Detailed analysis of mortality rates in the female progeny of 1,001 Holstein bulls allows the discovery of new dominant genetic defects.

Reducing juvenile mortality in cattle is important for both economic and animal welfare reasons. Previous studies have revealed a large variability in mortality rates between breeds and sire progeny groups, with some extreme cases due to dominant mutations causing various syndromes among the descendants of mosaic bulls. The purpose of this study was to monitor sire-family calf mortality within the French and Walloon Holstein populations, and to use this information to detect genetic defects that might have been overlooked by lack of specific symptoms. In a population of heifers born from 1,001 bulls between 2017 and 2020, the average sire-family mortality rates were of 11.8% from birth to 1 year of age and of 4.2, 2.9, 3.1, and 3.2% for the perinatal, postnatal, preweaning, and postweaning subperiods, respectively. After outlining the 5 worst bulls per category, we paid particular attention to the bulls Mo and Pa, because they were half-brothers. Using a battery of approaches, including necropsies, karyotyping, genetic mapping, and whole-genome sequencing, we described 2 new independent genetic defects in their progeny and their molecular etiology. Mo was found to carry a de novo reciprocal translocation between chromosomes BTA26 and BTA29, leading to increased embryonic and juvenile mortality because of aneuploidy. Clinical examination of 2 calves that were monosomic for a large proportion of BTA29, including an orthologous segment deleted in human Jacobsen syndrome, revealed symptoms shared between species. In contrast, Pa was found to be mosaic for a dominant de novo nonsense mutation of GATA 6 binding protein (GATA6), causing severe cardiac malformations. In conclusion, our results highlight the power of monitoring juvenile mortality to identify dominant genetic defects due to de novo mutation events.

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.

Determination of immunoglobulin concentrations and genetic parameters for colostrum and calf serum in Charolais animals.

Colostrum samples from 366 Charolais primiparous cows, as well as serum from their calves at 24 to 48 h of age, were collected to gain an overview of the situation regarding passive immune transfer in beef cattle, from both the phenotypic and genetic points of view. All samples were analyzed to quantify their G1 immunoglobulins by radial immunodiffusion (RID) and their IgG, IgA, and IgM using ELISA. The average concentrations obtained in colostrum were 84 mg/mL for RID-IgG1, and 158 mg/mL, 4.5 mg/mL and 10.8 mg/mL for ELISA-IgG, -IgA, and -IgM, respectively. The corresponding values in calf serum were 19.9, 30.6, 1.0, and 1.9 mg/mL. Apart from the general environmental effect (farm-year combination and laboratory conditions), the characteristics of the dams tested did not reveal any influence on colostrum immunoglobulin concentrations. Calving difficulty, as well as the birth weight and sex of calves, were found to be associated with serum concentrations in some cases. Heritability estimates were low to moderate, with the highest being for RID-IgG1 in colostrum (h2 = 0.28, standard error = 0.14) and serum (h2 = 0.36, standard error = 0.18). Phenotypic correlations among the different immunoglobulins were generally positive or null, and none of the genetic correlations were significant due to large standard errors. The phenotypic correlation between dam colostrum and calf serum values was 0.2 for RID-IgG1 and null for the 3 ELISA measurements. The correlation between RID-IgG1 and ELISA-IgG was, unexpectedly, null for colostrum and 0.4 for serum. Increased RID-IgG1 levels in calf serum were associated with improved survival, as well as better early growth and fewer health problems. These results thus showed that despite generally higher concentrations in beef than in dairy cattle, passive transfer was unsuccessful in a considerable number of calves. This should be brought to the attention of breeders to avoid negative effects on survival and subsequent performance. The heritability estimates were encouraging; however, obtaining phenotypes on a large scale constitutes a real limitation regarding these traits.

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species.

In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans.

A Generalized Caprine-like Hypoplasia Syndrome is localized within a 6-cM interval on bovine chromosome 13 in the Montbéliarde breed.

Caprine-like Generalized Hypoplasia Syndrome (or SHGC) is a new hereditary disorder described in the Montbéliarde breed. We report here the characterization of this new disease, based on the visual examination of animals affected by SHGC, and on physiological and biochemical studies undertaken on samples of both SHGC and normal animals. Biological samples for more than 150 affected calves and their parents have been collected over the past 4 years within the framework of the Bovine Genetic Disease Observatory. First, pedigree analyses showed that the mode of inheritance is most probably autosomal recessive. Then, a genome scan with 113 animals and 140 microsatellite markers revealed a single locus within a 35-cM region on bovine chromosome 13. Genotypes of 261 animals for 18 new microsatellite markers from the region confirmed the localization of the disorder to a 6-cM interval. Finally, based on the analysis of haplotypes in 463 Montbéliarde sires, we estimated the frequency of the SHGC mutated allele in the population and could propose a strategy for the systematic eradication of this disorder in the near future.

A first-generation microsatellite-based integrated genetic and cytogenetic map for the European rabbit (Oryctolagus cuniculus) and localization of angora and albino.

