Journal of applied genetics (J APPL GENET)

Publications in this journal

• Article: Studies on changes of estimated breeding values of U.S. Holstein bulls for final score from the first to second crop of daughters

  V. K. R. Koduru, S. Tsuruta, M. Łukaszewicz, I. Misztal, T. J. Lawlor
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  ABSTRACT: The purpose of this study was to find ways of reducing changes of sire predicted transmitting ability for type’s final scores (PTATs) from the first to second crop of daughters. The PTATs were estimated from two datasets: D01 (scores recorded up to 2001) and D05 (scores recorded up to 2005). The PTAT changes were calculated as the difference between the evaluations based on D01 and D05. The PTATs were adjusted to a common genetic base of all evaluated cows born in 1995. The single-trait (ST) animal model included the fixed effects of the herd–year–season–classifier, age by year group at classification, stage of lactation at classification, registry status of animals, and additive genetic and permanent environment random effects. Unknown parent groups (UPGs) were defined based on every other birth year starting from 1972. Modifications to the ST model included the usage of a single record per cow, separate UPGs for first and second crop daughters, separate UPGs for sires and dams, and deepened pedigrees for dams with missing phenotypic records. Also, the multiple-trait (MT) model treated records of registered and grade cows as correlated traits. The mean PTAT change, for all of the sires, was close to zero in all of the models analyzed. The estimated mean PTAT change for 145 sires with 40 to 100 first crop and ≥200 second crop daughters was −0.33, −0.20, −0.13, −0.28, and −0.12 with ST, only first records, only last records, updated pedigrees, and allowing separate parent groups (PGs) for sires and dams after updating the pedigrees, respectively. The percentages of sires showing PTAT decline were reduced from 74.5 (with ST) to 57.3 by using only the last records of cows, and to 56.4 by allowing separate UPGs for sires and dams after updating the pedigrees. Though updating of the pedigrees alone was not effective, separate UPGs for sires together with additional pedigree was helpful in reducing the bias. KeywordsBreeding value-Final score-Fluctuation-U.S. Holstein
  Journal of applied genetics 05/2012; 52(1):81-88.
• Article: Current genetic methodologies in the identification of disaster victims and in forensic analysis

  Ewa Ziętkiewicz, Magdalena Witt, Patrycja Daca, Jadwiga Żebracka-Gala, Mariusz Goniewicz, Barbara Jarząb, Michał Witt
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  ABSTRACT: This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures). KeywordsDNA profiling–Genetic markers in DVI–Statistical analysis in DVI–Automated technological platforms–Polymorphisms databases–Transcriptome analysis–DNA mixtures analysis
  Journal of applied genetics 04/2012; 53(1):41-60.
• Article: Identification of mutations in theNF2 gene in Polish patients with neurofibromatosis type 2

  Mikołaj Łaniewski-Wołłk, Monika Gos, Andrzej Koziarski, Agnieszka Szpecht-Potocka
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  ABSTRACT: Point mutation and loss of heterozygosity (LOH) analyses were performed in 12 Polish patients with a classic symptom of NF2 — bilateral vestibular schwannomas (BVS). In 5 patients (41.7%), germline mutations were found in theNF2 gene: 2 previously reported substitutions (c.592C>T and c.52C>T) and 3 novel mutations (c.1001_1002insG, c.1029_1030insCC, c.774_778dupGAATG). In addition, LOH analysis of 30 tumour samples from 10 patients revealed a molecular basis of NF2 in 3 patients (25%) that did not have any germline mutation. The molecular defects in sporadic cases of NF2 are still being discussed. Keywordsmutations-neurofibromatosis type 2-NF2
  Journal of applied genetics 04/2012; 49(3):297-300.
• Article: Fitting and validating the genomic evaluation model to Polish Holstein-Friesian cattle

