Management of lethal recessive alleles in beef cattle through the use of mate selection software

International audienceAbstractBackgroundRecessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions.MethodsTwo beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0–100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping.ResultsWith full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring (aa) as compared to indiscriminate selection against carrier parents (Aa). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses.ConclusionsGenotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding

Genotype imputation for the prediction of genomic breeding values in non-genotyped and low-density genotyped individuals

<p>Abstract</p> <p>Background</p> <p>There is wide interest in calculating genomic breeding values (GEBVs) in livestock using dense, genome-wide SNP data. The general framework for genomic selection assumes all individuals are genotyped at high-density, which may not be true in practice. Methods to add additional genotypes for individuals not genotyped at high density have the potential to increase GEBV accuracy with little or no additional cost. In this study a long haplotype library was created using a long range phasing algorithm and used in combination with segregation analysis to impute dense genotypes for non-genotyped dams in the training dataset (S1) and for non-genotyped or low-density genotyped individuals in the prediction dataset (S2), using the 14^th QTL-MAS Workshop dataset. Alternative low-density scenarios were evaluated for accuracy of imputed genotypes and prediction of GEBVs.</p> <p>Results</p> <p>In S1, females in the training population were not genotyped and prediction individuals were either not genotyped or genotyped at low-density (evenly spaced at 2, 5 or 10 Mb). The proportion of correctly imputed genotypes for training females did not change when genotypes were added for individuals in the prediction set whereas the number of correctly imputed genotypes in the prediction set increased slightly (S1). The S2 scenario assumed the complete training set was genotyped for all SNPs and the prediction set was not genotyped or genotyped at low-density. The number of correctly imputed genotypes increased with genotyping density in the prediction set. Accuracy of genomic breeding values for the prediction set in each scenario were the correlation of GEBVs with true breeding values and were used to evaluate the potential loss in accuracy with reduced genotyping. For both S1 and S2 the GEBV accuracies were similar when the prediction set was not genotyped and increased with the addition of low-density genotypes, with the increase larger for S2 than S1.</p> <p>Conclusions</p> <p>Genotype imputation using a long haplotype library and segregation analysis is promising for application in sparsely-genotyped pedigrees. The results of this study suggest that dense genotypes can be imputed for selection candidates with some loss in genomic breeding value accuracy, but with levels of accuracy higher than traditional BLUP estimated breeding values. Accurate genotype imputation would allow for a single low-density SNP panel to be used across traits.</p

Lowest Open Channels, Bound States, and Narrow Resonances of Dipositronium

The constraints imposed by symmetry on the open channels of dipositronium has been studied, and the symmetry-adapted lowest open channel of each quantum state has been identified. Based on this study, the existence of two more 0^+ bound states has been theoretically confirmed, and a 0^+ narrow resonance has been predicted. A variational calculation has been performed to evaluate the critical strength of the repulsive interaction . Two 0^- states are found to have their critical strengths very close to 1, they are considered as candidates of new narrow resonances or loosely bound states .Comment: 10 pages, 0 figure

Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Pitch discrimination is better for synthetic timbre than natural musical instrument timbres despite familiarity

Pitch discrimination is better for complex tones than pure tones, but how pitch discrimination differs between natural and artificial sounds is not fully understood. This study compared pitch discrimination thresholds for flat-spectrum harmonic complex tones with those for natural sounds played by musical instruments of three different timbres (violin, trumpet, and flute). To investigate whether natural familiarity with sounds of particular timbres affects pitch discrimination thresholds, this study recruited non-musicians and musicians who were trained on one of the three instruments. We found that flautists and trumpeters could discriminate smaller differences in pitch for artificial flat-spectrum tones, despite their unfamiliar timbre, than for sounds played by musical instruments, which are regularly heard in everyday life (particularly by musicians who play those instruments). Furthermore, thresholds were no better for the instrument a musician was trained to play than for other instruments, suggesting that even extensive experience listening to and producing sounds of particular timbres does not reliably improve pitch discrimination thresholds for those timbres. The results show that timbre familiarity provides minimal improvements to auditory acuity, and physical acoustics (e.g., the presence of equal-amplitude harmonics) determine pitch discrimination thresholds more than does experience with natural sounds and timbre-specific training

Second bound state of the positronium molecule and biexcitons

A new, hitherto unknown bound state of the positronium molecule, with orbital angular momentum L=1 and negative parity is reported. This state is stable against autodissociation even if the masses of the positive and negative charges are not equal. The existence of a similar state in two-dimension has also been investigated. The fact that the biexcitons have a second bound state may help the better understanding of their binding mechanism.Comment: Latex, 8 pages, 2 Postscript figure

How much do delayed health care seeking, delayed care provision and diversion from primary care contribute to the transmission of STIs

Objectives: To explore the changing pattern of condom use from 1990 to 2000; to identify sociodemographic and behavioural factors associated with condom use; and reasons for condom use in 2000. Methods: Large probability sample surveys administered among those resident in Britain aged 16–44 (n = 13 765 in 1990, n = 11 161 in 2000). Face to face interviews with self completion components collected sociodemographic, behavioural, and attitudinal data. Results: Condom use in the past year among sexually active 16–24 year old men increased from 61.0% in 1990 to 82.1% in 2000 (p<0.0001), and from 42.0% to 63.2% (p<0.0001) among women of the same age, with smaller increases among older age groups. Among individuals reporting at least two partners in the previous 4 week period, approximately two thirds reported inconsistent or no condom use (63.1% (95% CI 55.9% to 69.8%) of the men and 68.5% (95% CI 57.6% to 77.7%) of the women). Conclusions: Rates of condom use increased substantially between 1990 and 2000, particularly among young people. However, inconsistent condom use by individuals with high rates of partner acquisition may contribute significantly to the recent resurgence in STIs. This group is an important target for intensive and specific sexual health interventions