Molecular analysis of the desaturase2 (desat2) gene responsible for female cuticular hydrocarbon ... more Molecular analysis of the desaturase2 (desat2) gene responsible for female cuticular hydrocarbon synthesis, revealed that all tested Israeli populations of Drosophila melanogaster belong to the ‘Low’ type (low ratio of 5,9‐/7,11‐heptacosadiene) with a 16 bp deletion in the promoter region. Additional deletion leading to the appearance of the stop‐codon TGA was found in exon 1 in populations inhabiting opposite slopes at Nahal Oren canyon. Mating experiments between carriers of various desat2 alleles estimated the putative effect of desat2 status on courtship behaviour. The allele with an additional deletion in exon 1 seems to play some role in mating success, which is associated with shorter courtship latency and courtship duration. The appearance and maintenance of this mutant allele in populations inhabiting Nahal Oren canyon may reflect flies’ adaptation to peculiar microscale climatic conditions and may be associated with incipient sympatric differentiation.
Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can ... more Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can be quantified by the classical coefficient of coincidence (CoC) `but this characteristic is highly variable and specific to the pair of chromosomal intervals considered. Several models were proposed to characterize COI on a chromosome-wise level. In the gamma model, the strength of interference is characterized by a shape parameterν, while the gamma-sprinkled two-pathway model (GS) accounts for both interference-dependent and independent crossover (CO) events by fitting a mixture of gamma distributions withv>1 andv=1, correspondingly, and mixture proportions 1-pandp. In reality, COI can vary along chromosomes resulting in low compliance of the fitted model to real data. Additional inconsistency can be caused by common neglecting of possible negative COI in the model, earlier reported for several organisms. In this work, we propose an extension of the GS-model to take possible negative...
The objectives of this study were to identify genetic loci in the bread wheat genome that would i... more The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H2 = 0.5–0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 ...
The objective of the present study was to evaluate the response of Norfa White breeder layers pro... more The objective of the present study was to evaluate the response of Norfa White breeder layers producing ∼200 eggs annually or ∼33 g egg/d to different protein levels of 17, 14, and 11% when 14 or 11% was fed without or with supplementations of Met and Lys only or with Arg, Thr, Val, He, and Trp, in the presence or absence of glutamic and glycine acid as non essential amino acids in the 1st trial. In the 2nd and 3rd trials, 14% CP vegetable or practical diet was fed without or with Met and Lys, or Met, Lys, and Arg, or Met, Lys and Trp supplementation. A positive control diet containing 17% CP was also included. Results indicated that a minimum protein level of 14% CP supplemented with Met and Lys is required to achieve comparable egg production, egg weight, egg mass, feed/ egg mass ratio or feed conversion ratio (FCR), egg quality parameters as well as fertility, hatchability and weight of day-old chicks as those of the 17% CP diet. Diet containing 11% CP supplemented with Met, Lys,...
Key message Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on ... more Key message Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on highdensity SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Abstract Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F 6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
progress of analytical methods. In sexually reproducing organisms, recombination is one of the ma... more progress of analytical methods. In sexually reproducing organisms, recombination is one of the major sources of genetic variation. Being sensitive to both genomic and ecological factors, it ensures a fine-tuned balance between stability and flexibility of genetic organization, enabling the adaptation of populations to their current environments and, simultaneously, the adaptability in face of potential challenges. Bridging between heredity and environment, recombination is both a factor of and a subject to evolution, which feeds up the ever-increasing interest in this process within the biodiversity paradigm. Analysis of natural populations, laboratory experiments, and theoretical modeling shed new light on the short-and long-term effects of recombination, as well as on its interplay with other evolutionary factors, such as selection, mutation, transposable elements (TEs), genetic drift, and gene flow. This, in turn, contributes to a better understanding of how recombination itself could have originated, evolved, and maintained. Yet, numerous important aspects of recombination evolution remain obscure. This is especially true for the relatively new question of why recombination possesses a certain set of rather universal features (crossover interference, ecological plasticity, fitness dependence, etc.), which started to fascinate researchers much later than the classic question of why recombination exists.
Proceedings of the National Academy of Sciences, 2013
Significance The microclimatic contrast between opposing slopes of “Evolution Canyon” (Mount Carm... more Significance The microclimatic contrast between opposing slopes of “Evolution Canyon” (Mount Carmel, Israel) provides a natural laboratory for testing the effects of abiotic factors on biodiversity and population genetic differentiation in a geographical microscale. Drosophila melanogaster fruitflies originating from the opposite canyon slopes are subject to divergent selection leading to slope-specific adaptations, accompanied by incipient mating isolation, all in the face of pervasive demographic processes, including ongoing genetic exchange. We demonstrate that interslope genetic changes in this species accumulate in a number of chromosomal differentiation “islands” and that gene networks related to adaptive responses and reproductive processes are thus significantly affected.
Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in wat... more Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in water stress tolerance of wild barley (Hordeum spontaneoum), the progenitor of cultivated barley, were investigated using genotypes contrasting in their response to water stress. Gene expression profiles of water-stress tolerant vs. water-stress sensitive wild barley genotypes, under severe dehydration stress applied at the seedling stage, were compared using cDNA-AFLP analysis. Of the 1100 transcript-derived fragments (TDFs) amplified about 70 displayed differential expression between control and stress conditions. Eleven of them showed clear difference (up-or down-regulation) between tolerant and susceptible genotypes. These TDFs were isolated, sequenced and tested by RT-PCR. The differential expression of seven TDFs was confirmed by RT-PCR, and TDF-4 was selected as a promising candidate gene for water-stress tolerance. The corresponding gene, designated Hsdr4 (Hordeum spontaneum dehydration-responsive), was sequenced and the transcribed and flanking regions were determined. The deduced amino acid sequence has similarity to the rice Rho-GTPase-activating protein-like with a Sec14 p-like lipid-binding domain. Analysis of Hsdr4 promoter region that was isolated by screening a barley BAC library, revealed a new putative miniature inverted-repeat transposable element (MITE), and several potential stress-related binding sites for transcription factors (MYC, MYB, LTRE, and GT-1), suggesting a role of the Hsdr4 gene in plant tolerance to dehydration stress. Furthermore, the Hsdr4 gene was mapped using wild barley mapping population to the long arm of chromosome 3H between markers EBmac541 and EBmag705, within a region that previously was shown to affect osmotic adaptation in barley. Keywords cDNA-AFLP Á Dehydration stress Á Gene expression Á Drought tolerance Á Wild barley Abbreviations cDNA-AFLP cDNA-amplified fragment length polymorphism TDF transcript-derived fragment RT-PCR reverse transcription polymerase chain reaction Q-PCR quantitative expression analysis by real-time PCR UTR untranslated region SNP single nucleotide polymorphism QTL quantitative trait locus MITE miniature inverted-repeat transposable element The sequences reported in this paper have been deposited in the NCBI and dbEST databases. The accession numbers are incorporated in the text. The accession number of Hsdr4 is DQ464370. The accession numbers of the ESTs are: TDF
Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity... more Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity. A key question concerns the spatial scale at which genetic differentiation occurs and to what extent it is driven by natural selection. The Levant region exhibits a strong ecological gradient along the North-South axis, with numerous small canyons in an East-West direction and with small-scale environmental gradients on the opposing North-and South-facing slopes. We sequenced 34 short genomic regions in 54 accessions of wild barley collected throughout Israel and from the opposing slopes of two canyons. The nucleotide diversity of the total sample is 0.0042, which is about two-thirds of a sample from the whole species range (0.0060). Thirty accessions collected at 'Evolution Canyon' (EC) at Nahal Oren, close to Haifa, have a nucleotide diversity of 0.0036, and therefore harbor a large proportion of the genetic diversity. There is a high level of genetic clustering throughout Israel and within EC, which roughly differentiates the slopes. Accessions from the hot and dry South-facing slope have significantly reduced genetic diversity and are genetically more distinct from accessions from the North-facing slope, which are more similar to accessions from other regions in Northern Israel. Statistical population models indicate that wild barley within the EC consist of three separate genetic clusters with substantial gene flow. The data indicate a high level of population structure at large and small geographic scales that shows isolation-by-distance, and is also consistent with ongoing natural selection contributing to genetic differentiation at a small geographic scale.
A review of previous reports on indirect selection for recombination in Drosophila melanogaster. ... more A review of previous reports on indirect selection for recombination in Drosophila melanogaster. Table S2. Effect of desiccation selection on the coefficient of coincidence in adjacent and non-adjacent intervals of D. melanogaster. Table S3. Effect of hypoxia and hyperoxia selection on the coefficient of coincidence in adjacent and non-adjacent intervals of D. melanogaster. Table S4. Coincidence of interval-pair cases of changes in interference with significant positive correlation between rf values in the interval-pairs (a) and with significant increases in rf in desiccation, hypoxia, and hyperoxia selection variants (b). (PDF 486 kb)
Estimates of the coefficients of coincidence for non-adjacent intervals per replicate and entire ... more Estimates of the coefficients of coincidence for non-adjacent intervals per replicate and entire variants (selection and control). (PDF 2103 kb)
Estimates of the coefficients of coincidence for adjacent intervals per replicate and entire vari... more Estimates of the coefficients of coincidence for adjacent intervals per replicate and entire variants (selection and control). (PDF 2958 kb)
The evolutionary basis of reproductive success in different environments is of major interest in ... more The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. We sequenced mRNA extracted from spikelets at the flowering stage in drought-treated and control plants. The barley genome was used for a reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drou...
