Genetic resources of wild barley in the Near East: structure, evolution and application in breeding

Genetic diversity and structure of populations of the wild progenitor of barley, Hordeum spontaneum, from three countries, Israel, Turkey and Iran, in the Near East Fertile Crescent, are compared and contrasted. The analysis is based on electrophoretically discernible allozymic variation in proteins encoded by 27 shared loci in 2125 individuals representing 52 populations of wild barley. The results indicate that: (a) H. spontaneum in the Near East Fertile Crescent is very variable genetically; (b) genetic differentiation of populations includes some clinal but primarily regional and local patterns often displaying sharp geographic differentiation over short distances; (c) the average relative genetic differentiation (G_st) was 54% within populations, 39% among populations, and 8% between the three countries; (d) allele distribution is characterized by a high proportion of unique alleles (51%), and a high proportion of common alleles that are distributed either locally or sporadically; (e) discriminant analysis by allele frequencies successfully clustered wild barley of each of the three countries (96% correct classification); (f) a substantial portion of the patterns of allozyme variation in the wild gene pool is significantly correlated with the environment and is predictable ecologically, chiefly by a combination of humidity and temperature variables; (g) natural populations of wild barley are, on the average, more variable than two composite crosses and land races of cultivated barley. The spatial patterns and environmental correlates and predictors of genetic variation of H, spontaneum in the Fertile Crescent indicate that genetic variation in wild barley populations is not only rich but at least partly adaptive and predictable by ecology and allozyme markers. Consequently, conservation and utilization programmes should optimize sampling strategies by following the ecological-genetic factors and allozyme markers as effectively predictive guidelines.     

Genetic diversity among wild and cultivated barley as revealed by RFLP

Genetic variability of cultivated and wild barley, Hordeum vulgare ssp. vulgare and spontaneum, respectively, was assessed by RFLP analysis. The material consisted of 13 European varietes, single-plant offspring lines of eight land races from Ethiopia and Nepal, and five accessions of ssp. spontaneum from Israel, Iran and Turkey. Seventeen out of twenty-one studied cDNA and gDNA probes distributed across all seven barley chromosomes revealed polymorphism when DNA was digested with one of four restriction enzymes. A tree based on genetic distances using frequencies of RFLP banding patterns was estimated and the barley lines clustered into five groups reflecting geographical origin. The geographical groups of land-race lines showed less intragroup variation than the geographical groups of spontaneum lines. The group of European varieties, representing large variation in agronomic traits, showed an intermediate level. The proportion of gene diversity residing among geographical groups (F_ST) varied from 0.19 to 0.94 (average 0.54) per RFLP pattern, indicating large diversification between geographical groups.     

Genetic relationships among South-East Turkey wild barley populations and sampling strategies of Hordeum spontaneum

To assess the genetic diversity and the genetic structure of Turkish wild barley (Hordeum spontaneum Tell.) populations, 76 genotypes from ten ecologically and geographically different locations were analyzed by means of amplified fragment length polymorphism (AFLP) markers. Five primer combinations produced 187 scorable bands, of which 117 (62.6%) were polymorphic. Several population-specific and genotype-specific bands were identified, which differentiate populations or genotypes. Genetic distance, determined by Nei’s distance coefficient, varied from 0.07 to 0.21 with an average of 0.13. In the UPGMA dendrogram based on Nei genetic distances, the Hordeum spontaneum populations were separated into two major clusters. Genetic diversity was larger among (68%) than within (32%) populations. Eight AFLP bands were strongly correlated to the altitude of the collecting site, while no clear trend was detected between geographical origin and genetic diversity. Our results strongly suggest the need for a change in Hordeum spontaneum sampling strategy: more populations, rather then more individuals within population, should be sampled to appraise and safeguard genetic diversity in the wild barley gene pool.     

Genetic variation ofHordeum spontaneum in Israel: Eco-geographical races,detected by trait measurements

Samples from 11 populations of wild barley,Hordeum spontaneum, from Israel, were examined for morphological variation in a common garden plot design. Earliness traits had the highest between population variation of all traits studied. No relationship was found between dimensions of leaves and size of seeds.—Using numerical taxonomy methods, four races were found, which correspond to the geographical and environmental range of the species in Israel. It is concluded thatH. spontaneum shows a well developed tendency toward formation of highly adaptive races rather than exhibiting clinical variation.     

