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Pollott GE, Piercy RJ, Massey C, Salavati M, Cheng Z, Wathes DC. Locating a novel autosomal recessive genetic variant in the cattle glucokinase gene using only WGS data from three cases and six carriers. Front Genet 2022; 13:755693. [PMID: 36105082 PMCID: PMC9465091 DOI: 10.3389/fgene.2022.755693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
New Mendelian genetic conditions, which adversely affect livestock, arise all the time. To manage them effectively, some methods need to be devised that are quick and accurate. Until recently, finding the causal genomic site of a new autosomal recessive genetic disease has required a two-stage approach using single-nucleotide polymorphism (SNP) chip genotyping to locate the region containing the new variant. This region is then explored using fine-mapping methods to locate the actual site of the new variant. This study explores bioinformatic methods that can be used to identify the causative variants of recessive genetic disorders with full penetrance with just nine whole genome-sequenced animals to simplify and expedite the process to a one-step procedure. Using whole genome sequencing of only three cases and six carriers, the site of a novel variant causing perinatal mortality in Irish moiled calves was located. Four methods were used to interrogate the variant call format (VCF) data file of these nine animals, they are genotype criteria (GCR), autozygosity-by-difference (ABD), variant prediction scoring, and registered SNP information. From more than nine million variants in the VCF file, only one site was identified by all four methods (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF_002263795.1)). This site was a splice acceptor variant located in the glucokinase gene (GCK). It was verified on an independent sample of animals from the breed using genotyping by polymerase chain reaction at the candidate site and autozygosity-by-difference using SNP-chips. Both methods confirmed the candidate site. Investigation of the GCR method found that sites meeting the GCR were not evenly spread across the genome but concentrated in regions of long runs of homozygosity. Locating GCR sites was best performed using two carriers to every case, and the carriers should be distantly related to the cases, within the breed concerned. Fewer than 20 animals need to be sequenced when using the GCR and ABD methods together. The genomic site of novel autosomal recessive Mendelian genetic diseases can be located using fewer than 20 animals combined with two bioinformatic methods, autozygosity-by-difference, and genotype criteria. In many instances it may also be confirmed with variant prediction scoring. This should speed-up and simplify the management of new genetic diseases to a single-step process.
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Affiliation(s)
- Geoffrey E. Pollott
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
- *Correspondence: Geoffrey E. Pollott,
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Sciences and Services, Royal Veterinary College, London, United Kingdom
| | - Claire Massey
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Sciences and Services, Royal Veterinary College, London, United Kingdom
| | - Mazdak Salavati
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
- The Roslin Institute, Midlothian, United Kingdom
| | - Zhangrui Cheng
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - D. Claire Wathes
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
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Al-Khudhair A, Null DJ, Cole JB, Wolfe CW, Steffen DJ, VanRaden PM. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle. J Dairy Sci 2021; 105:1338-1345. [PMID: 34955244 DOI: 10.3168/jds.2021-20600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
A new undesirable genetic factor, neuropathy with splayed forelimbs (JNS), has been identified recently in the Jersey breed. Calves affected with JNS are unable to stand on splayed forelimbs that exhibit significant extensor rigidity and excessive lateral abduction at birth. Affected calves generally are alert at birth but exhibit neurologic symptoms, including spasticity of head and neck and convulsive behavior. Other symptoms reported include dislocated shoulders, congenital craniofacial anomalies, and degenerative myelopathy. Inheritance of an undesirable genetic factor was determined from a study of 16 affected calves reported by Jersey breeders across the United States. All of their pedigrees traced back on both paternal and maternal sides to a common ancestor born in 1995. Genotypes revealed that JNS is attributable to a specific haplotype on Bos taurus autosome 6. Currently 8.2% of the genotyped US Jersey population are carriers of the haplotype. Sequencing of the region of shared homozygosity revealed missense variant rs1116058914 at base 60,158,901 of the ARS-UCD1.2 reference map as the most concordant with the genetic condition and the most likely cause. The single-base G to A substitution is in the coding region of the last exon of UCHL1, which is conserved across species. Mutations in humans and gene knockouts in mice cause similar recessive symptoms and muscular degeneration. Since December 2020, carrier status has been tracked using the identified haplotype and reported for all 459,784 genotyped Jersey animals. With random mating, about 2,200 affected calves per year with losses of about $250,000 would result from the 1.3 million US Jersey cows in the national population. Selection and mating programs can reduce numbers of JNS-affected births using either the haplotype status or a direct gene test in the future. Breeders should report calf abnormalities to their breed association to help discover new defects such as JNS.