  Joanna Szyda, Andrzej Żarnecki, Tomasz Suchocki, Stanisław Kamiński
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  ABSTRACT: The aim of the study was to fit the genomic evaluation model to Polish Holstein-Friesian dairy cattle. A training data set for the estimation of additive effects of single nucleotide polymorphisms (SNPs) consisted of 1227 Polish Holstein-Friesian bulls. Genotypes were obtained by the use of Illumina BovineSNP50 Genotyping BeadChip. Altogether 29 traits were considered: milk-, fat- and protein- yields, somatic cell score, fourfemale fertility traits, and 21 traits describing conformation. The prediction of direct genomic values was based on a mixed model containing deregressed national proofs as a dependent variable and random SNP effects as independent variables. The correlations between direct genomic values and conventional estimated breeding values estimated for the whole data set were overall very high and varied between 0.98 for production traits and 0.78 for non return rates for cows. For the validation data set of 232 bulls the corresponding correlations were 0.38 for milk-, 0.37 for protein-, and 0.32 for fat yields, while the correlations between genomic enhanced breeding values and conventional estimated breeding values for the four traits were: 0.43, 0.44, 0.31, and 0.35. This model was able to pass the interbull validation criteria for genomic selection, which indicates that it is realistic to implement genomic selection in Polish Holstein-Friesian cattle. KeywordsDairy cattle–Genomic selection–Model validation–Single nucleotide polymorphism
  Journal of applied genetics 04/2012; 52(3):363-366.
• Article: Darwin’s contributions to genetics

  Y. -S. Liu, X. M. Zhou, M. X. Zhi, X. J. Li, Q. L. Wang
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  ABSTRACT: Darwin’s contributions to evolutionary biology are well known, but his contributions to genetics are much less known. His main contribution was the collection of a tremendous amount of genetic data, and an attempt to provide a theoretical framework for its interpretation. Darwin clearly described almost all genetic phenomena of fundamental importance, such as prepotency (Mendelian inheritance), bud variation (mutation), heterosis, reversion (atavism), graft hybridization (Michurinian inheritance), sex-limited inheritance, the direct action of the male element on the female (xenia and telegony), the effect of use and disuse, the inheritance of acquired characters (Lamarckian inheritance), and many other observations pertaining to variation, heredity and development. To explain all these observations, Darwin formulated a developmental theory of heredity — Pangenesis — which not only greatly influenced many subsequent theories, but also is supported by recent evidence. KeywordsDarwin-genetics-Pangenesis-variation and heredity-breeding
  Journal of applied genetics 04/2012; 50(3):177-184.
• Article: Campylobacter protein oxidation influences epithelial cell invasion or intracellular survival as well as intestinal tract colonization in chickens

  A. M. Łasica, A. Wyszyńska, K. Szymanek, P. Majewski, E. K. Jagusztyn-Krynicka
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  ABSTRACT: The Dsb family of redox proteins catalyzes disulfide bond formation and isomerization. Since mutations indsb genes change the conformation and stability of many extracytoplasmic proteins, and since many virulence factors of pathogenic bacteria are extracytoplasmic, inactivation ofdsb genes often results in pathogen attenuation. This study investigated the role of 2 membrane-bound oxidoreductases, DsbB and DsbI, in theCampylobacter jejuni oxidative Dsb pathway.Campylobacter mutants, lacking DsbB or DsbI or both, were constructed by allelic replacement and used in the human intestinal epithelial T84 cell line for the gentamicin protection assay (invasion assay) and chicken colonization experiments. InC. coli strain 23/1, the inactivation of thedsbB ordsbI gene separately did not significantly affect the colonization process. However, simultaneous disruption of both membrane-bound oxidoreductase genes significantly decreased the strain’s ability to colonize chicken intestines. Moreover,C. jejuni strain 81–176 with mutateddsbB ordsbI genes showed reduced invasion/intracellular survival abilities. No cells of the double mutants (dsbB − dsbI −) ofC. jejuni 81–176 were recovered from human cells after 3 h of invasion. Keywords Campylobacter -colonization, disulfide bonds-Dsb proteins-invasion-oxidoreductase
  Journal of applied genetics 04/2012; 51(3):383-393.
• Article: Chromosome pairing in triploid intergeneric hybrids ofFestuca pratensis withLolium multiflorum, revealed by GISH