Genetic diversity and environmental associations of wild barley,Hordeum spontaneum,in Turkey

Genetic variability within and between populations of the wild progenitor of barley was studied electrophoretically. Thirty enzyme loci were assayed in 437 individuals representing 11 populations ofH. spontaneum in Turkey. The results indicated that: (a)H. spontaneum in Turkey is genetically rich in allozyme variation, but because of predominant self-pollination the variation is maintained as different homozygotes in the population; (b) genetic differentiation of populations includes clinal, regional, and local patterns, sometimes displaying sharp geographic differentiation over short distances; (c) overall indices of allozymic diversity and some allele frequencies of wild barley are significantly correlated with the environment and are predictable ecologically, chiefly by combinations of temperature and humidity variables; (d) a high percentage of alleles (66%) occur in local areas or are distributed sporadically rather than widespread; (e) Wright Fixation index was very high, F=0.995; (f) genetic distance was high (D=0.11, ranging from 0.031 to 0.288) between populations, and (g) average relative genetic differentiation was high among populations (Gst=0.47, ranging from 0.02 to 0.66). The spatial patterns and environmental correlates and predictors of genetic variation ofH. spontaneum in Turkey, indicated that genetic variation in wild barley populations is not only common, but also at least partly, adaptive. Therefore, a much fuller exploitation of these genetic resources by breeding is warranted.     

Correlation of ecological factors and allozymic variations with resistance toErysiphe graminis hordei inHordeum spontaneum in Israel: Patterns and application

The association of ecological factors and allozymic markers of wild barley,Hordeum spontaneum, with genotypes varying in resistance to 3 cultures of the pathogenErysiphe graminis hordei, which incites the disease powdery mildew of barley, were explored theoretically and practically. The study involved 275 accessions comprising 16 populations largely representing the ecological range ofH. spontaneum in Israel. From earlier studies of allozymic variation and disease resistance it now becomes apparent that genetic polymorphisms for resistance toE. graminis hordei are structured geographically, and are predictable by climatic as well as allozymic variables. Three-variable combinations of temperature and water factors explain significantly 0.32 of the spatial variance in disease resistance between localities. Also, several allozyme genotypes, singly or in combination, are significantly associated with disease resistance. A high correlation was found between the standard deviation of infection types of the culture of the pathogen from Israel, and allozymic polymorphism,P (r_s = 0.86, p < 0.001). Consequently, the IsraelH. spontaneum populations, growing in the center of diversity of the species, contain large amounts of unexploited disease resistance polymorphism. These could be effectively screened and utilized for producing resistant barley varieties by using ecological factors and allozymic variants as guidelines.     

Analysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology,geography and flowering time

Wild barley, Hordeum spontaneum C. Koch, is the progenitor of cultivated barley, Hordeum vulgare. The centre of diversity is in the Fertile Crescent of the Near East, where wild barley grows in a wide range of conditions (temperature, water availability, day length, etc.). The genetic diversity of 39 wild barley genotypes collected from Israel, Turkey and Iran was studied with 33 SSRs of known map location. Analysis of molecular variance (AMOVA) was performed to partition the genetic variation present within from the variation between the three countries of origin. Using classification tree analysis, two (or three) specific SSRs were identified which could correctly classify most of the wild barley genotypes according to country of origin. Associations of SSR variation with flowering time and adaptation to site-of-origin ecology and geography were investigated by two contrasting statistical approaches, linear regression based on SSR length variation and linear regression based on SSR allele class differences. A number of SSRs were significantly associated with flowering time under four different growing regimes (short days, long days, unvernalised and vernalised). Most of the associations observed could be accounted for by close linkage of the SSR loci to earliness per se genes. No associations were found with photoperiodic and vernalisation response genes known to control flowering in cultivated barley suggesting that different genetic factors may be active in wild barley. Novel genomic regions controlling flowering time in wild barley were detected on chromosomes 1HS, 2HL, 3HS and 4HS. Associations of SSRs with site-of-origin ecological and geographic data were found primarily in genomic regions determining plant development. This study shows that the analyses of SSR variation by allele class and repeat length are complementary, and that some SSRs are not necessarily selectively neutral.     