Several problems in modern genome mapping analysis belong to the field of discrete
optimization ... more Several problems in modern genome mapping analysis belong to the field of discrete
optimization on a set of all possible orders. In this paper we propose formulations,
mathematical models and algorithms for genetic/genomic mapping problem, that can be formulated in TSP-like terms. These include: ordering of marker loci (or genes) in
multilocus genetic mapping (MGM), multilocus consensus mapping (MCGM), and
physical mapping problem (PMP). All these problems are considered as computationally challenging because of noisy marker scores, large-size data sets, specific constraints on certain classes of orders, and other complications. The presence of specific constraints on ordering of some elements in these problems does not allow applying effectively the well-known powerful discrete optimization algorithms like Cutting-plane, Genetic algorithm with EAX crossover and famous Lin-Kernighan. In the paper we demonstrate that developed by us Guided Evolution Strategy algorithms successfully solves this class of discrete constrained optimization problems. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on three genetic/genomic problems with up to 2,500 points.
Molecular analysis of the desaturase2 (desat2) gene responsible for female cuticular hydrocarbon ... more Molecular analysis of the desaturase2 (desat2) gene responsible for female cuticular hydrocarbon synthesis, revealed that all tested Israeli populations of Drosophila melanogaster belong to the ‘Low’ type (low ratio of 5,9‐/7,11‐heptacosadiene) with a 16 bp deletion in the promoter region. Additional deletion leading to the appearance of the stop‐codon TGA was found in exon 1 in populations inhabiting opposite slopes at Nahal Oren canyon. Mating experiments between carriers of various desat2 alleles estimated the putative effect of desat2 status on courtship behaviour. The allele with an additional deletion in exon 1 seems to play some role in mating success, which is associated with shorter courtship latency and courtship duration. The appearance and maintenance of this mutant allele in populations inhabiting Nahal Oren canyon may reflect flies’ adaptation to peculiar microscale climatic conditions and may be associated with incipient sympatric differentiation.
Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can ... more Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can be quantified by the classical coefficient of coincidence (CoC) `but this characteristic is highly variable and specific to the pair of chromosomal intervals considered. Several models were proposed to characterize COI on a chromosome-wise level. In the gamma model, the strength of interference is characterized by a shape parameterν, while the gamma-sprinkled two-pathway model (GS) accounts for both interference-dependent and independent crossover (CO) events by fitting a mixture of gamma distributions withv>1 andv=1, correspondingly, and mixture proportions 1-pandp. In reality, COI can vary along chromosomes resulting in low compliance of the fitted model to real data. Additional inconsistency can be caused by common neglecting of possible negative COI in the model, earlier reported for several organisms. In this work, we propose an extension of the GS-model to take possible negative...
The objectives of this study were to identify genetic loci in the bread wheat genome that would i... more The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H2 = 0.5–0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 ...
The objective of the present study was to evaluate the response of Norfa White breeder layers pro... more The objective of the present study was to evaluate the response of Norfa White breeder layers producing ∼200 eggs annually or ∼33 g egg/d to different protein levels of 17, 14, and 11% when 14 or 11% was fed without or with supplementations of Met and Lys only or with Arg, Thr, Val, He, and Trp, in the presence or absence of glutamic and glycine acid as non essential amino acids in the 1st trial. In the 2nd and 3rd trials, 14% CP vegetable or practical diet was fed without or with Met and Lys, or Met, Lys, and Arg, or Met, Lys and Trp supplementation. A positive control diet containing 17% CP was also included. Results indicated that a minimum protein level of 14% CP supplemented with Met and Lys is required to achieve comparable egg production, egg weight, egg mass, feed/ egg mass ratio or feed conversion ratio (FCR), egg quality parameters as well as fertility, hatchability and weight of day-old chicks as those of the 17% CP diet. Diet containing 11% CP supplemented with Met, Lys,...
