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ABSTRACT: Recessive alleles represent genetic risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and validation of these genetic defects, including haplotype-based detection, variant selection from sequence data, and validation using knockout embryos. Holstein haplotype 2 (HH2), which causes embryonic death, was used to demonstrate the approach. Holstein haplotype 2 was identified using a deficiency-of-homozygotes approach and confirmed to negatively affect conception rate and stillbirths. Five carriers were present in a group of 183 sequenced Holstein bulls selected to maximize the coverage of unique haplotypes. Three variants concordant with haplotype calls were found in HH2: a high-priority frameshift mutation resulting, and 2 low-priority variants (1 synonymous variant, 1 premature stop codon). The frameshift in intraflagellar 80 (IFT80) was confirmed in a separate group of Holsteins from the 1000 Bull Genomes Project that shared no animals with the discovery set. IFT80-null embryos were generated by truncating the IFT80 transcript at exon 2 or 11 using a CRISPR-Cas9 system. Abattoir-derived oocytes were fertilized in vitro, and zygotes were injected at the one-cell stage either with a guide RNA and CAS9 mRNA complex (n = 100) or Cas9 mRNA (control, n = 100) before return to culture, and replicated 3 times. IFT80 is activated at the 8-cell stage, and IFT80-null embryos arrested at this stage of development, which is consistent with data from mouse hypomorphs and HH2 carrier-to-carrier matings. This frameshift in IFT80 on chromosome 1 at 107,172,615 bp (p.Leu381fs) disrupts WNT and hedgehog signaling, and is responsible for the death of homozygous embryos.

ABSTRACT: A 60% pregnancy success for inseminations is targeted to optimize production efficiency for dairy cows within a seasonal, pasture-grazed system. Routine measures of pregnancy success are widely available but are limited, in practice, to a gestation stage beyond the first 28 d. Although some historical data exist on embryonic mortality before this stage, productivity of dairy systems and genetics of the cows have advanced significantly in recent decades. Accordingly, the aim was to construct an updated estimate of pregnancy success at key developmental stages during the first 70 d after insemination. Blood samples were collected for progesterone concentrations on d 0 and 7. A temporal series of 4 groups spanning fertilization through d 70 were conducted on 4 seasonal, pasture-grazed dairy farms (n = 1,467 cows) during the first 21 d of the seasonal breeding period. Morphological examination was undertaken on embryos collected on d 7 (group E7) and 15 (group E15), and pregnancy was diagnosed via ultrasonography on approximately d 28 and 35 (group E35) as well as d 70 (group E70). Fertilization, embryo, and fetal evaluation for viability established a pregnancy success pattern. Additionally, cow and on-farm risk factor variables associated with pregnancy success were evaluated. We estimated pregnancy success rates of 70.9%, 59.1%, 63.8%, 62.3%, and 56.7% at d 7, 15, 28, 35, and 70, respectively. Fertilization failure (15.8%) and embryonic arrest before the morula stage (10.3%) were the major developmental events contributing to first-week pregnancy failures. Embryo elongation failure of 7% contributed to pregnancy failure during the second week. The risk factors for pregnancy success that were related to the cows included interval between calving and insemination, and d-7 plasma progesterone concentrations, whereas insemination sire was associated with pregnancy outcome. Most pregnancy failure occurs during the first week among seasonal-calving pasture-grazed dairy cows.

A 60% pregnancy success for inseminations is targeted to optimize production efficiency for dairy cows within a seasonal, pasture-grazed system. Routine measures of pregnancy success are widely available but are limited, in practice, to a gestation stage beyond the first 28 d. Although some historical data exist on embryonic mortality before this stage, productivity of dairy systems and genetics of the cows have advanced significantly in recent decades. Accordingly, the aim was to construct an updated estimate of pregnancy success at key developmental stages during the first 70 d after insemination. Blood samples were collected for progesterone concentrations on d 0 and 7. A temporal series of 4 groups spanning fertilization through d 70 were conducted on 4 seasonal, pasture-grazed dairy farms (n = 1,467 cows) during the first 21 d of the seasonal breeding period. Morphological examination was undertaken on embryos collected on d 7 (group E7) and 15 (group E15), and pregnancy was diagnosed via ultrasonography on approximately d 28 and 35 (group E35) as well as d 70 (group E70). Fertilization, embryo, and fetal evaluation for viability established a pregnancy success pattern. Additionally, cow and on-farm risk factor variables associated with pregnancy success were evaluated. We estimated pregnancy success rates of 70.9%, 59.1%, 63.8%, 62.3%, and 56.7% at d 7, 15, 28, 35, and 70, respectively. Fertilization failure (15.8%) and embryonic arrest before the morula stage (10.3%) were the major developmental events contributing to first-week pregnancy failures. Embryo elongation failure of 7% contributed to pregnancy failure during the second week. The risk factors for pregnancy success that were related to the cows included interval between calving and insemination, and d-7 plasma progesterone concentrations, whereas insemination sire was associated with pregnancy outcome. Most pregnancy failure occurs during the first week among seasonal-calving pasture-grazed dairy cows. [Display omitted] [ABSTRACT FROM AUTHOR]

