A large population study to assess the magnitude of prenatal programming in dairy cattle

The performance of an adult dairy cow may be influenced by events that occur before her birth. The present study investigated potential effects of 2 prenatal groups of factors, Assisted Reproductive Techniques (ART) and maternal characteristics (e.g., dam parity), on offspring performance during their first lactation, in populations of 2 dairy cow breeds: French Holstein and Montbéliarde. The different ART studied included the type of semen (conventional or X-sorted) used for Artificial Insemination (AI) and the technology of conception used (AI, embryo transfer, or in vitro fertilization). Three maternal characteristics were considered: (1) the dam age at first calving, (2) dam parity number, and (3) indicators of dam udder health during gestation (somatic cell score and events of clinical mastitis). First, we investigated whether heifer survival from 3d to 18 mo old was associated with any of the prenatal factors considered. We then estimated the associations of these prenatal factors with 8 traits of commercial interest: (1) stature, (2-4) milk, fat, and protein yields, (5) somatic cell score, (6) clinical mastitis, and (7-8) heifer and cow conception rate, all measured on genotyped cows. Linear models were used for this study with the prenatal factors as covariates in the model, and for the 8 traits, phenotypes were adjusted for their corresponding genomic estimated breeding value. The results indicated that the survival rate of heifers born from embryo transfer was significantly higher than that of heifers born from AI (probably due to preferential management practices), while the other prenatal factors did not explain differences in heifer survival. Among the Montbéliarde cows born from AI, those born from X-sorted semen showed a lightly but significantly lower milk yield than those born without X-sorting of the semen (-52 kg of milk in the first lactation). Among the Holstein cows, those born from embryo transfer presented significantly lower milk performance than cows born from AI. Regarding the maternal characteristics, none or very weak associations were found between the dam age at first calving and the offspring performance in both breeds. Dam parity, on the other hand, was associated with offspring performance for milk, fat, and protein yield in both breeds, however not in the same direction. In the Holstein breed, an increase in dam parity was favorable for offspring performance for milk, fat, and protein yield, whereas in the Montbéliarde breed, an increase in dam parity was associated with lower milk and protein yield and no association was found for fat yield. The udder health of the dam during gestation was not or only weakly associated with the traits studied in the offspring. Although some significant associations were identified due to the large sample size, the effects were modest, typically less than 1% of the phenotypic mean, and were not consistently observed across the 2 breeds.

Short communication: Correlation of methane production, intensity, and yield with residual feed intake throughout lactation in Holstein cows

The environmental impact of dairy production can be reduced in several ways, including increasing feed efficiency and reducing methane (CH4) emissions. There is no consensus on their relationship. This study aimed at estimating the correlations between residual feed intake (RFI) and CH4 emissions expressed in g/d methane production (MeP), g/kg of fat- and protein-corrected milk methane intensity (MeI), or g/kg of DM intake methane yield (MeY) throughout lactation. We collected CH4 data using GreenFeed devices from 107 Holstein cows, as well as production and intake phenotypes. RFI was predicted from DM intake, fat- and protein-corrected milk, BW, and body condition score. Five-trait random regression models were used to estimate the individual variance components of the CH4 and production traits, which were used to calculate the correlations between RFI and CH4 traits throughout lactation. We found positive correlations of RFI with MeP and MeI ranging from 0.05 to 0.47 throughout the lactation. Correlations between RFI and MeY are low and vary from positive to negative, ranging from -0.18 to 0.17. Both MeP and MeI are favorably correlated with RFI, as is MeY during the first half of lactation. These correlations are mostly favorable for genetic selection, but the confirmation of these results is needed with genetic correlations over a larger dataset.

X-linked genes influence various complex traits in dairy cattle

BACKGROUND

The search for quantitative trait loci (QTL) affecting traits of interest in mammals is frequently limited to autosomes, with the X chromosome excluded because of its hemizygosity in males. This study aimed to assess the importance of the X chromosome in the genetic determinism of 11 complex traits related to milk production, milk composition, mastitis resistance, fertility, and stature in 236,496 cows from three major French dairy breeds (Holstein, Montbéliarde, and Normande) and three breeds of regional importance (Abondance, Tarentaise, and Vosgienne).

RESULTS

Estimates of the proportions of heritability due to autosomes and X chromosome (h²_X) were consistent among breeds. On average over the 11 traits, h²_X=0.008 and the X chromosome explained ~ 3.5% of total genetic variance. GWAS was performed within-breed at the sequence level (~ 200,000 genetic variants) and then combined in a meta-analysis. QTL were identified for most breeds and traits analyzed, with the exception of Tarentaise and Vosgienne and two fertility traits. Overall, 3, 74, 59, and 71 QTL were identified in Abondance, Montbéliarde, Normande, and Holstein, respectively, and most were associated with the most-heritable traits (milk traits and stature). The meta-analyses, which assessed a total of 157 QTL for the different traits, highlighted new QTL and refined the positions of some QTL found in the within-breed analyses. Altogether, our analyses identified a number of functional candidate genes, with the most notable being GPC3, MBNL3, HS6ST2, and DMD for dairy traits; TMEM164, ACSL4, ENOX2, HTR2C, AMOT, and IRAK1 for udder health; MAMLD1 and COL4A6 for fertility; and NRK, ESX1, GPR50, GPC3, and GPC4 for stature.

CONCLUSIONS

This study demonstrates the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and highlights new functional candidate genes and variants for these traits. These results could potentially be extended to other species as many X-linked genes are shared among mammals.

Comparison of methane production, intensity, and yield throughout lactation in Holstein cows

Genetic selection to reduce methane (CH4) emissions from dairy cows is an attractive means of reducing the impact of agricultural production on climate change. In this study, we investigated the feasibility of such an approach by characterizing the interactions between CH4 and several traits of interest in dairy cows. We measured CH4, dry matter intake (DMI), fat- and protein-corrected milk (FPCM), body weight (BW), and body condition score (BCS) from 107 first- and second-parity Holstein cows from December 2019 to November 2021. Methane emissions were measured using a GreenFeed device and expressed in terms of production (MeP, in g/d), yield (MeY, in g/kg DMI), and intensity (MeI, in g/kg FPCM). Because of the limited number of cows, only animal parameters were estimated. Both MeP and MeI were moderately repeatable (>0.45), whereas MeY presented low repeatability, especially in early lactation. Mid lactation was the most stable and representative period of CH4 emissions throughout lactation, with animal correlations above 0.9. The average animal correlations of MeP with DMI, FPCM, and BW were 0.62, 0.48, and 0.36, respectively. The MeI was negatively correlated with FCPM (<-0.5) and DMI (>-0.25), and positively correlated with BW and BCS. The MeY presented stable and weakly positive correlations with the 4 other traits throughout lactation, with the exception of slightly negative animal correlations with FPCM and DMI after the 35th week. The MeP, MeI, and MeY were positively correlated at all lactation stages and, assuming animal and genetic correlations do not strongly differ, selection on one trait should lead to improvements in all. Overall, selection for MeI is probably not optimal as its change would result more from CH4 dilution in increased milk yield than from real decrease in methane emission. Instead, MeY is related to rumen function and is only weakly associated with DMI, FPCM, BW, and BCS; it thus appears to be the most promising CH4 trait for selection, provided that this would not deteriorate feed efficiency and that a system of large-scale phenotyping is developed. The MeP is easier to measure and thus may represent an acceptable alternative, although care would need to be taken to avoid undesirable changes in FPCM and BW.

