Low water availability is the major environmental factor limiting crop productivity. Transcriptom... more 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 activ...
Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domesti... more Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domestication episode, its evolution under domestication has resulted in various genetic modifications. Grain weight, embryo weight, and the interaction between those factors were examined among domesticated durum wheat and its direct progenitor, wild emmer wheat. Experimental data show that grain weight has increased over the course of wheat evolution without any parallel change in embryo weight, resulting in a significantly reduced (30%) embryo weight/grain weight ratio in domesticated wheat. The genetic factors associated with these modifications were further investigated using a population of recombinant inbred substitution lines that segregated for chromosome 2A. A cluster of loci affecting grain weight and shape was identified on the long arm of chromosome 2AL. Interestingly, a novel locus controlling embryo weight was mapped on chromosome 2AS, on which the wild emmer allele promotes heavier embryos and greater seedling vigour. To the best of our knowledge, this is the first report of a QTL for embryo weight in wheat. The results suggest a differential selection of grain and embryo weight during the evolution of domesticated wheat. It is argued that conscious selection by early farmers favouring larger grains and smaller embryos appears to have resulted in a significant change in endosperm weight/embryo weight ratio in the domesticated wheat. Exposing the genetic factors associated with endosperm and embryo size improves our understanding of the evolutionary dynamics of wheat under domestication and is likely to be useful for future wheat-breeding efforts.
OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A... more OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A transcriptomic analysis of the drought response of transgenic rice plants expressing P SARK ::IPT, validated by qPCR, indicated that OsWRKY47 expression was induced under drought stress in P SARK ::IPT plants. A PCR-assisted site selection assay (SELEX) of recombinant OsWRKY47 protein showed that the preferred sequence bound in vitro is (G/T)TTGACT. Bioinformatics analyses identified a number of gene targets of OsWRKY47; among these two genes encode a Calmodulin binding protein and a Cys-rich secretory protein. Using Oswrk47 knockout mutants and transgenic rice overexpressing OsWRKY47 we show that the transcription of these putative targets were regulated by OsWRKY47. Phenotypic analysis carried out with transgenic rice plants showed that Oswrky47 mutants displayed higher sensitivity to drought and reduced yield, while plants overexpressing OsWRKY47 were more tolerant.
Background
Drought is the major environmental stress threatening crop-plant productivity worldwid... more Background Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research.
Results We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism.
Conclusions Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved in novel drought adaptation mechanisms. The identified shared genes can provide a useful resource for subsequent research to better understand the mechanisms involved in drought adaptation across-species and can serve as a potential set of molecular biomarkers for progressive drought experiments.
Most wild Cicer species have narrow eco-geographic amplitude. Likewise, domesticated chickpea suf... more Most wild Cicer species have narrow eco-geographic amplitude. Likewise, domesticated chickpea suffers from severe adaptive limitations due to its unique evolutionary history. The wild progenitor may offer only limited adaptive allelic variation for improving the chickpea crop. Therefore, there is a need to explore allelic diversity between and within annual Cicer sp. that span diverse natural habitats. Here we characterized the allelic diversity between and within wild populations of C. pinnatifidum, C. judaicum and C. cuneatum spanning most of their documented native range in Turkey, Israel and Ethiopia. Eco-geographical analysis resulted in clear separation between the collection sites of C. cuneatum in east Africa and the other two east Mediterranean species. Analysis of molecular variance shows that only 18 % of the allelic variation accounts for differences between the three species, while 34 % was contributed from difference between populations. Interestingly, most (48 %) of the allelic variation was detected among accessions within populations. PCoA analysis confirmed the independent taxonomic and indeed the genetic integrity of the two east Mediterranean sister species C. pinnatifidum and C. judaicum. Conservation of large rich populations seems a more effective strategy than the preservation of small thin populations of annual Cicer sp. Given the relatively narrow geographic range of most annual Cicer sp., accessing germplasm lines from ecologically distinct habitats emerges as the most promising strategy for the identification of useful adaptive allelic variation.
Herbicide resistant weeds are becoming increasingly common, threatening global food security. Her... more Herbicide resistant weeds are becoming increasingly common, threatening global food security. Here, we present BrIFAR: a new model system for the functional study of mechanisms of herbicide resistance in grass weeds. We have developed a large collection of Brachypodium accessions, the BrI collection, representing a wide range of habitats. Wide screening of the responses of the accessions to four major herbicide groups (PSII, ACCase, ALS/AHAS and EPSPS inhibitors) identified 28 herbicide-resistance candidate accessions. Target-site resistance to PSII inhibitors was found in accessions collected from habitats with a known history of herbicide applications. An amino acid substitution in the psbA gene (serine264 to glycine) conferred resistance and also significantly affected the flowering and shoot dry weight of the resistant accession, as compared to the sensitive accession. Non-target site resistance to ACCase inhibitors was found in accessions collected from habitats with a history of herbicide application and from a nature reserve. In-vitro enzyme activity tests and responses following pre-treatment with malathion (a cytochrome-P450 inhibitor) indicated sensitivity at the enzyme level, and give strong support to diclofop-methyl and pinoxaden enhanced detoxification as NTS resistance mechanism. BrIFAR can promote better understanding of the evolution of mechanisms of herbicide resistance and aid the implementation of integrative management approaches for sustainable agriculture.
