Considering genetic characteristics in German Holstein breeding programs

Invited review: Management of genetic defects in dairy cattle populations

When related animals are mated to one another, genetic defects may become apparent if recessive mutations are inherited from both sides of the pedigree. The widespread availability of high-density DNA genotypes for millions of animals has made it possible to identify and track known defects as well as to identify and track previously unknown defects that cause early embryonic losses. Although the number of known defects has increased over time, the availability of carrier information has been used to dramatically reduce the frequency of many disorders. The economic impact of known genetic defects in the US dairy cattle population has decreased by ∼2/3 since 2016, due largely to the avoidance of carrier-to-carrier matings. Effective population management requires robust systems for reporting new defects, identification of causal mechanisms, and development of commercially available tests. The United States and Canada depend on informal cooperation among many groups, including farmers, purebred cattle associations, genetics companies, and researchers, to identify emerging and causal defects. The structure of a collaborative system including all key sectors of the dairy cattle industry to support long-term population management is described. This review provides a comprehensive overview of the landscape surrounding genetic defects in dairy cattle. Topics covered include current defects of relevance to commercial dairy producers, trends in carrier frequencies over time, how best to manage these defects, strategies for detecting emerging diseases, and marketing and trade considerations.

Distribution of Recessive Genetic Defect Carriers in Holstein Friesian Cattle: A Polish Perspective

Genetic disorders are caused by a hereditary change in the structure of DNA that may hurt the health and life of animals. Several recessive haplotypes and a few causative mutations are known in Holstein Friesian cattle: CDH (Holstein cholesterol deficiency), haplotypes with a homozygous deficiency in Holstein (HH1, HH3, HH4, HH5, HH6, HH7), BLAD (bovine leukocyte adhesion deficiency), DUMPS (deficiency of uridine monophosphate synthase), FXI (factor XI deficiency), HHM (mule foot, syndactyly), and BC (citrullinaemia). From a breeding point of view, these genetic diseases have highly negative effects and are a significant problem for breeders, exposing them to economic losses and hurting animal welfare. This study aimed to characterize the Polish population of Holstein Friesian dairy cattle, considering the carrier status of twelve selected genetic defects. This study was based on genotype data collected from 78,884 cows and 691 bulls of the Holstein Friesian variety. The studies were performed using Illumina Infinium microarrays. Among both bulls and cows, the highest numbers of carriers were detected for HH5 (appropriately 6.7% and 5.4%). The lowest numbers of carriers were detected for DUMPS, factor XI, and HHM. The study revealed one calf suffering from cholesterol deficiency.

Selected Monogenic Genetic Diseases in Holstein Cattle-A Review

Genetic disorders arise from alterations in the hereditary information encoded in DNA, leading to potential detrimental effects on the well-being and vitality of organisms. Within the bovine population, genetic conditions inherited in an autosomal recessive manner are frequently associated with particular breeds. In recent years, several recessive haplotypes and a few causative mutations have been discovered in Holstein cattle: CDH (Holstein cholesterol deficiency), haplotypes with a homozygous deficiency in Holstein (HH1, HH3, HH4, HH5, HH6 and HH7), BLAD (bovine leukocyte adhesion deficiency) and DUMPS (deficiency of uridine monophosphate synthase). All of these diseases are inherited in an autosomal recessive manner. From a breeding perspective, recessive mutations specifically exhibit considerable detrimental effects and are a significant problem for breeders, exposing them to economic losses. Individual mutations can cause embryo death at any stage of pregnancy. Only genetic research and conscious selection of animals for mating will lead to a reduction in the number of carriers and elimination of mutations from the population.