Mutation of the MYH3 gene causes recessive cleft palate in Limousine cattle

Background

The palate is a structure separating the oral and nasal cavities and its integrity is essential for feeding and breathing. The total or partial opening of the palate is called a cleft palate and is a common malformation in mammals with environmental or hereditary aetiologies. Generally, it compromises life expectancy in the absence of surgical repair. A new form of non-syndromic cleft palate arose recently in Limousine cattle, with animals referred to the French National Observatory of Bovine Abnormalities since 2012. Since the number of affected animals has increased steadily, this study was undertaken to identify the cause of this disease.

Results

Based on pedigree analysis, occurrence of cleft palate in Limousine cattle was concordant with an autosomal recessive mode of inheritance. Genotyping of 16 affected animals and homozygosity mapping led to the identification of a single disease-associated haplotype on Bos taurus chromosome (BTA)19. The genome of two affected animals was sequenced, and their sequences were compared to the ARS-UCD1.2 reference genome to identify variants. The likely causal variants were compared to the variant database of the 1000 bull genome project and two fully linked mutations in exon 24 of the MYH3 (myosin heavy chain) gene were detected: a 1-bp non-synonymous substitution (BTA19:g.29609623A>G) and a 11-bp frameshift deletion (BTA19:g.29609605-29609615del). These two mutations were specific to the Limousine breed, with an estimated allele frequency of 2.4% and are predicted to be deleterious. The frameshift leads to a premature termination codon. Accordingly, mRNA and protein analyses in muscles from wild-type and affected animals revealed a decrease in MYH3 expression in affected animals, probably due to mRNA decay, as well as an absence of the MYH3 protein in these animals. MYH3 is mostly expressed in muscles, including craniofacial muscles, during embryogenesis, and its absence may impair palate formation.

Conclusions

We describe a new form of hereditary cleft palate in Limousine cattle. We identified two fully linked and deleterious mutations, ultimately leading to the loss-of-function of the MYH3 protein. The mutations were included on the Illumina EuroG10k v8 and EuroGMD v1 SNP chips and are used to set up a reliable eradication strategy in the French Limousine breed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00762-2.

New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation

Background

Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be improved through selective breeding. Using a large dataset of Holstein cows (161,253 animals including 56,766 cows with ELISA serological phenotypes and 12,431 animals with genotypes), we applied a single-step single nucleotide polymorphism (SNP) best linear unbiased prediction approach to investigate the genetic determinism underlying resistance to this disease (heritability estimate and identification of relevant genomic regions) and estimated genetic trends, reliability, and relative risk factors associated with genomic predictions.

Results

Resistance to JD was moderately heritable (0.14) and 16 genomic regions were detected that accounted for at least 0.05% of the breeding values variance (GV) in resistance to JD, and were located on chromosomes 1, 3, 5, 6, 7, 19, 20, 21, 23, 25, and 27, with the highest percentage of variance explained by regions on chromosomes 23 (0.36% GV), 5 (0.22% GV), 1 (0.14% GV), and 3 (0.13% GV). When estimated for the whole chromosomes, the autosomes with the largest overall contributions were chromosomes 3 (5.3% GV), 10 (4.8%), 23 (4.7%), 1 (3.6%), 7 (3.4%), 5 (2.9%), 12 (2.5%), 11 (2.2%), and 13 (2%). We estimated a slightly favorable genetic trend in resistance to JD over the last two decades, which can be explained by a low positive genetic correlation between resistance to JD and total merit index (+ 0.06). Finally, in a validation population of 907 cows, relatively reliable genomic predictions (reliability = 0.55) were obtained, which allowed the identification of cows at high risk of infection.

Conclusions

This study provides new insights into the genetic determinism of resistance to JD and shows that this trait can be predicted from SNP genotypes. It has led to the implementation of a single-step genomic evaluation that should rapidly become an effective tool for controlling paratuberculosis on French Holstein farms.

Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records

BACKGROUND

Conflicting results regarding alterations to sperm DNA methylation in cases of spermatogenesis defects, male infertility and poor developmental outcomes have been reported in humans. Bulls used for artificial insemination represent a relevant model in this field, as the broad dissemination of bull semen considerably alleviates confounding factors and enables the precise assessment of male fertility. This study was therefore designed to assess the potential for sperm DNA methylation to predict bull fertility.

RESULTS

A unique collection of 100 sperm samples was constituted by pooling 2-5 ejaculates per bull from 100 Montbéliarde bulls of comparable ages, assessed as fertile (n = 57) or subfertile (n = 43) based on non-return rates 56 days after insemination. The DNA methylation profiles of these samples were obtained using reduced representation bisulfite sequencing. After excluding putative sequence polymorphisms, 490 fertility-related differentially methylated cytosines (DMCs) were identified, most of which were hypermethylated in subfertile bulls. Interestingly, 46 genes targeted by DMCs are involved in embryonic and fetal development, sperm function and maturation, or have been related to fertility in genome-wide association studies; five of these were further analyzed by pyrosequencing. In order to evaluate the prognostic value of fertility-related DMCs, the sperm samples were split between training (n = 67) and testing (n = 33) sets. Using a Random Forest approach, a predictive model was built from the methylation values obtained on the training set. The predictive accuracy of this model was 72% on the testing set and 72% on individual ejaculates collected from an independent cohort of 20 bulls.

CONCLUSION

This study, conducted on the largest set of bull sperm samples so far examined in epigenetic analyses, demonstrated that the sperm methylome is a valuable source of male fertility biomarkers. The next challenge is to combine these results with other data on the same sperm samples in order to improve the quality of the model and better understand the interplay between DNA methylation and other molecular features in the regulation of fertility. This research may have potential applications in human medicine, where infertility affects the interaction between a male and a female, thus making it difficult to isolate the male factor.