Microgeographic edaphic differentiation in allozyme polymorphisms of wild barley (Hordeum spontaneum,Poaceae)

Allozymic variation in proteins encoded by 22 loci was analyzed electrophoretically in 278 individual plants of wild barley,Hordeum spontaneum, the progenitor of cultivated barley, in four 100 meter transects, in Israel, each equally subdivided into basalt and terra rossa soil types. Significant differentiation according to soil was found in 9 alleles. Our results suggest that allozyme polymorphisms in wild barley are at least partly adaptive, and differentiate by edaphic natural selection rather than by stochastic processes, and/or neutrality of allozymic variants.     

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent

Wild barley shows a large morphological and phenotypic variation, which is associated with ecogeographical factors and correlates with genotypic differences. Diversity of defense related genes and their expression in wild barley has been recognized and has led to attempts to exploit genes from H. spontaneum in breeding programs. The aim of this study was to determine the variation in the accumulation of hordatines, which are Hordeum-specific preformed secondary metabolites with strong and broad antimicrobial activity in vitro, in 50 accessions of H. spontaneum from different habitats in Israel. Differences in the accumulation of hordatines in the seedling stage were significant between different H. spontaneum genotypes from different regional locations and micro-sites. Variation in the hordatine accumulation within genotypes was between 9% and 45%, between genotypes from the same location between 13% and 38%, and between genotypes from different locations up to 121%. Principal component analysis showed that water related factors explain 39%, temperature related factors explain 33% and edaphic factors account for 11% of the observed variation between the populations of H. spontaneum. Genetic analysis of the tested accessions with LP-PCR primers that are specific for genes involved in the biosynthetic pathway of hordatines showed tight correlations between hordatine abundance and genetic diversity of these markers. Multiple regression analyses indicated associations between genetic diversity of genes directly involved in hordatine biosynthesis, ecogeographical factors and the accumulation of hordatines.     

Genetic diversity and environmental associations of wild wheat,Triticum dicoccoides,in Israel

Summary Allozyme variation in the tetraploid wild progenitor of wheat, Triticum dicoccoides, was studied for the proteins encoded by about 50 gene loci in 457 individuals representing 12 populations from Israel. Six spikelet morphological traits were measured in the same populations. The results indicate that: (a) 16 loci (= 32%) were monomorphic in all 12 populations, 15 loci (= 30%) were locally polymorphic, and 19 loci (= 38%) were regionally polymorphic. All polymorphic loci (but one) displayed high levels of polymorphism ( 10%). In Israel, the proportion of polymorphic loci per population, P, in wild wheat averaged 0.25 (range, 0.16–0.38), and the genetic diversity index, H_e averaged 0.07, (range, 0.03 – 0.12). (b) Altogether there were 110 alleles at the 50 putative loci tested (c) Genetic differentiation of populations included regional and local patterns: (i) The coefficients of genetic distance between populations were high (mean D = 0.10 range, 0.02 – 0.25), and indicated sharp genetic differentiation over short distances, (ii) Common ( 10%) but sporadic and localized alleles were frequent (76%), and (iii) Rare alleles were few (only 5 alleles). (d) The patterns of allozyme and spikelet variation in the wild gene pool were significantly correlated with, and partly predictable by, water factors, including those of precipitation, evaporation, and relative humidity as well as of soil type, (e) All six spikelet characters showed statistically significant variation among localities and (f) Allozymic variation was correlated with spikelet variation.These results suggest in T. dicoccoides: (i) the operation of natural selection in population genetic structure, (ii) local adaptive genetic differentiation caused by diversifying selection through climate and soil, and (iii) the guidelines for sampling these resources for use in wheat breeding programs.     

Allozyme Variation in Turkmenian Populations of Wild Barley, Hordeum spontaneum Koch.

The extent and structure of genetic variation in 720 individualsrepresenting 36 populations of wild barley, Hordeum spontaneum,from Central Asia (Turkmenistan) were determined using starchgel electrophoresis of eight water soluble leaf proteins encodedby 13 loci. The populations were grouped into seven ecogeographicregions. The study found: (a) a similar amount of within populationgenetic diversity (H_e = 0.106), but lower total genetic diversity(H_T = 0.166) to that reported for Middle East populations ofH. spontaneum; (b) of the total genetic diversity, 61% was attributableto variation within populations, 27% between populations ofa region, and 12% among regions; (c) of the 42 alleles found,11 were ubiquitous, 22 were widespread and common, three localand common and seven local and rare; (d) there was a poor correlationbetween population genetic and geographic distances; and (e)the frequencies of only a few alleles correlated significantlywith climatic or geographic parameters. The extent and structureof genetic variation of Turkmenian populations, which representthe Central Asian part of the species' range, were significantlydifferent in some important aspects from Middle Eastern andeastern Mediterranean populations. The mosaic pattern of geneticvariation found in wild barley in the Middle East is less pronouncedin populations from Central Asia where there is less geneticdifferentiation among populations and regions, and more ubiquitousor common and fewer localized alleles. Copyright 2001 Annalsof Botany Company Allozyme, Central Asia, genetic diversity, Hordeum spontaneum, wild barley     