The effect of genetic defects on pregnancy loss in Swedish dairy cattle

The effect of carrier status of 10 lethal recessive genetic defects on pregnancy maintenance in Swedish dairy cattle was examined. The genetic defects were Ayrshire Haplotype 1, Ayrshire Haplotype 2, BTA12, BTA23, and Brown Swiss Haplotype 2 in Red Dairy Cattle (RDC), and Holstein Haplotype 1, 3, 4, 6, and 7 (HH1-HH7) in Holstein. Effects of carrier status of BTA12 and HH3 on conception rate (CR), interval from first to last service (FLS), and milk production were also examined. Data were obtained for 1,429 herds in the Swedish milk recording system, while information on carrier status of genetic defects was obtained from the Nordic Cattle Genetic Evaluation. In total, data on 158,795 inseminations in 28,432 RDC and 22,018 Holstein females were available. Data permitted separate analyses of BTA12 and HH3, but carrier frequencies of other defects were too low to enable further analysis. Pregnancy loss was defined as failure to maintain pregnancy, where pregnancy status was confirmed with manual and chemical pregnancy diagnosis, insemination, calving, sales and culling data. Odds ratios (OR) and probabilities of pregnancy loss and CR were estimated using generalized linear mixed models, while pregnancy loss, CR, FLS, milk, protein, and fat yields were analyzed using linear mixed models. Pregnancy losses were reported on average within the first month post-AI. At-risk matings were more prone to suffer pregnancy loss in BTA12 (OR = 1.79) and HH3 carriers (OR = 1.77) than not-at-risk matings. At-risk matings also had lower CR (OR = 0.62 and 0.63 for BTA12 and HH3, respectively) than not-at-risk matings. Carrier females of BTA12 had longer FLS and higher milk production than noncarriers. Conception rate and pregnancy maintenance could be improved by avoiding at-risk matings. This finding could help reduce pregnancy loss due to genetic defects in the breeding program for improved fertility.

Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India

Fertility is an important trait associated with reproductive performance and animal welfare concern. Lethal alleles affect fertility through early embryonic death, abortions, and stillbirth depending on the genetic expression of the allele. Holstein Friesian and Jersey are two major Bos taurus breeds used widely for increasing milk yield along with purebreds of Bos indicus breeds like Gir, Kankrej, Sahiwal, and Tharparkar. In the present study, prevalence of lethal mutants in crossbred Holstein Friesian (CBHF, n = 2435), crossbred Jersey (CBJY, n = 2874), Gir (n = 3288), Kankrej (n = 593), Sahiwal (n = 965), and Tharparkar (n = 18) were studied. Heterozygous carrier animals were identified for bovine leukocyte adhesion deficiency (BLAD), Citrullinemia, complex vertebral malformation (CVM), Brachyspina, Holstein Haplotype 1 (HH1), Holstein Haplotype 3 (HH3),Holstein Haplotype 4 (HH4) and Jersey Haplotype 1 (JH1). Breed purity analysis confirmed inheritance of Bos taurus genes contributing to the presence of lethal mutant alleles like BLAD, Citrullinemia, HH1, and JH1 in apparently phenotypic Bos indicus animals. Screening and elimination of heterozygous carrier bulls/cows is essential to control fertility loss associated with lethal alleles.

Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level

In this study, we explored mating allocation in Holstein using genomic information for 24,333 Holstein females born in Denmark, Finland, and Sweden. We used 2 data sets of bulls: the top 50 genotyped bulls and the top 25 polled genotyped bulls on the Nordic total merit scale. We used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and β-casein. We found that it was possible to reduce genetic relationships and eliminate expression of genetic defects with minimal effect on the genetic level in total merit index. Compared with maximizing only Nordic total merit index, the relative frequency of polled offspring increased from 13.5 to 22.5%, and that of offspring homozygous for β-casein (A2A2) from 66.7 to 75.0% in one generation, without any substantial negative impact on other comparison criteria. Using only semen from polled bulls, which might become necessary if dehorning is banned, considerably reduced the genetic level. We also found that animals carrying the polled allele were less likely to be homozygous for β-casein (A2A2) and more likely to be carriers of the genetic defect HH1. Hence, adding economic value to a monogenic trait in the economic score used for mating allocation sometimes negatively affected another monogenetic trait. We recommend that the comparison criteria used in this study be monitored in a modern genomic mating program.

Integrated analysis of whole genome and transcriptome sequencing reveals a frameshift mutation associated with recessive embryonic lethality in Holstein cattle

Embryo loss is an important factor affecting fertility in dairy production. HH2 was identified as a haplotype on chromosome 1 associated with embryonic lethality in Holstein cattle. In the current study, both short- and long-read WGS was performed on four carriers and four non-carriers of HH2 to screen for variants in concordance with HH2 haplotype status. Sequence variation analysis revealed five putative functional variants of protein-coding genes, including a frameshift mutation (g.107172616delT) in intraflagellar transport protein 80 (IFT80) gene. Transcriptome analysis of whole blood indicated that no gene exhibited significantly differential expression or allele-specific expression between carriers and non-carriers in the candidate region. This evidence points to g.107172616delT as the highest priority causative mutation for HH2. Protein prediction reveals that the frameshift mutation results in a premature stop codon to reduce the peptide chain from 760 to 383 amino acids and greatly alters the structure and function of IFT80 protein. Our results demonstrate that the use of a combination of multiple high-throughput sequencing technologies is an efficient strategy to screen for the candidate causative mutations responsible for Mendelian traits, including genetic disorders.

