Showing papers in "Journal of Applied Genetics in 2009"
TL;DR: Genes involved in cell wall integrity and the actin cytoskeleton are required for both alcohol tolerance and thermotolerance, whereas the RNA polymerase II mediator complex seems to be specific to heat tolerance.
Abstract: During fermentation, yeast cells are exposed to a number of stresses -- such as high alcohol concentration, high osmotic pressure, and temperature fluctuation - so some overlap of mechanisms involved in the response to these stresses has been suggested. To identify the genes required for tolerance to alcohol (ethanol, methanol, and 1-propanol), heat, osmotic stress, and oxidative stress, we performed genome-wide screening by using 4828 yeast deletion mutants. Our screens identified 95, 54, 125, 178, 42, and 30 deletion mutants sensitive to ethanol, methanol, 1-propanol, heat, NaCl, and H2O2, respectively. These deleted genes were then classified based on their cellular functions, and cross-sensitivities between stresses were determined. A large number of genes involved in vacuolar H(+)-ATPase (V-ATPase) function, cytoskeleton biogenesis, and cell wall integrity, were required for tolerance to alcohol, suggesting their protective role against alcohol stress. Our results revealed a partial overlap between genes required for alcohol tolerance and those required for thermotolerance. Genes involved in cell wall integrity and the actin cytoskeleton are required for both alcohol tolerance and thermotolerance, whereas the RNA polymerase II mediator complex seems to be specific to heat tolerance. However, no significant overlap of genes required for osmotic stress and oxidative stress with those required for other stresses was observed. Interestingly, although mitochondrial function is likely involved in tolerance to several stresses, it was found to be less important for thermotolerance. The genes identified in this study should be helpful for future research into the molecular mechanisms of stress response.
155 citations
TL;DR: Leaf lignin content is a useful index for evaluation of drought tolerance in maize and molecular selection markers can be developed on the basis of differential expression of the candidate genes and applied to maize improvement for drought tolerance.
Abstract: In order to provide information for the development of molecular selection markers for drought tolerance improvement, the methods of prometric analysis, quantitative real-time PCR and field evaluation were employed for the identification of the differential expression of candidate genes under drought stress in maize. At seventeen, twenty-four and forty-eight hours of polyethylene glycol-simulated drought stress at the seventh leaf stage, leaf samples were collected from two drought-tolerant inbred lines for prometric analysis by two-dimensional electrophoresis and peptide mass fingerprinting. Fifty-eight proteins out of more than 500 were found in response to drought stress. Three drought-induced spots 2506, 3507 and 4506 showed sequence similarity with cinnamyl alcohol dehydrogenase, cytochrome protein 96A8 and S-adenosyl-L-methionine synthase, respectively. The expression of two key enzymes to lignin biosynthesis was quantified by quantitative real-time PCR among three drought-tolerant and one drought-sensitive inbred lines under drought stress and well-watered control conditions. After a decrease at the beginning of drought stress, the expression of cinnamyl alcohol dehydrogenase and caffeateO-methyltransferase recovered at twenty-four hours of the drought stress in the three drought-tolerant lines, but not in the drought-sensitive lines. Leaf lignin content, anthesis-silking interval and grain weight per plant were investigated with six inbred lines of varying drought tolerance under drought stress and well-watered control. Drought tolerance coefficients of these three characters were calculated and the correlation coefficients among these drought tolerance coefficients were estimated. Significant difference in leaf lignin content was found among the inbred lines and in response to drought stress. Close correlations were observed between the drought tolerant coefficients for leaf lignin content and grain weight per plant, and between the drought tolerant coefficients for leaf lignin content and anthesis-silking interval. These results indicate that leaf lignin content is a useful index for evaluation of drought tolerance in maize. Molecular selection markers can be developed on the basis of differential expression of the candidate genes and applied to maize improvement for drought tolerance.
119 citations
TL;DR: A combination of the molecular and quantitative approaches should be used to develop tools helping farmers in the selection of their animals to improve the nutritional quality of the produced milk fat.
Abstract: The milk fatty acid (FA) profile is far from the optimal fat composition in regards to human health. The natural sources of variation, such as feeding or genetics, could be used to increase the concentrations of unsaturated fatty acids. The impact of feeding is well described. However, genetic effects on the milk FA composition begin to be extensively studied. This paper summarizes the available information about the genetic variability of FAs. The greatest breed differences in FA composition are observed between Holstein and Jersey milk. Milk fat of the latter breed contains higher concentrations of saturated FAs, especially short-chain FAs. The variation of the delta-9 desaturase activity estimated from specific FA ratios could explain partly these breed differences. The choice of a specific breed seems to be a possibility to improve the nutritional quality of milk fat. Generally, the proportions of FAs in milk are more heritable than the proportions of these same FAs in fat. Heritability estimates range from 0.00 to 0.54. The presence of some single nucleotide polymorphisms could explain partly the observed individual genetic variability. The polymorphisms detected onSCD1 andDGAT1 genes influence the milk FA composition. TheSCD1 V allele increases the unsaturation of C16 and C18. TheDGAT1 A allele is related to the unsaturation of C18. So, a combination of the molecular and quantitative approaches should be used to develop tools helping farmers in the selection of their animals to improve the nutritional quality of the produced milk fat.