Durum wheat, Triticum turgidum ssp. durum Desf., is an important crop particularly in the Mediter... more Durum wheat, Triticum turgidum ssp. durum Desf., is an important crop particularly in the Mediterranean basin. Powdery mildew, caused by the pathogen Blumeria graminis f. sp. tritici (Bgt), is a major disease of wheat that results in significant yield losses worldwide. A recombinant inbred line (RIL) population, derived from a cross between durum wheat and wild emmer wheat, T. turgidum ssp. dicoccoides, was used for genomic dissection of quantitative and qualitative resistance loci against wheat powdery mildew based on a genomic map of >600 markers, evenly distributed across the A and B genomes of tetraploid wheat. The genetic analysis of the phenotypic reactions of the RIL population to two Bgt isolates revealed two different resistance mechanisms. The first is monogenic: a wild emmer wheat allele in a single locus conferring complete resistance to Bgt#15, previously designated as PmG16. The second one is polygenic: a set of durum wheat alleles, in five independent QTLs that control partial resistance to Bgt#66 in the RIL population, with a LOD score range of 3.4–19.8. One of them is a major quantitative resistance locus (QRL) that was mapped on chromosome 1A and explains 26.4 % of the variance. In most of the detected QRLs, the durum wheat alleles conferred resistance to powdery mildew. These findings are exceptional in the sense that, so far, only a few Pm alleles originated from a durum wheat background. Therefore, our results emphasize the high potential of exploiting the wide genetic diversity of tetraploid wheat germplasm for wheat breeding using modern wheat genomics tools.
Low water availability is the major environmental factor limiting crop productivity. Transcriptom... more 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 activ...
Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domesti... more Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domestication episode, its evolution under domestication has resulted in various genetic modifications. Grain weight, embryo weight, and the interaction between those factors were examined among domesticated durum wheat and its direct progenitor, wild emmer wheat. Experimental data show that grain weight has increased over the course of wheat evolution without any parallel change in embryo weight, resulting in a significantly reduced (30%) embryo weight/grain weight ratio in domesticated wheat. The genetic factors associated with these modifications were further investigated using a population of recombinant inbred substitution lines that segregated for chromosome 2A. A cluster of loci affecting grain weight and shape was identified on the long arm of chromosome 2AL. Interestingly, a novel locus controlling embryo weight was mapped on chromosome 2AS, on which the wild emmer allele promotes heavier embryos and greater seedling vigour. To the best of our knowledge, this is the first report of a QTL for embryo weight in wheat. The results suggest a differential selection of grain and embryo weight during the evolution of domesticated wheat. It is argued that conscious selection by early farmers favouring larger grains and smaller embryos appears to have resulted in a significant change in endosperm weight/embryo weight ratio in the domesticated wheat. Exposing the genetic factors associated with endosperm and embryo size improves our understanding of the evolutionary dynamics of wheat under domestication and is likely to be useful for future wheat-breeding efforts.
OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A... more OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A transcriptomic analysis of the drought response of transgenic rice plants expressing P SARK ::IPT, validated by qPCR, indicated that OsWRKY47 expression was induced under drought stress in P SARK ::IPT plants. A PCR-assisted site selection assay (SELEX) of recombinant OsWRKY47 protein showed that the preferred sequence bound in vitro is (G/T)TTGACT. Bioinformatics analyses identified a number of gene targets of OsWRKY47; among these two genes encode a Calmodulin binding protein and a Cys-rich secretory protein. Using Oswrk47 knockout mutants and transgenic rice overexpressing OsWRKY47 we show that the transcription of these putative targets were regulated by OsWRKY47. Phenotypic analysis carried out with transgenic rice plants showed that Oswrky47 mutants displayed higher sensitivity to drought and reduced yield, while plants overexpressing OsWRKY47 were more tolerant.
Background
Drought is the major environmental stress threatening crop-plant productivity worldwid... more Background Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research.
Results We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism.
Conclusions Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved in novel drought adaptation mechanisms. The identified shared genes can provide a useful resource for subsequent research to better understand the mechanisms involved in drought adaptation across-species and can serve as a potential set of molecular biomarkers for progressive drought experiments.