Opportunities for genomic selection of cheese-making traits in Montbéliarde cows

As part of the From'MIR project, traits related to the composition and cheese-making properties (CMP) of milk were predicted from 6.6 million mid-infrared spectra taken from 410,622 Montbéliarde cows (19,862 with genotypes). Genome-wide association studies of imputed whole-genome sequences highlighted candidate SNPs that were then added to the EuroG10K BeadChip, which is routinely used in genomic selection. In the present study, we (1) assessed the reliability of single-step genomic BLUP breeding values (ssEBVs) for cheese yields, coagulation traits, and casein and calcium content generated from test-day records of the first 3 lactations, (2) estimated realized genetic trends for these traits over the last decade, and (3) simulated different cheese-making breeding objectives and estimated the responses for CMP as well as for other traits currently selected in the Montbéliarde breed. To estimate the reliability of ssEBVs, the available data were split into 2 independent training and validation sets that respectively contained cows with the oldest and the most recent lactation data. The training set included 155,961 cows (12,850 with genotypes) and was used to predict ssEBVs of 2,125 genotyped cows in the validation set. We first tested 4 models that included either lactation (LACT) or test-day (TD) records from the first (1) or the first 3 (3) lactations, giving equal weight to all 50K SNP effects. Mean reliabilities were 61%, 62%, 63%, and 64% for the LACT1, LACT3, TD1, and TD3 models, respectively. Using the most accurate model (TD3), we then compared the reliabilities of 3 scenarios with: SNPs from the Illumina BovineSNP50 BeadChip only, equally weighted (50K); 50K SNPs plus additional candidate SNPs, equally weighted (50K+); and 50K and candidate SNPs with additional weight given to 7 to 14 candidate SNPs, depending on the trait (CAND). The 50K+ and CAND scenarios led to similar mean reliabilities (67%) and both outperformed the 50K scenario (64%), whereas the CAND scenario generated the less biased ssEBVs. To assess genetic trends, SNP effects were estimated with a single-step GBLUP based on the TD3 model and the 50K scenario applied to the whole population (2.6 million performance records from 190,261 cows and 423,348 animals in the pedigree, of which 21,874 were genotyped) and then applied to 50K genotypes of 21,171 males and 311,761 females. We detected a positive genetic trend for all CMP during the last decade, probably due to selection for an increase in milk protein and fat content in Montbéliarde cows. Finally, we compared the selection responses to 3 different breeding objectives: the current Montbéliarde total merit index (TMI) and 2 alternative scenarios that gave a weight of 70% to TMI and the remaining 30% to either milk casein content (TMI-COMP) or a combination of 3 CMP (TMI-Cheese). The TMI-Cheese scenario yielded the best responses for all the CMP analyzed, whereas values in the TMI-COMP scenario were intermediate, with a slight effect on other traits currently included in TMI. Based on these results, a program of genomic evaluation for CMP predicted from mid-infrared spectra was designed and implemented for the Montbéliarde breed.

Genetic merit for fertility alters the bovine uterine luminal fluid proteome†

Over the last decades, fertility of dairy cows has declined due to selection strategies focusing on milk yield. To study the effect of genetic merit for fertility on the proteome of the bovine uterine luminal fluid, Holstein heifers with low- and two groups of heifers with high-fertility index (high-fertility Holstein and Montbéliarde) were investigated. To focus on the maternal effect, heifers from all groups were synchronized and received on Day 7 high-quality embryos. Uterine luminal fluid from Day 19 pregnant heifers was analyzed in a holistic proteomic approach using nano-LC-MS/MS analysis combined with a label-free quantification approach. In total, 1737 proteins were identified, of which 597 differed significantly in abundance between the three groups. The vast majority of proteome differences was found comparing both high-fertility groups to the low-fertility Holstein group, showing that the genetic predisposition for fertility is prevalent regarding the uterine luminal fluid proteome. Evaluation of this dataset using bioinformatic tools revealed an assignment of higher abundant proteins in low-fertility Holstein to several metabolic processes, such as vitamin metabolic process, which comprises folate receptor alpha (FOLR1) and retinol-binding protein, indicating an involvement of disturbed metabolic processes in decreased fertility. Moreover, immune system-related proteins - lactotransferrin and chromogranin A - were enriched in low-fertility cows together with interferon tau 3 h and interferon tau-2. Our results indicate that the genetic merit for fertility leads to substantial quantitative differences at the level of proteins in uterine fluid of pregnant animals, thus altering the microenvironment for the early conceptus.

A missense mutation in the FZD7 gene is associated with dilution of the red areas of the coat in Montbéliarde cattle

Recently, a new genetically autosomal recessive color phenotype emerged in the red pied bovine Montbéliarde breed. It is characterized by a dilution of the red areas of the coat and was denominated 'milca'. A genome-wide homozygosity scan of 106 cases followed by haplotype analysis revealed a candidate region within BTA2 between positions 89.95 and 91.63 Mb. Analysis of whole-genome sequence data generated from milca animals identified a strong candidate variant within the coding region of the Frizzled-7 gene (FZD7). This gene encodes for a G-protein coupled receptor for Wnt signaling proteins. The variant induces a glycine to alanine substitution in the second extracellular loop, p.(Gly414Ala). Cross-species amino acid alignments revealed that this glycine is conserved among orthologs and most paralogs, suggesting that it plays an important role in FZD function. In addition, genotyping data revealed that the mutant allele is restricted to the Montbéliarde breed, at a 3.7% frequency. All homozygous cows for the mutant allele exhibited the milca phenotype whereas all heterozygotes had no coat color defects. In conclusion, this study strongly suggests that, in cattle, a mutation of FZD7 alone is sufficient to cause a coat color phenotype without any strong other adverse effect.

Gene networks for three feed efficiency criteria reveal shared and specific biological processes

Background

French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria.

Results

A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency.

Conclusions

The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.

Influence of metabolic status and genetic merit for fertility on proteomic composition of bovine oviduct fluid†

The oviduct plays a crucial role in fertilization and early embryo development providing the microenvironment for oocyte, spermatozoa, and early embryo. Since dairy cow fertility declined steadily over the last decades, reasons for early embryonic loss have gained increasing interest. Analyzing two animal models, this study aimed to investigate the impact of genetic predisposition for fertility and of metabolic stress on the protein composition of oviduct fluid. A metabolic model comprised maiden Holstein heifers and postpartum lactating (Lact) and non-lactating (Dry) cows, while a genetic model consisted of heifers from the Montbéliarde breed and Holstein heifers with low- and high-fertility index. In a holistic proteomic analysis of oviduct fluid from all groups using nano-liquid chromatography tandem-mass spectrometry analysis and label-free quantification, we were able to identify 1976 proteins, among which 143 showed abundance alterations in the pairwise comparisons within both models. Most differentially abundant proteins were revealed between low fertility Holstein and Montbéliarde (52) in the genetic model and between lactating and maiden Holstein (19) in the metabolic model, demonstrating a substantial effect of genetic predisposition for fertility and metabolic stress on the oviduct fluid proteome. Functional classification of affected proteins revealed actin binding, translation, and immune system processes as prominent gene ontology (GO) clusters. Notably, Actin-related protein 2/3 complex subunit 1B and the three immune system-related proteins SERPIND1 protein, immunoglobulin kappa locus protein, and Alpha-1-acid glycoprotein were affected in both models, suggesting that abundance changes of immune-related proteins in oviduct fluid play an important role for early embryonic loss.

Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle

Background

Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. We detected the most-promising candidate variants (CV) using imputed WGS of 2515 MON, 2203 NOR, and 6321 HOL bulls, and validated their effects in three younger populations of 23,926 MON, 9400 NOR, and 51,977 HOL cows.