97 citations
TL;DR: A simple and efficient plant DNA extraction procedure for isolation of high-quality DNA from plant tissues is presented in this paper, which requires maceration of plant tissue of about 1.0 cm(2) (e.g. of a leaf blade) in DNA extraction buffer (100 mM Tris-HCl, 100 mM EDTA, 250 mM NaCl) using 1.5-mL microfuge tubes, followed by cell lysis with 20% SDS, and DNA extraction with phenol: chloroform: iso-amyl alcohol (25:24:
Abstract: Polymerase chain reaction has found wide applications in modern research involving transformations and other genomic studies. For reproducible PCR results, however, the quantity and quality of template DNA is of considerable importance. A simple and efficient plant DNA extraction procedure for isolation of high-quality DNA from plant tissues is presented here. It requires maceration of plant tissue of about 1.0 cm(2) (e.g. of a leaf blade) in DNA extraction buffer (100 mM Tris-HCl, 100 mM EDTA, 250 mM NaCl) using 1.5-mL microfuge tubes, followed by cell lysis with 20% SDS, and DNA extraction with phenol: chloroform: iso-amyl alcohol (25:24:1). Hydrated ether is then used to remove polysaccharides and other contaminants from the DNA preparation. Average DNA yield is 20-30 microg cm(-2) for fresh tissues, and ratio of absorbance at 260 nm to absorbance at 280 nm is 1.5-1.8. The DNA is quite suitable for PCR using microsatellites, RAPD and specific markers for recombinant selection. Amplifications have been obtained for these markers by using template DNA extracted from fresh as well as frozen leaf tissues of various plants, including barley, oat, potato and tomato. DNA stored for more than 2 years has been successfully amplified with microsatellite markers, which shows suitability of this method after long-term storage of DNA. Besides, the ease of use and cost-effectiveness make the procedure attractive.
88 citations
TL;DR: The most significant associations were found between the A/C polymorphism located in exon 14 of ABCG2 and milk fat production traits as well as calving-to-first insemination interval, and between the T/C substitution in intron 9 of thePPARGC1A and non-return rate in heifers.
Abstract: This study investigated the impact of 6 polymorphisms located in theABCG2, PPARGC1A, OLR1 andSCD1 genes on estimated breeding values for milk production, longevity, somatic cell count and reproductive traits. The analysis was conducted on 453 Polish Holstein-Friesian bulls. Genotypes were identified using PCR-RFLP, and haplotype inferences were performed for 3 linked mutations ofPPARGC1A. The most significant associations were found between the A/C polymorphism located in exon 14 ofABCG2 and milk fat production traits as well as calving-to-first insemination interval, and between the T/C substitution in intron 9 of thePPARGC1A and non-return rate in heifers.
73 citations
TL;DR: Results indicate that the cold response activation of dehydrin gene in tomato fruits is the consequence of an alternative pathway, different from theSl-CBF1 regulon, which is used as a transcriptional marker of cold stress in leaves and ripening fruits.
Abstract: Tomato is sensitive to cold during vegetative growth, fruit set, development, and ripening. We have characterized the effect of cold stress (6°C for up to 48 h) on the transcriptome of Micro-Tom tomato fruits during ripening by subtractive PCR. The cold stress caused modifications in gene expression of housekeeping genes. From a total of 38 genes up-regulated by cold, only one clone — a dehydrin homologue — was related to previously identified cold-stress genes. Phylogenetic analysis showed its clustering with other cold-induced dehydrins, and increased distances from dehydrins activated by abscisic acid. Quantitative expression analysis of tomato dehydrin showed it was activated by cold treatment in leaves and fruits. As dehydrin is a member of theSl-CBF1 regulon from tomato, we analyzed the cold-responsive transcription factorSl-CBF1 in mature leaves and ripening fruits stored at 6°C. Leaves of Micro-Tom showed high basal levels of the transcription factorSl-CBF1, compared to fruits. Cold treatment caused increased levels ofSl-CBF1 expression in leaves but not in fruits of Micro-Tom and Demisem (a commercial cultivar). Tomato dehydrin can be used as a transcriptional marker of cold stress in leaves and ripening fruits. However, our results indicate that the cold response activation of dehydrin gene in tomato fruits is the consequence of an alternative pathway, different from theSl-CBF1 regulon.
63 citations
TL;DR: Results of this study showed that fluctuations in timing of ascospore release corresponded to the dynamics of combined concentrations of DNA from Leptosphaeria maculans and L. biglobosa, with significant positive correlations between Ascospore number and DNA yield, and real-time PCR was more sensitive than traditional PCR, especially in years with low ascospores numbers.
