The chromatin determinants and Ph1 gene effect at wheat sites with contrasting recombination frequency

INTRODUCTION

Meiotic recombination is one of the most important processes of evolution and adaptation to environmental conditions. Even though there is substantial knowledge about proteins involved in the process, targeting specific DNA loci by the recombination machinery is not well understood.

OBJECTIVES

This study aims to investigate a wheat recombination hotspot (H1) in comparison with a "regular" recombination site (Rec7) on the sequence and epigenetic level in conditions with functional and non-functional Ph1 locus.

METHODS

The DNA sequence, methylation pattern, and recombination frequency were analyzed for the H1 and Rec7 in three mapping populations derived by crossing introgressive wheat line 8.1 with cv. Chinese Spring (with Ph1 and ph1 alleles) and cv. Tähti.

RESULTS

The H1 and Rec7 loci are 1.586 kb and 2.538 kb long, respectively. High-density mapping allowed to delimit the Rec7 and H1 to 19 and 574 bp and 593 and 571 bp CO sites, respectively. A new method (ddPing) allowed screening recombination frequency in almost 66 thousand gametes. The screening revealed a 5.94-fold higher recombination frequency at the H1 compared to the Rec7. The H1 was also found out of the Ph1 control, similarly as gamete distortion. The recombination was strongly affected by larger genomic rearrangements but not by the SNP proximity. Moreover, chromatin markers for open chromatin and DNA hypomethylation were found associated with crossover occurrence except for the CHH methylation.

CONCLUSION

Our results, for the first time, allowed study of wheat recombination directly on sequence, shed new light on chromatin landmarks associated with particular recombination sites, and deepened knowledge about role of the Ph1 locus in control of wheat recombination processes. The results are suggesting more than one recombination control pathway. Understanding this phenomenon may become a base for more efficient wheat genome manipulation, gene pool enrichment, breeding, and study processes of recombination itself.

Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene

A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.

Characterization of new allele influencing flowering time in bread wheat introgressed from Triticum militinae

Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat.

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line

Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.

Adult plant and seedling resistance to powdery mildew in a Triticum aestivum x Triticum militinae hybrid line

In the progeny of a cross between the common wheat cultivar Tähti and Triticum militinae, a member of the timopheevii group of tetraploid wheats, several hybrid lines were selected that are characterized by improved seedling and adult plant resistance (APR) to powdery mildew. An F2 single-seed descendant mapping population segregating for seedling resistance and APR to powdery mildew was analysed for the identification of quantitative trait loci (QTL). The main QTL responsible for APR was detected on the long arm of chromosome 4A tightly linked to the Xgwm160 locus on a T. militinae translocation explaining up to 54% of phenotypic variance. The same translocation influenced seedling resistance to powdery mildew upon inoculation of plants with a synthetic population of Blumeria graminis DC. f. sp. tritici, and explained 28-33% of the phenotypic variance.

Venous blood levels of inhaled trichloroethylene in female rats and changes induced by interacting agents

The concentration from inhalation of trichloroethylene (TCE) in venous blood from female rats was studied. Exposure consisted of 200, 400 and 500 ppm for 6 hrs, or 50 and 100 ppm for 2 hrs. In each experiment, 1 rat was exposed at a constant concentration of TCE. Blood samples were obtained from an indwelling jugular cannula throughout the experiment. Combination effects with chloral hydrate (0.2 g/kg), ethanol (0.8 ml/kg), isopropanol (0.8 ml/kg), pyrazole (0.2 g/kg), tetraethylthiuram disulfide (TETD; 0.2 g/kg) or tetrachloroethylene (TTCE; 1 g/kg) given orally were observed. The experimental data on the uptake of TCE in blood were fitted, by use of nonlinear regression analysis, to a simple toxicokinetic model. TETD caused the greatest increase in the steady state concentration of TCE (3.7 X), compared to TCE alone at 200 ppm. Isopropanol, pyrazole and TTCE also produced pronounced effects, but chloral hydrate treatment resulted in no significant change. At 50 and 100 ppm TCE exposure for 2 hrs, a significant increase (almost 3 X) in the steady state concentration of TCE from both ethanol and isopropanol was observed.

