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Shook G.E.,University of Wisconsin - Madison | Chaffer M.,Kimron Veterinary Institute | Chaffer M.,University of Prince Edward Island | Wu X.-L.,University of Wisconsin - Madison | Ezra E.,Israel Cattle Breeders Association
Animal Genetics | Year: 2012

Paratuberculosis (Johne's disease) is an infectious enteric disease in dairy cattle and other species that causes substantial economic loss worldwide. In this study, two recursive Gaussian-threshold models were employed in order to infer the effects of Johne's disease on milk yield, fat yield, and protein yield while simultaneously estimating genetic parameters (i.e. heritability and genetic correlation) in an Israeli Holstein population. Disease diagnosis was based on ELISA serum antibody tests. Data were available for 4694 daughters of 361 sires; 3.5% were positive; and 1.6% were suspect for the disease test. Disease status was coded either as a binary character (negative vs. positive) or as an ordered categorical trait (negative, suspect, and positive) in the two recursive models and as a binary trait in a linear model. Among sires with ≥50 daughters, predicted probability of Mycobacterium avium ssp. paratuberculosis (MAP) infection in future daughters ranged from <1% to 16.5%. Heritability estimates for Johne's disease were near 0.15, confirming a genetic contribution to disease susceptibility. Genetic correlation estimates for Johne's disease with the three yield traits were 0.15-0.22. Residual correlations for Johne's disease with the yield traits were between -0.01 and -0.10. For the linear regression model, yield losses associated with a positive disease diagnosis during 305 days of lactation were 300 kg milk and around 10 kg for fat and protein. Yield loss estimates from the recursive models were 25-50% less than linear model estimates. Recursive modeling has theoretical advantages over linear models for these phenotypes, but the estimated genetic parameters in this study did not differ significantly between the two types of models. © 2012 Stichting International Foundation for Animal Genetics.

Seroussi E.,Institute of Animal science | Glick G.,Institute of Animal science | Shirak A.,Institute of Animal science | Yakobson E.,Institute of Animal science | And 3 more authors.
BMC Genomics | Year: 2010

Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions.Results: We used the BeadChip data obtained for 912 Israeli bulls to investigate the effects of CNV on SNP calls. For each of the SNPs, we estimated the frequencies of occurrence of loss of heterozygosity (LOH) and of gain, based either on deviation from the expected Hardy-Weinberg equilibrium (HWE) or on signal intensity (SI) using the PennCNV "detect" option. Correlations between LOH/CNV frequencies predicted by the two methods were low (up to r = 0.08). Nevertheless, 418 locations displayed significantly high frequencies by both methods. Efficiency of designating large genomic clusters of olfactory receptors as CNVs was 29%. Frequency values for copy loss were distinguishable in non-autosomal regions, indicating misplacement of a region in the current BTA7 map. Analysis of BTA18 placed major quantitative trait loci affecting net merit in the US Holstein population in regions rich in segmental duplications and CNVs. Enrichment of transporters in CNV loci suggested their potential effect on milk-production traits.Conclusions: Expansion of HWE and PennCNV analyses allowed estimating LOH/CNV frequencies, and combining the two methods yielded more sensitive detection of inherited CNVs and better estimation of their possible effects on cattle genetics. Although this approach was more effective than methodologies previously applied in cattle, it has severe limitations. Thus the number of CNVs reported here for the Holstein breed may represent as little as one-tenth of inherited common structural variation. © 2010 Seroussi et al; licensee BioMed Central Ltd.

