Genome-wide association study for age at puberty and resumption of cyclicity in a crossbred dairy cattle population

Fertility is of primary economic importance in dairy cattle and the most common reason for involuntary culling. However, standard fertility traits have very low heritability that renders genetic selection slow and difficult. In this study, we explored fertility from an endocrine standpoint. A total of 1,163 crossbred Holstein-Normande females in a 3-generation familial design were studied for progesterone level measured every 10 d to determine age at puberty (PUB) and commencement of postpartum luteal activity (CPLA). Genetic parameters were estimated using REML with WOMBAT software. The heritability estimates were 0.38 ± 0.10 and 0.16 ± 0.07 for PUB and CPLA, respectively. Moreover, the 2 traits were genetically correlated (0.45 ± 0.23), suggesting a partially common determinism. Because of the family structure, a linkage disequilibrium and linkage analysis approach was preferred over standard genome-wide association study to map genomic regions associated with these traits. Ten quantitative trait loci (QTL) were detected for PUB on chromosomes 1, 3, 11, 13, 14, 21, and 29, whereas 3 QTL were associated with CPLA on chromosomes 21 and 26. Only the QTL on chromosome 21 was common to both traits. Four functional candidate genes (NCOA2, GAS2, OVOL1, and FOSL1) were identified in the detected regions. These findings will contribute to a clearer understanding of fertility determinism and enhance the value of introducing endocrinological data in fertility studies.

Genetic parameters of milk production traits in response to a short once-daily milking period in crossbred Holstein × Normande dairy cows

Despite its potential utility for predicting cows' milk yield responses to once-daily milking (ODM), the genetic basis of cow milk trait responses to ODM has been scarcely if ever described in the literature, especially for short ODM periods. This study set out to (1) estimate the genetic determinism of milk yield and composition during a 3-wk ODM period, (2) estimate the genetic determinism of milk yield responses (i.e., milk yield loss upon switching cows to ODM and milk yield recovery upon switching them back to twice-daily milking; TDM), and (3) seek predictors of milk yield responses to ODM, in particular using the first day of ODM. Our trial used 430 crossbred Holstein × Normande cows and comprised 3 successive periods: 1 wk of TDM (control), 3 wk of ODM, and 2 wk of TDM. Implementing ODM for 3 wk reduced milk yield by 27.5% on average, and after resuming TDM cows recovered on average 57% of the milk lost. Heritability estimates in the TDM control period and 3-wk ODM period were, respectively, 0.41 and 0.35 for milk yield, 0.66 and 0.61 for milk fat content, 0.60 and 0.80 for milk protein content, 0.66 and 0.36 for milk lactose content, and 0.20 and 0.15 for milk somatic cell score content. Milk yield and composition during 3-wk ODM and TDM periods were genetically close (within-trait genetic correlations between experimental periods all exceeding 0.80) but were genetically closer within the same milking frequency. Heritabilities of milk yield loss observed upon switching cows to ODM (0.39 and 0.34 for milk yield loss in kg/d and %, respectively) were moderate and similar to milk yield heritabilities. Milk yield recovery (kg/d) upon resuming TDM was a trait of high heritability (0.63). Because they are easy to measure, TDM milk yield and composition and milk yield responses on the first day of ODM were investigated as predictors of milk yield responses to a 3-wk ODM to easily detect animals that are well adapted to ODM. Twice-daily milking milk yield and composition were found to be partly genetically correlated with milk yield responses but not closely enough for practical application. With genetic correlations of 0.98 and 0.96 with 3-wk ODM milk yield losses (in kg/d and %, respectively), milk yield losses on the first day of ODM proved to be more accurate in predicting milk yield responses on longer term ODM than TDM milk yield.

Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (P_C) and four candidate mutations for the Friesian allele (P_F). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in P_C/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.

Effect of dairy production system, breed and co-product handling methods on environmental impacts at farm level