Abstract: Spores of many fungal pathogens are dispersed by wind. Detection of these airborne inocula is important in forecasting both the onset and the risk of epiphytotics. Species-specific primers targeted at the internal transcribed spacer (ITS) region ofLeptosphaeria maculans andL. biglobosa — the causal organisms of phoma stem canker and stem lesions ofBrassica spp., including oilseed rape — were used to detect DNA extracted from particles deposited on tapes obtained from a spore trap operated in Rarwino (northwest Poland) from September to November in 2004 and 2006. The quantities of DNA assessed by traditional end-point PCR and quantitative real-time PCR were compared to microscopic counts of airborne ascospores. Results of this study showed that fluctuations in timing of ascospore release corresponded to the dynamics of combined concentrations of DNA fromL. maculans andL. biglobosa, with significant positive correlations between ascospore number and DNA yield. Thus the utilization of PCR-based molecular diagnostic techniques enabled the detection, identification, and accurate quantification of airborne inoculum at the species level. Moreover, real-time PCR was more sensitive than traditional PCR, especially in years with low ascospore numbers.
43 citations
TL;DR: Surprisingly, splicing, nuclear transport, and extramatrix proteins may be involved in sex determination.
Abstract: Genetic control of gonadal development proceeds through either the male or female molecular pathways, driving bipotential gonadal anlage differentiation into a testis or ovary. Antagonistic interactions between the 2 pathways determine the gonadal sex. Essentially sex determination is the enhancement of one of the 2 pathways according to genetic sex. Initially, Sry with other factors upregulates Sox9 expression in XY individuals. Afterwards the expression of Sox9 is maintained by a positive feedback loop with Fgf9 and prostaglandin D2 as well as by autoregulative ability of Sox9. If these factors reach high concentrations, then Sox9 and/or Fgf9 may inhibit the female pathway. Surprisingly, splicing, nuclear transport, and extramatrix proteins may be involved in sex determination. The male sex determination pathway switches on the expression of genes driving Sertoli cell differentiation. Sertoli cells orchestrate testicular differentiation. In the absence of Sry, the predomination of the female pathway results in the realization of a robust genetic program that drives ovarian differentiation.
42 citations
TL;DR: These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea.
Abstract: The presence and distribution of CRISPR (clustered regularly interspaced short palindrome repeat) elements in the archaeal order Thermococcales were analyzed. Four complete genome sequences from the species Pyrococcus abyssi, P. furiosus, P. horikoshii, and Thermococcus kodakaraensis were studied. A fragment of the genome of P. furiosus was flanked by CRISPR elements upstream and by a single element downstream. The composition of the gene sequences contained in this genome fragment (positions 699013 to 855319) showed significant differences from the other genes in the P. furiosus genome. Differences were observed in the GC content at the third codon positions and the frequency of codon usage between the genes located in the analyzed fragment and the other genes in the P. furiosus genome. These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea.
38 citations
TL;DR: A model of the regulation of skeletal muscle growth and differentiation, with a principal role of the somatotropic pathway is proposed, which may explain at least in part the development of muscle phenotype in Limousin bulls.
Abstract: A cDNA microarray (18 263 probes) was used for transcriptome analysis of bovine skeletal muscle (m. semitendinosus) in 12-month-old bulls of the beef breed Limousin (LIM) and the typical dairy breed Holstein-Friesian (HF, used as a reference). We aimed to identify the genes whose expression may reflect the muscle phenotype of beef bulls. A comparison of muscle transcriptional profiles revealed significant differences in expression of 393 genes between HF and LIM. We classified biological functions of 117 genes with over 2-fold differences in expression between the examined breeds. Among them, 72 genes were up-regulated and 45 genes were down-regulated in LIM vs. HF. The genes were involved in protein metabolism and modifications (22 genes), signal transduction (15), nucleoside, nucleotide and nucleic acid metabolism (13), cell cycle (9), cell structure and motility (9), developmental processes (9), intracellular protein traffic (7), cell proliferation and differentiation (6), cell adhesion (6), lipid, fatty acid and steroid metabolism (5), transport (5), and other processes. For the purpose of microarray data validation, we randomly selected 4 genes:trip12, mrps30, pycrl, andc-erbb3. Real-time RT-PCR results showed similar trends in gene expression changes as those observed in microarray studies. Basing on results of the present study, we proposed a model of the regulation of skeletal muscle growth and differentiation, with a principal role of the somatotropic pathway. It may explain at least in part the development of muscle phenotype in LIM bulls. We assume that the growth hormone directly or indirectly (through IGF-1) activates the calcium-signaling pathway with calcineurin, which stimulates myogenic regulatory factors (MRFs) and inhibits early growth response gene. The inhibition results in indirect activation of MRFs and impaired activation of TGF-beta1 and myostatin, which finally facilitates terminal muscle differentiation.