Key message Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on ... more Key message Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on highdensity SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Abstract Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F 6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
progress of analytical methods. In sexually reproducing organisms, recombination is one of the ma... more progress of analytical methods. In sexually reproducing organisms, recombination is one of the major sources of genetic variation. Being sensitive to both genomic and ecological factors, it ensures a fine-tuned balance between stability and flexibility of genetic organization, enabling the adaptation of populations to their current environments and, simultaneously, the adaptability in face of potential challenges. Bridging between heredity and environment, recombination is both a factor of and a subject to evolution, which feeds up the ever-increasing interest in this process within the biodiversity paradigm. Analysis of natural populations, laboratory experiments, and theoretical modeling shed new light on the short-and long-term effects of recombination, as well as on its interplay with other evolutionary factors, such as selection, mutation, transposable elements (TEs), genetic drift, and gene flow. This, in turn, contributes to a better understanding of how recombination itself could have originated, evolved, and maintained. Yet, numerous important aspects of recombination evolution remain obscure. This is especially true for the relatively new question of why recombination possesses a certain set of rather universal features (crossover interference, ecological plasticity, fitness dependence, etc.), which started to fascinate researchers much later than the classic question of why recombination exists.
Proceedings of the National Academy of Sciences, 2013
Significance The microclimatic contrast between opposing slopes of “Evolution Canyon” (Mount Carm... more Significance The microclimatic contrast between opposing slopes of “Evolution Canyon” (Mount Carmel, Israel) provides a natural laboratory for testing the effects of abiotic factors on biodiversity and population genetic differentiation in a geographical microscale. Drosophila melanogaster fruitflies originating from the opposite canyon slopes are subject to divergent selection leading to slope-specific adaptations, accompanied by incipient mating isolation, all in the face of pervasive demographic processes, including ongoing genetic exchange. We demonstrate that interslope genetic changes in this species accumulate in a number of chromosomal differentiation “islands” and that gene networks related to adaptive responses and reproductive processes are thus significantly affected.
Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in wat... more Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in water stress tolerance of wild barley (Hordeum spontaneoum), the progenitor of cultivated barley, were investigated using genotypes contrasting in their response to water stress. Gene expression profiles of water-stress tolerant vs. water-stress sensitive wild barley genotypes, under severe dehydration stress applied at the seedling stage, were compared using cDNA-AFLP analysis. Of the 1100 transcript-derived fragments (TDFs) amplified about 70 displayed differential expression between control and stress conditions. Eleven of them showed clear difference (up-or down-regulation) between tolerant and susceptible genotypes. These TDFs were isolated, sequenced and tested by RT-PCR. The differential expression of seven TDFs was confirmed by RT-PCR, and TDF-4 was selected as a promising candidate gene for water-stress tolerance. The corresponding gene, designated Hsdr4 (Hordeum spontaneum dehydration-responsive), was sequenced and the transcribed and flanking regions were determined. The deduced amino acid sequence has similarity to the rice Rho-GTPase-activating protein-like with a Sec14 p-like lipid-binding domain. Analysis of Hsdr4 promoter region that was isolated by screening a barley BAC library, revealed a new putative miniature inverted-repeat transposable element (MITE), and several potential stress-related binding sites for transcription factors (MYC, MYB, LTRE, and GT-1), suggesting a role of the Hsdr4 gene in plant tolerance to dehydration stress. Furthermore, the Hsdr4 gene was mapped using wild barley mapping population to the long arm of chromosome 3H between markers EBmac541 and EBmag705, within a region that previously was shown to affect osmotic adaptation in barley. Keywords cDNA-AFLP Á Dehydration stress Á Gene expression Á Drought tolerance Á Wild barley Abbreviations cDNA-AFLP cDNA-amplified fragment length polymorphism TDF transcript-derived fragment RT-PCR reverse transcription polymerase chain reaction Q-PCR quantitative expression analysis by real-time PCR UTR untranslated region SNP single nucleotide polymorphism QTL quantitative trait locus MITE miniature inverted-repeat transposable element The sequences reported in this paper have been deposited in the NCBI and dbEST databases. The accession numbers are incorporated in the text. The accession number of Hsdr4 is DQ464370. The accession numbers of the ESTs are: TDF
Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity... more Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity. A key question concerns the spatial scale at which genetic differentiation occurs and to what extent it is driven by natural selection. The Levant region exhibits a strong ecological gradient along the North-South axis, with numerous small canyons in an East-West direction and with small-scale environmental gradients on the opposing North-and South-facing slopes. We sequenced 34 short genomic regions in 54 accessions of wild barley collected throughout Israel and from the opposing slopes of two canyons. The nucleotide diversity of the total sample is 0.0042, which is about two-thirds of a sample from the whole species range (0.0060). Thirty accessions collected at 'Evolution Canyon' (EC) at Nahal Oren, close to Haifa, have a nucleotide diversity of 0.0036, and therefore harbor a large proportion of the genetic diversity. There is a high level of genetic clustering throughout Israel and within EC, which roughly differentiates the slopes. Accessions from the hot and dry South-facing slope have significantly reduced genetic diversity and are genetically more distinct from accessions from the North-facing slope, which are more similar to accessions from other regions in Northern Israel. Statistical population models indicate that wild barley within the EC consist of three separate genetic clusters with substantial gene flow. The data indicate a high level of population structure at large and small geographic scales that shows isolation-by-distance, and is also consistent with ongoing natural selection contributing to genetic differentiation at a small geographic scale.