Six dairy farms with the same on-farm area and milk production were compared. One farm (G-No) used grass as the sole forage for a herd of Normande cows, a dual-purpose breed. Three farms, with Holstein cows, varied forage for the herd from grass only (G-Ho) to low (G/LM-Ho) or high (G/HM-Ho) proportion of maize silage in the total forage area. Finally, two farms based on G/LM-Ho and G/HM-Ho systems aimed to increase omega-3 fatty acids in the winter diets of cows (G/LM/O3-Ho, G/HM/O3-Ho). Allocation methods (biophysical, protein, economic allocation) and system expansion applied for co-product (milk and meat) handling were examined. The impact categories considered were climate change, climate change including the effects of land use and land use change (CC/LULUC), cumulative energy demand, eutrophication, acidification and land occupation. The impacts per kg of fat-and-protein-corrected milk (FPCM) of G-No were highest, followed by those of G-Ho, G/LM-Ho and G/HM-Ho, regardless co-product handling methods and impact categories (except for eutrophication). CC/LULUC per kg FPCM of G/LM/O3-Ho and G/HM/O3-Ho were both 1% and 3% lower than those of G/LM-Ho and G/HM-Ho, respectively, but other impacts were higher. With system expansion, impacts per kg FPCM were lower than when allocation methods were used. Enteric fermentation was the greatest contributor (45-50%) to CC/LULUC, while grass production was the most important contributor to other impacts. The highest CC/LULUC (for G-No) can be explained by (1) G-No having the lowest milk yield/cow (though it produced the most meat) and (2) the fact that grass required more N fertiliser, but had lower yields than silage maize, even though grassland sequestered C. Among Holstein systems, increasing cow productivity by increasing feed intake (including maize silage and supplementing with concentrate) decreased impacts of milk. Reducing replacement rate and age of first calving also decreased impacts of milk. Increasing cow productivity reduced the amount of on-farm area required to produce a given amount of milk. Thus, the "liberated" on-farm area of Holstein systems was used to produce cash crops, and total impacts of these systems were lower than those of G-No (except for eutrophication and land occupation).

A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull

Polled and Multisystemic Syndrome (PMS) is a novel developmental disorder occurring in the progeny of a single bull. Its clinical spectrum includes polledness (complete agenesis of horns), facial dysmorphism, growth delay, chronic diarrhea, premature ovarian failure, and variable neurological and cardiac anomalies. PMS is also characterized by a deviation of the sex-ratio, suggesting male lethality during pregnancy. Using Mendelian error mapping and whole-genome sequencing, we identified a 3.7 Mb deletion on the paternal bovine chromosome 2 encompassing ARHGAP15, GTDC1 and ZEB2 genes. We then produced control and affected 90-day old fetuses to characterize this syndrome by histological and expression analyses. Compared to wild type individuals, affected animals showed a decreased expression of the three deleted genes. Based on a comparison with human Mowat-Wilson syndrome, we suggest that deletion of ZEB2, is responsible for most of the effects of the mutation. Finally sperm-FISH, embryo genotyping and analysis of reproduction records confirmed somatic mosaicism in the founder bull and male-specific lethality during the first third of gestation. In conclusion, we identified a novel locus involved in bovid horn ontogenesis and suggest that epithelial-to-mesenchymal transition plays a critical role in horn bud differentiation. We also provide new insights into the pathogenicity of ZEB2 loss of heterozygosity in bovine and humans and describe the first case of male-specific lethality associated with an autosomal locus in a non-murine mammalian species. This result sets PMS as a unique model to study sex-specific gene expression/regulation.

How to improve the hygienic quality of forages for horse feeding

BACKGROUND

Improving the hygienic quality of forages for horse nutrition seems to be a reasonable target for decreasing the prevalence of pulmonary diseases. The aim of the experiment was to study the effects of different agricultural practices on the main aero-allergens contained in forages, including breathable dust, fungi, mycotoxins and pollens.

RESULTS

Results showed that the late harvest of hay, a second crop or a haylage production provides a good alternative to increase hygienic quality by reducing fungi contamination and breathable dust content. Barn drying of hay, while having no effect on breathable dust, similarly reduced fungi contamination. In contrast, when hay was harvested at a lower dry mass content (750 g DM kg⁻¹ versus 850 g DM kg⁻¹), both breathable dust and fungi contaminations were increased, which could at least be reversed by adding propionic acid just before baling. Zearalenone was detected in different hays, and even in one case, in breathable dust.

CONCLUSION

Overall, our data suggest that different approaches can be used to increase forage hygienic quality for horse feeding and thus reduce their exposure to factors involved in equine pulmonary disease.

172 PRE-IMPLANTATION GENETIC DIAGNOSIS COMBINED WITH FREEZING AND TRANSFER OF IN VITRO-PRODUCED EMBRYOS ALLOWS CREATING GENETIC RESOURCES FROM A MOSAIC BULL

