Associations of reproductive indices with fertility outcomes, milk yield, and survival in Holstein cows

The study is part of a research effort investigating potential associations between genomic variation and fertility of Holstein cows. The objective was to compare the reproductive performance of Holstein cows in 3 categories of 2 reproductive indices (RI) that were developed for the allocation of cows in a ranking for potential fertility, based on the predicted probability of pregnancy. The associations between categories of the developed indices and multiple fertility variables in a large multistate population of Holstein cows were tested. In addition, we analyzed associations among the RI categories with milk yield and survival. Based on phenotypic information from individual cows, 2 reproductive indices (RI1 and RI2) were developed, representing a predicted probability that a cow will become pregnant at first artificial insemination postpartum, as a function of explanatory variables used in a logistic model. Data from a total of 11,733 cows calving in 16 farms located in 4 regions of the United States (Northeast, Midwest, Southeast, and Southwest) were available. Cows were enrolled at parturition and monitored weekly for reproductive events, health status, milk yield, and survival. To develop the indices, potential significant effects were initially tested by univariate analyses. Effects with P ≤ 0.05 were offered to the multivariate analysis, and the final models were determined through backward elimination, considering potentially significant interactions. The final model for RI1 included the random effect of farm and a complement of significant fixed effects as explanatory variables influencing a pregnancy outcome: (1) incidence of retained fetal membranes; (2) metritis; (3) clinical endometritis; (4) lameness at 35 days in milk (DIM); (5) resumption of postpartum ovulation by 50 DIM; (6) season of calving; and (7) parity number. The model for RI2 included (1) parity number; (2) body condition score at 40 DIM; (3) incidence of retained fetal membranes; (4) metritis; (5) resumption of postpartum ovulation by 50 DIM; (6) region; (7) subclinical ketosis; (8) mastitis; (9) clinical endometritis; and (10) milk yield at the first milk test after calving; as well as the interaction effects of postpartum resumption of ovulation by 50 DIM × region; mastitis × region; and milk yield at the first milk test after calving × parity number. Multivariate logistic regression, ANOVA, and survival analysis were used to test the correspondence between the resulting RI and individual fertility, milk yield, and survival from the population. To facilitate the analyses, the resulting RI values were categorized as low for cows in the lowest quartile, medium for cows within the interquartile range, or high for cows in the top quartile. We found consistent agreement between categories of the predicted RI and the measures of fertility and survival collected from individual cows. We conclude that the proposed RI represent a viable approach to refine the allocation of cows into potential low- and high-fertility populations.

Genome-enable prediction for health traits using high-density SNP panel in US Holstein cattle

The objective of this study was to compare accuracies of different Bayesian regression models in predicting molecular breeding values for health traits in Holstein cattle. The dataset was composed of 2505 records reporting the occurrence of retained fetal membranes (RFM), metritis (MET), mastitis (MAST), displaced abomasum (DA), lameness (LS), clinical endometritis (CE), respiratory disease (RD), dystocia (DYST) and subclinical ketosis (SCK) in Holstein cows, collected between 2012 and 2014 in 16 dairies located across the US. Cows were genotyped with the Illumina BovineHD (HD, 777K). The quality controls for SNP genotypes were HWE P‐value of at least 1 × 10⁻¹⁰; MAF greater than 0.01 and call rate greater than 0.95. The fimpute program was used for imputation of missing SNP markers. The effect of each SNP was estimated using the Bayesian Ridge Regression (BRR), Bayes A, Bayes B and Bayes Cπ methods. The prediction quality was assessed by the area under the curve, the prediction mean square error and the correlation between genomic breeding value and the observed phenotype, using a leave‐one‐out cross‐validation technique that avoids iterative cross‐validation. The highest accuracies of predictions achieved were: RFM [Bayes B (0.34)], MET [BRR (0.36)], MAST [Bayes B (0.55), DA [Bayes Cπ (0.26)], LS [Bayes A (0.12)], CE [Bayes A (0.32)], RD [Bayes Cπ (0.23)], DYST [Bayes A (0.35)] and SCK [Bayes Cπ (0.38)] models. Except for DA, LS and RD, the predictive abilities were similar between the methods. A strong relationship between the predictive ability and the heritability of the trait was observed, where traits with higher heritability achieved higher accuracy and lower bias when compared with those with low heritability. Overall, it has been shown that a high‐density SNP panel can be used successfully to predict genomic breeding values of health traits in Holstein cattle and that the model of choice will depend mostly on the genetic architecture of the trait.

Mantle flow beneath a continental strike-slip fault: postseismic deformation after the 1999 Hector Mine earthquake

Two recent large earthquakes in the Mojave Desert, California-the magnitude 7.3 1992 Landers and magnitude 7.1 1999 Hector Mine earthquakes-have each been followed by elevated crustal strain rates over periods of months and years. Geodetic data collected after the Hector Mine earthquake exhibit a temporally decaying horizontal velocity field and a quadrant uplift pattern opposite to that expected for localized shear beneath the earthquake rupture. We interpret the origin of this accelerated crustal deformation to be vigorous flow in the upper mantle in response to the stress changes generated by the earthquake. Our results suggest that transient flow in the upper mantle is a fundamental component of the earthquake cycle and that the lower crust is a coherent stress guide coupling the upper crust with the upper mantle.

