A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including , , , , and inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including , , , , and inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows

Prediction of first test day milk yield using historical records in dairy cows

The transition between two lactations remains one of the most critical periods during the productive life of dairy cows. In this study, we aimed to develop a model that predicts the milk yield of dairy cows from test day milk yield data collected in the previous lactation. In the past, data routinely collected in the context of herd improvement programmes on dairy farms have been used to provide insights in the health status of animals or for genetic evaluations. Typically, only data from the current lactation is used, comparing expected (i.e., unperturbed) with realised milk yields. This approach cannot be used to monitor the transition period due to the lack of unperturbed milk yields at the start of a lactation. For multiparous cows, an opportunity lies in the use of data from the previous lactation to predict the expected production of the next one. We developed a methodology to predict the first test day milk yield after calving using information from the previous lactation. To this end, three random forest models (nextMILKFULL, nextMILKPH, and nextMILKP) were trained with three different feature sets to forecast the milk yield on the first test day of the next lactation. To evaluate the added value of using a machine-learning approach against simple models based on contemporary animals or production in the previous lactation, we compared the nextMILK models with four benchmark models. The nextMILK models had an RMSE ranging from 6.08 to 6.24 kg of milk. In conclusion, the nextMILK models had a better prediction performance compared to the benchmark models. Application-wise, the proposed methodology could be part of a monitoring tool tailored towards the transition period. Future research should focus on validation of the developed methodology within such tool

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae. We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into different pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, , and tb) or third-generation leptons (τν and ττ) are included in this kind of combination for the first time. A simplified model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confidence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Search for non-resonant Higgs boson pair production in the 2b+2l+ETmiss final state in pp collisions at s = 13 TeV with the ATLAS detector

A search for non-resonant Higgs boson pair (HH) production is presented, in which one of the Higgs bosons decays to a b-quark pair (bb ̄) and the other decays to WW*, ZZ*, or τ+τ−, with in each case a final state with l+l−+ neutrinos (l = e, μ). The analysis targets separately the gluon-gluon fusion and vector boson fusion production modes. Data recorded by the ATLAS detector in proton-proton collisions at a centre-of-mass energy of 13 TeV at the Large Hadron Collider, corresponding to an integrated luminosity of 140 fb−1, are used in this analysis. Events are selected to have exactly two b-tagged jets and two leptons with opposite electric charge and missing transverse momentum in the final state. These events are classified using multivariate analysis algorithms to separate the HH events from other Standard Model processes. No evidence of the signal is found. The observed (expected) upper limit on the cross-section for non-resonant Higgs boson pair production is determined to be 9.7 (16.2) times the Standard Model prediction at 95% confidence level. The Higgs boson self-interaction coupling parameter κλ and the quadrilinear coupling parameter κ2V are each separately constrained by this analysis to be within the ranges [−6.2, 13.3] and [−0.17, 2.4], respectively, at 95% confidence level, when all other parameters are fixed

Determination of the Relative Sign of the Higgs Boson Couplings to W and Z Bosons Using WH Production via Vector-Boson Fusion with the ATLAS Detector

The associated production of Higgs and W bosons via vector-boson fusion is highly sensitive to the relative sign of the Higgs boson couplings to W and Z bosons. In this Letter, two searches for this process are presented, using 140 fb^{-1} of proton-proton collision data at sqrt[s]=13 TeV recorded by the ATLAS detector at the LHC. The first search targets scenarios with opposite-sign couplings of the W and Z bosons to the Higgs boson, while the second targets standard model-like scenarios with same-sign couplings. Both analyses consider Higgs boson decays into a pair of b quarks and W boson decays with an electron or muon. The data exclude the opposite-sign coupling hypothesis with a significance beyond 5σ, and the observed (expected) upper limit set on the cross section for vector-boson fusion WH production is 9.0 (8.7) times the standard model value at 95% confidence level

Studies of the Energy Dependence of Diboson Polarization Fractions and the Radiation-Amplitude-Zero Effect in WZ Production with the ATLAS Detector

: This Letter presents the first study of the energy dependence of diboson polarization fractions in WZ→lνl^{'}l^{'}(l,l^{'}=e,μ) production. The dataset used corresponds to an integrated luminosity of 140 fb^{-1} of proton-proton collisions at a center-of-mass energy of 13 TeV recorded by the ATLAS detector. Two fiducial regions with an enhanced presence of events featuring two longitudinally polarized bosons are defined. A nonzero fraction of events with two longitudinally polarized bosons is measured with an observed significance of 5.3 standard deviations in the region with 100200 GeV, where p_{T}^{Z} is the transverse momentum of the Z boson. This Letter also reports the first study of the radiation-amplitude-zero effect. Events with two transversely polarized bosons are analyzed for the ΔY(l_{W}Z) and ΔY(WZ) distributions defined respectively as the rapidity difference between the lepton from the W boson decay and the Z boson and the rapidity difference between the W boson and the Z boson. Significant suppression of events near zero is observed in both distributions. Unfolded ΔY(l_{W}Z) and ΔY(WZ) distributions are also measured and compared to theoretical predictions