  Arkadiusz Kosmala, Elżbieta Zwierzykowska, Zbigniew Zwierzykowski
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  ABSTRACT: Genomicin situ hybridisation (GISH) was used to reveal chromosome pairing in two partly fertile, triploid (2n = 3x = 21) hybrids obtained by crossing the diploid (2n = 2x = 14)Festuca pratensis Huds. (designated FpFp), used as a female parent, with the autotetraploid (2n = 4x = 28)Lolium multiflorum Lam. (designated LmLmLmLm), used as a male parent. The pattern of chromosome pairing calculated on the basis of the mean values of chromosome configurations identified in all 100 PMCs analysed, was: 0.71I Lm + 2.24I Fp + 2.18II Lm/Lm + 0.54II Lm/Fp + 4.18III Lm/Lm/Fp. A relatively high number of Lm/Lm bivalents and Fp univalents, and a low number of Lm/Fp bivalents and Lm univalents indicated that the pairing was preferential betweenL. multiflorum chromosomes. Other observations regarding chromosome pairing within the Lm/Lm/Fp trivalents also confirmed this preferential pairing in the analysed triploids, as the Fp chromosome was not randomly located in the chain- and frying-pan-shaped trivalents. The similarities and differences in chromosome pairing at metaphase I and the level of preferential pairing betweenLolium chromosomes in the different triploidLolium-Festuca hybrids are discussed. Key wordschromosome pairing- Festuca pratensis -GISH-intergeneric hybrids- Lolium multiflorum -triploids
  Journal of applied genetics 04/2012; 47(3):215-220.
• Article: Marker-assisted selection of diploid and tetraploid potatoes carryingRpi-phu1, a major gene for resistance toPhytophthora infestans

  J. Śliwka, H. Jakuczun, P. Kamiński, E. Zimnoch-Guzowska
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  ABSTRACT: TheRpi-phu1 gene originates from an interspecific hybrid betweenSolanum stenotomum andS. phureja, and confers a high level of resistance toPhytophthora infestans (late blight) in potato. TheRpi-phu1 was introduced by crossing at the diploid level into theS. tuberosum gene pool and then transferred to the tetraploid level by means of2n gametes. Tetraploid lines carrying theRpi-phu1 were selected for further crosses. A molecular marker GP94, linked in mapping population 97-30 with theRpi-phu1 (6.4 cM), was applied to other unselected populations (2 diploid and 1 tetraploid), and was shown to be useful in marker-assisted selection (MAS) of the resistant individuals. GP94 was applied also in commercial breeding in 2 tetraploid populations. Although the marker allele of GP94, characteristic for theRpi-phu1 presence, was rare in theS. tuberosum gene pool, it seemed to be common in 2 other sources of resistance to late blight:S. ruizceballosii andS. kurtzianum. Keywordslate blight-molecular marker-Phytophthora infestans-R gene-resistance-Solanum tuberosum
  Journal of applied genetics 04/2012; 51(2):133-140.
• Article: Variability of ribosomal DNA sites inFestuca pratensis, Lolium perenne, and their intergeneric hybrids, revealed by FISH and GISH

  T. Książczyk, M. Taciak, Z. Zwierzykowski
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  ABSTRACT: This study focuses on the variability of chromosomal location and number of ribosomal DNA (rDNA) sites in some diploid and autotetraploidFestuca pratensis andLolium perenne cultivars, as well as on identification of rDNA-bearing chromosomes in their triploid and tetraploidF. pratensis ×L. perenne hybrids. The rDNA loci were mapped using fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes, and the origin of parental genomes was verified by genomic in situ hybridization (GISH) withL. perenne genomicDNAas a probe, andF. pratensis genomic DNA as a block. FISH detected variation in the number and chromosomal location of both 5S and 45S rDNA sites. InF. pratensis mostly additional signals of 5S rDNA loci occurred, as compared with standardF. pratensis karyotypes. Losses of 45S rDNA loci were more frequent inL. perenne cultivars and intergeneric hybrids. Comparison of theF. pratensis andL. perenne genomes approved a higher number of rDNA sites as well as variation in chromosomal rDNA location inL. perenne. A greater instability ofF. pratensis-genome-like andL. perenne-genome-like chromosomes in tetraploid hybrids was revealed, indicating gains and losses of rDNA loci, respectively. Our data indicate that the rDNA loci physically mapped on chromosomes 2 and 3 inF. pratensis and on chromosome 3 inL. perenne are useful markers for these chromosomes in intergenericFestuca ×Lolium hybrids. Keywords Festuca ×Lolium hybrids-5S rDNA-45S rDNA-GISH-rDNA-FISH
  Journal of applied genetics 04/2012; 51(4):449-460.
• Article: High-fat diet leads to a decreased methylation of theMc4r gene in the obese BFMI and the lean B6 mouse lines