Results

Bull sequence-based GWAS detected 84 QTL: 13, 10, and 30 for milk production traits; 3, 0, and 2 for somatic cell score (SCS); and 8, 2 and 16 for udder morphology traits, in MON, NOR, and HOL respectively. Five genomic regions with effects on milk production traits were shared among the three breeds whereas six (2 for production and 4 for udder morphology and health traits) had effects in two breeds. In 80 of these QTL, 855 CV were highlighted based on the significance of their effects and functional annotation. The subsequent GWAS on MON, NOR, and HOL cows validated 8, 9, and 23 QTL for production traits; 0, 0, and 1 for SCS; and 4, 1, and 8 for udder morphology traits, respectively. In 47 of the 54 confirmed QTL, the CV identified in bulls had more significant effects than single nucleotide polymorphisms (SNPs) from the standard 50K chip. The best CV for each validated QTL was located in a gene that was functionally related to production (36 QTL) or udder (9 QTL) traits.

Conclusions

Using this two-step GWAS approach, we identified and validated 54 QTL that included CV mostly located within functional candidate genes and explained up to 6.3% (udder traits) and 37% (production traits) of the genetic variance of economically important dairy traits. These CV are now included in the chip used to evaluate French dairy cattle and can be integrated into routine genomic evaluation.

Frequencies of milk protein variants and haplotypes estimated from genotypes of more than 1 million bulls and cows of 12 French cattle breeds

Due to their major effects on milk composition and cheese-making properties and their putative effects on human health, there is a great deal of interest in bovine milk protein variants. The objectives of this study were to estimate frequencies of milk protein variants and haplotypes in 12 cattle breeds as well as their trends over time to assess the effect of selection on milk traits. Milk protein variants and haplotypes were identified from SNP genotype data from more than 1 million animals from 12 dairy, beef, or dual-purpose cattle breeds that had been genotyped for genomic selection. We examined a total of 15 loci in the genes that encode β-lactoglobulin (β-LG) and 3 caseins (α_S1-CN, β-CN, and κ-CN); genotypes were directly called from customized SNP chips (50.6%) or imputed (49.4%). Variants A and B of β-LG were frequent in the 12 breeds. For the caseins, we found 3 variants for α_S1-CN (B, C, and D), 6 for β-CN (A1, A2, A3, B, C, and I), and 5 for κ-CN (A, B, C, D, and E). For α_S1-CN, the B variant was the most frequent in all breeds except Jersey. For β-CN, the A2 variant was the most abundant in all breeds except Tarentaise, although in Normande animals, the I variant (30.9%) was almost as common as A2 (39.7%). The C variant was very rare except in the Tarentaise sample (4.8%). The most frequent variant for κ-CN was A in 5 breeds (including Holstein), and B in the 7 other breeds. The B variant was present at a particularly high frequency in Jersey (82.6%) and Normande (85.5%) animals. The C and E variants of κ-CN appeared to be particularly frequent in the Tarentaise (12.7%) and Holstein (9%) breeds, respectively. We found 20 haplotype combinations of α_S1-β-κ CN that were present at a frequency >0.1% in at least one breed; however, only 6 to 9 haplotypes were found in any given breed, demonstrating a strong degree of linkage disequilibrium. The most frequent haplotypes were B-A1-A, B-A2-A, B-A2-B, B-I-B, C-A2-A, and C-A2-B. Some alleles were predominantly found in only one haplotype, such as the E and C variants of κ-CN and the I variant of β-CN, which were mainly found in the B-A1-E, B-A1-C, and B-I-B haplotypes, respectively. We observed changes in the frequency of certain variants over time in several breeds, such as an increase in the frequency of variants A of β-LG, I of β-CN, and B of κ-CN. With these results, we update and complete frequency data that were first estimated 30 to 50 yr ago, and, for the first time in these breeds, we assess the effect of selection on milk protein variants.

Genetic architecture of individual variation in recombination rate on the X chromosome in cattle

Meiotic recombination is an essential biological process that ensures proper chromosome segregation and creates genetic diversity. Individual variation in global recombination rates has been shown to be heritable in several species, and variants significantly associated with this trait have been identified. Recombination on the sex chromosome has often been ignored in these studies although this trait may be particularly interesting as it may correspond to a biological process distinct from that on autosomes. For instance, recombination in males is restricted to the pseudo-autosomal region (PAR). We herein used a large cattle pedigree with more than 100,000 genotyped animals to improve the genetic map of the X chromosome and to study the genetic architecture of individual variation in recombination rate on the sex chromosome (XRR). The length of the genetic map was 46.4 and 121.2 cM in males and females, respectively, but the recombination rate in the PAR was six times higher in males. The heritability of CO counts on the X chromosome was comparable to that of autosomes in males (0.011) but larger than that of autosomes in females (0.024). XRR was highly correlated (0.76) with global recombination rate (GRR) in females, suggesting that both traits might be governed by shared variants. In agreement, a set of eleven previously identified variants associated with GRR had correlated effects on female XRR (0.86). In males, XRR and GRR appeared to be distinct traits, although more accurate CO counts on the PAR would be valuable to confirm these results.

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

Background

Mature sperm carry thousands of RNAs, including mRNAs, lncRNAs, tRNAs, rRNAs and sncRNAs, though their functional significance is still a matter of debate. Growing evidence suggests that sperm RNAs, especially sncRNAs, are selectively retained during spermiogenesis or specifically transferred during epididymis maturation, and are thus delivered to the oocyte at fertilization, providing resources for embryo development. However , a deep characterization of the sncRNA content of bull sperm and its expression profile across breeds is currently lacking. To fill this gap, we optimized a guanidinium–Trizol total RNA extraction protocol to prepare high-quality RNA from frozen bull sperm collected from 40 representative bulls from six breeds. Deep sequencing was performed (40 M single 50-bp reads per sample) to establish a comprehensive repertoire of cattle sperm sncRNA.

Results

Our study showed that it comprises mostly piRNAs (26%), rRNA fragments (25%), miRNAs (20%) and tRNA fragments (tsRNA, 14%). We identified 5p-halves as the predominant tsRNA subgroup in bull sperm, originating mostly from Gly and Glu isoacceptors. Our study also increased by ~ 50% the sperm repertoire of known miRNAs and identified 2022 predicted miRNAs. About 20% of sperm miRNAs were located within genomic clusters, expanding the list of known polycistronic pri-miRNA clusters and defining several networks of co-expressed miRNAs. Strikingly, our study highlighted the great diversity of isomiRs, resulting mainly from deletions and non-templated additions (A and U) at the 3p end. Substitutions within miRNA sequence accounted for 40% of isomiRs, with G>A, U>C and C>U substitutions being the most frequent variations. In addition, many sncRNAs were found to be differentially expressed across breeds.

Conclusions

Our study provides a comprehensive overview of cattle sperm sncRNA, and these findings will pave the way for future work on the role of sncRNAs in embryo development and their relevance as biomarkers of semen fertility.

Identification of the ABCC4, IER3, and CBFA2T2 candidate genes for resistance to paratuberculosis from sequence-based GWAS in Holstein and Normande dairy cattle

Background

Bovine paratuberculosis is a contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), with adverse effects on animal welfare and serious economic consequences. Published results on host genetic resistance to MAP are inconsistent, mainly because of difficulties in characterizing the infection status of cows. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to MAP in Holstein and Normande cows with an accurately defined status for MAP.