The polled and multisystemic syndrome (PMS) is a genetic abnormality observed in the progeny of a unique bull affected by a large chromosomal deletion and cellular mosaicism. Hemizygous females, representing 15% of total progeny, are hornless and show organ malformations, including of the ovaries. Hemizygous males are assumed to die in early fetal development. This study was initiated to produce sufficiently affected fetuses using the semen of the sire as a unique genetic resource. Oocytes from slaughterhouse ovaries were in vitro matured, fertilized with the same bull and cultured in SOF medium using standard in vitro procedures currently performed in the laboratory. On Day 7, grade 1 to 3 embryos were biopsied (5 to 10 cells) and frozen using a conventional glycerol procedure. Whole-biopsy amplification of genomic DNA was performed using a Qiagen Repli-g® Mini Kit (Qiagen, Valencia, CA, USA). Sex determination was done by PCR (UNCEIA Sexing Kit, UNCEIA, Paris, France). The PMS status was indirectly determined using both tetra-primer amplification refractory mutation system-PCR and PCR-restriction fragment length polymorphism procedures to genotype a single SNP located within the deleted region. Because the sire was both homo- and hemizygous for this SNP, 3 categories of progeny were defined according to their genotypes: unaffected (heterozygous), potentially affected (homo- or hemizygous for the same allele as their sire) and affected (hemizygous for the alternate allele). Thirteen affected and 21 potentially affected female embryos were thawed and transferred (1 ≤ n ≤ 4) into 17 Day 7 recipients. Pregnant females were slaughtered on Day 9 and fetuses were recovered; sex and PMS status were then verified. From 2133 inseminated oocytes (7 replicates), 64% cleaved and 10% (n = 216) developed to the blastocyst stage on Day 7. This was significantly lower than the 87% cleavage and 25% blastocyst development rates observed with a control bull used to inseminate 368 oocytes from the same batches. Finally, 174 embryos were biopsied and 169 were frozen. Fifty percent were sexed as female (n = 87). Among them, 15% (n = 13) were affected and 29% (n = 25) were potentially affected. The 24-h survival rate averaged 67% from 54 thawed, unaffected embryos, whereas the hatching rate at 72 h was 59%. Seven female fetuses were recovered from 6 recipient cows. Clinical examination revealed an absence of horn buds for 3 of them. This status was subsequently confirmed by a non-Mendelian inheritance study based on Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA, USA) genotyping data. This combination of in vitro procedures allowed us to increase the number of affected fetuses from 15 to 43% (3/7) in the mosaic bull progeny. In addition, it enabled us to produce valuable material from a very limited resource to perform clinical and functional studies. Finally, it demonstrates the feasibility of a pre-implantation genetic diagnosis combined with freezing and transfer of IVP embryos.

Anti-Müllerian hormone: a predictive marker of embryo production in cattle?

In cattle, the embryo production rate after superovulation varies between individuals and is difficult to predict. Recently, we proposed that anti-Müllerian hormone (AMH) plasma levels measured before treatment can help predict superovulatory responses. To establish whether blood measurement of AMH can help predict the number of embryos produced by a given cow after superovulation, data collected over 4 years from 45 dairy cows submitted to repeated embryo production were analysed in a retrospective study. A high within-animal repeatability (0.38 and 0.36) and a strong effect of the father of the donor cow (P < 0.01) were observed for the numbers of collected and transferable embryos, respectively. AMH concentration, measured in the plasma of donor cows during first lactation and several months before the start of the embryo production campaigns, was found to be highly correlated with the maximal number of collected (P < 0.0001) and transferable (P < 0.01) embryos per cow. In conclusion, the capacity of embryo production is a repeatable and probably heritable trait in the cow, and blood measurement of AMH in potential donor cows could be of value in determining a cow’s intrinsic capacity to produce transferable embryos.

The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregulation of the Normande Agouti gene

Mammalian pigmentation is controlled by the concerted action of Tyr, Tyrp1 and Dct producing eumelanin and/or pheomelanin in melanocytes. The ratio of these two pigments is determined by the agonist alpha-melanocyte stimulating hormone and the antagonist Agouti protein acting on the Mc1r. Here we show that the Agouti gene is over-expressed in Normande breed compared with Prim'Holstein breed. The Normande cattle have a characteristic coat color phenotype with a variable presence of black (eumelanin) hair over a red/brown background. We have found a previously undescribed full-length L1-BT element inserted in the 5'-genomic sequence of the Agouti gene in Normande cattle which promotes the over-expression of alternative transcripts. The variable expression of the alternative transcript directed by the long interspersed nuclear element promoter may be the origin of the brindle coat color pattern of the Normande breed. This new bovine Agouti allele isolated in Normande breed has been named Abr. Finally, as ectopic over-expression of Agouti in Ay mice is responsible for the obesity syndrome, we discuss the possible consequences of Abr for meat and milk production in cattle.

Identification of a doublet missense substitution in the bovine LRP4 gene as a candidate causal mutation for syndactyly in Holstein cattle

Syndactyly in Holstein cattle is an autosomal recessive abnormality characterized by the fusion of the functional digits. This disorder has been previously mapped to the telomeric part of bovine chromosome 15. Here, we describe the fine-mapping of syndactyly in Holstein cattle to a 3.5-Mb critical interval using a comparative mapping approach and an extended pedigree generated by embryo transfer. We report genetic evidence for the exclusion of two genes previously suggested as candidates (EXT2 and ALX4) and describe the identification of a doublet mutation in complete linkage disequilibrium with syndactyly in one gene of the critical interval: LRP4. Finally, based on recent discoveries concerning the mouse mutants dan and mdig and a mouse knockout for Lrp4, we present solid evidence that the subsequent substitution in LRP4 exon 33 is a strong candidate causal mutation for syndactyly in Holstein cattle.