Mating allocations in Nordic Red Dairy Cattle using genomic information

In this study, we compared mating allocations in Nordic Red Dairy Cattle using genomic information. We used linear programming to optimize different economic scores within each herd, considering genetic level, semen cost, the economic impact of recessive genetic defects, and genetic relationships. We selected 9,841 genotyped females born in Denmark, Finland, or Sweden in 2019 for mating allocations. We used 2 different pedigree relationship coefficients, the first tracing the pedigree 3 generations back from the parents of the potential mating and the second based on all available pedigree information. We used 3 different genomic relationship coefficients, 1 SNP-by-SNP genomic relationship and 2 based on shared genomic segments. We found high correlations (≥0.83) between the pedigree and genomic relationship measures. The mating results showed that it was possible to reduce the different genetic relationships between parents with minimal effect on genetic level. Including the cost of known recessive genetic defects eliminated expression of genetic defects. It was possible to reduce genomic relationships between parents with pedigree measures, but it was best done with genomic measures. Linear programming maximized the economic score for all herds studied within seconds, which means that it is suitable for implementation in mating software to be used by advisors and farmers.

Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection

BACKGROUND

We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step.

METHODS

We used stochastic simulation to estimate true genetic gain realised at a 0.01 rate of true inbreeding (ΔF_true) by breeding schemes that combined one of four pre-selection strategies with one of three selection strategies. The four pre-selection strategies were: (1) no carriers culled, (2) male carriers culled, (3) female carriers culled, and (4) all carriers culled. Carrier-status was known prior to selection. The three selection strategies were: (1) OCS in which [Formula: see text] was predicted and controlled using pedigree relationships (POCS), (2) OCS in which [Formula: see text] was predicted and controlled using genomic relationships (GOCS), and (3) truncation selection of parents. All combinations of pre-selection strategies and selection strategies were tested for three starting frequencies of the LRA (0.05, 0.10, and 0.15) and two linkage statuses with the locus that has the LRA being on a chromosome with or without loci affecting the breeding goal trait. The breeding schemes were simulated for 10 discrete generations (t = 1, …, 10). In all breeding schemes, ΔF_true was calibrated to be 0.01 per generation in generations t = 4, …, 10. Each breeding scheme was replicated 100 times.

RESULTS

We found no significant difference in true genetic gain from generations t = 4, …, 10 between breeding schemes with or without pre-selection within selection strategy. POCS and GOCS schemes realised similar true genetic gains from generations t = 4, …, 10. POCS and GOCS schemes realised 12% more true genetic gain from generations t = 4, …, 10 than truncation selection schemes.

CONCLUSIONS

We advocate for OCS schemes with pre-selection against the LRA that cause animal suffering and high costs. At LRA frequencies of 0.10 or lower, OCS schemes in which male carriers are culled reduce the frequency of LRA, control rate of inbreeding, and realise no significant reduction in true genetic gain compared to OCS schemes without pre-selection against LRA.

Prevalence of nine genetic defects in Chinese Holstein cattle

Worldwide use of elite sires has caused inbreeding accumulation and high frequencies of genetic defects in dairy cattle populations. In recent years, several genetic defect genes or haplotypes have been identified in Holstein cattle. A rapid and reliable microfluidic chip with Kompetitive allele-specific PCR (KASP) assay was developed in our previous study for the detection of heterozygotes at eight genetic defect loci of bovine leukocyte adhesion deficiency (BLAD), Brachyspina syndrome (BS), complex vertebral malformation (CVM), Holstein haplotype 1 (HH1), Holstein haplotype 3 (HH3), Holstein haplotype 4 (HH4), Holstein haplotype 5 (HH5) and haplotype for cholesterol deficiency (HCD). This study aimed to extend that assay to include a newly identified genetic defect of Holstein haplotype 6 (HH6) and to estimate the frequencies of carriers for each of the nine genetic defects in six Chinese Holstein herds. Of the 1633 cows, carrier frequencies of the genetic defects were 6.92%, 5.76%, 4.46%, 4.30%, 3.62%, 2.94%, 1.86% and 0.37% for HH1, HH3, CVM, HH5, HCD, BS, HH6 and BLAD, respectively. No carrier was found for HH4. Notably, 27.43% of cows carried at least one genetic defect, while 2.27% and 0.12% of cows carried double and triple genetic defect alleles, respectively. The existence of genetic defects calls for routine molecular testing and effective management of genetic defects by avoiding carrier-to-carrier mating in production herds and eliminating or at least reducing the frequency of the defective alleles through marker-assisted selection in breeding herds.