Results

From MAP-infected herds, cows without clinical signs of disease were subjected to at least four repeated serum ELISA and fecal PCR tests over time to determine both infected and non-infected statuses. Clinical cases were confirmed using PCR. Only cows that had concordant results for all tests were included in further analyses. Positive and control cows were matched within herd according to their birth date to ensure a same level of exposure to MAP. Cows with accurate phenotypes, i.e. unaffected (control) or affected (clinical or non-clinical cases), were genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were imputed to whole-genome sequences using the 1000 Bull Genomes reference population (run6). A genome-wide association study (GWAS) of MAP status of 1644 Holstein and 649 Normande cows, using either two (controls versus cases) or three classes of phenotype (controls, non-clinical and clinical cases), revealed three regions, on Bos taurus (BTA) chromosomes 12, 13, and 23, presenting significant effects in Holstein cows, while only one of those was identified in Normande cows (BTA23). The most significant effect was found on BTA13, in a short 8.5-kb region. Conditional analyses revealed that only one causal variant may be responsible for the effects observed on each chromosome with the ABCC4 (BTA12), CBFA2T2 (BTA13), and IER3 (BTA23) genes as good functional candidates.

Conclusions

A sequence-based GWAS on cows for which resistance to MAP was accurately defined, was able to identify candidate variants located in genes that were functionally related to resistance to MAP; these explained up to 28% of the genetic variance of the trait. These results are very encouraging for efforts towards implementation of a breeding strategy aimed at improving resistance to paratuberculosis in Holstein cows.

Short communication: A splice site mutation in CENPU is associated with recessive embryonic lethality in Holstein cattle

A genome scan for homozygous haplotype deficiency coupled with whole-genome sequence data analysis is a very effective method to identify embryonic lethal mutations in cattle. Among other factors, the power of the approach depends on the availability of a greater amount of genotyping and sequencing data. In the present study, we analyzed the largest known panel of Illumina BovineSNP50 (Illumina Inc., San Diego, CA) genotypes, comprising 401,896 Holstein animals, and we report the mapping of a new embryonic lethal haplotype on chromosome 27, called HH7. We fine mapped the locus in a 2.0-Mb interval using an identical-by-descent approach and analyzed genome sequence data from 4 carrier and 143 noncarrier Holstein bulls to identify the causative mutation. We detected a strong candidate variant in the gene encoding centromere protein U (CENPU), a centromere component essential for proper chromosome segregation during mitosis. The mutant allele is a deletion of 4 nucleotides located at position +3 to +6 bp after the splicing donor site of exon 11. Cross-species nucleotide alignment revealed that the nucleotide at position +3 is entirely conserved among vertebrates, suggesting that it plays an important role in the regulation of CENPU splicing. For verification, we genotyped the candidate variant in 232,775 Holstein individuals and did not observe any homozygotes, whereas 16 were expected (Poisson P-value = 1.1 × 10^-7; allele frequency = 0.8%). In addition, genotyping of 250,602 animals from 19 additional breeds revealed that the mutant allele is restricted to animals of Holstein descent. Finally, we estimated the effect of the candidate variant on 2 fertility traits in at-risk mating (i.e., between carrier bulls and daughters of carrier bulls) versus non-risk mating. In agreement with a recessive lethal inheritance pattern, we observed a marked reduction in both conception rate and 56-d nonreturn rate in heifers and cows. The effect on 56-d nonreturn rate suggests that a substantial proportion of homozygous mutants die before 35 d after insemination, which is consistent with the early embryonic death previously reported in CENPU^-/- mouse embryos. In conclusion, we demonstrate that with more than 400,000 genotypes, we can map very rare recessive lethal mutations segregating at a frequency below 1% in the population. We recommend performing new analyses regularly as data are accumulating.

The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds

Background

In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved.

Methods

We compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection.

Results

Genomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds.

Conclusions

With the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future.

Abstract OT1-11-01: The BRandO BiO registry – A multicenter regional registry for patients with primary breast and ovarian cancer with longitudinal biobanking and evaluation of epidemiological, life style and quality of life factors

Background:

Further progress in the treatment of breast cancer will likely come from contributions of molecular biology and immunologic approaches. The search for druggable molecular aberrations may enable treatment based on the molecular profile. A better identification of patients with a high risk of relapse facilitates the selection of these pts for clinical trials investigating early therapeutic molecular-based interventions.

Trial Design:

The BRandO BiO Registry is a multi-center regional registry to record clinical, epidemiological, and biological data from patients with newly diagnosed breast and ovarian cancer at the University of Ulm, Dept. of Gynecology and 19 affiliated network hospitals and practices in the Alb-Allgäu Bodensee region (outreach area of the Comprehensive Cancer Center Ulm). Longitudinal biobanking is included with collection of paraffin-embedded samples of the primary tumor as well as blood samples at first diagnosis, after 6 and 12 months and at first relapse to isolate and investigate cell-free and germline DNA. Epidemiological, life style and quality of life (QOL) questionnaires are collected at first diagnosis, after 12, 36 and 60 months. The follow up is planned for 10 years.

Eligibility criteria:

Patients with primary newly diagnosed untreated breast or ovarian cancer of ≥ 18 years are eligible; primary metastatic untreated disease is allowed. Exclusion criteria comprise severe neurological or psychiatric disorders interfering with the ability to give an informed consent, no consent for registration, storage and processing of the individual disease characteristics and bio samples, and any malignant tumor in the last 3 years (except in situ disease).

Specific aims:

To register the majority of patients with newly diagnosed breast or ovarian cancer in all BRandO-BiO participating centers of a well-defined geographical area. To assess clinical characteristics and outcome data (event-free survival, overall survival) of these patients. To evaluate the primary tumor of all patients for mutational (druggable) aberrations. Further to assess cell-free DNA in the serial blood samples at baseline, 6 and 12 months and correlate these results with clinical outcome data as well as tumor and patient characteristics to look for early markers predicting relapse. To perform a longitudinal assessment of the patients' sociodemographic factors, comorbidities, lifestyle and QOL factors by analyzing serial questionnaires collected at recruitment and at 12, 36 and 60 months.

Present accrual and target accrual:

The BRandO BiO Registry started January 2016 in the Dept. of Gynecology, University of Ulm and February 2017 at the network hospitals and practices. Until June 2018, 1180 patients with primary breast or ovarian cancer have been enrolled. The current adherence to serial blood testing and serial questionnaires is good with a return rate of 90%. A sample size of 3000 patients is planned.

Contact information:

Jens Huober, University of Ulm, Dept of Gynecology, Breast Center, jens.huober@uniklinik-ulm.de

Amelie de Gregorio, University of Ulm, Dept of Gynecology, Breast Center, Amelie.de Gregorio@uniklinik-ulm.de

Citation Format: Huober J, Nagel G, Rempen A, Schlicht E, Flock F, Fritz S, Thiel F, Wiesmüller L, Felderbaum R, Heilmann V, Bekes I, Fink V, Albrecht S, De Gregorio N, Tzschaschel M, Ernst K, Wolf C, Kuhn P, Friedl T, Janni W, De Gregorio A. The BRandO BiO registry – A multicenter regional registry for patients with primary breast and ovarian cancer with longitudinal biobanking and evaluation of epidemiological, life style and quality of life factors [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT1-11-01.

