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Weller JI, Ezra E, Seroussi E, Gershoni M. Genetic and Genomic Analysis of Cow Mortality in the Israeli Holstein Population. Genes (Basel) 2023; 14:genes14030588. [PMID: 36980860 PMCID: PMC10048625 DOI: 10.3390/genes14030588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
“Livability” was defined as the inverse of the probability of death. The objectives of this study were to estimate the heritability, genetic and phenotypic trends for the livability of Israeli Holstein cows; estimate the genetic and environmental correlations between livability and the nine traits included in the Israeli breeding index; estimate the effect of the inclusion of livability in the Israeli breeding index on expected genetic gains; and compute a genome-wide association study (GWAS) for livability. Seven data sets were analyzed. All data were derived from the database of the Israeli dairy cattle herd-book. The mean livability for the complete data set of 523,954 cows born from 2000 through 2016 was 89.6%. Pregnancy reduced livability by 15%. Livability generally increased with parity and days in milk within parity. Heritability of livability was 0.0082. Phenotypic and genetic trends over the 14-year period from 2000 through 2013 were −0.42% and −0.22% per year. If livability is included in the Israeli breeding index, accounting for 9% of the index, livability would increase by 1.3% and protein production would decrease by 11 kg over the next decade, as compared to the current index. A marker in proximity to the oxytocin–vasopressin locus had the greatest effect in the GWAS. Oxytocin activity in cattle affects calving-associated pathologies and maternal death. Inclusion of livability in the Israeli breeding index is not recommended.
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Affiliation(s)
- Joel Ira Weller
- Israel Cattle Breeders Association, Caesarea 38900, Israel
- Correspondence: ; Tel.: +972-506220430
| | - Ephraim Ezra
- Israel Cattle Breeders Association, Caesarea 38900, Israel
| | - Eyal Seroussi
- ARO, The Volcani Center, Rishon LeZion 15159, Israel
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Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation. Genes (Basel) 2023; 14:genes14030547. [PMID: 36980820 PMCID: PMC10048120 DOI: 10.3390/genes14030547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (n = 114 cows), for mutations in the FABP4 gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (n = 19 bulls) and the cows’ BovineHD BeadChip allowed imputing genotypes for these mutations that were verified by Sanger sequencing, whereas, an error rate of 11.6% and 10.7% were encountered for HRM and TaqMan, respectively. We show that this error rate seriously affected the linkage-disequilibrium analysis that supported this gene candidacy over other BTA14 gene candidates. Thus, imputation produced superior genotypes and should also be regarded as a method of choice to validate the reliability of the genotypes obtained by other methodologies that are prone to genotyping errors due to technical conditions. These results support the view that RFI is a complex trait and that searching for the causative sequence variation underlying cattle RFI should await the development of statistical methods suitable to handle additive and epistatic interactions.
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Weller JI, Gershoni M, Ezra E. Breeding Dairy Cattle for Female Fertility and Production in the Age of Genomics. Vet Sci 2022; 9:vetsci9080434. [PMID: 36006349 PMCID: PMC9416766 DOI: 10.3390/vetsci9080434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Phenotypic and genetic changes for female fertility and production traits in the Israeli Holstein population over the last three decades were studied in order to determine if long term selection has resulted in reduced heritability and negative genetic correlations. Annual means for conception status, defined as the inverse of the number of inseminations to conception in percent, decreased from 55.6 for cows born in 1983 to 46.5 for cows born in 2018. Mean estimated breeding values increased by 1.8% for cow born in 1981 to cows born in 2018. Phenotypic records from 1988 to 2016 for the nine Israeli breeding index traits were divided into three time periods for multi-trait REML analysis by the individual animal model. For all traits, heritabilities increased or stayed the same for the later time periods. Heritability for conception status was 0.05. The first parity genetic correlation between conception status and protein yield was −0.38. Heritabilities decreased with the increase in parity for protein but remained the same for conception status. Realized genetic trends were greater than expected for cows born from 2008 through 2016 for somatic cell score, conception status and herd-life, and lower than expected for the production traits.
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Affiliation(s)
- Joel Ira Weller
- Israel Cattle Breeders Association, Caesarea 38900, Israel
- Agricultural Research Organization, The Volcani Center, Rishon LeZion 15159, Israel
- Correspondence: ; Tel.: +972-506220430
| | - Moran Gershoni
- Agricultural Research Organization, The Volcani Center, Rishon LeZion 15159, Israel
| | - Ephraim Ezra
- Israel Cattle Breeders Association, Caesarea 38900, Israel
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