Weller J.I.,Israel Agricultural Research Organization | Ezra E.,Israel Cattle Breeders Association
Journal of Dairy Science | Year: 2016

The objective was to test the hypothesis that more frequent but less accurately analyzed milk components may give a more representative measure of a cow's total lactation production. Daily records for milk production and fat and protein concentration collected by the AfiLab recording system (Afimilk, Kibbutz Afikim, Israel) from January 2014 to January 2016 from 47 large kibbutz (communal) herds distributed throughout Israel with a total of 37,486 Israeli Holstein cows were compared with the same statistics derived from monthly test day records derived by Bentley and Foss milk analyzers at the central laboratory of the Israel Cattle Breeders Association. The lactation means for all traits were quite similar for the 2 methods in both parities, except for fat production, which was lower for the daily records. This finding corresponded to fat lactation curves, which showed that daily results were lower with low days in milk (DIM) but almost equal to the monthly results after 125 DIM. Relative to monthly records, daily records overestimated protein percentage before 150 DIM and underestimated protein percentage in the second half of the lactation. The standard deviation for first- and second-parity daily records scored by the monthly and daily system were least similar for fat percentage, but even for this trait the difference was no more than 0.1 percentage points. The standard deviations for complete lactation production were slightly lower for the daily results for all traits but protein production. First-parity heritabilities were higher for lactations computed from daily records for all traits except for protein percentage, but differences were not significant. For daily records, coefficients of determination to predict future milk, fat, and protein lactation production from truncated lactations were greatest and root mean squared errors were least if the mean production from the last 2 weeks before the truncation date was used to estimate future production. Daily first-parity partial lactations for milk, fat, and protein production with <150 DIM predicted future lactation more accurately than corresponding monthly partial lactations. With only 30 DIM, genetic correlations between predicted and actual lactations ranged from 0.73 to 0.79 for milk, fat, and protein production. Real-time daily recording of fat and protein concentration by the daily recording system may be preferable to monthly analysis for herd-management decisions and genetic evaluation. Further study is required to compare the results of individual cows in multiple lactations. © 2016 American Dairy Science Association.

Kedmi M.,Hebrew University of Jerusalem | Kedmi M.,The Mutual | Van Straten M.,The Mutual | Ezra E.,Israel Cattle Breeders Association | And 2 more authors.
Journal of Dairy Science | Year: 2010

Epizootic hemorrhagic disease is caused by a Culicoides-borne Orbivirus. In cattle, the disease is characterized by reduced milk production and mortality. Recent outbreaks of epizootic hemorrhagic disease virus (EHDV) in North Africa, Israel, and Turkey increase the risk of its invasion into central and northern Europe. An outbreak of EHDV in Israel during the fall of 2006 enabled an assessment of the consequent production losses to the dairy cattle industry. Reduction in milk production and involuntary culling were modeled using a 4-yr database of monthly milk and mortality records from 48 affected and 63 unaffected herds. These indices were compared between periods of outbreak and no outbreak and assessed for various levels and exposure onset. Geospatial kriging interpolation of serological results from 127 herds was used to assess the total outbreak losses for the dairy cattle industry in Israel. Herds affected during the first, second, and third month of the outbreak (September-November) experienced an average loss of 207 (95% CI=154-261), 137 (63-211), and 52 (27-76) kg of milk/milking cow, respectively, during the outbreak period. An average excess mortality and involuntary culling of 1.47/100 cows was documented in herds affected in September. High correlation was observed between EHDV seroprevalence and milk loss; average milk loss for herds with seropositivity of 26 to 50, 51 to 75, and 76 to 100% was 84, 133, and 204. kg of milk/milking cow, respectively. A 1.42% (0.91-1.93%) increase in mortality was observed in herds with seroprevalence above 50%. Losses for the dairy cattle industry interpolated from these data were estimated at US2,491,000 (US1,591,000-3,391,000), an average loss of US26.5/cow in the Israeli dairy cattle. This equals 0.55% of the average total value production of a dairy cow in Israel. This is the first study to estimate the production losses caused by EHDV or any bluetongue-like disease. © 2010 American Dairy Science Association.