A variance component estimation approach to infer associations between Mendelian polledness and quantitative production and female fertility traits in German Simmental cattle

BACKGROUND

Managing beneficial Mendelian characteristics in dairy cattle breeding programs implies that the correlated genetic effects are considered to avoid possible adverse effects in selection processes. The Mendelian trait polledness in cattle is traditionally associated with the belief that the polled locus has unfavorable effects on breeding goal traits. This may be due to the inferior breeding values of former polled bulls and cows in cattle breeds, such as German Simmental, or to pleiotropic or linkage effects of the polled locus.

METHODS

We focused on a variance component estimation approach that uses a marker-based numerator relationship matrix reflecting gametic relationships at the polled locus to test for direct pleiotropic or linked quantitative trait loci (QTL) effects of the polled locus on relevant traits. We applied the approach to performance, health, and female fertility traits in German Simmental cattle.

RESULTS

Our results showed no evidence for any pleiotropic QTL effects of the polled locus on test-day production traits milk yield and fat percentage, on the mastitis indicator 'somatic cell score', and on several female fertility traits, i.e. 56 days non return rate, days open and days to first service. We detected a significant and unfavorable QTL effect accounting for 6.6% of the genetic variance for protein percentage only.

CONCLUSIONS

Pleiotropy does not explain the lower breeding values and phenotypic inferiority of polled German Simmental sires and cows relative to the horned population in the breed. Thus, intensified selection in the polled population will contribute to increased selection response in breeding goal traits and genetic merit and will narrow the deficit in breeding values for production traits.

Comparison of Gene Editing Versus Conventional Breeding to Introgress the POLLED Allele Into the Tropically Adapted Australian Beef Cattle Population

Dehorning is the process of physically removing horns to protect animals and humans from injury, but the process is costly, unpleasant, and faces increasing public scrutiny. Genetic selection for polled (hornless), which is genetically dominant to horned, is a long-term solution to eliminate the need for dehorning. However, due to the limited number of polled Australian Brahman bulls, the northern Australian beef cattle population remains predominantly horned. The potential to use gene editing to produce high-genetic-merit polled cattle was recently demonstrated. To further explore the concept, this study simulated introgression of the POLLED allele into a tropically adapted Australian beef cattle population via conventional breeding or gene editing (top 1% or 10% of seedstock bulls/year) for 3 polled mating schemes and compared results to baseline selection on genetic merit (Japan Ox selection index, $JapOx) alone, over the course of 20 years. The baseline scenario did not significantly decrease the 20-year HORNED allele frequency (80%), but resulted in one of the fastest rates of genetic gain ($8.00/year). Compared to the baseline, the conventional breeding scenarios where polled bulls were preferentially used for breeding, regardless of their genetic merit, significantly decreased the 20-year HORNED allele frequency (30%), but resulted in a significantly slower rate of genetic gain ($6.70/year, P ≤ 0.05). The mating scheme that required the exclusive use of homozygous polled bulls, resulted in the lowest 20-year HORNED allele frequency (8%), but this conventional breeding scenario resulted in the slowest rate of genetic gain ($5.50/year). The addition of gene editing the top 1% or 10% of seedstock bull calves/year to each conventional breeding scenario resulted in significantly faster rates of genetic gain (up to $8.10/year, P ≤ 0.05). Overall, our study demonstrates that, due to the limited number of polled Australian Brahman bulls, strong selection pressure on polled will be necessary to meaningfully increase the number of polled animals in this population. Moreover, these scenarios illustrate how gene editing could be a tool for accelerating the development of high-genetic-merit homozygous polled sires to mitigate the current trade-off of slower genetic gain associated with decreasing HORNED allele frequency in the Australian Brahman population.

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.

Technical note: Development and application of KASP assays for rapid screening of 8 genetic defects in Holstein cattle

Specific DNA mutations underlying several genetic defects associated with embryo loss or reduced calf survivability have been identified in dairy cattle, and a convenient and cost-effective platform is required for their routine screening. We developed Kompetitive allele-specific PCR (KASP) assays for discrimination of the wild-type alleles from the associated defective alleles at each of 8 common genetic defects in Holstein cattle, involving 5 SNP [HH1, HH3, HH4, bovine leukocyte adhesion deficiency (BLAD), and complex vertebral malformation (CVM)] and 3 insertion or deletion mutations [HH5, haplotype for cholesterol deficiency (HCD), and brachyspina (BS)]. A total of 390 cows from a Chinese Holstein herd were genotyped and the carriers identified at 7 of these 8 loci (except HH4), with the highest carrier frequencies found for CVM (10.5%) and HH1 (10.0%), followed by HH3 (2.6%), BS (2.1%), HCD (1.3%), HH5 (0.8%), and BLAD (0.5%). Surprisingly, 102 cows (26.2%) carried at least 1 of the 7 defective alleles. Our results demonstrate that these KASP assays are simple, rapid, and reliable for the detection of multiple genetic defects. The high carrier frequency of these genetic defects indicates an urgent need for routine molecular testing to eliminate the deleterious alleles from Chinese Holstein cattle.

