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Barley is a model species for the investigation of the evolution, adaptation and spread of the world's important crops. In this article, we describe the first application of an oligonucleotide pool assay single nucleotide polymorphism (SNP) platform to assess the evolution of barley in a portion of the Fertile Crescent, a key region in the development of farming. A large collection of >1000 genetically mapped, genome-wide SNPs was assayed in geographically matched landrace and wild barley accessions (N=448) from Jordan and Syria. Landrace and wild barley categories were clearly genetically differentiated, but a limited degree of secondary contact was evident. Significant chromosome-level differences in diversity between barley types were observed around genes known to be involved in the evolution of cultivars. The region of Jordan and southern Syria, compared with the north of Syria, was supported by SNP data as a more likely domestication origin. Our data provide evidence for hybridization as a possible mechanism for the continued adaptation of landrace barley under cultivation, indicate regions of the genome that may be subject to selection processes and suggest limited origins for the development of the cultivated crop., (© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.)

In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.

Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Delta(l)-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley.

The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers. Four of the 22 markers (Bmac316, scssr03907, HVM67 and Bmag770) were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H, bin 13) in two different environments with common significant alleles (175, 177), whereas the HVHOTR1 marker (2H, bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398.

Associations between markers and drought related traits were investigated on a set of 57 advanced barley breeding lines, carrying various levels of introgression from Hordeum spontaneum lines 41-1 and 41-5, the best sources of drought tolerance in the ICARDA barley breeding program, using 74 simple sequences repeats (SSR) and 20 single nucleotide polymorphism markers. The 57 lines were evaluated for grain yield and drought related traits for three years (2003/04, 2004/05, 2005/06) in nine Mediterranean low rainfall environments. A high level of polymorphism was found with SSR markers, and the mean polymorphism information content and gene diversity values were 0.67 and 0.71, respectively. The number of alleles per locus varied from 2 to 11, with an average of 5.8 alleles per marker. Considering all the 57 lines, the linkage disequilibrium (LD) analysis was significant at a comparison-wise P < 0.01 level in nearly 9 % of the SSR marker pairs used and a decay of LD was observed to a value of r < 0.2 at a genetic distance of 40 cM. The association analysis revealed a total of 147 significant marker-trait associations for grain yield and drought related traits. A total of 72 (49 %) marker-trait associations showed favorable effects of the exotic germplasm where the H. spontaneum lines contributed to an improvement of the trait under drought stress conditions. The number of significant marker-trait associations per trait were: 12 for growth habit; 2 for growth vigor; 11 for peduncle extrusion; 5 for number of grains per spike; 20 for peduncle length; 16 for days to heading; 20 for plant height; 8 for spike length; 17 for thousand kernel weight; 30 for grain yield; 4 for harvest index and 2 for biological yield. The phenotypic variation explained by individual marker-trait associations ranged from 7.6 % to 36.2 %. The identification of genomic regions associated with grain yield and drought related traits is useful for the genetic improvement of cultivars better adapted to drought stress environments. Thus, the present study is encouraging in identifying significant marker-trait associations through LD based association mapping analysis, which could complement and augment previous quantitative trait loci information for the potential use of Marker Assisted Selection for drought. [ABSTRACT FROM AUTHOR]

Unpredictable drought conditions combined with extreme heat stress are major constraints limiting the production of barley (Hordeum vulgare L.), one of the most important rain-fed crops in West Asia and North Africa. Yield and yield stability might be improved by raising levels of both heterozygosity and heterogeneity, which could be achieved through increased outcrossing in barley landrace populations. Selection for outcrossing-related traits such as high anther extrusion, large anther sizes, and vigorous stigmas may increase the level of outcrossing. This investigation was conducted to quantify the genetic variance and calculate correlation coefficients for spikelet traits related to mating characteristics. For this purpose, F3-line populations derived from nine crosses between genotypes showing contrasting expression of anther extrusion were produced. F3-line populations were grown in field trials at three locations in Jordan during the 2001-2002 growing season. Anther extrusion was higher in the more favorable environment than in environments with low and variable precipitation. Anther extrusion and outcrossings related spikelet traits were influenced by genetic and environmental factors. Early heading F3-lines within populations showed a tendency toward higher anther extrusion, presumably because of escape from drought stress expected later in the growing season. The variation of outcrossing-related spikelet traits in F3-line populations was continuous, suggesting a polygenic inheritance, and exhibited transgressive segregation in some populations toward high anther extrusion. Most populations showed intermediate to high broad sense heritabilities for anther extrusion and anther length. However, low to intermediate heritabilities were detected for all other outcrossing-related traits. Positive genetic correlations were recorded between anther extrusion and anther and stigma size. Results suggest that outcrossing-related spikelet traits may respond to selection in particular in the case of anther extrusion and anther and stigma size. [ABSTRACT FROM AUTHOR]

A partial genetic linkage map was constructed on 71 doubled-haploid lines derived from a cross between the barley lines Tadmor and WI2291 with 181 molecular markers. The segregating population was used to detect markers linked to the geneMlg conferring resistance to powdery mildew (Erysiphe graminis f. sp. hordei) and to genes for quantitative resistance to scald (Rhynchosporium secalis). The gene Mlg on chromosome 4H was flanked by two AFLP markers at a distance of 2.0 and 2.4 cM, respectively. QTLs for resistance to scald were detected on chromosomes 2H and 3H. This association of molecular markers with qualitative and quantitative disease resistance loci represents a valuable starting-point for marker-assisted selection. [ABSTRACT FROM AUTHOR]