33 citations
TL;DR: Methodology based on random regression animal models can be recommended for genetic evaluation of laying hens with relatively high heritabilities in the first and final periods of production with a substantial decrease in heritability during the egg production peak.
Abstract: Heritability and genetic correlations of monthly egg production under random regression models were estimated. Three layer lines (A22, A88, K66) in six consecutive generations were analysed. A22 (13, 770 recorded hens) and A88 (13, 950 recorded hens) are maternal lines of Rhode Island White birds selected on egg production and shell colour; K66 (9, 351 recorded birds) is a paternal line of Rhode Island Red birds selected on egg weight. Eight models with different orders of Legendre polynomials were applied. Adequacy of the models was checked by the Akaike Information Criterion. According to the most adequate model including second order Legendre polynomials for fixed effects and third order for additive genetic and permanent environmental effects, relatively high heritabilities were estimated in the first (h2=0.3) and final (h2 above 0.3) periods of production with a substantial decrease in heritability during the egg production peak. Methodology based on random regression animal models can be recommended for genetic evaluation of laying hens.
TL;DR: Genetic modification of cereals with puroindoline genes and/or their promoters enable more detailed functional analyses and the production of plants with the desired characteristics.
Abstract: Kernel hardness is an important agronomic trait that influences end-product properties. In wheat cultivars, this trait is determined by thePuroindoline a (Pina) andPuroindoline b (Pinb) genes, located in theHardness locus (Ha) on chromosome 5DS of the D genome. Wild type alleles code puroindoline a (PINA) and puroindoline b (PINB) proteins, which form a 15-kDa friabilin present on the surface of water-washed starch granules. Both the proteins are accumulated in the starch endosperm cells and aleurone of the mature kernels.Puroindoline-like genes coding puroindoline-like proteins in the starch endosperm occur in some of the genomes of Triticeae and Aveneae cereals. Orthologs are present in barley, rye and oats. However, some genomes of these diploid and polyploid cereals, like that ofTriticum turgidum var.durum (AABB) lack thepuroindoline genes, having a very hard kernel texture. The two wild type alleles in opposition (dominant loci) control the soft pheno-type. Mutation either inPina orPinb or in both leads to a medium-hard or hard kernel texture. The most frequent types ofPin mutations are point mutations within the coding sequence resulting in the substitution of a single amino acid or a null allele. The latter is the result of a frame shift determined by base deletion or insertion or a one-point mutation to the stop codon. The lipid-binding properties of the puroindolines affect not only the dough quality but also the plants’ resistance to pathogens. Genetic modification of cereals withPuroindoline genes and/or their promoters enable more detailed functional analyses and the production of plants with the desired characteristics.
TL;DR: The results suggest that selection based on theIGF2 mutation in Poland may be very useful in PL and LW pigs, where theG allele is still relatively frequent.
Abstract: IGF2 is one of the genes that control muscle development. Moreover,IGF2 is imprinted, as only the paternal allele is expressed in the offspring. Using real-time PCR forIGF2 genotyping (Carrodegous et al. 2005), we evaluated the frequency of theIGF2 A3072G mutation (Van Laere et al. 2003) in pigs: Polish Landrace (PL,N = 271) and Large White (LW,N = 267). Our results are consistent with previous reports, showing that theA allele is common in breeds subjected to strong selection for lean meat content (A allele frequency was 0.79 in LW and 0.69 in PL). Moreover, we compared body composition, growth performance and meat quality traits in pigs carrying opposite genotypes (A/A andG/G) inthe IGF2 gene. The association study revealed that theA allele increases the weight of loin (WL) (additive gene effect = 450±50 g in LW and 213±64g in PL), weight of ham (WH) (544±48 g in LW and 302±72 g in PL), loin eye area (LEA) (4.9±0.46 cm2 in LW and 2.1 ±0.95 cm2 in PL), carcass meat percentage (CP) (3.12±0.27% in LW and 1.89±0.47% in PL), and decreases average backfat thickness (ABF) (−0.2±0.036 cm in LW and −0.2±0.048 cm in PL). Additionally, in PL, theA allele increases the weight of tenderloin (WT) (11±0.01 g), average daily gain (ADG) (30.7±17.29 g), and decreases feed intake (F) (−121±45 g) and days of feeding (DF) (−3.5±2.08 days). No significant effects were observed for meat quality traits. Our results suggest that selection based on theIGF2 mutation in Poland may be very useful in PL and LW pigs, where theG allele is still relatively frequent.
TL;DR: A novel missense single-nucleotide polymorphism (SNP) within the goatPRL gene in 1367 individuals is reported by PCR-SSCP (polymerase chain reaction with single-strand conformation polymorphism) analysis and DNA sequencing.