Although the European rabbit (Oryctolagus cuniculus) is used both in agronomics and in research, genomic resources for this species are still limited and no microsatellite-based genetic map has been reported. Our aim was to construct a rabbit genetic map with cytogenetically mapped microsatellites so as to build an integrated genetic and cytogenetic map. A reference population of 187 rabbits comprising eight three-generation families with 10-25 offspring per family was produced. One hundred and ninety-four of 305 previously identified microsatellites were included in this study. Of these, 158 were polymorphic with two to seven alleles. The map reported here comprises 111 markers, including 104 INRA microsatellites, five microsatellites from another source and two phenotypic markers (angora and albino). Ninety markers were integrated into 20 linkage groups. The remaining 21 microsatellites mapped to separate linkage groups, 19 with a precise cytogenetic position and two with only a chromosomal assignment. The genetic map spans 2766.6 cM and covers 20 rabbit chromosomes, excluding chromosomes 20, 21 and X. The density of this map is limited, but we used it to verify the location of angora and albino on chromosomes 15q and 1q, respectively, in agreement with previously published data. This first generation genetic/cytogenetic map will help gene identification and quantitative trait loci mapping projects in rabbit.

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.

Genomic identification of the breed of an individual or its tissue.

To elaborate a methodological approach for the assignment of a breed to a carcass or other animal tissue, DNA microsatellites were utilized. Four Italian beef breeds were studied; examining these breeds is a challenge because they display similar morphological and productive characteristics. As comparison 54 Holstein-Friesian subjects were used. To measure the genetic similarities between animals or between groups of animals we used our method (Ciampolini et al, 1995, Individual multilocus genotypes using microsatellite polymorphisms to permit the analysis of the genetic variability within and between italian beef cattle breeds. Journal of Animal science,73, 3259-3268.) based on the consideration of a multilocus genotype of each animal, which enabled us to establish breed genomic formulae. Although the results are only preliminary, they show that we can distinguish easily between Holstein-Friesian subjects and beef animals; moreover we can identify, with a high resolution potential, animals from breeds (the four Italian white) with very high genetic similarities. However all the Holstein-Friesian subjects were identified.

A genetic and physical map of bovine chromosome 3.

This paper reports a map of nine polymorphic microsatellite markers previously assigned to bovine chromosome 3 (BTA3) by somatic cell genetics. The linkage group covers 101 cM on the chromosome with an average intermarker distance of 13.9 cM. One marker (INRA200) was isolated from a peak of flow sorted chromosomes 2 and 3. Another marker (INRA197) was derived from a cosmid. The localization of the cosmid by in situ hybridization enabled the orientation of the linkage group on BTA3. Markers were relatively evenly spaced and consequently can be used to complement other mapping data about this chromosome. This establishes a framework of polymorphic markers that can be used to search for quantitative trait loci (QTL).

A genetic and physical map of bovine chromosome 11.

A genetic map of bovine Chromosome (Chr) 11 (BTA11, synteny group U16) has been constructed from 330 animals belonging to 21 families, which constitute the international bovine reference panel (IBRP). This map is based on 13 polymorphic microsatellite markers, two of which were chosen in previously published maps. Three markers have been isolated from cosmids. Two of the three cosmids have been physically localized by fluorescence in situ hybridization (FISH), to anchor the genetic map on the chromosome. In addition, a biallelic polymorphism in the beta-lactoglobulin gene (LGB) has been genetically positioned relative to the microsatellite markers. The most probable order of the markers is: cen-INRA044-BM716-INRA177-(TGLA327, INRA198, INRA131)-INRA111-INRABERN169-(INRA115, INRA032)-INRA108-INRABERN162-INRA195-LGB. The total linkage group spans 126 cM, which probably corresponds to most of the chromosome length. The average intermarker distance is about 10.5 cM, allowing the potential detection of a genetic linkage with any Economic Trait Loci (ETL) of this chromosome. Seven of these markers have been previously published by Vaiman and coworkers (1994), two will be published as part of a set of markers (Eggen et al. in preparation), two are described in this paper, and two (BM716, TGLA327) were chosen from the published maps of BTA11 in order to integrate our data with existing maps. All these markers were assigned to synteny group U16 by use of a previously characterized panel of hamster/bovine somatic hybrid cell lines (Guérin et al. 1994).(ABSTRACT TRUNCATED AT 250 WORDS)

A microsatellite within the bovine kappa-casein gene reveals a polymorphism correlating strongly with polymorphisms previously described at the protein as well as the DNA level.

The polymorphism of a (TA)n(CA)n repeat microsatellite present in the third intron of the bovine kappa-casein gene (CASK) has been investigated. The existence of six alleles differing only in the number of dinucleotide repeats has been established. A total of 330 animals belonging to nine different pure bred Bos taurus French breeds or to a cross-bred Bos taurus x Bos indicus population (Créole) were genotyped. The distribution of the microsatellite alleles was examined and clear breed differences were noted. Genotyping of animals by isoelectric focusing (IEF) or restriction fragment length polymorphism (RFLP) (TaqI) was performed, in order to examine the relationship of the microsatellite polymorphism to other previously described CASK polymorphisms, at the protein and DNA levels. Strong correlation was seen, indicating that evolution of the various polymorphisms was not independent, and nine CASK haplotypes were observed.

Characterization of five new bovine dinucleotide repeats.

Five new bovine (TG)n microsatellite sequences were characterized. During the screening procedure, one-third of the clones had essentially the same flanking sequences. A fast technique was devised to eliminate these clones.