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Affiliation(s)
- A Al-Khudhair
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - D J Null
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - J B Cole
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - C W Wolfe
- American Jersey Cattle Association, Reynoldsburg, OH 43068-2362
| | - D J Steffen
- School of Veterinary and Biomedical Sciences, University of Nebraska, Lincoln 68583-0905
| | - P M VanRaden
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350.
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Nosková A, Hiltpold M, Janett F, Echtermann T, Fang ZH, Sidler X, Selige C, Hofer A, Neuenschwander S, Pausch H. Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing. Genetics 2021; 217:6041611. [PMID: 33724408 DOI: 10.1093/genetics/iyaa033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Maya Hiltpold
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Fredi Janett
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Echtermann
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Xaver Sidler
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Stefan Neuenschwander
- Animal Genetics, Institute of Agricultural Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
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Scheper C, Emmerling R, Götz KU, König S. A variance component estimation approach to infer associations between Mendelian polledness and quantitative production and female fertility traits in German Simmental cattle. Genet Sel Evol 2021; 53:60. [PMID: 34261443 PMCID: PMC8278706 DOI: 10.1186/s12711-021-00652-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022] Open
Abstract
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.
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Affiliation(s)
- Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Giessen, Germany
| | - Reiner Emmerling
- Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Prof. Dürrwaechter‑Platz 1, 85586 Poing‑Grub, Germany
| | - Kay-Uwe Götz
- Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Prof. Dürrwaechter‑Platz 1, 85586 Poing‑Grub, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Giessen, Germany
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Nicholas FW. Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics, freely available on the Internet for 25 years. Anim Genet 2020; 52:3-9. [PMID: 33156546 DOI: 10.1111/age.13010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2020] [Indexed: 02/02/2023]
Abstract
For the last 25 years, Online Mendelian Inheritance in Animals (OMIA) has been providing free global access to an ever-increasing record of discoveries made by animal geneticists around the world. To mark this 25-year milestone, this document provides a brief account (including some pre-history) of how OMIA came to be; some timelines of important discoveries and advances in the genetics of the animal species covered by OMIA, gleaned from the OMIA database; and an analysis of the current state of knowledge regarding likely causal variants of single-locus traits in OMIA species, also gleaned from the OMIA database.
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Affiliation(s)
- F W Nicholas
- Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
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6
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Murgiano L, Militerno G, Sbarra F, Drögemüller C, G P Jacinto J, Gentile A, Bolcato M. KDM2B-associated paunch calf syndrome in Marchigiana cattle. J Vet Intern Med 2020; 34:1657-1661. [PMID: 32515858 PMCID: PMC7379006 DOI: 10.1111/jvim.15789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Chianina, Romagnola, and Marchigiana are the 3 most important Italian breeds of cattle raised in the Apennine Mountains. Inherited disorders have been reported in the Chianina and Romagnola breeds but not in the Marchigiana breed. Recently, a case resembling recessively inherited KDM2B-associated paunch calf syndrome (PCS) in Romagnola cattle was identified in Marchigiana cattle. HYPOTHESIS/OBJECTIVES To characterize the features of the observed congenital anomaly, evaluate its possible genetic etiology, and determine the prevalence of the deleterious allele in the Marchigiana population. ANIMALS A single stillborn Marchigiana calf was referred for clinicopathological examination because of the presence of PCS-like morphological lesions. METHODS The animal was necropsied and the calf and its parents were genotyped. A PCR-based direct gene test was applied to determine the KDM2B genotype and 114 Marchigiana bulls were genotyped. RESULTS The pathological phenotype included facial deformities, enlarged fluid-filled abdomen, and hepatic fibrosis. The affected animal was the offspring of consanguineous mating and homozygous presence of the KDM2B missense variant was confirmed. Both parents were heterozygous for KDM2B and the prevalence of carriers in a selected population of Marchigiana bulls was <2%. CONCLUSIONS AND CLINICAL IMPORTANCE The characteristic malformations and genetic findings were consistent with the diagnosis of PCS and provide evidence that the deleterious KDM2B variant initially detected in Romagnola cattle also occurs in the Marchigiana breed.
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Affiliation(s)
- Leonardo Murgiano
- Department of Clinical Sciences & Advanced Medicine , University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gianfranco Militerno
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders, Perugia, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics 2020; 21:27. [PMID: 31914939 PMCID: PMC6950892 DOI: 10.1186/s12864-020-6446-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich, Switzerland.