The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TBF1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB

Background

With the availability of massive SNP data for several economically important cattle breeds, haplotype tests have been performed to identify unknown recessive disorders. A number of so-called lethal haplotypes, have been uncovered in Holstein Friesian cattle and, for at least seven of these, the causative mutations have been identified in candidate genes. However, several lethal haplotypes still remain elusive. Here we report the molecular genetic causes of lethal haplotype 5 (HH5) and cholesterol deficiency (CDH). A targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used to interrogate for causative mutations in a case/control approach.

Methods

Targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used in a case/control approach. PCRs for the causing mutations were developed and compared to routine imputing in 2,100 (HH5) and 3,100 (CDH) cattle.

Results

HH5 is caused by a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event. TFB1M di-methylates adenine residues in the hairpin loop at the 3’-end of mitochondrial 12S rRNA, being essential for synthesis and function of the small ribosomal subunit of mitochondria. Homozygous TFB1M^-/- mice reportedly exhibit embryonal lethality with developmental defects. A 2.8% allelic frequency was determined for the German HF population. CDH results from a 1.3kbp insertion of an endogenous retrovirus (ERV2-1-LTR_BT) into exon 5 of the APOB gene at BTA11:77,959kb. The insertion is flanked by 6bp target site duplications as described for insertions mediated by retroviral integrases. A premature stop codon in the open reading frame of APOB is generated, resulting in a truncation of the protein to a length of only <140 amino acids. Such early truncations have been shown to cause an inability of chylomicron excretion from intestinal cells, resulting in malabsorption of cholesterol. The allelic frequency of this mutation in the German HF population was 6.7%, which is substantially higher than reported so far. Compared to PCR assays inferring the genetic variants directly, the routine imputing used so far showed a diagnostic sensitivity of as low as 91% (HH5) and 88% (CDH), with a high specificity for both (≥99.7%).

Conclusion

With the availability of direct genetic tests it will now be possible to more effectively reduce the carrier frequency and ultimately eliminate the disorders from the HF populations. Beside this, the fact that repetitive genomic elements (RE) are involved in both diseases, underline the evolutionary importance of RE, which can be detrimental as here, but also advantageous over generations.

A frameshift mutation in GON4L is associated with proportionate dwarfism in Fleckvieh cattle

Background

Low birth weight and postnatal growth restriction are the most evident symptoms of dwarfism. Accompanying skeletal aberrations may compromise the general condition and locomotion of affected individuals. Several paternal half-sibs with a low birth weight and a small size were born in 2013 in the Fleckvieh cattle population.

Results

Affected calves were strikingly underweight at birth in spite of a normal gestation length and had craniofacial abnormalities such as elongated narrow heads and brachygnathia inferior. In spite of a normal general condition, their growth remained restricted during rearing. We genotyped 27 affected and 10,454 unaffected animals at 44,672 single nucleotide polymorphisms and performed association tests followed by homozygosity mapping, which allowed us to map the locus responsible for growth failure to a 1.85-Mb segment on bovine chromosome 3. Analysis of whole-genome re-sequencing data from one affected and 289 unaffected animals revealed a 1-bp deletion (g.15079217delC, rs723240647) in the coding region of the GON4L gene that segregated with the dwarfism-associated haplotype. We showed that the deletion induces intron retention and premature termination of translation, which can lead to a severely truncated protein that lacks domains that are likely essential to normal protein function. The widespread use of an undetected carrier bull for artificial insemination has resulted in a tenfold increase in the frequency of the deleterious allele in the female population.

Conclusions

A frameshift mutation in GON4L is associated with autosomal recessive proportionate dwarfism in Fleckvieh cattle. The mutation has segregated in the population for more than 50 years without being recognized as a genetic disorder. However, the widespread use of an undetected carrier bull for artificial insemination caused a sudden accumulation of homozygous calves with dwarfism. Our findings provide the basis for genome-based mating strategies to avoid the inadvertent mating of carrier animals and thereby prevent the birth of homozygous calves with impaired growth.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0207-z) contains supplementary material, which is available to authorized users.