Weller J.I.,Institute of Animal science | Ezra E.,Israel Cattle Breeders Association
Journal of Dairy Science | Year: 2015

The objectives were to investigate the effects of various environmental factors that may affect herd-life of Israeli Holsteins, including first-calving age and season, calving ease, number of progeny born, and service sire for first calving in complete and truncated records; and to estimate heritabilities and genetic correlations between herd-life and the other traits included in the Israeli breeding index. The basic data set consisted of 590,869 cows in milk recording herds with first freshening day between 1985 and at least 8 yr before the cut-off date of September 15, 2013. Herd-life was measured as days from first calving to culling. The phenotypic and genetic trends for herd-life were 5.7 and 16.8. d/yr. The genetic trend was almost linear, whereas the phenotypic trend showed 4 peaks and 3 valleys. Cows born in February and March had the shortest herd-life, whereas cows born in September had the longest herd-life. Herd-life was maximal with calving age of 23. mo, which is 1. mo less than the mean calving age, and minimal at 19 and 31. mo of calving age. Dystocia and twinning on first-parity calving reduced herd-life by approximately180 and 120. d, but the interaction effect increased herd-life by 140. d. Heritability for herd-life was 0.14. Despite the fact that the service sire effect was significant in the fixed model analysis, service sire effect accounted for <0.05% of the total variance. In the analysis of 1,431,938 truncated records, the effects of dystocia and twinning rate were very similar but less than 50% of the effects found in the analysis of complete records. Pregnancy at the truncation date increased expected herd-life by 432. d. The correlation between actual herd-life and predicted herd-life based on truncated records was 0.44. Genetic correlations between the truncated records and actual herd-life were 0.75 for records truncated after 6. mo but approached unity for records truncated after 3 yr. The genetic correlations of herd-life with first-parity milk, fat, and protein production, somatic cell score (SCS), and female fertility were all positive, except for SCS, in which negative values are economically favorable. The highest correlations with herd-life in absolute value were with female fertility and SCS. © 2015 American Dairy Science Association.

Friedman E.,the Hebrew University | Roth Z.,the Hebrew University | Voet H.,University of Management and Economics | Lavon Y.,Israel Cattle Breeders Association | Wolfenson D.,the Hebrew University
Journal of Dairy Science | Year: 2012

Reduced fertility of dairy cows during periods of elevated temperature, humidity, or both might be associated with low plasma progesterone concentration. Alleviation of thermal stress by efficient cooling is a prerequisite for improving fertility by hormonal treatment. We examined whether insertion of a controlled intravaginal drug-releasing (CIDR) insert containing progesterone following artificial insemination (AI) would improve summer conception rate. Control (n = 195) and treated (CIDR; n = 165) cows, yielding on average 42.3. kg milk/d, were inseminated following estrus detection during the summer (July to October) in 2 commercial dairy herds in Israel. Mean maximal air temperature and relative humidity during the study were 30.2°C and 86%, respectively. All experimental cows were efficiently cooled throughout the study, as confirmed by measuring the body temperature of random cows. Treated cows received a CIDR insert on d 5 ± 1 post-AI for 13 d and pregnancy was confirmed by palpation 45 d post-AI. Plasma progesterone concentration in treated cows was elevated by approximately 1.5. ng/mL. Multiple logistic regressions were used to analyze conception rate. Treatment did not alter the overall conception rate; however, probability of conception increased in CIDR-treated cows with low body condition score (BCS) compared with their control counterparts (53 vs. 27%, respectively). A pronounced increase in probability of conception was recorded in CIDR-treated cows exhibiting both low BCS and postpartum reproductive disorders, compared with their control counterparts (58 vs. 14%, respectively). Exogenous progesterone supplementation on d 5 post-AI for 13 d improves summer fertility of subpopulations of cows exhibiting low BCS and postpartum reproductive disorders. Reproductive management based on specific hormonal treatment of designated subgroups of cows known to derive beneficial effects from it might improve treatment efficiency and reduce expenses. © 2012 American Dairy Science Association.