Abstract: Concentrations of the single-chain polypeptide hormone prolactin (PRL) are associated with wool or cashmere traits, and its seasonal changes may determine patterns of enzymatic activity and may affect cashmere fibre growth and moult. So, thePRL gene is a potential candidate gene for cashmere traits in marker-assisted selection (MAS). In this paper, we report a novel missense single-nucleotide polymorphism (SNP) within the goatPRL gene in 1367 individuals by PCR-SSCP (polymerase chain reaction with single-strand conformation polymorphism) analysis and DNA sequencing. The novel X76049:g.576C>A mutation is confirmed byEco24I PCR-RFLP (restriction fragment length polymorphism) analysis and causes a missense codon (Pro176Thr). The frequencies of allele C varied from 0.79 to 0.93 in 9 analysed goat populations. C allele was correlated with higher fibre length (P = 0.014).
TL;DR: It is concluded that presence of the T allele is a risk factor for ischemic stroke in Polish subjects.
Abstract: Hyperhomocysteinemia is reported to be an independent risk factor for the development of ischemic stroke. Several studies on genetic variants of methylenetetrahydrofolate reductase (MTHFR, which plays a crucial role in regulation of plasma homocysteine concentration) reported an association between C677T gene polymorphism and stroke in some Asian populations. No study but one detected this association in Caucasians. The purpose of the present case-control study was to find a relationship betweenMTHFR genotypes and stroke in a Polish population.MTHFR genotypes were determined by PCR in 152 patients with ischemic stroke from northwestern Poland and in 135 consecutive newborns from the same population. The TT genotype and the T allele were significantly more frequent in patients than in the control group (11.8% vs. 4.4%, and 34.5% vs. 21.5%,P < 0.01). When males and females were analyzed separately, the differences were statistically significant in both genders. It is concluded that presence of the T allele is a risk factor for ischemic stroke in Polish subjects.
TL;DR: The results suggest for the first time that sporadic and recurrent spontaneous abortions as well as miscarriage in the presence or absence of autoantibodies may have different KIR genotypic backgrounds.
Abstract: Natural killer (NK) cells are the most abundant lymphocyte population in the decidua. These cells express killer immunoglobulin-like receptors (KIRs), which upon recognition of HLA class I molecules on trophoblasts may either stimulate NK cells (activating KIRs) or inhibit them (inhibitory KIRs) to produce soluble factors necessary for the maintenance of pregnancy.KIR genes exhibit extensive haplotype polymorphism; individuals differ in both the number and kind (activating vs. inhibitory) ofKIR genes. This polymorphism affects NK cell reactivity and susceptibility to diseases, including gynecological disorders. Therefore weKIR-genotyped 149 spontaneously aborting women and 117 control multiparae (at least 2 healthy-born children). Several genotypes (i.e. combinations of variousKIR genes) were differently distributed among the patients and control subjects. Differences were observed in the numbers and the ratios of activating to inhibitory KIRs between patients and healthy women: (i) genotypes containing 6 activatingKIR genes were less frequent and those containing 6 inhibitoryKIR genes were more frequent in patients than in control subjects, and (ii) an excess of inhibitory KIRs (activating-to-inhibitoryKIR gene ratios of 0.33 to 0.83) was associated with miscarriage, whereas ratios close to equilibrium (0.86–1.25) seemed to be protective. In addition, the results suggest for the first time that sporadic and recurrent spontaneous abortions as well as miscarriage in the presence or absence of autoantibodies may have differentKIR genotypic backgrounds.
TL;DR: The results showed that QTL detection for PH was dependent on the genetic background of dent corn inbreds and multiple-trait joint QTL analysis could increase the number of detected QTLs.
Abstract: QTL mapping for plant-height traits has not been hitherto reported in high-oil maize. A high-oil maize inbred ‘GY220’ was crossed with two dent maize inbreds (‘8984’ and ‘8622’) to generate two connected F2:3 populations. Four plant-height traits were evaluated in 284 and 265 F2:3 families. Single-trait QTL mapping and multiple-trait joint QTL mapping was used to detect QTLs for the traits and the genetic relationship between plant height (PH) and two other plant-height traits. A total of 28 QTLs and 12 pairs of digenic interactions among detected QTLs for four traits were detected in the two F2:3 families. Only one marker was shared between the two populations. Joint analysis of PH with ear height (EH) and PH with top height (TH) detected 32 additional QTLs. Our results showed that QTL detection for PH was dependent on the genetic background of dent corn inbreds. Multiple-trait joint QTL analysis could increase the number of detected QTLs.
TL;DR: This review focuses on the differences in the level and profile of cytogenetic aberrations observed in donors of different age and gender, which may help explain the commonly observed gender differences in longevity.
Abstract: Analysis of relationships between the ageing cell phenotype and the age of cell donors is one of the ways towards understanding the link between cellular and organismal ageing. Cytogenetically, ageing is associated with a number of gross cellular changes, including altered size and morphology, genomic instability, and changes in expression and proliferation. Genomic instability can be easily assessed by analyzing the level of cytogenetic aberrations. In this review, we focus on the differences in the level and profile of cytogenetic aberrations observed in donors of different age and gender. Centenarians are a small fraction of the population at the extreme of human longevity. Their inclusion in such studies may shed light on one of the basic questions: whether genome stability is better maintained in successfully aged individuals compared to the rest of the population. At the same time, comparing the profile of age-related amount of chromosomal aberrations in men and women may help explaining the commonly observed gender differences in longevity.
