How to Use Fewer Markers in Admixture Studies

Swiss Fleckvieh has been established from 1970 as a composite of Simmental and Red Holstein Friesian cattle. Breed composition is currently reported based on pedigree information. Information on ancestry informative molecular markers potentially provides more accurate information. For the analysis Illumina Bovine SNP50 Beadchip data for 495 bulls were used. Markers were selected based on difference in allele frequencies in the pure populations, using FST as an indicator. Performance of sets with decreasing number of markers was compared. The scope of the study was to see how much we can reduce the number of markers based on FST to get a reliability that is close to that with the full set of markers. On these sets of markers hidden Markov models (HMM) and methods used in genomic selection (BayesB, partial least squares regression, LASSO variable selection) were applied. Correlations of admixture levels were estimated and compared with admixture levels based on pedigree information. FST chosen SNP gave very high correlations with pedigree based admixture. Only when using 96 and 48 SNP with the highest FST, correlations dropped to 0.92 and 0.90, respectively

Electron-impact rotational and hyperfine excitation of HCN, HNC, DCN and DNC

Rotational excitation of isotopologues of HCN and HNC by thermal electron-impact is studied using the molecular {\bf R}-matrix method combined with the adiabatic-nuclei-rotation (ANR) approximation. Rate coefficients are obtained for electron temperatures in the range 5$-$6000 K and for transitions among all levels up to J=8. Hyperfine rates are also derived using the infinite-order-sudden (IOS) scaling method. It is shown that the dominant rotational transitions are dipole allowed, that is those for which $\Delta J=1$. The hyperfine propensity rule $\Delta J=\Delta F$ is found to be stronger than in the case of He$-$HCN collisions. For dipole allowed transitions, electron-impact rates are shown to exceed those for excitation of HCN by He atoms by 6 orders of magnitude. As a result, the present rates should be included in any detailed population model of isotopologues of HCN and HNC in sources where the electron fraction is larger than 10$^{-6}$, for example in interstellar shocks and comets.Comment: 12 pages, 4 figures, accepted in MNRAS (2007 september 3

The Impact of Cytoplasmic Inheritance on Sperm Quality in Fleckvieh Bulls

Detrimental impact of certain mitogenome mutations on sperm quality traits, and consequently on male fertility is well documented in humans. With a quantitative genetic mixed model, we analysed the impact of cytoplasmic effects, maternal lineages treated as random effect, on sperm quality traits in 554 Austrian Fleckvieh bulls. We have observed that 2% of the phenotypic variance for transformed total number of spermatozoa is due to cytoplasmic (maternal lineage) effects. Regarding percent of viable live spermatozoa, no cytoplasmic effects were detected. However, the observed effects still need to be further evaluated from three perspectives, the analysis of the mitogenome polymorphism effects and the impact of the mitogenome effects on the realised fertility as well as on the whole production economically

The Impact of Cytoplasmic Inheritance on Sperm Quality in Fleckvieh Bulls

Detrimental impact of certain mitogenome mutations on sperm quality traits, and consequently on male fertility is well documented in humans. With a quantitative genetic mixed model, we analysed the impact of cytoplasmic effects, maternal lineages treated as random effect, on sperm quality traits in 554 Austrian Fleckvieh bulls. We have observed that 2% of the phenotypic variance for transformed total number of spermatozoa is due to cytoplasmic (maternal lineage) effects. Regarding percent of viable live spermatozoa, no cytoplasmic effects were detected. However, the observed effects still need to be further evaluated from three perspectives, the analysis of the mitogenome polymorphism effects and the impact of the mitogenome effects on the realised fertility as well as on the whole production economically

Genetski polimorfizam β-laktoglobulina u paške ovce

Milk samples from 248 Pag ewes, belonging to 14 different flocks and located through the Pag Island (Croatia), were analyzed by isoelectrofocusing and PCR-RFLP. Two genetic variants (A and B) and three genotypes (AA, AB and BB) of β-lactoglobulin have been identified. According to the allele frequency (A=0.48, B=0.52) and occurrence of genetic variants, the Pag breed is similar to other Mediterranean dairy sheep breeds. The observed genotype frequencies at the β-lactoglobulin locus (AA=0.185, AB=0.589 and BB=0.226) were significantly different from those expected from Hardy-Weinberg equilibrium. In comparison with 12 different studies related to Mediterranean dairy sheep populations, the significant departure from Hardy-Weinberg was also obtained in Valle del Belice sheep. However, the sample size required for detection of the same amount of departure from the Hardy-Weinberg as it was observed in Pag sheep was only sufficient in four studies (including Pag sheep). The superiority of the AB β-lactoglobulin genotype for milk production could be one of possible reasons for the observed excess of heterozygotes and allele frequencies at intermediate level.Uzorci mlijeka od 248 paških ovaca iz 14 različitih stada lociranih po cijelom otoku Pagu analizirani su tehnikama izoelektričnog fokusiranja i PCR-RFLP. Identificirane su dvije genetske varijante (A i B) i tri genotipa (AA, AB i BB) β-laktoglobulina. Po frekvenciji alela (A=0.48, B=0.52) i prisutnosti genetskih varijanti paška je ovca slična ostalim mediteranskim mliječnim pasminama ovaca. Dobivene genotipske frekvencije β-laktoglobulinskog lokusa (AA=0.185, AB=0.588 i BB=0.226) pokazale su signifikantno odstupanje od očekivanog Hardy-Weinbergove ravnoteže. U 12 različitih istraživanja koja se odnose na mediteranske mliječne pasmine ovaca, signifikantno odstupanje primijećeno je još samo u pasmine Valle del Belice. Međutim, samo u četiri istraživanja (obuhvaćajući i istraživanje autora) veličina uzorka bila je dovoljna za detekciju istog odstupanja od Hardy-Weinbergove ravnoteže. Superiornost AB genotipa β-laktoglobulina za proizvodnju mlijeka mogući je uzrok veće prisutnosti heterozigote te intermedijarne frekvencije alela