Ezra E.,Israel Cattle Breeders Association | Van Straten M.,Hachaklait | Weller J.I.,Institute of Animal science
Animal | Year: 2016

A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were analyzed for production, calving traits, fertility, calving diseases, body condition score, abortion rate and survival under intensive commercial management conditions. Holstein cows were higher than crossbreds for 305-day milk, fat and protein production. Differences were 764, 1244, 1231 for kg milk; 23.4, 37.4, 35.6 for kg fat, and 16.7, 29.8, 29.8 for kg protein; for parities 1 through 3. Differences for fat concentration were not significant; while crossbred cows were higher for protein concentration by 0.06% to 0.08%. Differences for somatic cells counts were not significant. Milk production persistency was higher for Holstein cows by 5, 8.3 and 8% in parities 1 through 3. Crossbred cows were higher for conception status by 3.1, 3.6 and 4.7% in parities 1 through 3. Rates of metritis for Holsteins were higher than the crossbred cows by 7.8, 4.6 and 3.4% in parities 1 to 3. Differences for incidence of abortion, dystocia, ketosis and milk fever were not significant. Holstein cows were lower than crossbred cows for body condition score for all three parities, with differences of 0.2 to 0.4 units. Contrary to comparisons in other countries, herd-life was higher for Holsteins by 79 days. A total of 6321 Holstein cows born between 2007 and 2011 were higher than 765 progeny of crossbred cows backcrossed to Israeli Holsteins of the same ages for milk, fat and protein production. Differences were 279, 537, 542 kg milk; 10.5, 17.7, 17.0 kg fat and 6.2, 12.9, 13.2 kg protein for parities 1 through 3. Differences for fat concentration were not significant, while backcross cows were higher for protein percentage by 0.02% to 0.04%. The differences for somatic cell score, conception rate, and calving diseases other than metritis, were not significant. Holstein cows were lower than backcross cows by 1.5% to 2.5% for conception status in parities 1 to 3 and lower for body condition score for parities 1 and 2, with differences in the range of 0.06 to 0.09 units. Culling rates were higher, and herd-life lower for the crossbred cows. The gains obtained in secondary traits for crossbred cows did not compensate for the major reduction in production. © The Animal Consortium 2016

Glick G.,Hebrew University of Jerusalem | Shirak A.,Institute of Animal science | Uliel S.,Israel Cattle Breeders Association | Zeron Y.,Sion AI Institute | And 4 more authors.
Animal Genetics | Year: 2012

Strong selection in the Israeli Holstein dairy cattle population over the last three decades should have left clear signatures of selection. Two experimental approaches were applied to detect evidence of contemporary selection based on the 54K BeadChip genotypes of ~1000 Israeli Holstein bulls: (i) the long-range haplotype test, which searches for structural evidence resulting from selective sweep, and (ii) direct analysis of the changes in haplotypes frequencies over time combined with linkage disequilibrium blocks haplotype-based association analysis. Ten traits were analyzed: the PD07 Israeli selection index, milk, milk fat, % fat, milk protein, % protein, somatic cell score, female fertility, milk production persistency and herd life. The long-range haplotype test detected ~15% of the 3288 haplotypes that showed significant positive frequency trends (P < 0.05) and was significantly correlated with the substitution effects of the haplotypes and the selection intensities for the different traits. Thirty signatures of recent selection, which correspond to both approaches and affect the Israeli PD07 selection index, were identified on 17 of the 29 autosomes. The second experimental approach also was used to estimate the selection intensity of the different traits. The correlation between the selection intensities for the traits analyzed, derived from changes in haplotype frequencies in the population of bulls, and those derived from trait-based analysis of the cow population was 0.93 over all traits. Thus, the changes in haplotypes frequencies in the bulls' population accurately estimate genetic trends in the general cow population and can be used to detect signatures of recent selection. © 2012 Stichting International Foundation for Animal Genetics.