Most wild Cicer species have narrow eco-geographic amplitude. Likewise, domesticated chickpea suf... more Most wild Cicer species have narrow eco-geographic amplitude. Likewise, domesticated chickpea suffers from severe adaptive limitations due to its unique evolutionary history. The wild progenitor may offer only limited adaptive allelic variation for improving the chickpea crop. Therefore, there is a need to explore allelic diversity between and within annual Cicer sp. that span diverse natural habitats. Here we characterized the allelic diversity between and within wild populations of C. pinnatifidum, C. judaicum and C. cuneatum spanning most of their documented native range in Turkey, Israel and Ethiopia. Eco-geographical analysis resulted in clear separation between the collection sites of C. cuneatum in east Africa and the other two east Mediterranean species. Analysis of molecular variance shows that only 18 % of the allelic variation accounts for differences between the three species, while 34 % was contributed from difference between populations. Interestingly, most (48 %) of the allelic variation was detected among accessions within populations. PCoA analysis confirmed the independent taxonomic and indeed the genetic integrity of the two east Mediterranean sister species C. pinnatifidum and C. judaicum. Conservation of large rich populations seems a more effective strategy than the preservation of small thin populations of annual Cicer sp. Given the relatively narrow geographic range of most annual Cicer sp., accessing germplasm lines from ecologically distinct habitats emerges as the most promising strategy for the identification of useful adaptive allelic variation.
Herbicide resistant weeds are becoming increasingly common, threatening global food security. Her... more Herbicide resistant weeds are becoming increasingly common, threatening global food security. Here, we present BrIFAR: a new model system for the functional study of mechanisms of herbicide resistance in grass weeds. We have developed a large collection of Brachypodium accessions, the BrI collection, representing a wide range of habitats. Wide screening of the responses of the accessions to four major herbicide groups (PSII, ACCase, ALS/AHAS and EPSPS inhibitors) identified 28 herbicide-resistance candidate accessions. Target-site resistance to PSII inhibitors was found in accessions collected from habitats with a known history of herbicide applications. An amino acid substitution in the psbA gene (serine264 to glycine) conferred resistance and also significantly affected the flowering and shoot dry weight of the resistant accession, as compared to the sensitive accession. Non-target site resistance to ACCase inhibitors was found in accessions collected from habitats with a history of herbicide application and from a nature reserve. In-vitro enzyme activity tests and responses following pre-treatment with malathion (a cytochrome-P450 inhibitor) indicated sensitivity at the enzyme level, and give strong support to diclofop-methyl and pinoxaden enhanced detoxification as NTS resistance mechanism. BrIFAR can promote better understanding of the evolution of mechanisms of herbicide resistance and aid the implementation of integrative management approaches for sustainable agriculture.
Durum wheat, Triticum turgidum ssp. durum Desf., is an important crop particularly in the Mediter... more Durum wheat, Triticum turgidum ssp. durum Desf., is an important crop particularly in the Mediterranean basin. Powdery mildew, caused by the pathogen Blumeria graminis f. sp. tritici (Bgt), is a major disease of wheat that results in significant yield losses worldwide. A recombinant inbred line (RIL) population, derived from a cross between durum wheat and wild emmer wheat, T. turgidum ssp. dicoccoides, was used for genomic dissection of quantitative and qualitative resistance loci against wheat powdery mildew based on a genomic map of >600 markers, evenly distributed across the A and B genomes of tetraploid wheat. The genetic analysis of the phenotypic reactions of the RIL population to two Bgt isolates revealed two different resistance mechanisms. The first is monogenic: a wild emmer wheat allele in a single locus conferring complete resistance to Bgt#15, previously designated as PmG16. The second one is polygenic: a set of durum wheat alleles, in five independent QTLs that control partial resistance to Bgt#66 in the RIL population, with a LOD score range of 3.4–19.8. One of them is a major quantitative resistance locus (QRL) that was mapped on chromosome 1A and explains 26.4 % of the variance. In most of the detected QRLs, the durum wheat alleles conferred resistance to powdery mildew. These findings are exceptional in the sense that, so far, only a few Pm alleles originated from a durum wheat background. Therefore, our results emphasize the high potential of exploiting the wide genetic diversity of tetraploid wheat germplasm for wheat breeding using modern wheat genomics tools.
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Papers by zvi peleg
Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research.
Results
We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism.
Conclusions
Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved in novel drought adaptation mechanisms. The identified shared genes can provide a useful resource for subsequent research to better understand the mechanisms involved in drought adaptation across-species and can serve as a potential set of molecular biomarkers for progressive drought experiments.
Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research.
Results
We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism.
Conclusions
Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved in novel drought adaptation mechanisms. The identified shared genes can provide a useful resource for subsequent research to better understand the mechanisms involved in drought adaptation across-species and can serve as a potential set of molecular biomarkers for progressive drought experiments.