Error structure as a function of substrate and inhibitor concentration in enzyme kinetic experiments

Optimal design of experiments as well as proper analysis of data are dependent on knowledge of the experimental error. A detailed analysis of the error structure of kinetic data obtained with acetylcholinesterase showed conclusively that the classical assumptions of constant absolute or constant relative error are inadequate for the dependent variable (velocity). The best mathematical models for the experimental error involved the substrate and inhibitor concentrations and reflected the rate law for the initial velocity. Data obtained with other enzymes displayed similar relationships between experimental error and the independent variables. The new empirical error functions were shown superior to previously used models when utilized in weighted non-linear-regression analysis of kinetic data. The results suggest that, in the spectrophotometric assays used in the present study, the observed experimental variance is primarily due to errors in determination of the concentrations of substrate and inhibitor and not to error in measuring the velocity.

Mechanism of S-(1,2-dichlorovinyl)glutathione-induced nephrotoxicity

S-(1,2-Dichlorovinyl)glutathione and S-(1,2-dichlorovinyl)-DL-cysteine are potent nephrotoxins. Agents that inhibit gamma-glutamyl transpeptidase, cysteine conjugate beta-lyase, and renal organic anion transport systems, namely L-(alpha S,5S)-alpha-amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid (AT-125), aminooxyacetic acid, and probenecid, respectively, protected against S-conjugate-induced nephrotoxicity. Furthermore, S-(1,2-dichlorovinyl)-DL-alpha-methylcysteine, which cannot be cleaved by cysteine conjugate beta-lyase, was not nephrotoxic. These results strongly support a role for renal gamma-glutamyl transpeptidase, cysteine conjugate beta-lyase, and organic anion transport systems in S-(1,2-dichlorovinyl)glutathione- and S-(1,2-dichlorovinyl)cysteine-induced nephrotoxicity.

The binding of substrates and a product of the enzymatic reaction to glutathione S-transferase A

The binding of substrates and a product to glutathione S-transferase A from rat liver was studied by use of equilibrium dialysis and equilibrium partition in a two-phase system. The radioactive substrates glutathione and bromosulfophthalein as well as a product of glutathione and 3,4-dichloro-1-nitrobenzene, S-(2-chloro-4-nitrophenyl)glutathione, gave hyperbolic binding isotherms with a stoichiometry of 2 mol per mol of enzyme (i.e. 1 molecule per subunit). Glutathione (and glutathione disulfide) had an equilibrium (dissociation) constant for the binding of about 10 microM, whereas bromosulfophthalein and the product had equilibrium constants of about 0.5 microM. All ligands showed the same binding stoichiometry, and competition experiments involving unlabeled ligands indicated that glutathione and the glutathione derivatives were binding to the same site. Low affinity sites appeared to exist in addition to the specific high affinity sites (one per subunit) for all ligands tested. The binding studies are fully consistent with a steady state random kinetic mechanism for the enzyme.

A new procedure to derive weighting factors for nonlinear regression analysis applied to enzyme kinetic data

The experimental variance of enzymic steady-state kinetic experiments depends on velocity as approximated by a power function (Var(v) = K1 . valpha (Askelöf, P., Korsfeldt, M. and Mannervik, B. (1976) Eur. J. Biochem. 69, 61--67). The values of the constants (K1, alpha) can be estimated by making replicate measurements of velocity, and the inverse of the function can then be used as a weighting factor. In order to avoid measurement of a large number of replicates to establish the error structure of a kinetic data set, a different approach was tested. After a preliminary regression using a 'good model', which satisfies reasonable goodness-of-fit criteria, the residuals were taken to represent the experimental error. The neighbouring residuals were grouped together and the sum of their mean squared values was used as a measure of the variance in the neighbourhood of the corresponding measurements. The values of the constants obtained in this way agreed with those obtained by replicates.