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Agerholm JS, McEvoy FJ, Heegaard S, Charlier C, Jagannathan V, Drögemüller C. A de novo missense mutation of FGFR2 causes facial dysplasia syndrome in Holstein cattle. BMC Genet 2017; 18:74. [PMID: 28768473 PMCID: PMC5541750 DOI: 10.1186/s12863-017-0541-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/27/2017] [Indexed: 01/17/2023] Open
Abstract
Background Surveillance for bovine genetic diseases in Denmark identified a hitherto unreported congenital syndrome occurring among progeny of a Holstein sire used for artificial breeding. A genetic aetiology due to a dominant inheritance with incomplete penetrance or a mosaic germline mutation was suspected as all recorded cases were progeny of the same sire. Detailed investigations were performed to characterize the syndrome and to reveal its cause. Results Seven malformed calves were submitted examination. All cases shared a common morphology with the most striking lesions being severe facial dysplasia and complete prolapse of the eyes. Consequently the syndrome was named facial dysplasia syndrome (FDS). Furthermore, extensive brain malformations, including microencephaly, hydrocephalus, lobation of the cerebral hemispheres and compression of the brain were present. Subsequent data analysis of progeny of the sire revealed that around 0.5% of his offspring suffered from FDS. High density single nucleotide polymorphism (SNP) genotyping data of the seven cases and their parents were used to map the defect in the bovine genome. Significant genetic linkage was obtained for three regions, including chromosome 26 where whole genome sequencing of a case-parent trio revealed two de novo variants perfectly associated with the disease: an intronic SNP in the DMBT1 gene and a single non-synonymous variant in the FGFR2 gene. This FGFR2 missense variant (c.927G>T) affects a gene encoding a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and across species. It is predicted to change an evolutionary conserved tryptophan into a cysteine residue (p.Trp309Cys). Both variant alleles were proven to result from de novo mutation events in the germline of the sire. Conclusions FDS is a novel genetic disorder of Holstein cattle. Mutations in the human FGFR2 gene are associated with various dominant inherited craniofacial dysostosis syndromes. Given the phenotypic similarities in FDS affected calves, the genetic mapping and absence of further high impact variants in the critical genome regions, it is highly likely that the missense mutation in the FGFR2 gene caused the FDS phenotype in a dominant mode of inheritance. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0541-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jørgen S Agerholm
- Department of Clinical Veterinary Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, 1870, Frederiksberg C, DK, Denmark.
| | - Fintan J McEvoy
- Department of Clinical Veterinary Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, 1870, Frederiksberg C, DK, Denmark
| | - Steffen Heegaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen Ø, DK, Denmark.,Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen Ø, DK, Denmark
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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Heaton MP, Smith TPL, Freking BA, Workman AM, Bennett GL, Carnahan JK, Kalbfleisch TS. Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity. F1000Res 2017; 6:1303. [PMID: 28928950 PMCID: PMC5590088 DOI: 10.12688/f1000research.12216.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/20/2022] Open
Abstract
Background: Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals. Methods: A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams. The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line. The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U.S. sheep. Results: The genomes had a combined average read depth of 16, and an average WGS genotype scoring rate and accuracy exceeding 99%. The utility of this resource was illustrated by characterizing three genes with 14 known coding variants affecting litter size in global sheep populations: growth and differentiation factor 9 (
GDF9), bone morphogenetic protein 15 (
BMP15), and bone morphogenetic protein receptor 1B (
BMPR1B). In the 96 U.S. rams, nine missense variants encoding 11 protein variants were identified. However, only one was previously reported to affect litter size (
GDF9 V371M, Finnsheep). Two missense variants in
BMP15 were identified that had not previously been reported: R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in
BMPR1B: M64I in Katahdin, and T345N in Romanov and Finnsheep breeds. Based on the strict conservation of amino acid residues across placental mammals, the four variants encoded by
BMP15 and
BMPR1B are predicted to interfere with their function. However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in
BMP15 and
BMPR1B with daughters of these rams. Conclusions: Collectively, this report describes a new resource for discovering protein variants
in silico and identifies alleles for further testing of their effects on litter size in U.S. breeds.