Diversity within and between populations of two sympatrically distributed Hordeum species in Jordan

Summary The diversity of two sympatrically distributed barley species (Hordeum vulgare L. and Hordeum spontaneum C. Koch.) has been assessed for 7 morphometric and 13 qualitative traits. Phenotypically, Hordeum vulgare was more stable than Hordeum spontaneum for all morphometric traits; this is a reflection of domestication and selection. The overall diversity indexes were 0.546±0.125 and 0.502±0.113 for Hordeum vulgare and Hordeum spontaneum, respectively (P=0.095). However, Hordeum spontaneum expressed a higher level of diversity for most qualitative traits. The observed similarity for a number of diversity indexes is probably due to gene flow between the two species.     

Protein resources in wild barley,Hordeum spontaneum,in Israel: Predictive method by ecology and allozyme markers

Geographic variation in protein content of wild barley,Hordeum spontaneum, and the associations of protein content with ecological and allozyme markers were tested in an attempt to derive predictive guidelines for conservation and utilization in breeding programs. The study involved 195 genotypes of wild barley from 25 populations, 15 central and 10 marginal. These populations had been tested earlier for allozymic variation (Nevo & al. 1979 a, b). The results indicate that protein content varies both within, but particularly between populations. Notably, the 10 marginal populations exhibit high protein content but low kernel weight, as compared with the 15 central populations which displayed lower protein content but high kernel weight. Three variable combinations of climatic factors explain 40% of the variability in protein content among populations. Likewise, 3 variable combinations of allozyme allele frequencies explain a significant degree of spatial variance in protein content (R square = 0.63). — We conclude that natural populations of wild barley in Israel contain large amounts of yet untapped genes for protein content. These could be effectively screened and utilized for producing high protein cultivars of barley by following ecological and allozymic markers as predictive guidelines in screening natural populations of wild barley.     

Phenotypic landscapes: phenological patterns in wild and cultivated barley

Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study, we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection) and 18 cultivated barley (H. vulgare) varieties was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographical distribution: north, coast and desert. Population differentiation (Q_ST) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (F_ST) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components, yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographical origin of domesticated barley.     

Genetic diversity of four esterase loci in natural populations of Hordeum spontaneum C. Koch from Jordan

Summary The diversity of four esterase loci was studied electrophoretically in 690 individual spikes representing 12 populations of wild barley (Hordeum spontaneum C. Koch.) collected from central, peripheral and marginal regions of its distribution in Jordan. A minimum of 6, 10, 5 and 5 alleles were observed at the Est-1, Est-2, Est-4 and Est-5 loci, respectively. Est-2 and Est-4 were the most diverse loci (H_c=0.53±0.05 and 0.46±0.07, respectively). Est-5 was intermediate (H_c=0.33+0.07) and Est-1 was the lowest (H_c=0.22±0.04). Polymorphism was highest in the central populations (H_e=0.52±0.04), followed by the peripheral (H_e=0.40±0.05) and the marginal (H_e=0.22±0.05) populations. Average allelic diversity between (G_st=0.49) and within (H_s=0.51) populations reflects a high allelic differentiation among these populations. Log-linear analyses revealed that four two-locus terms and two three-locus terms were significantly associated (P<0.05). Geographical distances between populations were not significantly correlated with Nei's genetic similarity index (r=0.16; P<0.19). It is postulated that diversifying selection is a major factor in the population genetic differentiation of these esterase loci.     

Diurnal rhythms of the chlorophyll a/b binding protein mRNAs in wild emmer wheat and wild barley (Poaceae) in the Fertile Crescent

The mRNAs encoding the chlorophyll a/b binding (cab) proteins of the light harvesting system were monitored in the wild cereals, wild emmer wheat,Triticum dicoccoides, and wild barley,Hordeum spontaneum, the progenitors of all cultivated wheats and barley, respectively. Significantly different mRNA levels were detected at different time points during the day, with generally low levels around sunrise, sunset and midnight, and maximum levels around noon. These results indicate that a diurnal control of thecab gene expression is present in these ancient species.     