A Meta-Analysis Including Pre-selected Sequence Variants Associated With Seven Traits in Three French Dairy Cattle Populations

A within-breed genome-wide association study (GWAS) is useful when identifying the QTL that segregates in a breed. However, an across-breed meta-analysis can be used to increase the power of identification and precise localization of QTL that segregate in multiple breeds. Precise localization will allow including QTL information from other breeds in genomic prediction due to the persistence of the linkage phase between the causal variant and the marker. This study aimed to identify and confirm QTL detected in within-breed GWAS through a meta-analysis in three French dairy cattle breeds. A set of sequence variants selected based on their functional annotations were imputed into 50 k genotypes for 46,732 Holstein, 20,096 Montbeliarde, and 11,944 Normande cows to identify QTL for milk production, the success rate at insemination of cows (fertility) and stature. We conducted within-breed GWAS followed by across-breed meta-analysis using a weighted Z-scores model on the GWAS summary data (i.e., P-values, effect direction, and sample size). After Bonferroni correction, the GWAS result identified 21,956 significantly associated SNP (P _FWER < 0.05), while meta-analysis result identified 9,604 significant SNP (P _FWER < 0.05) associated with the phenotypes. The meta-analysis identified 36 QTL for milk yield, 48 QTL for fat yield and percentage, 29 QTL for protein yield and percentage, 13 QTL for fertility, and 16 QTL for stature. Some of these QTL were not significant in the within-breed GWAS. Some previously identified causal variants were confirmed, e.g., BTA14:1802265 (fat percentage, P = 1.5 × 10^-760; protein percentage, P = 7.61 × 10^-348) both mapping the DGAT1-K232A mutation and BTA14:25006125 (P = 8.58 × 10^-140) mapping PLAG1 gene was confirmed for stature in Montbeliarde. New QTL lead SNP shared between breeds included the intronic variant rs109205829 (NFIB gene), and the intergenic variant rs41592357 (1.38 Mb upstream of the CNTN6 gene and 0.65 Mb downstream of the CNTN4 gene). Rs110425867 (ZFAT gene) was the top variant associated with fertility, and new QTL lead SNP included rs109483390 (0.1 Mb upstream of the TNFAIP3 gene and 0.07 Mb downstream of PERP gene), and rs42412333 (0.45 Mb downstream of the RPL10L gene). An across-breed meta-analysis had greater power to detect QTL as opposed to a within breed GWAS. The QTL detected here can be incorporated in routine genomic predictions.

Progressive ataxia of Charolais cattle highlights a role of KIF1C in sustainable myelination

Hereditary spastic paraplegias (HSPs) are clinically and genetically heterogeneous human neurodegenerative diseases. Amongst the identified genetic causes, mutations in genes encoding motor proteins such as kinesins have been involved in various HSP clinical isoforms. Mutations in KIF1C are responsible for autosomal recessive spastic paraplegia type 58 (SPG58) and spastic ataxia 2 (SPAX2). Bovines also develop neurodegenerative diseases, some of them having a genetic aetiology. Bovine progressive ataxia was first described in the Charolais breed in the early 1970s in England and further cases in this breed were subsequently reported worldwide. We can now report that progressive ataxia of Charolais cattle results from a homozygous single nucleotide polymorphism in the coding region of the KIF1C gene. In this study, we show that the mutation at the heterozygous state is associated with a better score for muscular development, explaining its balancing selection for several decades, and the resulting high frequency (13%) of the allele in the French Charolais breed. We demonstrate that the KIF1C bovine mutation leads to a functional knock-out, therefore mimicking mutations in humans affected by SPG58/SPAX2. The functional consequences of KIF1C loss of function in cattle were also histologically reevaluated. We showed by an immunochemistry approach that demyelinating plaques were due to altered oligodendrocyte membrane protrusion, and we highlight an abnormal accumulation of actin in the core of demyelinating plaques, which is normally concentrated at the leading edge of oligodendrocytes during axon wrapping. We also observed that the lesions were associated with abnormal extension of paranodal sections. Moreover, this model highlights the role of KIF1C protein in preserving the structural integrity and function of myelin, since the clinical signs and lesions arise in young-adult Charolais cattle. Finally, this model provides useful information for SPG58/SPAX2 disease and other demyelinating lesions.

Hereditary spastic paraplegias (HSPs) are human neurodegenerative diseases mainly associated with lower extremity weakness and spasticity. Motor-sensory axons degeneration, implying heterogeneous cellular and molecular mechanisms and various genetic causes, is the neuropathological hallmark of this disease. Recently, mutations in KIF1C were associated with human spastic paraplegia type 58 (SPG58) and spastic ataxia 2 (SPAX2), where the radiological brain examination showed demyelination features. We report herein that progressive ataxia of Charolais cattle, a neurodegenerative disease with autosomal recessive inheritance, is caused by a substitution in the KIF1C gene, which leads to a functional knock-out. Interestingly this mutation is associated, in a heterozygous state, with a better muscular development, and thus a zootechnic advantage. Identification of the mutation will therefore be helpful to eradicate this disease. Further study of the lesions in ataxic bovine central nervous system highlighted a peculiar link to oligodendrocytes which were hypertrophied and harbored many membrane protrusions. The demyelinating plaques were enriched by these membranes and actin accumulation indicating close relationship between KIF1C, actin transport and axonal wrapping by oligodendrocyte tongues. Since kif1c knock-out mouse do not display any neurological symptoms, progressive ataxia of Charolais cattle thus provides a useful model for studying SPG58/SPAX2 and other demyelinating diseases.

A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features

BACKGROUND

Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis.

RESULTS

The quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats.

CONCLUSIONS

These results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention.

Oxidative Stress and Cardiovascular Risk in Type 1 Diabetes Mellitus: Insights From the DCCT/EDIC Study

Background

Hyperglycemia leading to increased oxidative stress is implicated in the increased risk for the development of macrovascular and microvascular complications in patients with type 1 diabetes mellitus.

Methods and Results

A random subcohort of 349 participants was selected from the DCCT / EDIC (Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications) cohort. This included 320 controls and 29 cardiovascular disease cases that were augmented with 98 additional known cases to yield a case cohort of 447 participants (320 controls, 127 cases). Biosamples from DCCT baseline, year 1, and closeout of DCCT , and 1 to 2 years post‐ DCCT ( EDIC years 1 and 2) were measured for markers of oxidative stress, including plasma myeloperoxidase, paraoxonase activity, urinary F 2α isoprostanes, and its metabolite, 2,3 dinor‐8 iso prostaglandin F 2α . Following adjustment for glycated hemoblobin and weighting the observations inversely proportional to the sampling selection probabilities, higher paraoxonase activity, reflective of antioxidant activity, and 2,3 dinor‐8 iso prostaglandin F 2α , an oxidative marker, were significantly associated with lower risk of cardiovascular disease (−4.5% risk for 10% higher paraoxonase, P <0.003; −5.3% risk for 10% higher 2,3 dinor‐8 iso prostaglandin F 2α , P =0.0092). In contrast, the oxidative markers myeloperoxidase and F 2α isoprostanes were not significantly associated with cardiovascular disease after adjustment for glycated hemoblobin. There were no significant differences between DCCT intensive and conventional treatment groups in the change in all biomarkers across time segments.