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Affiliation(s)
- Michael P Heaton
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Bradley A Freking
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Aspen M Workman
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Gary L Bennett
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Jacky K Carnahan
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
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10
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Denholm L. Genotype disclosure in the genomics era: roles and responsibilities. Aust Vet J 2017; 95:308-316. [PMID: 28677120 DOI: 10.1111/avj.12606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 05/08/2017] [Indexed: 01/26/2023]
Abstract
Disclosure of affected breed without disclosure of major progenitors has been the usual practice in scientific papers reporting recessive heritable disorders of cattle. Before molecular genetics, carrier identity could not be used by breeders to control causal mutations because phenotypically normal heterozygotes among genetically related animals could not be detected other than by test mating. Accurate, low-cost DNA tests fundamentally changed this situation. Genomics can provide relief from the old problem of emerging recessive disorders in cattle breeding, but greater transparency of genotype data between breeders is necessary to fully exploit the opportunities for cost-efficient genetic disease control. Effective control of several recessive disorders has been demonstrated in Angus cattle, based entirely on voluntary DNA testing by breeders but mandatory public disclosure of test results and genotype probabilities for all registered animals. When a DNA test is available, major progenitors (particularly bulls from which semen has been distributed) should be identified and disclosed concurrently with the affected breed. As a minimum, whenever possible the closest common ancestors in the pedigrees of the parents of homozygous mutants should be disclosed after confirmation of carrier status. Progenitor disclosure in scientific publications should occur in cooperation with breed societies, which should have the opportunity to advise breeders and initiate management programs before scientific publication. Unless properly managed, genomic enhancement of animal selection using SNP markers may increase inbreeding, co-ancestry and emergence of recessive disorders. The information systems and genotype disclosure policies of some breed societies will be increasingly challenged, particularly with accelerating mutation discovery using next-generation sequencing.
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Affiliation(s)
- L Denholm
- Principal Policy Analyst, NSW Department of Premier & Cabinet, Orange, New South Wales 2800, Australia
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Shaffer LG, Ramirez CJ, Sundin K, Connell LB, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the ceský fousek. VETERINARY RECORD CASE REPORTS 2017. [DOI: 10.1136/vetreccr-2016-000346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
| | - Laurie B Connell
- Department of Molecular and Biomedical SciencesSchool of Marine SciencesUniversity of MaineOronoMaineUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
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12
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Pausch H, Ammermüller S, Wurmser C, Hamann H, Tetens J, Drögemüller C, Fries R. A nonsense mutation in the COL7A1 gene causes epidermolysis bullosa in Vorderwald cattle. BMC Genet 2016; 17:149. [PMID: 27905875 PMCID: PMC5131490 DOI: 10.1186/s12863-016-0458-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 11/25/2016] [Indexed: 12/27/2022] Open
Abstract
Background The widespread use of individual sires for artificial insemination promotes the propagation of recessive conditions. Inadvertent matings between unnoticed carriers of deleterious alleles may result in the manifestation of fatal phenotypes in their progeny. Breeding consultants and farmers reported on Vorderwald calves with a congenital skin disease. The clinical findings in affected calves were compatible with epidermolysis bullosa. Results Pedigree analysis indicated autosomal recessive inheritance of epidermolysis bullosa in Vorderwald cattle. We genotyped two diseased and 41 healthy animals at 41,436 single nucleotide polymorphisms and performed whole-genome haplotype-based association testing, which allowed us to map the locus responsible for the skin disease to the distal end of bovine chromosome 22 (P = 8.0 × 10−14). The analysis of whole-genome re-sequencing data of one diseased calf, three obligate mutation carriers and 1682 healthy animals from various bovine breeds revealed a nonsense mutation (rs876174537, p.Arg1588X) in the COL7A1 gene that segregates with the disease. The same mutation was previously detected in three calves with dystrophic epidermolysis bullosa from the Rotes Höhenvieh cattle breed. We show that diseased animals from Vorderwald and Rotes Höhenvieh cattle are identical by descent for an 8.72 Mb haplotype encompassing rs876174537 indicating they inherited the deleterious allele from a recent common ancestor. Conclusions Autosomal recessive epidermolysis bullosa in Vorderwald and Rotes Höhenvieh cattle is caused by a nonsense mutation in the COL7A1 gene. Our findings demonstrate that deleterious alleles may segregate across cattle populations without apparent admixture. The identification of the causal mutation now enables the reliable detection of carrier animals. Genome-based mating strategies can avoid inadvertent matings of carrier animals thereby preventing the birth of homozygous calves that suffer from a painful skin disease. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0458-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hubert Pausch
- Chair of Animal Breeding, Technical University of Munich, Freising, 85354, Germany. .,Present address: Biosciences Research, Agriculture Victoria, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, 3083, Australia.