TL;DR: Another putative QTL in linkage group 4 of ‘Doyenne du Comice’ seems to indicate that sources of fire blight resistance can be identified also in the susceptible cultivars, which are considered to be potential sources of resistance to fire blight.
Abstract: Fire blight, caused by the gram-negative bacteriumErwinia amylovora (Burrill) Winslow et al., is a dangerous disease of pome fruits, including pear. A pear breeding program for fire blight resistance was initiated in 2003 at the Department of Pomology, Warsaw University of Life Sciences, Poland. Since several Asian species are considered to be potential sources of resistance to fire blight, the susceptiblePyrus communis ‘Doyenne du Comice’ was crossed with the resistantP. ussuriensis. The F1 full-sib progeny composed of 155 seedlings was tested for susceptibility to fire blight by artificial shoot inoculation. A framework linkage map of both parents was constructed based on 48 AFLP and 32 SSR markers and covered a length of 595 cM and 680 cM in ‘Doyenne du Comice’ andP. ussuriensis, respectively. For the first time a putative QTL for fire blight resistance inP. ussuriensis linkage group 11 was identified. Another putative QTL in linkage group 4 of ‘Doyenne du Comice’ seems to indicate that sources of fire blight resistance can be identified also in the susceptible cultivars.
TL;DR: Basing on the sequence of pSaO5411, a pair of sequence-characterized amplified region (SCAR) primers were designed, and the resultant SCAR marker was able to target both cultivated rye and the wildSecale species, which enabled to identify effectively the S. africanum chromatin introduced into the wheat genome.
Abstract: A repetitive sequence of 411 bp, named pSaO5411, was identified in theSecale africanum genome (Ra) by random amplified polymorphic DNA (RAPD) analysis of wheat and wheat—S. africanum amphiploids. GenBank BLAST search revealed that the sequence of pSaO5411 was highly homologous to a part of a Ty1-copia retrotransposon. Fluorescence in situ hybridization (FISH) analyses indicated that pSaO5411 was significantly hybridized toS. africanum chromosomes of a wheat—S. africanum amphiploid, and it was dispersed along theSecale chromosome arms except the terminal regions. Basing on the sequence of pSaO5411, a pair of sequence-characterized amplified region (SCAR) primers were designed, and the resultant SCAR marker was able to target both cultivated rye and the wildSecale species, which also enabled to identify effectively theS. africanum chromatin introduced into the wheat genome.
TL;DR: Cl clones from the genomic BAC library of the narrow-leafed lupin were used for cytogenetic mapping of mitotic metaphase chromosomes of that species by the BAC-FISH technique, and data concerning linkage of resistance to 2 fungal pathogens as well as assignment of the second linkage group to the appropriate chromosome are given for the first time.
Abstract: BAC (bacterial artificial chromosome) clones from the genomic BAC library of the narrow-leafed lupin (Lupinus angustifolius) were used for cytogenetic mapping of mitotic metaphase chromosomes of that species by the BAC-FISH technique. Location of the clones, together with cytogenetic markers localised earlier by FISH (fluorescencein situ hybridisation) and PRINS (primedin situ DNA labelling), was combined with computer-aided chromosome measurements, to construct the first idiogram of the narrow-leafed lupin. The chromosomes are meta- or submetacentric; the mean absolute chromosome lengths range from 1.9 μm to 3.8 μm, and mean relative lengths from 1.6% to 3.3%. Data concerning linkage of resistance to 2 fungal pathogens as well as assignment of the second linkage group to the appropriate chromosome are given for the first time.
TL;DR: The findings suggest the potential benefits from pharmacogenetic testing, and provide evidence that theVKORC1 −1639 G>A gene polymorphism may explain at least in part the low responsiveness to acenocoumarol.
Abstract: A daily dose of vitamin K antagonists (VKAs) may vary and its range depends on various interrelated factors. Low responsiveness to VKA (defined as a failure to achieve a target international normalized ratio [INR]) is associated with polymorphisms of the vitamin K epoxide reductase-oxidase complex gene (VKORC1). A highly prevalent promoter single-nucleotide polymorphism (VKORC1−1639 G>A, rs 17878363) impairsVKORC1 expression and determines the interindividual variability of the target INR. We studied 57 patients receiving oral anticoagulation, including 50 subjects treated with acenocoumarol (mean dose: 5.7±2.3 mg/day) and 7 treated with warfarin (mean dose: 9.6±4.2 mg/day). The indications for the use of oral anticoagulant therapy were as follows: deep-vein thrombosis (N = 23); pulmonary embolism (N = 20); arterial thrombosis (N = 5); stroke (N = 4); atrial fibrillation with transient ischemic attacks (N = 2), and history of multiple thromboembolic events (N = 3). Identification of theVKORC1 genomic variation was performed using DNA sequencing methods. The prevalence of the mutated allele (VKORC1-1639A) was 41%. TheVKORC1-1639G allele carriers required a higher daily dose of acenocoumarol (5.9±1.9 mg) than the noncarriers (4.1±3.3 mg;P A gene polymorphism may explain at least in part the low responsiveness to acenocoumarol.