Polimorfizam κ-kazeina talijanskih pasmina koza: novi ACRS-PCR test za razlikovanje A i B alela

The objective of this study was to develop a DNA test for rapid characterisation of goat κ-casein (κ-CN) A and B variants and to study this polymorphism in Italian goat breeds. Genetic polymorphism of κ-CN gene was, in addition to isoelectric focusing, analysed according to a new technique designated as amplification created restriction site. Two alleles that differ in one nucleotide mutation (G Ø A) in exon 4 were characterised. The 167-bp PCR product surrounding the nucleotide mutation was amplified from genomic DNA and the PCR product was digested with MaeIII. After digestion the A allele gives three fragments of 77, 65 and 25 bp in comparison with the B allele which gives two fragments of 90 and 77 bp. The analysis of allele frequency distribution at κ-CN locus, based on 401 individual samples, revealed significant differences among three goat breeds from the north of Italy (Nera di Verzasca, Frontalasca and Alpine) with frequency of κ-CN B allele around 0.3, versus two goat breeds from the south of Italy (Maltese and Sarda) with frequency of κ-CN B allele around 0.5. While two goat breeds (Maltese and Nera di Verzasca) did not show significant deviations from the Hardy-Weinberg equilibrium, a highly significant excess of heterozygote genotype (AB) was observed in Alpine, Frontalasca and Sarda goats. Here the developed DNA method and observed relatively high frequency of κ-CN B allele give a prerequisite for the assessment of research related to the simultaneous estimation of the effects of composite αs1/κ-CN genotypes on milk production and cheese-making properties.Svrha je bila razviti DNA test za brzo određivanje genetičkih varijanti κ-kazeina u talijanskih pasmina koza. Genetički je polimorfizam istraživan izoelektričnim fokusiranjem (IEF) i amplifikacijom nastalim restrikcijskim mjestom na genomu (ACRS). PCR produkt na ekzonu 4, dug 167-bp koji okružuje nukleotidnu mutaciju (G Ø A), amplificiran s genomske DNA i razgrađen je s MaeIII enzimom. Identificirana su dva alela koja se razlikuju u jednoj nukleotidnoj mutaciji (G Ø A). Dobiveni su fragmenti 77 i 65 bp za alel A te 90 i 77 bp za alel B. Signifikantna razlika za frekvenciju alela B ustanovljena je za tri pasmine koza sa sjevera Italije (Nera di Verzasca, Frontalasca i Alpine) s frekvencijom κ-kazeina B oko 0,3, u usporedbi s dvjema pasminama s juga Italije (Maltese i Sarda), s frekvencijom κ-kazeina B otprilike 0,5. Pasmine Maltese i Nera di Verzasca nisu pokazale signifikantno odstupanje od Hardy-Weinbergove ravnoteže, za razliku od pasmina Alpine, Frontalasca i Sarda u kojima je uočeno veliko signifikantno odstupanje. Prikazana DNA metoda i promatrana relativno velika frekvencija κ-kazeina B alela omogućavaju daljnja istraživanja zajedničkog utjecaja αs1-kazeina i κ-kazeina na proizvodnju mlijeka i sira

Genomic characterization of the three Balkan Livestock Guardian Dogs

Balkan Livestock Guardian Dogs (LGD) were bred to help protect sheep flocks in sparsely populated, remote mountainous areas in the Balkans. The aim of this study was genomic characterization (107,403 autosomal SNPs) of the three LGD breeds from the Balkans (Karst Shepherd, Sharplanina Dog, and Tornjak). Our analyses were performed on 44 dogs representing three Balkan LGD breeds, as well as on 79 publicly available genotypes representing eight other LGD breeds, 70 individuals representing seven popular breeds, and 18 gray wolves. The results of multivariate, phylogenetic, clustering (STRUCTURE), and FST differentiation analyses showed that the three Balkan LGD breeds are genetically distinct populations. While the Sharplanina Dog and Tornjak are closely related to other LGD breeds, the Karst Shepherd is a slightly genetically distinct population with estimated influence from German Shepard (Treemix analysis). Estimated genomic diversity was high with low inbreeding in Sharplanina Dog (Ho = 0.315, He = 0.315, and FROH>2Mb = 0.020) and Tornjak (Ho = 0.301, He = 0.301, and FROH>2Mb = 0.033) breeds. Low diversity and high inbreeding were estimated in Karst Shepherds (Ho = 0.241, He = 0.222, and FROH>2Mb = 0.087), indicating the need for proper diversity management. The obtained results will help in the conservation management of Balkan LGD dogs as an essential part of the specific grazing biocultural system and its sustainable maintenance

Analysis of the impact of cytoplasmic and mitochondrial inheritance on litter size and carcass in rabbits

The effects of mitogenome variation on economically important traits have been reported in a number of domestic animal species. In this study, the first of its kind on rabbits, we have performed the estimation of the contribution of cytoplasmic and D-loop mitochondrial DNA (mtDNA) sequence effects on the litter size and carcass traits in three Pannon rabbit breeds (Pannon Ka, Pannon Large and Pannon White). The observed effects of both estimates, coming from cytoplasmic or D-loop mtDNA variation, were negligible. The most likely explanation for the results obtained is the lack of mitogenome polymorphism in all three populations, as suggested from the analysis performed on the D-loop mtDNA sequence, here assigned to the two most frequent rabbit haplotypes. The extent of potential benefits of the introduction, or alteration, of mitogenome variation in rabbit breeding remains an open question for future research