Lavon Y.,Hebrew University | Ezra E.,Israel Cattle Breeders Association | Leitner G.,The Veterinary Institute | Wolfenson D.,Hebrew University
Journal of Dairy Science | Year: 2011

The aim was to evaluate the effects of mastitis, determined by the pattern and level of somatic cell count (SCC) around first artificial insemination (AI), on conception rate (CR). Data from 287,192 first AI and milk records covering a 7-yr period were obtained from the Israeli Herd Book. Analyses examined the association of probability of conception with SCC elevation relative to timing of AI, using generalized linear mixed models. A SCC threshold of 150,000 cells/mL of milk was set to distinguish between uninfected cows and cows with mastitis. Accordingly, cows with high SCC before and low SCC after AI were designated cured, those with low SCC before and high SCC after AI were designated newly infected, and cows with high SCC before and after AI were designated chronic (likely subclinical) mastitic cows. Compared with uninfected cows, the cured, newly infected, and chronic subgroups showed reduced CR (39.4±0.1, 36.6±0.2, 32.9±0.3, and 31.5±0.2, respectively). In the chronic, subclinical group, probability of conception was lowered by 14.5% in the mild and moderately elevated SCC subgroups and by 20.5% in cows with high SCC elevation compared with the uninfected group (CR of 29.7 vs. 39.4%, respectively). A single high elevation of SCC (>10 6 cells/mL on only 1 milk test day) lowered the probability of conception by 23.6% when it occurred during the 10 d immediately before AI, but not when it occurred earlier. For 30 d after AI, probability of conception was lowered by about 23%, as reflected in a CR of about 27% compared with the uninfected group. Probability of conception was lowered in cows with uterine and foot health problems (33.9%), in multiparous cows (34.1%), and in cows in the summer (29.1%), but no interactions with mastitis were detected. Results indicate that SCC elevation around AI, typical for subclinical mastitis, was associated with a significant reduction in probability of conception, and that even mild SCC elevation reduced CR. Severe elevation of SCC before AI, typical for clinical intramammary infection, reduced the probability of conception. © 2011 American Dairy Science Association.

Weller J.I.,Institute of Animal science | Ezra E.,Israel Cattle Breeders Association
Journal of Dairy Science | Year: 2016

Five alternative models were applied for analysis of dystocia and stillbirth in first and second parities. Models 1 and 2 were included only to estimate the parameters required for model 4, and models 3 and 5 are included only as comparisons to the model 4 estimates. Variance components were estimated by multi-trait REML, including cows with valid calving records for both parities. For the effects of sire of calf on first and second parities, variance components were estimated including only calvings with the same sire of calf for both parities. All heritabilities for the cow effect were quite low, but higher for dystocia than for stillbirth and higher in first parity. The sire-of-calf heritabilities were higher than the cow effect heritabilities, except for stillbirth in parity 2. Unlike the effect of cow correlations, all sire of calf correlations were >0.6, and the correlations for the same trait in parities 1 and 2 were >0.9. Thus, a multi-trait analysis should yield a significant gain in accuracy with respect to the sire of calf effects for bulls not mated to virgin heifers. A multi-trait individual animal model algorithm was developed for joint analysis of dystocia and stillbirth in first and second parities. Relationships matrices were included both for the effects of cow and sire of calf. In addition, random herd-year-season and fixed sex of calf effects were included in the model. Records were preadjusted for calving month and age. A total of 899,223 Israeli Holstein cows with first calvings since 1985 were included in the complete analysis. Approximate reliabilities were computed for both sire of cow and sire of calf effects. Correlations between these reliabilities and reliabilities obtained by direct inversion of the coefficient matrix for a sire of cow-sire of calf model were all close to 0.99. Phenotypic trends for cows born from 1983 through 2007 were economically unfavorable for dystocia and favorable for stillbirth in both parities. Genetic trends were economically unfavorable for both dystocia and stillbirth in first parity. First-parity sire of calf trends were unfavorable for dystocia, but favorable for stillbirth. All environmental trends were nearly zero. Regressions of evaluations of the complete analysis on a model including only calvings before 2011 were all >0.8. All evaluations met the Interbull Method 3 criterion for unbiasedness. Model 4, which computed genetic evaluations for all animals for all 4 traits accounting for all known relationships and correlations among the traits, is recommended for routine genetic evaluation of calving traits. © 2016 American Dairy Science Association.

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