TL;DR: Comparison of the phenotypes of the patient and 5 individuals with c.1582C>T showed that only the hallmark triad of the syndrome — consisting of hypertelorism, aortic root dilatation/aneurysm, and cleft palate or bifid uvula — was present in all 6 cases.
Abstract: We report on a 2-year-old Polish girl with typical manifestations of Loeys-Dietz syndrome (LDS), a rare genetic condition belonging to the group of Marfan-related disorders. The characteristic LDS symptoms observed in the girl included craniofacial dysmorphism (craniosynostosis, cleft palate, hypertelorism), arachnodactyly, camptodactyly, scoliosis, joint laxity, talipes equinovarus, translucent and hyperelastic skin, and umbilical hernia. Mild dilatation of the ascending aorta and tortuous course of the left internal carotid artery were recognized during her second year of life. Molecular genetic testing revealed a heterozygous missense mutation (c.1582C>T, p.R528C) in the transforming growth factor beta receptor II gene (TGFBR2). This mutation has been previously associated with LDS in 5 unrelated cases, and was never reported in patients with other Marfan-related disorders. Comparison of the phenotypes of our patient and these 5 individuals with c.1582C>T showed that only the hallmark triad of the syndrome — consisting of hypertelorism, aortic root dilatation/aneurysm, and cleft palate or bifid uvula — was present in all 6 cases. Interestingly, none of the 5 individuals who underwent psychological evaluation showed developmental delay. The pattern of all other LDS features showed interindividual variability. Our data support the recently reported observation that symptoms of LDS can develop at a very young age, making early diagnosis and management essential for these patients. This is the first report on a Polish infant with typical LDS symptoms caused by aTGFBR2 mutation.
TL;DR: Haplotypes containing Δ32 CCR5,190GCCR2 and 744ACX3CR1 were found to be significantly more common in the control group, which suggests an association between these haplotypes and resistance to HIV-1 infection.
Abstract: Genetic susceptibility to HIV infection was previously proven to be influenced by some chemokine receptor polymorphisms clustering on chromosome 3p21. Here the influence of 5 genetic variants was studied: Δ32CCR5, G(-2459)ACCR5, G190ACCR2, G744ACX3CR1 and C838TCX3CR1. They were screened in a cohort of 168 HIV-1 positive adults [HIV(+) group] and 151 newborns [control group] from northwestern Poland. PCR-RFLP was performed to screen for the variants (except for A32CCR5 polymorphism, where PCR fragment size was sufficient to identify the alleles) and then electrophoresed on agarose gel to determine fragment size. Distribution of genotypes and alleles was not significantly different between the groups except for theCCR5 polymorphisms, with the A32 allele and the (-2459)ACCR5 allele more frequent among neonates than in the HIV(+) group. No Δ32/Δ32 homozygotes were found in the HIV(+) group, but 16.1% were Δ32/wt heterozygotes. In the control group, 1.3% were Δ32/Δ32 homozygotes and 26.0% were Δ32/wt heterozygotes. Linkage between the chemokine polymorphisms was calculated using the most informative loci for haplotype reconstruction. Haplotypes containing Δ32 CCR5,190GCCR2 and 744ACX3CR1 were found to be significantly more common in the control group. This suggests an association between these haplotypes and resistance to HIV-1 infection.
TL;DR: This is the first report providing suggestive evidence for association of —1023A/GADRB2 polymorphism with an increased risk of asthma, and the analyzed SNPs may not play a major role in response to β2-agonists in asthmatic children.
Abstract: The aims of this study were: (1) to find associations of asthma with single-nucleotide polymorphisms (SNPs) within the ADRB2 gene: Arg16Gly, Gln27Glu, -1023 G/A, -367 T/C, -47 C/T ; (2) to define linkage disequilibrium in the gene region, basing on the analyzed SNPs; and (3) to analyze the importance of ADRB2 polymorphism for response to bronchodilator drugs in children diagnosed with bronchial asthma. We compared 113 asthmatic children and 123 healthy subjects from the Polish population. Genotyping was performed by PCR-RFLP. We found an association of the A allele of -1023A/G ADRB2 polymorphism with asthma (P = 0.024). No significant associations with other SNPs were detected. Moderate linkage was found between Gln27Glu and -47C/T polymorphisms in linkage disequilibrium analysis (D' = 0.85, r(2) = 0.429, LOD = 31.97). No significant differences were found in haplotype frequencies in comparison to the control group, implicating that they are not associated with susceptibility to asthma in the analyzed population. There was no significant correlation between the analyzed SNPs of the ADRB2 gene and the response to beta(2)-agonists. This is the first report providing suggestive evidence for association of -1023A/G ADRB2 polymorphism with an increased risk of asthma. The analyzed SNPs may not play a major role in response to beta(2)-agonists in asthmatic children.