| | - Simon Ammermüller
- Chair of Animal Breeding, Technical University of Munich, Freising, 85354, Germany
| | - Christine Wurmser
- Chair of Animal Breeding, Technical University of Munich, Freising, 85354, Germany
| | - Henning Hamann
- Federal Bureau for Geo Information and Rural Development of Baden-Württemberg, Kornwestheim, 70806, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Kiel, 24098, Germany
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - Ruedi Fries
- Chair of Animal Breeding, Technical University of Munich, Freising, 85354, Germany
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13
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Heaton MP, Smith TPL, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Res 2016; 5:2003. [PMID: 27746904 PMCID: PMC5040160 DOI: 10.12688/f1000research.9254.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 01/08/2023] Open
Abstract
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants
in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene (
EPAS1), a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by
EPAS1 (E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The six
EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of
EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates
in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.
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Affiliation(s)
| | | | | | | | | | | | - Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, USA
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14
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Heaton MP, Smith TP, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Res 2016; 5:2003. [PMID: 27746904 PMCID: PMC5040160 DOI: 10.12688/f1000research.9254.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 08/24/2023] Open
Abstract
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by EPAS1 (E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The six EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.
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Affiliation(s)
| | | | | | | | | | | | - Theodore S. Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, USA
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15
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Agerholm JS, Menzi F, McEvoy FJ, Jagannathan V, Drögemüller C. Lethal chondrodysplasia in a family of Holstein cattle is associated with a de novo splice site variant of COL2A1. BMC Vet Res 2016; 12:100. [PMID: 27296271 PMCID: PMC4906884 DOI: 10.1186/s12917-016-0739-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/07/2016] [Indexed: 12/29/2022] Open
Abstract
Background Lethal chondrodysplasia (bulldog syndrome) is a well-known congenital syndrome in cattle and occurs sporadically in many breeds. In 2015, it was noticed that about 12 % of the offspring of the phenotypically normal Danish Holstein sire VH Cadiz Captivo showed chondrodysplasia resembling previously reported bulldog calves. Pedigree analysis of affected calves did not display obvious inbreeding to a common ancestor, suggesting the causative allele was not a rare recessive. The normal phenotype of the sire suggested a dominant inheritance with incomplete penetrance or a mosaic mutation. Results Three malformed calves were examined by necropsy, histopathology, radiology, and computed tomography scanning. These calves were morphologically similar and displayed severe disproportionate dwarfism and reduced body weight. The syndrome was characterized by shortening and compression of the body due to reduced length of the spine and the long bones of the limbs. The vicerocranium had severe dysplasia and palatoschisis. The bones had small irregular diaphyses and enlarged epiphyses consisting only of chondroid tissue. The sire and a total of four affected half-sib offspring and their dams were genotyped with the BovineHD SNP array to map the defect in the genome. Significant genetic linkage was obtained for several regions of the bovine genome including chromosome 5 where whole genome sequencing of an affected calf revealed a COL2A1 point mutation (g.32473300 G > A). This private sequence variant was predicted to affect splicing as it altered the conserved splice donor sequence GT at the 5’-end of COL2A1 intron 36, which was changed to AT. All five available cases carried the mutant allele in heterozygous state and all five dams were homozygous wild type. The sire VH Cadiz Captivo was shown to be a gonadal and somatic mosaic as assessed by the presence of the mutant allele at levels of about 5 % in peripheral blood and 15 % in semen. Conclusions The phenotypic and genetic findings are comparable to a previously reported COL2A1 missense mutation underlying lethal chondrodysplasia in the offspring of a mosaic French Holstein sire (Igale Masc). The identified independent spontaneous splice site variant in COL2A1 most likely caused chondrodysplasia and must have occurred during the early foetal development of the sire. This study provides a first example of a dominant COL2A1 splice site variant as candidate causal mutation of a severe lethal chondrodysplasia phenotype. Germline mosaicism is a relatively frequent mechanism in the origin of genetic disorders and explains the prevalence of a certain fraction of affected offspring. Paternal dominant de novo mutations are a risk in cattle breeding, especially because the ratio of defective offspring may be very high and be associated with significant animal welfare problems. Electronic supplementary material The online version of this article (doi:10.1186/s12917-016-0739-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jørgen S Agerholm
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 68, Frederiksberg C, DK-1870, Denmark.
| | - Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, CH-3001, Switzerland
| | - Fintan J McEvoy
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, Frederiksberg C, DK-1870, Denmark
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, CH-3001, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, CH-3001, Switzerland
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16
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Yudin NS, Lukyanov KI, Voevoda MI, Kolchanov NA. Application of reproductive technologies to improve dairy cattle genomic selection. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s207905971603014x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Frischknecht M, Signer-Hasler H, Leeb T, Rieder S, Neuditschko M. Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed. Anim Genet 2016; 47:227-9. [DOI: 10.1111/age.12406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 12/01/2022]
Affiliation(s)
- M. Frischknecht
- Agroscope; Swiss National Stud Farm; Les Longs-Prés 1580 Avenches Switzerland
- Institute of Genetics; Vetsuisse Faculty; University of Bern; Bremgartenstrasse 109a 3012 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; Bremgartenstrasse 109a 3001 Bern Switzerland
| | - H. Signer-Hasler
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; Bremgartenstrasse 109a 3001 Bern Switzerland
- Bern University of Applied Sciences; School of Agricultural; Forest and Food Sciences; Länggasse 85 3052 Zollikofen Switzerland
| | - T. Leeb
- Agroscope; Swiss National Stud Farm; Les Longs-Prés 1580 Avenches Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; Bremgartenstrasse 109a 3001 Bern Switzerland
| | - S. Rieder
- Institute of Genetics; Vetsuisse Faculty; University of Bern; Bremgartenstrasse 109a 3012 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; Bremgartenstrasse 109a 3001 Bern Switzerland
| | - M. Neuditschko
- Institute of Genetics; Vetsuisse Faculty; University of Bern; Bremgartenstrasse 109a 3012 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; Bremgartenstrasse 109a 3001 Bern Switzerland
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18
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Affiliation(s)
- Kathrin F. Stock
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schroeder-Weg 1, 27283 Verden, Germany
| | - Lina Jönsson
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
- Danish Warmblood Association, Vilhelmsborg Alle 1, 8320 Mårslet, Denmark
| | - Anne Ricard
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative, 78352 Jouy-en-Josas, France
- IFCE, Recherche et Innovation, 61310 Exmes, France
| | - Thomas Mark
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
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19
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Cole JB. A simple strategy for managing many recessive disorders in a dairy cattle breeding program. Genet Sel Evol 2015; 47:94. [PMID: 26620491 PMCID: PMC4666089 DOI: 10.1186/s12711-015-0174-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/23/2015] [Indexed: 11/26/2022] Open
Abstract
Background High-density single nucleotide polymorphism genotypes have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle, as well as to track other conditions such as red coat color and polled. Most current methods for mate allocation fail to consider this information, and it will become increasingly difficult to manage matings as the number of recessive mutations to be accounted for increases. Methods A modified version of a mating strategy that constrains inbreeding based on genomics (the Pryce method) was developed that also accounts for the economic effects of Mendelian disorders on overall economic merit (modified Pryce method) and compared with random mating, truncation selection, and the Pryce scheme. Several scenarios were considered, including scenarios with six hypothetical recessive alleles and 12 recessive alleles that are currently segregating in the US Holstein population. Results The Pryce method and the modified Pryce method showed similar ability to reduce frequencies of recessive alleles, particularly for loci with frequencies greater than 0.30. The modified Pryce method outperformed the Pryce method for low-frequency alleles with small economic value. Cumulative genetic gain for the selection objective was slightly greater when using the Pryce method, but rates of inbreeding were similar across methods. Conclusions The proposed method reduces allele frequencies faster than other methods, and also can be used to maintain or increase the frequency of desirable recessives. It can be easily implemented in software for mate allocation, and the code used in this study is freely available as a reference implementation.
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Affiliation(s)
- John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
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20
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Segelke D, Täubert H, Reinhardt F, Thaller G. Considering genetic characteristics in German Holstein breeding programs. J Dairy Sci 2015; 99:458-67. [PMID: 26601581 DOI: 10.3168/jds.2015-9764] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/27/2015] [Indexed: 11/19/2022]
Abstract
Recently, several research groups have demonstrated that several haplotypes may cause embryonic loss in the homozygous state. Up to now, carriers of genetic disorders were often excluded from mating, resulting in a decrease of genetic gain and a reduced number of sires available for the breeding program. Ongoing research is very likely to identify additional genetic defects causing embryonic loss and calf mortality by genotyping a large proportion of the female cattle population and sequencing key ancestors. Hence, a clear demand is present to develop a method combining selection against recessive defects (e.g., Holstein haplotypes HH1-HH5) with selection for economically beneficial traits (e.g., polled) for mating decisions. Our proposed method is a genetic index that accounts for the allele frequencies in the population and the economic value of the genetic characteristic without excluding carriers from breeding schemes. Fertility phenotypes from routine genetic evaluations were used to determine the economic value per embryo lost. Previous research has shown that embryo loss caused by HH1 and HH2 occurs later than the loss for HH3, HH4, and HH5. Therefore, an economic value of € 97 was used against HH1 and HH2 and € 70 against HH3, HH4, and HH5. For polled, € 7 per polled calf was considered. Minor allele frequencies of the defects ranged between 0.8 and 3.3%. The polled allele has a frequency of 4.1% in the German Holstein population. A genomic breeding program was simulated to study the effect of changing the selection criteria from assortative mating based on breeding values to selecting the females using the genetic index. Selection for a genetic index on the female path is a useful method to control the allele frequencies by reducing undesirable alleles and simultaneously increasing economical beneficial characteristics maintaining most of the genetic gain in production and functional traits. Additionally, we applied the genetic index to real data and found a decrease of the genetic trend for the birth years 1990 to 2006. Since 2010 the genetic index has increased due to a strong increase in the polled frequency. However, further investigation is needed to better understand the biology to determine the correct time of embryo loss and the economic value of fertility disorders.