Conclusions

Heightened antioxidant activity (rather than diminished oxidative stress markers) is associated with lower cardiovascular disease risk in type 1 diabetes mellitus, but these biomarkers did not change over time with intensification of glycemic control.

Clinical Trial Registration

URL : https://www.clinicaltrials.gov . Unique identifiers: NCT 00360815 and NCT 00360893.

Genome-wide association study for milking speed in French Holstein cows

Using a combination of data from the BovineSNP50 BeadChip SNP array (Illumina, San Diego, CA) and a EuroGenomics (Amsterdam, the Netherlands) custom single nucleotide polymorphism (SNP) chip with SNP pre-selected from whole genome sequence data, we carried out an association study of milking speed in 32,491 French Holstein dairy cows. Milking speed was measured by a score given by the farmer. Phenotypes were yield deviations as obtained from the French evaluation system. They were analyzed with a linear mixed model for association studies. We identified SNP on 22 chromosomes significantly associated with milking speed. As clinical mastitis and somatic cell score have an unfavorable genetic correlation with milking speed, we tested whether the most significant SNP on these 22 chromosomes associated with milking speed were also associated with clinical mastitis or somatic cell score. Nine hundred seventy-one genome-wide significant SNP were associated with milking speed. Of these, 86 were associated with clinical mastitis and 198 with somatic cell score. The most significant association signals for milking speed were observed on chromosomes 7, 8, 10, 14, and 18. The most significant signal was located on chromosome 14 (ZFAT gene). Eleven novel milking speed quantitative trait loci (QTL) were observed on chromosomes 7, 10, 11, 14, 18, 25, and 26. Twelve candidate SNP for milking speed mapped directly within genes. Of these, 10 were QTL lead SNP, which mapped within the genes HMHA1, POLR2E, GNB5, KLHL29, ZFAT, KCNB2, CEACAM18, CCL24, and LHPP. Limited pleiotropy was observed between milking speed QTL and clinical mastitis.

67 Influence of Metabolic Status and Genetic Merit for Fertility on Proteomic Composition of Bovine Uterine Luminal Fluid

Intensive selection strategies focusing on increased milk yield over several decades has been associated with a decline in fertility in dairy cows. To study the effect of the genetic merit for fertility and the metabolic status of the female on the oocyte, early embryo and the maternal environment, 2 animal models were established. The genetic merit model involved Holstein heifers with a low (LFH) and high fertility (HFH) index and heifers from the Montbéliarde breed (MBD), known to have good reproductive performance. The metabolic model comprised samples from maiden heifers (MH), postpartum lactating cows (Lact), and non-lactating cows (dried off immediately after calving; Dry). A common pool of Day 7 embryos recovered from superovulated and artificially inseminated Holstein heifers were transferred into synchronised recipients (1/recipient) of the above-mentioned animal models and uterine lumen fluid (ULF) of confirmed pregnant animals was recovered on Day 19 post-oestrus. As communication between the conceptus and the uterine environment is crucial for the successful establishment of pregnancy, we analysed uterine luminal fluid of pregnant cows from both models using a holistic proteomic approach. Using nano-liquid chromatography-tandem mass spectrometry analysis combined with a label-free quantification approach, we analysed the uterine luminal fluid from the uterine horn ipsilateral to the corpus luteum (where the conceptus was located in all cases). A total of 2127 proteins were quantified in all samples of both models. Among this set of proteins, 458 were found to differ significantly (P-value < 0.05) in abundance between the groups of the genetic model, and 141 were altered in abundance in the metabolic model. The majority of proteome differences in ULF samples was found comparing HFH to the LFH group (358) and between Dry and Lact cows (70) in the metabolic model. Evaluation of this dataset using bioinformatic tools comprising DAVID GO and gene set enrichment analysis revealed that the affected proteins were predominantly assigned to the terms “translation”, “monosaccharide metabolic process”, “enzyme inhibitor activity”, “lipid binding”, and “response to oxidative stress”. Our study revealed that metabolic status and genetic merit for fertility lead to quantitative molecular differences at the level of proteins in uterine fluid of pregnant animals, thus altering the microenvironment for the early conceptus. This research was funded by European Union Seventh Framework Programme FP7/2007-2013 under grant agreement no. 312097 (‘FECUND’).

KIRREL is differentially expressed in adipose tissue from 'fertil+' and 'fertil-' cows: in vitro role in ovary?

We have previously shown that dairy cows carrying the 'fertil-' haplotype for one quantitative trait locus affecting female fertility located on the bovine chromosome three (QTL-F-Fert-BTA3) have a significantly lower conception rate and body weight after calving than cows carrying the 'fertil+' haplotype. Here, we compared by Tiling Array the expression of genes included in the QTL-F-Fert-BTA3 in 'fertil+' and 'fertil-' adipose tissue one week after calving when plasma non-esterified fatty acid concentrations were greater in 'fertil-' animals. We observed that thirty-one genes were overexpressed whereas twelve were under-expressed in 'fertil+' as compared to 'fertil-' cows (P < 0.05). By quantitative PCR and immunoblot we confirmed that adipose tissue KIRREL mRNA and protein were significantly greater expressed in 'fertil+' than in 'fertil-'. KIRREL mRNA is abundant in bovine kidney, adipose tissue, pituitary, and ovary and detectable in hypothalamus and mammary gland. Its expression (mRNA and protein) is greater in kidney of 'fertil+' than 'fertil-' cows (P < 0.05). KIRREL (mRNA and protein) is also present in the different ovarian cells with a greater expression in granulosa cells of 'fertil+' than 'fertil-' cows. In cultured granulosa cells, recombinant KIRREL halved steroid secretion in basal state (P < 0.05). It also decreased cell proliferation (P < 0.05) and in vitro oocyte maturation (P < 0.05). These results were associated to a rapid increase in MAPK1/3 and MAPK14 phosphorylation in granulosa cells and to a decrease in MAPK1/3 phosphorylation in oocyte. Thus, KIRREL could be a potential metabolic messenger linking body composition and fertility.

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Background

Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.

Results

We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.

Conclusions

Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.