Tectonic contraction across Los Angeles after removal of groundwater pumping effects

After the 1987 Whittier Narrows and 1994 Northridge earthquakes revealed that blind thrust faults represent a significant threat to metropolitan Los Angeles, a network of 250 continuously recording global positioning system (GPS) stations was deployed to monitor displacements associated with deep slip on both blind and surface faults. Here we augment this GPS data with interferometric synthetic aperture radar imagery to take into account the deformation associated with groundwater pumping and strike-slip faulting. After removing these non-tectonic signals, we are left with 4.4 mm yr-1 of uniaxial contraction across the Los Angeles basin, oriented N 36 degrees E (perpendicular to the major strike-slip faults in the area). This indicates that the contraction is primarily accommodated on thrust faults rather than on the northeast-trending strike-slip faults. We have found that widespread groundwater and oil pumping obscures and in some cases mimics the tectonic signals expected from the blind thrust faults. In the 40-km-long Santa Ana basin, groundwater withdrawal and re-injection produces 12 mm yr-1 of long-term subsidence, accompanied by an unprecedented seasonal oscillation of 55 mm in the vertical direction and 7 mm horizontally.

Present-Day deformation across the basin and range province, western united states

The distribution of deformation within the Basin and Range province was determined from 1992, 1996, and 1998 surveys of a dense, 800-kilometer-aperture, Global Positioning System network. Internal deformation generally follows the pattern of Holocene fault distribution and is concentrated near the western extremity of the province, with lesser amounts focused near the eastern boundary. Little net deformation occurs across the central 500 kilometers of the network in western Utah and eastern Nevada. Concentration of deformation adjacent to the rigid Sierra Nevada block indicates that external plate-driving forces play an important role in driving deformation, modulating the extensional stress field generated by internal buoyancy forces that are due to lateral density gradients and topography near the province boundaries.

Migration of fluids beneath yellowstone caldera inferred from satellite radar interferometry

Satellite interferometric synthetic aperture radar is uniquely suited to monitoring year-to-year deformation of the entire Yellowstone caldera (about 3000 square kilometers). Sequential interferograms indicate that subsidence within the caldera migrated from one resurgent dome to the other between August 1992 and August 1995. Between August 1995 and September 1996, the caldera region near the northeast dome began to inflate, and accompanying surface uplift migrated to the southwest dome between September 1996 and June 1997. These deformation data are consistent with hydrothermal or magmatic fluid migration into and out of two sill-like bodies that are about 8 kilometers directly beneath the caldera.

Correlation of Changes in Gravity, Elevation, and Strain in Southern California

Measurements made once or twice a year from 1977 through 1982 show large correlated changes in gravity, elevation, and strain in several southern California networks. Precise gravity surveys indicate changes of as much as 25 microgals between surveys 6 months apart. Repeated surveys show that annual elevation changes as large as 100 millimeters occur along baselines 40 to 100 kilometers long. Laser-ranging surveys reveal coherent changes in areal strain of 1 to 2 parts per million occurred over much of southern California during 1978 and 1979. Although the precision of these measuring systems has been questioned, the rather good agreement among them suggests that the observed changes reflect true crustal deformation.

Episodic Strain Accumulation in Southern California

Reexamination of horizontal geodetic data in the region of recently discovered aseismic uplift has demonstrated that equally unusual horizontal crustal deformation accompanied the development of the uplift. During this time interval compressive strains were oriented roughly normal to the San Andreas fault, suggesting that the uplift produced little shear strain accumulation across this fault. On the other hand, the orientation of the anomalous shear straining is consistent with strain accumulation across northdipping range-front thrusts like the San Fernando fault. Accordingly, the horizontal and vertical crustal deformation disclosed by geodetic observation is interpreted as a short epoch of rapid strain accumulation on these frontal faults. If this interpretation is correct, thrust-type earthquakes will eventually release the accumulated strains, but the geodetic data examined here cannot be used to estimate when these events might occur. However, observation of an unusual sequence of tilts prior to 1971 on a level line lying to the north of the magnitude 6.4 San Fernando earthquake offers some promise for precursor monitoring. The data are adequately explained by a simple model of up-dip aseismic slip propagation toward the 1971 epicentral region. These observations and the simple model that accounts for them suggest a conceptually straightforward monitoring scheme to search for similar uplift and tilt precursors within the uplifted region. Such premonitory effects could be detected by a combination of frequenlty repeated short (30 to 70 km in length) level line measurements, precise gravity traverses, and continuously recording gravimeters sited to the north of the active frontal thrust faults. Once identified, such precursors could be closely followed in space and time, and might then provide effective warnings of impending potentially destructive earth-quakes.

Strain Release Mechanism of the 1906 San Francisco Earthquake

Reexamination of geodetic data has shown that aseismic slip occurred on or near the San Andreas fault in the period of about 20 years after 1906. The inferred displacements are comparable to but at greater depths than the sudden slip that occurred at the time of the earthquake. The postseismic slip is constrained only between late 1906 and 1925, and data are insufficient to determine the movements, if any, below about 20 kilometers on the fault. Two independent observations also indicate stubstantial anomalous crustal deformation away from the fault at least 30 years before the earthquake.