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Affiliation(s)
- D Segelke
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heideweg 1, 27283 Verden, Germany.
| | - H Täubert
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heideweg 1, 27283 Verden, Germany
| | - F Reinhardt
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heideweg 1, 27283 Verden, Germany
| | - G Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098 Kiel, Germany
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21
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Abstract
A novel canine muscular dystrophy in Landseer dogs was observed. We had access to five affected dogs from two litters. The clinical signs started at a few weeks of age, and the severe progressive muscle weakness led to euthanasia between 5 and 15 months of age. The pedigrees of the affected dogs suggested a monogenic autosomal-recessive inheritance of the trait. Linkage and homozygosity mapping indicated two potential genome segments for the causative variant on chromosomes 10 and 31 harboring a total of 4.8 Mb of DNA or 0.2% of the canine genome. Using the Illumina sequencing technology, we obtained a whole-genome sequence from one affected Landseer. Variants were called with respect to the dog reference genome and compared with the genetic variants of 170 control dogs from other breeds. The affected Landseer dog was homozygous for a single, private nonsynonymous variant in the critical intervals, a nonsense variant in the COL6A1 gene (Chr31:39,303,964G>T; COL6A1:c.289G>T; p.E97*). Genotypes at this variant showed perfect concordance with the muscular dystrophy phenotype in all five cases and more than 1000 control dogs. Variants in the human COL6A1 gene cause Bethlem myopathy or Ullrich congenital muscular dystrophy. We therefore conclude that the identified canine COL6A1 variant is most likely causative for the observed muscular dystrophy in Landseer dogs. On the basis of the nature of the genetic variant in Landseer dogs and their severe clinical phenotype these dogs represent a model for human Ullrich congenital muscular dystrophy.
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22
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Nicholas FW, Mäki-Tanila A. An important anniversary: 150 years since Mendel's laws of inheritance made their first public appearance. J Anim Breed Genet 2015; 132:277-80. [PMID: 26138341 DOI: 10.1111/jbg.12175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Shaffer LG, Ramirez CJ, Sundin K, Carl C, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the Drentsche patrijshond. VETERINARY RECORD CASE REPORTS 2015. [DOI: 10.1136/vetreccr-2015-000185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWA99164USA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Casey Carl
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
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24
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Sartelet A, Li W, Pailhoux E, Richard C, Tamma N, Karim L, Fasquelle C, Druet T, Coppieters W, Georges M, Charlier C. Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genomics 2015; 16:316. [PMID: 25895751 PMCID: PMC4404575 DOI: 10.1186/s12864-015-1528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of genome-wide association studies combined with next generation DNA sequencing, provided that the causative mutations are conventional loss-of-function variants. We show in this work how the combined use of next generation DNA and RNA sequencing allows for the rapid identification of otherwise difficult to identify splice-site variants. RESULTS We report the use of haplotype-based association mapping to identify a locus on bovine chromosome 10 that underlies autosomal recessive arthrogryposis in Belgian Blue Cattle. We identify 31 candidate mutations by resequencing the genome of four cases and 15 controls at ~10-fold depth. By analyzing RNA-Seq data from a carrier fetus, we observe skipping of the second exon of the PIGH gene, which we confirm by RT-PCR to be fully penetrant in tissues from affected calves. We identify - amongst the 31 candidate variants - a C-to-G transversion in the first intron of the PIGH gene (c211-10C > G) that is predicted to affect its acceptor splice-site. The resulting PIGH protein is likely to be non-functional as it lacks essential domains, and hence to cause arthrogryposis. CONCLUSIONS This work illustrates how the growing arsenal of genome exploration tools continues to accelerate the identification of an even broader range of disease causing mutations, therefore improving the management and control of genetic defects in livestock.