TL;DR: Because the disorder seems to have an impact on reproductive traits and udder health in cattle, 103 randomly selected cows, 28 cows with repeat breeding, and 9 cows with recurrent mastitis were tested for the presence of an abnormalFXI allele.
Abstract: Factor XI (FXI) deficiency is a hereditary coagulation disorder observed in various mammalian species. The molecular basis of coagulopathy has been recognized in Holstein cattle as a 76-bp insertion in the coding region of theFXI gene. Because the disorder seems to have an impact on reproductive traits and udder health in cattle, we tested 103 randomly selected cows, 28 cows with repeat breeding, and 9 cows with recurrent mastitis for the presence of an abnormalFXI allele. Three related cows were diagnosed as carriers.
TL;DR: In a Polish child with the clinical symptoms typical of ODDD, a novel missense mutation c.C31T resulting in p.L11F substitution is demonstrated, providing evidence on the importance of this highly conserved amino acid residue for the proper functioning of GJA1 protein.
Abstract: Oculodentodigital dysplasia (ODDD) (OMIM #164200) is a rare congenital, autosomal dominant disorder comprising craniofacial, ocular, dental, and digital anomalies. The syndrome is caused byGJA1 mutations. The clinical phenotype of ODDD involves a characteristic dysmorphic facies, ocular findings (microphthalmia, microcornea, glaucoma), syndactyly type III of the hands, phalangeal abnormalities, diffuse skeletal dysplasia, enamel dysplasia, and hypotrichosis. In a Polish child with the clinical symptoms typical of ODDD, we demonstrated a novel missense mutation c.C31T resulting in p.L11F substitution. Our report provides evidence on the importance of this highly conserved amino acid residue for the proper functioning of GJA1 protein.
TL;DR: There are many theories of aging and a number ofthem encompass the role of mitochondria in this process, but there is little evidence that these mutations could affect the functioning of aging tissues.
Abstract: There are many theories of aging and a number ofthem encompass the role of mitochondria in this process. Mitochondrial DNA mutations and deletions have been shown to accumulate in many tissues in mammals during aging. However, there is little evidence that these mutations could affect the functioning of aging tissues.
TL;DR: The aim of this study was to detect polymorphism in the bovine bone morphogenetic protein 15 (BMP 15) gene and a 4-bp deletion was identified in the coding region of the gene.
Abstract: The aim of this study was to detect polymorphism in the bovine bone morphogenetic protein 15 (BMP 15) gene. On the basis of PCR-SSCP and DNA sequencing, a 4-bp deletion was identified in the coding region of the gene. Sequence analysis revealed that the deletion altered the reading frame and introduced a stop codon at position 264. Eight breeds (Luxi, Qinchuan, Nanyang, Jinnan, Bohai Black, Menggolian, Holstein, and Simmental) were genotyped by PCR-SSCP. No cows homozygous for this mutation were observed in these breeds. Heterozygous cows were detected in Luxi, Qinchuan, Nanyang, Jinnan and Bohai Black cattle. Fecundity was not increased in heterozygous individuals.
TL;DR: The frequency of losses of selected microsatellite markers localized on chromosomes 17 and 13q in hereditary and sporadic ovarian tumors is not strongly related to the presence of BRCA1 germline mutations.
Abstract: Loss of heterozygosity atBRCA1/2 loci in breast and ovarian tumors is a suggested risk factor for germlineBRCA1/2 mutation status. We evaluated the presence of losses of selected microsatellite markers localized on chromosomes 17 and 13q in hereditary and sporadic ovarian tumors. 151 consecutive primary ovarian tumors (including 21 withBRCA1/2 mutations and 130 without the mutations) were screened for loss of heterozygosity at loci on chromosomes 17 and 13q. Losses of heterozygosity of at least one microsatellite marker localized on chromosomes 17 and 13q were revealed in 123 (81.5%) and 104 (68.9%) tumors, respectively. Losses of all informative markers on chromosomes 17 and 13 occurred in 30 (19.9%) and 31 (20.5%) tumors, respectively. There was no difference in the frequency of losses atBRCA1 intragenic markers (D17S855 and D17S1323) between BRCA1-positive and BRCA1-negative patients. The frequency of losses on chromosome 17 was higher in high-grade than in low-grade carcinomas. Loss of heterozygosity on chromosomes 17 and 13q is a frequent phenomenon in both hereditary and sporadic ovarian cancers. The frequency of losses atBRCA1 intragenic markers in the ovarian tumor tissue is not strongly related to the presence ofBRCA1 germline mutations.