Within-breed and multi-breed GWAS on imputed whole-genome sequence variants reveal candidate mutations affecting milk protein composition in dairy cattle

Background

Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R² ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations. Milk composition was evaluated as average test-day measurements adjusted for environmental effects. Next, we genotyped a subset of 8080 cows (2967 MON, 2737 NOR, and 2306 HOL) with the BovineSNP50 Beadchip. For each breed, genotypes were first imputed to high-density (HD) using HD single nucleotide polymorphisms (SNPs) genotypes of 522 MON, 546 NOR, and 776 HOL bulls. The resulting HD SNP genotypes were subsequently imputed to the sequence level using 27 million high-quality sequence variants selected from Run4 of the 1000 Bull Genomes consortium (1147 bulls). Within-breed, multi-breed, and conditional GWAS were performed.

Results

Thirty-four distinct genomic regions were identified. Three regions on chromosomes 6, 11, and 20 had very significant effects on milk composition and were shared across the three breeds. Other significant effects, which partially overlapped across breeds, were found on almost all the autosomes. Multi-breed analyses provided a larger number of significant genomic regions with smaller confidence intervals than within-breed analyses. Combinations of within-breed, multi-breed, and conditional analyses led to the identification of putative causative variants in several candidate genes that presented significant protein–protein interactions enrichment, including those with previously described effects on milk composition (SLC37A1, MGST1, ABCG2, CSN1S1, CSN2, CSN1S2, CSN3, PAEP, DGAT1, AGPAT6) and those with effects reported for the first time here (ALPL, ANKH, PICALM).

Conclusions

GWAS applied to fine-scale phenotypes, multiple breeds, and whole-genome sequences seems to be effective to identify candidate gene variants. However, although we identified functional links between some candidate genes and milk phenotypes, the causality between candidate variants and milk protein composition remains to be demonstrated. Nevertheless, the identification of potential causative mutations that underlie milk protein composition may have immediate applications for improvements in cheese-making.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0344-z) contains supplementary material, which is available to authorized users.

Genomic evaluation of regional dairy cattle breeds in single-breed and multibreed contexts

An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic evaluation was 5-11% more accurate than a pedigree-based BLUP in three of the four breeds, while the numerically smallest breed showed a < 1% increase in accuracy. Multibreed genomic evaluation was beneficial for two breeds (Abondance and French Simmental) with maximum gains of 5 and 8% in correlation coefficients between yield deviations and genomic estimated breeding values, when compared to the single-breed genomic evaluation results. Inflation of genomic evaluation of young candidates was also reduced. Our results indicate that genomic selection can be effective in regional breeds as well. Here, we provide empirical evidence proving that genetic distance between breeds is only one of the factors affecting the efficiency of multibreed genomic evaluation.

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Background

In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.

Results

In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.

Conclusions

To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.

Genomic selection in domestic animals: Principles, applications and perspectives

The principles of genomic selection are described, with the main factors affecting its efficiency and the assumptions underlying the different models proposed. The reasons of its fast adoption in dairy cattle are explained and the conditions of its application to other species are discussed. Perspectives of development include: selection for new traits and new breeding objectives; adoption of more robust approaches based on information on causal variants; predictions of genotype×environment interactions.

Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.

Genetic tools to improve reproduction traits in dairy cattle

Fertility is a major concern in the dairy cattle industry and has been the subject of numerous studies over the past 20 years. Surprisingly, most of these studies focused on rough female phenotypes and, despite their important role in reproductive success, male- and embryo-related traits have been poorly investigated. In recent years, the rapid and important evolution of technologies in genetic research has led to the development of genomic selection. The generalisation of this method in combination with the achievements of the AI industry have led to the constitution of large databases of genotyping and sequencing data, as well as refined phenotypes and pedigree records. These resources offer unprecedented opportunities in terms of fundamental and applied research. Here we present five such examples with a focus on reproduction-related traits: (1) detection of quantitative trait loci (QTL) for male fertility and semen quality traits; (2) detection of QTL for refined phenotypes associated with female fertility; (3) identification of recessive embryonic lethal mutations by depletion of homozygous haplotypes; (4) identification of recessive embryonic lethal mutations by mining whole-genome sequencing data; and (5) the contribution of high-density single nucleotide polymorphism chips, whole-genome sequencing and imputation to increasing the power of QTL detection methods and to the identification of causal variants.

Risk of pancreatic fistula after enucleation of pancreatic tumours

Background

Enucleation is used increasingly for small pancreatic tumours. Data on perioperative outcome after pancreatic enucleation, especially regarding the significance and risk factors associated with postoperative pancreatic fistula (POPF), are limited. This study aimed to assess risk-dependent perioperative outcome after pancreatic enucleation, with a focus on POPF.

Methods

Patients undergoing enucleation for pancreatic lesions between October 2001 and February 2014 were identified from a prospective database. A detailed analysis of morbidity was performed. Risk factors for POPF were assessed by univariable and multivariable analyses.

Results

Of 166 enucleations, 94 (56·6 per cent) were performed for cystic and 72 (43·4 per cent) for solid lesions. Morbidity was observed in 91 patients (54·8 per cent). Severe complications occurred in 30 patients (18·1 per cent), and one patient (0·6 per cent) died. Reoperation was necessary in nine patients (5·4 per cent). POPF was the main determinant of outcome and occurred in 68 patients (41·0 per cent): grade A POPF, 34 (20·5 per cent); grade B, ten (6·0 per cent); and grade C, 24 (14·5 per cent). Risk factors independently associated with POPF were: cystic tumour, localization in the pancreatic tail, history of pancreatitis and cardiac co-morbidity. Only cystic morphology was independently associated with clinically relevant POPF (grade B or C), occurring after enucleation in 25 (27 per cent) of 94 patients with cystic tumours versus nine (13 per cent) of 72 patients with solid tumours. Tumour size and distance to the main duct were not associated with risk of POPF.

Conclusion

Enucleation is a safe procedure in appropriately selected patients with a low rate of severe complications. POPF is the main determinant of outcome and is more frequent after the enucleation of cystic lesions.

An integrated approach to bovine oocyte quality: from phenotype to genes

In cattle, early embryonic failure plays a major role in the limitation of reproductive performance and is influenced by genetic effects. Suboptimal oocyte quality, including an inadequate store of maternal factors, is suspected to contribute to this phenomenon. In the present study, 13 Montbeliarde cows were phenotyped on oocyte quality, based on their ability to produce viable embryos after in vitro maturation, fertilisation and culture for 7 days. This discriminated two groups of animals, exhibiting developmental rates below 18.8% or above 40.9% (relative to cleaved embryos). Using microarrays, transcriptomic profiles were compared between oocytes collected in vivo from these two groups of animals. The difference in oocyte development potential was associated with changes in transcripts from 60 genes in immature oocytes and 135 genes in mature oocytes (following Bonferroni 5% correction). Of these, 16 and 32 genes were located in previously identified fertility quantitative trait loci. A subset of differential genes was investigated on distinct samples by reverse transcription-quantitative polymerase chain reaction. For SLC25A16, PPP1R14C, ROBO1, AMDHD1 and MEAF6 transcripts, differential expression was confirmed between high and low oocyte potential animals. Further sequencing and searches for polymorphisms will pave the way for implementing their use in genomic selection.

A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species

Background

With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods.

Results

For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations.

Conclusions

All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0087-7) contains supplementary material, which is available to authorized users.