Tamar Krugman

RAPD polymorphism of wild emmer wheat populations, Triticum dicoccoides, in Israel

Abstract Genetic diversity in random amplified polymorphic DNAs (RAPDs) was studied in 110 genotypes of the tetraploid wild progenitor of wheat, Triticum dicoccoides, from 11 populations sampled in Israel and Turkey. Our results show high level of diversity of RAPD markers in wild wheat populations in Israel. The ten primers used in this study amplified 59 scorable RAPD loci of which 48 (81.4%) were polymorphic and 11 monomorphic. RAPD analysis was found to be highly effective in distinguishing genotypes of T. dicoccoides originating from diverse ecogeographical sites in Israel and Turkey, with 95.5% of the 100 genotypes correctly classified into sites of origin by discriminant analysis based on RAPD genotyping. However, interpopulation genetic distances showed no association with geographic distance between the population sites of origin, negating a simple isolation by distance model. Spatial autocorrelation of RAPD frequencies suggests that migration is not influential. Our present RAPD results are non-random and in agreement with the previously obtained allozyme patterns, although the genetic diversity values obtained with RAPDs are much higher than the allozyme values. Significant correlates of RAPD markers with various climatic and soil factors suggest that, as in the case of allozymes, natural selection causes adaptive RAPD ecogeographical differentiation. The results obtained suggest that RAPD markers are useful for the estimation of genetic diversity in wild material of T. dicoccoides and the identification of suitable parents for the development of mapping populations for the tagging of agronomically important traits derived from T. dicoccoides.

Genomic dissection of drought resistance in durum wheat × wild emmer wheat recombinant inbreed line population.

Drought is the major factor limiting wheat productivity worldwide. The gene pool of wild emmer wheat, Triticum turgidum ssp. dicoccoides, harbours a rich allelic repertoire for morpho-physiological traits conferring drought resistance. The genetic and physiological bases of drought responses were studied here in a tetraploid wheat population of 152 recombinant inbreed lines (RILs), derived from a cross between durum wheat (cv. Langdon) and wild emmer (acc# G18-16), under contrasting water availabilities. Wide genetic variation was found among RILs for all studied traits. A total of 110 quantitative trait loci (QTLs) were mapped for 11 traits, with LOD score range of 3.0-35.4. Several QTLs showed environmental specificity, accounting for productivity and related traits under water-limited (20 QTLs) or well-watered conditions (15 QTLs), and in terms of drought susceptibility index (22 QTLs). Major genomic regions controlling productivity and related traits were identified on chromosomes 2B, 4A, 5A and 7B. QTLs for productivity were associated with QTLs for drought-adaptive traits, suggesting the involvement of several strategies in wheat adaptation to drought stress. Fifteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. The identified QTLs may facilitate the use of wild alleles for improvement of drought resistance in elite wheat cultivars.

Natural selection of allozyme polymorphisms: a microgeographical differentiation by edaphic, topographical, and temporal factors in wild emmer wheat (Triticum dicoccoides)

SummaryAllozymic variation in proteins encoded by 47 loci was analyzed electrophoretically in 1983/4 and 1984/5 in 356 individual plants of wild emmer wheat, Triticum dicoccoides, from a microsite at Tabigha, north of the Sea of Galilee, Israel. Each year the test involved two 100-meter transects, each equally subdivided into basalt and terra rossa soil types, and comparisons were based on 16 common polymorphic loci. Significant genetic differentiation, genetic phase disequilibria, and genome organization according to soil type were found over very short distances. Our results suggest that allozyme polymorphisms in wild emmer wheat are partly adaptive, and that they differentiate at both single and multilocus structures primarily from environmental stress of such ecological factors as soil type, topography, and temporal changes, probably through aridity stress.

Genetic basis of barley caryopsis dormancy and seedling desiccation tolerance at the germination stage.

The genomic regions controlling caryopsis dormancy and seedling desiccation tolerance were identified using 152 F4 lines derived from a cross between Mona, a Swedish cultivar, and an Israeli xeric wild barley Hordeum spontaneum genotype collected at Wadi Qilt, Israel. Dormancy, the inability of a viable seed to germinate, and desiccation tolerance, the ability of the desiccated seedlings to revive after rehydration, were characterized by fitting the germination and revival data with growth curves, using three parameters: minimum, maximum, and slope of germination or revival rate derived by the least square method. The genetic map was constructed with 85 genetic markers (SSRs, AFLPs, STSs, and Dhn genes) using the multipoint-mapping algorithm. Quantitative trait loci (QTLs) mapping was conducted with the multiqtl package. Ten genomic regions were detected that affected the target traits, seven of which affected both dormancy and desiccation tolerance traits. Both the wild barley genotype and the Swedish cultivar contributed the favorite alleles for caryopsis dormancy, whereas seedling desiccation tolerance was attributed to alleles descending from the cultivar. The results indicate that some barley dormancy genes are lost during domestication and that dormancy QTLs are associated with abiotic stress tolerance.

Edaphic natural selection of allozyme polymorphisms in Aegilops peregrina at a Galilee microsite in Israel

Allozymic diversity in proteins encoded by 19 loci was analysed electrophoretically in 70 individual plants of the wild tetraploid wheat Aegilops peregrina, from a microsite at Tabigha, north of the Sea of Galilee, Israel. The test involved a 100 m transect, equally subdivided into basalt and terra-rossa soil types and comparisons were based on the two polymorphic esterase loci. Significant genetic differentiation according to soil type was found over very short distances. Our results suggest that allozyme polymorphisms in A. peregrina are adaptive and that they differentiate primarily by soil selection, probably through aridity stress.

Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat

Low water availability is the major environmental factor limiting crop productivity. Transcriptome analysis was used to study terminal drought response in wild emmer wheat, Triticum dicoccoides, genotypes contrasting in their productivity and yield stability under drought stress. A total of 5,892 differentially regulated transcripts were identified between drought and well-watered control and/or between drought resistant (R) and drought susceptible (S) genotypes. Functional enrichment analyses revealed that multilevel regulatory and signalling processes were significantly enriched among the drought-induced transcripts, in particular in the R genotype. Therefore, further analyses were focused on selected 221 uniquely expressed or highly abundant transcripts in the R genotype, as potential candidates for drought resistance genes. Annotation of the 221 genes revealed that 26% of them are involved in multilevel regulation, including: transcriptional regulation, RNA binding, kinase activity and calcium and abscisic acid signalling implicated in stomatal closure. Differential expression patterns were also identified in genes known to be involved in drought adaptation pathways, such as: cell wall adjustment, cuticular wax deposition, lignification, osmoregulation, redox homeostasis, dehydration protection and drought-induced senescence. These results demonstrate the potential of wild emmer wheat as a source for candidate genes for improving drought resistance.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

BackgroundThe wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.ResultsFingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.ConclusionsThis study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

Wild barley eibi1 mutation identifies a gene essential for leaf water conservation

Drought is a major abiotic stress that limits plant growth and crop productivity. A spontaneous wilty mutant (eibi1) hypersensitive to drought was identified from wild barley (Hordeum spontaneum Koch). eibi1 showed the highest relative water loss rate among the known wilty mutants, which indicates that eibi1 is one of the most drought-sensitive mutants. eibi1 had the same abscisic acid (ABA) level, the same ability to accumulate stress-induced ABA, and the same stomatal movement in response to light, dark, drought, and exogenous ABA as the wild type, revealing that eibi1 was neither an ABA-deficient nor an ABA-insensitive mutant. The eibi1 leaves had a larger chlorophyll efflux rate in 80% ethanol than the wild-type leaves; and the transpiration rate of eibi1 was more closely related to chlorophyll efflux rate than to stomatal density, demonstrating that the cuticle of eibi1 was defective. eibi1 will be a promising candidate to study the actual barrier layer in the cuticle that limits water loss of the plant. Exogenous ABA reduced leaf length growth in eibi1 more than in the wild type, implying an interaction on plant growth of ABA signal transduction and the eibi1 product. One may infer that the eibi1 product may reverse the growth inhibition induced by ABA.

Alteration in expression of hormone-related genes in wild emmer wheat roots associated with drought adaptation mechanisms.

Transcriptomic and metabolomic profiles were used to unravel drought adaptation mechanisms in wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of cultivated wheat, by comparing the response to drought stress in roots of genotypes contrasting in drought tolerance. The differences between the drought resistant (R) and drought susceptible (S) genotypes were characterized mainly by shifts in expression of hormone-related genes (e.g., gibberellins, abscisic acid (ABA) and auxin), including biosynthesis, signalling and response; RNA binding; calcium (calmodulin, caleosin and annexin) and phosphatidylinositol signalling, in the R genotype. ABA content in the roots of the R genotype was higher in the well-watered treatment and increased in response to drought, while in the S genotype ABA was invariant. The metabolomic profiling revealed in the R genotype a higher accumulation of tricarboxylic acid cycle intermediates and drought-related metabolites, including glucose, trehalose, proline and glycine. The integration of transcriptomics and metabolomics results indicated that adaptation to drought included efficient regulation and signalling pathways leading to effective bio-energetic processes, carbon metabolism and cell homeostasis. In conclusion, mechanisms of drought tolerance were identified in roots of wild emmer wheat, supporting our previous studies on the potential of this genepool as a valuable source for novel candidate genes to improve drought tolerance in cultivated wheat.

Parallel microgeographic patterns of genetic diversity and divergence revealed by allozyme, RAPD, and microsatellites in Triticum dicoccoides at Ammiad, Israel

The levels of genetic diversity were compared by means of 35 allozyme, 60 RAPD, and 25 microsatellite (SSR) markers for 75–175 individuals of tetraploid wild emmer wheat (Triticum dicoccoides) collected in 1993 from a microgeographic microsite, Ammiad, north of the Sea of Galilee, Israel. This microsite included four major habitats, which showed highly significant differentiation in ecological factors, in particular with respect to rock cover, proximity and height, and surface soil moisture in the early growing season of T. dicoccoides. Higher within-subpopulation genetic diversity was found in the primarily non-coding DNA regions (RAPD and SSR) rather than in the protein-coding (allozymes) regions. However, much larger gene differentiation (GST) among the subpopulations was observed in the protein-coding allozymes than in the RAPDs and SSRs. Larger genetic distance was found at SSR loci, followed by allozyme and RAPD loci. The subpopulations in drier habitats tend to have higher allozyme, RAPD and SSR diversities (He), the relatively wet Karst subpopulation showed only about half He of the other relatively drier habitats. The subpopulations with larger difference of soil moisture between habitats tend to show larger genetic distances at allozyme, RAPD and SSR loci. These results suggest that climatic selection through aridity stress may be an important factor acting on both structural protein-coding and presumably partly regulatory non-coding DNA regions, resulting in microscale adaptive patterns, although hitchhiking and random drift may also intervene. These results have profound implications for genetic conservation both in situ and ex situ.