Ecotypes and genetic divergence among sympatrically distributed populations of Hordeum vulgare and Hordeum spontaneum from the xeric region of Jordan

Summary The progeny of paired samples of Hordeum vulgare L. and Hordeum spontaneum C. Koch, collected from Jordan's xeric region was used in this study. Statistical analyses of seven easily measured morphometric traits were used to elucidate the relationships and distances between populations of both species, to detect any ecogeographical races, and to study the interrelationships and adjustments in the morphometric traits under study. Flag leaf area and plant height were the two most important discriminating variables which totally separated Hordeum vulgare from Hordeum spontaneum and accounted for 85.3% of total phenotypic variance in the collection. Cluster analysis indicated that the level of divergence among populations of both species was considerably different. Populations of Hordeum vulgare clustered at a maximum Euclidean distance of 2.08, while the maximum distance at which populations of Hordeum spontaneum clustered was 1.49. Three ecotypes each of Hordeum vulgare and Hordeum spontaneum were identified. These ecotypes corresponded to the environmental range of the collection sites. The interrelationships between the seven morphometric traits were adjusted in different ways as revealed by the principal components analysis. Sampling from the different clusters identified in this analysis is expected to increase the allelic diversity for selection and breeding purposes.     

Natural Variation in Grain Selenium Concentration of Wild Barley, <Emphasis Type="Italic">Hordeum spontaneum</Emphasis>, Populations from Israel

Wild barley (Hordeum spontaneum), the progenitor of cultivated barley, is an important genetic resource for cereal improvement. Selenium (Se) is an essential trace mineral for humans and animals with antioxidant, anticancer, antiarthropathy, and antiviral effects. In the current study, the grain Se concentration (GSeC) of 92 H. spontaneum genotypes collected from nine populations representing different habitats in Israel was investigated in the central area of Guizhou Province, China. Remarkable variations in GSeC were found between and within populations, ranging from 0 to 0.387 mg kg⁻¹ among the 92 genotypes with an average of 0.047 mg kg⁻¹. Genotype 20_C from the Sede Boqer population had the highest GSeC, while genotype 25_1 from the Atlit population had the lowest. The mean value of GSeC in each population varied from 0.010 to 0.105 mg kg⁻¹. The coefficient of variation for each population ranged from 12% to 163%. Significant correlations were found between GSeC and 12 ecogeographical factors out of 14 studied. Habitat soil type also significantly affected GSeC. The wild barley exhibited wider GSeC ranges and greater diversity than its cultivated counterparts. The higher Se grain concentrations found in H. spontaneum populations suggest that wild barley germplasm confer higher abilities for Se uptake and accumulation, which can be used for genetic studies of barley nutritional value and for further improvement of domesticated cereals.     

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley

Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high‐quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high‐confidence protein‐coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single‐copy plant genes, illustrating that the gene‐containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1‐specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research.     

Genetic Diversity Analysis of Tibetan Wild Barley Using SSR Markers

One hundred and six accessions of wild barley collected from Tibet, China, including 50 entries of the two-rowed wild barley Hordeum vulgare ssp. spontaneum (HS), 29 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon (HA), and 27 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon var. lagunculiforme (HL), were analyzed using 30 SSR markers selected from the seven barley linkage groups for studying genetic diversity and evolutionary relationship of the three subspecies of Tibetan wild barley to cultivated barley in China. Over the 30 genetic loci that were studied, 229 alleles were identified among the 106 accessions, of which 70 were common alleles. H. vulgare ssp. spontaneum possesses about thrice more private alleles (2.83 alleles/locus) than HS (0.93 alleles/locus), whereas almost no private alleles were detected in HL. The genetic diversity among-subspecies is much higher than that within-subspecies. Generally, the genetic diversity among the three subspecies is of the order HS > HL > HA. Phylogenetic analysis of the 106 accessions showed that all the accessions of HS and HA was clustered in their own groups, whereas the 27 accessions of HL were separated into two groups (14 entries with group HS and the rest with group HA). This indicated that HL was an intermediate form between HS and HA. Based on this study and previous works, we suggested that Chinese cultivated barley might evolve from HS via HL to HA.