these SNPs, three in amy1-2 and nine in amy2-2 were significantly associated with ecological factors. The genetic divergence of amy sequences was significantly different among the populations. Natural microclimatic selection was apparently the major evolutionary driving force causing interslope divergence and adaptive evolution of these genes. The genetic variation in amy1-2 and amy2-2 was at least partly ecologically determined in these populations, representing adaptive patterns generated by natural selection. The SNPs were apparently generated by natural selection in climatic environmental patterns at both the micro (“Evolution Canyon”) and macro (across Israel, Galilee, and Negev) scales.     

HvNax3—a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum)

Previous work identified the wild barley (Hordeum vulgare ssp. spontaneum) accession CPI-71284-48 as being capable of limiting sodium (Na⁺) accumulation in the shoots under saline hydroponic growth conditions. Quantitative trait locus (QTL) analysis using a cross between CPI-71284-48 and a selection of the cultivated barley (H. vulgare ssp. vulgare) cultivar Barque (Barque-73, a moderate Na⁺ excluder) attributed the control of the Na⁺ exclusion trait from CPI-71284-48 to a single locus on the short arm of chromosome 7H, which was named HvNax3. The locus reduced shoot Na⁺ accumulation by 10–25% in plants grown in 150 mM NaCl. Markers generated using colinearity with rice and Brachypodium, together with the analysis of introgression lines and F₂ and F₃ families, enabled HvNax3 to be mapped to a 1.3-cM interval. Genes from the corresponding rice and Brachypodium intervals encode 16 different classes of proteins and include several plausible candidates for HvNax3. The potential of HvNax3 to provide a useful trait contributing to salinity tolerance in cultivated barley is discussed.     

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. F_ST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.     

Exogenous spermidine enhances Epichloë endophyte-induced tolerance to NaCl stress in wild barley (Hordeum brevisubulatum)

Plant and Soil - We investigated morphological variations in podzols caused by changes in soil porosity and permeability upon the growth of large tree-roots in a tropical barrier island (Ilha...     

Geographie variation of α-amylase, β-amylase, β-glucanase,pullulanase and chitinase activity in germinating Hordeum spontaneum barley from Israel and Jordan

The enzyme activities of -amylase, -amylase, -glucanase, pullulanase and chitinase were determined in extracts of wild barley (Hordeum vulgare ssp. spontaneum) germinated for five days under axenic standard conditions. The material comprises 257 accessions, for 242 of which the botanical territory of origin in Israel or Jordan is known. The enzyme activities based on soluble protein in the extracts showed significant differences (P<0.001) among the eleven territories. The territorial moisture parameters mostly correlate with the enzyme activities. As determined by one gene or oligogenes, the significant territorial differences and the correlation with moisture are thought to reflect natural selection of genes responsible for favourable activity, or of genes linked to the enzyme coding loci, or in a coadaptive manner, of physiologically allied genes. Genes for high -glucanase activity at germination are probably coadaptive with genes for high -glucan content of the grain. The generally low starch content of wild barley grains probably makes any high -amylase activity unnecessary at the germination stage. An inverse relationship appears between -glucanase and chitinase activity; these two enzymes are also pathogenesis related proteins.     

Effect of the fungal endophyte Epichloë bromicola on polyamines in wild barley (Hordeum brevisubulatum) under salt stress

Plant and Soil - The endophytic fungus Epichloë bromicola forms mutualistic symbiotic associations with wild barley (Hordeum brevisubulatum) in the saline-alkali areas of northwestern China....     

Fungal endophyte Epichloë bromicola infection regulates anatomical changes to account for salt stress tolerance in wild barley (Hordeum brevisubulatum)

Plant and Soil - Plants can minimize the adverse effects of salinity by modifying morphological and anatomical features. Previous studies showed that endophytic Epichloë bromicola play an...     

Identification of barley genetic regions influencing plant–microbe interactions and carbon cycling in soil

Plant and Soil - Forest management towards increased carbon (C) sequestration has repeatedly been suggested as a “natural climate solution”. We evaluated the potential of altered...     

Regional subdivision in wild barley allozyme variation: adaptive or neutral?

We examined the adaptive importance of allozyme variation in wild barley (Hordeum spontaneum). The test involved a nested sampling design with four population groups, each representing a different environment, and a comparison of observed allozyme variation with that expected under the assumption that allozymes are not neutral. Measurements of plant fitness in indigenous and alien environments in reciprocal introductions of seeds and seedlings in the four environments provided a guideline for the expected pattern of allozyme variation. The results showed considerable variation in both the degree of regional and population subdivision and the pattern of the subdivision among loci. The observed pattern of variation was ambiguous. Although two alleles exhibited a pattern of distribution that cannot be explained by genetic drift as a function of geographic distance, we failed to detect either a significant relationship between genetic distance and environmental similarity or any favored epistatic allele combinations across the four environments. Our results suggest that interpretation of allozyme variation in wild barley as adaptive and directly related to local environment still needs justification. Although we could not reject the null hypothesis, a proposed methodology seeking a concordance between observed and "adaptive" (i.e., expected under hypothesis that allozymes are not neutral) allozyme variation may prove to be effective in resolving the neutralist-selectionist debate when applied to other species.     

A genetic study of human interferon-α-induced repair of DNA damage in hepatitis B patients

In vitro treatment with human interferon-α (HuIFN-α) of hepatitis B virus-infected peripheral lymphocytes from 17 hepatitis B patients induced a decrease in the frequency of sister-chromatid exchanges (SCE). There was a significant difference in mean SCE frequencies between the HuIFN-α-treated patients and the control group, but not between acute and chronic hepatitis B patients treated with HuIFN-α     

Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?

Accurately estimating genetic variance components is important for studying evolution in the wild. Empirical work on domesticated and wild outbred populations suggests that dominance genetic variance represents a substantial part of genetic variance, and theoretical work predicts that ignoring dominance can inflate estimates of additive genetic variance. Whether this issue is pervasive in natural systems is unknown, because we lack estimates of dominance variance in wild populations obtained in situ. Here, we estimate dominance and additive genetic variance, maternal variance, and other sources of nongenetic variance in eight traits measured in over 9000 wild nestlings linked through a genetically resolved pedigree. We find that dominance variance, when estimable, does not statistically differ from zero and represents a modest amount (2-36%) of genetic variance. Simulations show that (1) inferences of all variance components for an average trait are unbiased; (2) the power to detect dominance variance is low; (3) ignoring dominance can mildly inflate additive genetic variance and heritability estimates but such inflation becomes substantial when maternal effects are also ignored. These findings hence suggest that dominance is a small source of phenotypic variance in the wild and highlight the importance of proper model construction for accurately estimating evolutionary potential.     

Mapping malting quality and yield characteristics in a north American two-rowed malting barley × wild barley advanced backcross population

Molecular Breeding - The brown midrib (bmr) phenotype is a recessive trait of sorghum (Sorghum bicolor L. Moench) that results in overall lignin reduction and is associated with enhanced ruminant...     

Suppression of spontaneous mutagenesis in human cells by DNA base excision–repair

The chemical instability of the covalent structure of DNA, and in vivo exposure of DNA to reactive oxygen species and endogenously produced alkylating agents, has triggered the evolution of several specific DNA repair pathways. A major strategy of repair involves the initial removal of an altered base from DNA by a member of the enzyme family of DNA glycosylases. The currently known enzymes of this type in mammalian cells are reviewed, and the subsequent base excision–repair (BER) steps that achieve restoration of the intact DNA structure are also described. The specific problem of retaining high accuracy in this essentially error-free repair process is discussed.