  S. Widiker, S. Kärst, A. Wagener, G. A. Brockmann
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  ABSTRACT: The melanocortin-4 receptor (Mc4r) plays an important role in body-weight regulation. This study examines the methylation status and expression levels of theMc4r gene in response to a standard and a high-fat diet in the obese Berlin fat mouse inbred (BFMI) line and the lean C57BL/6NCrl (B6) line ofMus musculus. The methylation status of CpG sites located within theMc4r exon was analyzed by bisulfite genomic sequencing of genomic DNA of brain tissues, and gene expression analysis was performed by real-time PCR. In both lines, the methylation of CpGs 1–8 (near the transcription start) was lower than methylation of CpGs 9–16 (located towards the end of the selected amplicon). On the standard diet, the methylation status did not differ between the lines. In response to high-fat diet, methylation of the CpGs near the transcription start was decreased in both lines. TheMc4r gene expression, however, was only marginally increased in BMFI mice, whereas there was no change in B6 mice. The results suggest that a long-term high-fat diet might have an effect on the methylation status of theMc4r gene. However, the effect of methylation onMc4r expression seems to be a variable compensated by other regulating factors in a line-specific manner. Keywordsepigenetics-gene expression-methylation pattern-Mus musculus-obesity
  Journal of applied genetics 04/2012; 51(2):193-197.
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  Article: Random variability of map distances based on Kosambi’s and Haldane’s mapping functions

  M. Huehn
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  ABSTRACT: The majority of published genetic maps are based on Kosambi distances or on Haldane distances. For a comparison of both map distance measures, their random variability is of particular interest. For the statistic ‘variance’, this paper presents a relationship between Kosambi distances and Haldane distances. The results suggest that Kosambi distances exhibit a smaller random variability. The theoretical results are applied to an experimental data set for molecular AFLP markers linked to the bolting gene of sugar beet (Beta vulgaris L.). KeywordsAFLP markers-Beta vulgaris-bolting gene-genetic maps-Haldane distance-Kosambi distance
  Journal of applied genetics 04/2012; 51(1):27-31.
• Article: Novel SNP of the goatprolactin gene (PRL) associated with cashmere traits

  X. -Y. Lan, Ch. -Y. Pan, H. Chen, Ch. -Z. Lei, F. -Y. Li, H. -Y. Zhang, Y. -S. Ni
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  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). Keywordscaprine-fibre length-prolactin- PRL gene-restriction fragment length polymorphism-single-strand conformation polymorphism-single-nucleotide polymorphism
  Journal of applied genetics 04/2012; 50(1):51-54.
• Article: Ade novo interstitial 6q deletion in a boy with a split hand malformation

  Jorge Duran-Gonzalez, Melva Gutierrez-Angulo, Diana Garcia-Cruz, Ma. de la Luz Ayala, Miguel Padilla, Ingrid P. Davalos
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  ABSTRACT: We report on ade novo interstitial deletion of (6)(q15q22.2) in a 5-year-old boy with developmental delay, microcephaly, facial dysmorphism, cryptorchidism, congenital heart defect, and split-hand malformation. Previous reports and this patient suggest that 6q21 may contain a gene or genes related either directly or indirectly to limb development. Keywordschromosome 6q-interstitial deletion 6q-split hand
  Journal of applied genetics 04/2012; 48(4):405-407.