Recessive alleles represent genetic risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and validation of these genetic defects, including haplotype-based detection, variant selection from sequence data, and validation using knockout embryos. Holstein haplotype 2 (HH2), which causes embryonic death, was used to demonstrate the approach. Holstein haplotype 2 was identified using a deficiency-of-homozygotes approach and confirmed to negatively affect conception rate and stillbirths. Five carriers were present in a group of 183 sequenced Holstein bulls selected to maximize the coverage of unique haplotypes. Three variants concordant with haplotype calls were found in HH2: a high-priority frameshift mutation resulting, and 2 low-priority variants (1 synonymous variant, 1 premature stop codon). The frameshift in intraflagellar 80 (IFT80) was confirmed in a separate group of Holsteins from the 1000 Bull Genomes Project that shared no animals with the discovery set. IFT80-null embryos were generated by truncating the IFT80 transcript at exon 2 or 11 using a CRISPR-Cas9 system. Abattoir-derived oocytes were fertilized in vitro, and zygotes were injected at the one-cell stage either with a guide RNA and CAS9 mRNA complex (n = 100) or Cas9 mRNA (control, n = 100) before return to culture, and replicated 3 times. IFT80 is activated at the 8-cell stage, and IFT80-null embryos arrested at this stage of development, which is consistent with data from mouse hypomorphs and HH2 carrier-to-carrier matings. This frameshift in IFT80 on chromosome 1 at 107,172,615 bp (p.Leu381fs) disrupts WNT and hedgehog signaling, and is responsible for the death of homozygous embryos. [ABSTRACT FROM AUTHOR]

Widespread genotyping has enabled the identification of putative recessive mutations that affect fertility through early embryonic fetal loss, or that compromise neonate or calf viability. The use of artificial insemination in the global dairy population can rapidly spread these harmful mutations, and testing for multiple mutations can become relatively expensive if not all tests are available on the same SNP panel. However, it is possible to provide heifer and cow predicted carrier status to farmers at no additional cost if the animals are genotyped with a standard SNP panel. Additionally, for defects where the causal mutation is unknown but a haplotype of markers has been associated with the defect, the carrier status can be predicted based on that haplotype. The aims of this study were 3-fold: (1) to determine the accuracy of imputation of putative causal mutations for recessive deleterious conditions in Australian dairy cattle, (2) to impute carrier status for known recessive deleterious conditions in all genotyped Australian Holstein, Jersey, and Red breed cows, and (3) to determine the changes in carrier frequencies across time for these recessive deleterious mutations. We used the F1 statistic, combining precision and recall, to assess the accuracy of carrier status prediction. We showed that known deleterious mutations can be accurately imputed in Australian Holstein and Jersey cattle that are not directly genotyped for the causal mutation, with F1 ranging between 0.88 and 0.99. For recessive deleterious conditions not included on the standard Australian SNP panel, carrier status could be predicted using a marker haplotype, with F1 ranging from 0.91 to 0.92. Most putative causals and haplotypes were either stable with a low carrier percentage or had a declining carrier percentage. However, several recessive mutations showed a relatively high or increasing percentage, highlighting the importance of detecting carriers to reduce the number of at-risk matings. Furthermore, the high carrier percentage of the recently identified bovine lymphocyte intestinal retention defect mutation emphasizes the importance of detection of novel mutations., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Several tools exist to diagnose pregnancy in dairy cattle. However, substantial pregnancy loss occurs within the first 60 d of gestation in cattle, and these losses have a profound adverse economic impact on the dairy and beef cattle industries. Detecting these impending pregnancy losses could offer producers an opportunity to reduce costs associated with this source of reproductive inefficiency. Several of the pregnancy diagnostic tools currently available and new technologies are being examined for their ability to predict pregnancies at risk for failing in early pregnancy. This review provides a synopsis of work undertaken recently to predict pregnancy losses in cattle. Currently, opportunities to predict pregnancy loss include (1) using transrectal ultrasonography to detect loss of the fetal heartbeat, floating debris within the placental fluids, and reductions in fetal size; (2) observing reductions in circulating progesterone concentrations; (3) detecting reductions in concentrations of circulating placental products; namely, pregnancy-associated glycoproteins and microRNAs; and (4) detecting reductions in the early pregnancy-dependent increase in interferon-stimulatory gene expression in peripheral blood leukocytes. An achievable goal may be to identify markers of embryo mortality so that researchers and clinicians can focus their efforts on developing intervention strategies for cows identified to be at risk for pregnancy failure. [ABSTRACT FROM AUTHOR]