Multiple inhibition of glutathione S-transferase A from rat liver by glutathione derivatives: kinetic analysis supporting a steady-state random sequential mechanism

Glutathione derivatives inhibit glutathione S-transferase A [cf. Biochem. J. (1975) 147, 513--522]. The steady-state kinetics of this inhibition have been investigated in detail by using S-octyglutathione, glutathione disulphide and S-(2-chloro-4-nitrophenyl)glutathione: the last compound is a product of the enzyme-catalused reaction. Interpreted in terms of generalized denotations of inhibition patterns, the compounds were found to be competitive with the substrate glutathione. Double-inhibition experiments involving simultaneous use of two inhibitors indicated exclusive binding of the inhibitors to the enzyme. The discrimination between alternative rate equations has been based on the results of weighted non-linear regression analysis. The experimental error was determined by replicate measurements and was found to increase with velocity. The established error structure was used as a basis for weighting in the regression and to construct confidence levels for the judgement of goodness-of-fit of rate equations fitted to experimental data. The results obtained support a steady-state random model for the mechanism of action of glutathione S-transferase A and exclude a number of simple kinetic models.

Variations in the blood concentration of 1,1,2-trichloroethane by percutaneous absorption and other routes of administration in the guinea pig

The blood concentration of 1,1,2-trichloroethane was studied after epicutaneous application, by an intracutaneous, subcutaneous or intraperitoneal injection. An equation with three exponential terms was necessary for a satisfactory description of the experimental data in the case of intraperitoneal injection. Subcutaneous and intracutaneous injections seem to give essentially the same king of blood concentration curves as for intraperitoneal injection. In the case of percutaneous absorption an equation with three exponential terms and a constant was necessary to account for the experimental data. The complex toxicokinetics of 1,1,2-trichloroethane by percutaneous absorption was assumed to be associated with progressive skin damage observed in previously reported experiments, a damage apparently involving a change in barrier function.

A study on the distribution of methylchloroform and n-octane in the mouse during and after inhalation

The distribution of methylchloroform and n-octane, respectively, in the blood, liver, kidney, and brain of mice was studied at different inspired air concentrations and after different exposure times. The air concentration varied between 10 and 10,000 ppm; and the exposure time, between 0.5 and 24 h. The resulting solvent concentrations in kidney and brain were about the same, but the liver concentrations were usually somewhat higher for both solvents. There was a linear dependence between inspired air concentration and tissue concentrations at fixed exposure times. A correlation between blood and organ concentrations was observed in animals exposed at different inhalation air concentrations but not in animals exposed only at one fixed concentration. The ratios between the concentrations of the solvents in the organs and blood were higher for n-octane than for methylchloroform. The ratios increased as the exposure concentration increased for all organs studied in the case of n-octane but only for the liver in the case of methylchloroform. When the exposure dose, i.e., inspired air concentration X time, was generated in different ways, a high concentration during a short exposure resulted in a ten times higher organ concentration than a low concentration during a long exposure. The liver, kidney, and brain concentrations generally did not differ more than twice between methylchloroform and n-octane after exposure of the same concentration and duration. The blood concentration, however, was much less in n-octane exposed animals than in methylchloroform exposed ones. A pharmacokinetic model with both uptake and elimination of the first order fitted the empirical data better for methylchloroform than a model with zero order uptake and first order elimination. Postexposure concentrations of methylchloroform were linear in a semilog graph. A one-compartment pharmacokinetic model was in accordance with the experimental data for methylchloroform. For n-octane, however, at least a two-compartment model must be assumed.

Purification and characterization of two glutathione S-aryltransferase activities from rat liver

Two forms of glutathione S-aryltransferase were purified from rat liver. The only differences noted between the two forms were in the chromatographic and electrophoretic properties, which permitted the separation of the two species. The molecular weights of the enzyme and its subunits were estimated as about 50000 and 23000 respectively. The steady-state kinetics did no follow Michaelis-Menten kinetics when one substrate concentration was kept constant while the second substrate concentration was varied. Several S-substituted GSH derivatives were tested as inhibitors of the enzymic reaction. The enzyme was inactivated by thiol-group reagents.