A review of previous reports on indirect selection for recombination in Drosophila melanogaster. ... more A review of previous reports on indirect selection for recombination in Drosophila melanogaster. Table S2. Effect of desiccation selection on the coefficient of coincidence in adjacent and non-adjacent intervals of D. melanogaster. Table S3. Effect of hypoxia and hyperoxia selection on the coefficient of coincidence in adjacent and non-adjacent intervals of D. melanogaster. Table S4. Coincidence of interval-pair cases of changes in interference with significant positive correlation between rf values in the interval-pairs (a) and with significant increases in rf in desiccation, hypoxia, and hyperoxia selection variants (b). (PDF 486 kb)
Estimates of the coefficients of coincidence for non-adjacent intervals per replicate and entire ... more Estimates of the coefficients of coincidence for non-adjacent intervals per replicate and entire variants (selection and control). (PDF 2103 kb)
Estimates of the coefficients of coincidence for adjacent intervals per replicate and entire vari... more Estimates of the coefficients of coincidence for adjacent intervals per replicate and entire variants (selection and control). (PDF 2958 kb)
The evolutionary basis of reproductive success in different environments is of major interest in ... more The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. We sequenced mRNA extracted from spikelets at the flowering stage in drought-treated and control plants. The barley genome was used for a reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drou...
Several problems in modern genome mapping analysis belong to the field of discrete
optimization ... more Several problems in modern genome mapping analysis belong to the field of discrete
optimization on a set of all possible orders. In this paper we propose formulations,
mathematical models and algorithms for genetic/genomic mapping problem, that can be formulated in TSP-like terms. These include: ordering of marker loci (or genes) in
multilocus genetic mapping (MGM), multilocus consensus mapping (MCGM), and
physical mapping problem (PMP). All these problems are considered as computationally challenging because of noisy marker scores, large-size data sets, specific constraints on certain classes of orders, and other complications. The presence of specific constraints on ordering of some elements in these problems does not allow applying effectively the well-known powerful discrete optimization algorithms like Cutting-plane, Genetic algorithm with EAX crossover and famous Lin-Kernighan. In the paper we demonstrate that developed by us Guided Evolution Strategy algorithms successfully solves this class of discrete constrained optimization problems. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on three genetic/genomic problems with up to 2,500 points.
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Papers by Abraham Korol
optimization on a set of all possible orders. In this paper we propose formulations,
mathematical models and algorithms for genetic/genomic mapping problem, that can be formulated in TSP-like terms. These include: ordering of marker loci (or genes) in
multilocus genetic mapping (MGM), multilocus consensus mapping (MCGM), and
physical mapping problem (PMP). All these problems are considered as computationally challenging because of noisy marker scores, large-size data sets, specific constraints on certain classes of orders, and other complications. The presence of specific constraints on ordering of some elements in these problems does not allow applying effectively the well-known powerful discrete optimization algorithms like Cutting-plane, Genetic algorithm with EAX crossover and famous Lin-Kernighan. In the paper we demonstrate that developed by us Guided Evolution Strategy algorithms successfully solves this class of discrete constrained optimization problems. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on three genetic/genomic problems with up to 2,500 points.
optimization on a set of all possible orders. In this paper we propose formulations,
mathematical models and algorithms for genetic/genomic mapping problem, that can be formulated in TSP-like terms. These include: ordering of marker loci (or genes) in
multilocus genetic mapping (MGM), multilocus consensus mapping (MCGM), and
physical mapping problem (PMP). All these problems are considered as computationally challenging because of noisy marker scores, large-size data sets, specific constraints on certain classes of orders, and other complications. The presence of specific constraints on ordering of some elements in these problems does not allow applying effectively the well-known powerful discrete optimization algorithms like Cutting-plane, Genetic algorithm with EAX crossover and famous Lin-Kernighan. In the paper we demonstrate that developed by us Guided Evolution Strategy algorithms successfully solves this class of discrete constrained optimization problems. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on three genetic/genomic problems with up to 2,500 points.