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Affiliation(s)
- Arnaud Sartelet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wanbo Li
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Eric Pailhoux
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Christophe Richard
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Nico Tamma
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Latifa Karim
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Corinne Fasquelle
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Tom Druet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wouter Coppieters
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Michel Georges
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Carole Charlier
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
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Pausch H, Wurmser C, Reinhardt F, Emmerling R, Fries R. Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation. J Dairy Sci 2015; 98:4162-7. [PMID: 25892690 DOI: 10.3168/jds.2015-9402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/13/2015] [Indexed: 12/15/2022]
Abstract
Most association studies for pinpointing trait-associated variants are performed within breed. The availability of sequence data from key ancestors of several cattle breeds now enables immediate assessment of the frequency of trait-associated variants in populations different from the mapping population and their imputation into large validation populations. The objective of this study was to validate the effects of 4 putatively causative variants on milk production traits, male fertility, and stature in German Fleckvieh and Holstein-Friesian animals using targeted sequence imputation. We used whole-genome sequence data of 456 animals to impute 4 missense mutations in DGAT1, GHR, PRLR, and PROP1 into 10,363 Fleckvieh and 8,812 Holstein animals. The accuracy of the imputed genotypes exceeded 95% for all variants. Association testing with imputed variants revealed consistent antagonistic effects of the DGAT1 p.A232K and GHR p.F279Y variants on milk yield and protein and fat contents, respectively, in both breeds. The allele frequency of both polymorphisms has changed considerably in the past 20 yr, indicating that they were targets of recent selection for milk production traits. The PRLR p.S18N variant was associated with yield traits in Fleckvieh but not in Holstein, suggesting that it may be in linkage disequilibrium with a mutation affecting yield traits rather than being causal. The reported effects of the PROP1 p.H173R variant on milk production, male fertility, and stature could not be confirmed. Our results demonstrate that population-wide imputation of candidate causal variants from sequence data is feasible, enabling their rapid validation in large independent populations.
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Affiliation(s)
- Hubert Pausch
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany.
| | - Christine Wurmser
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
| | - Friedrich Reinhardt
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283 Verden, Germany
| | - Reiner Emmerling
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, 85586 Poing, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
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Peters M, Reber I, Jagannathan V, Raddatz B, Wohlsein P, Drögemüller C. DNA-based diagnosis of rare diseases in veterinary medicine: a 4.4 kb deletion of ITGB4 is associated with epidermolysis bullosa in Charolais cattle. BMC Vet Res 2015; 11:48. [PMID: 25890340 PMCID: PMC4351973 DOI: 10.1186/s12917-015-0366-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/23/2015] [Indexed: 11/16/2022] Open
Abstract
Background Rare diseases in livestock animals are traditionally poorly diagnosed. Other than clinical description and pathological examination, the underlying causes have, for the most part, remained unknown. A single case of congenital skin fragility in cattle was observed, necropsy, histological and ultrastructural examinations were carried out and whole genome sequencing was utilized to identify the causative mutation. Results A single purebred female Charolais calf with severe skin lesions was delivered full-term and died spontaneously after birth. The clinical and pathological findings exactly matched the gross description given by previous reports on epitheliogenesis imperfecta and epidermolysis bullosa (EB) in cattle. Histological and ultrastructural changes were consistent with EB junctionalis (EBJ). Genetic analysis revealed a previously unpublished ITGB4 loss-of-function mutation; the affected calf was homozygous for a 4.4 kb deletion involving exons 17 to 22, and the dam carried a single copy of the deletion indicating recessive inheritance. The homozygous mutant genotype did not occur in healthy controls of various breeds but some heterozygous carriers were found among Charolais cattle belonging to the affected herd. The mutant allele was absent in a representative sample of unrelated sires of the German Charolais population. Conclusion This is the first time in which a recessively inherited ITGB4 associated EBJ has been reported in cattle. The identification of heterozygous carriers is of importance in avoiding the transmission of this defect in future. Current DNA sequencing methods offer a powerful tool for understanding the genetic background of rare diseases in domestic animals having a reference genome sequence available. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0366-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Zur Taubeneiche 10-12, 59821, Arnsberg, Germany.
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | - Barbara Raddatz
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
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Frischknecht M, Neuditschko M, Jagannathan V, Drögemüller C, Tetens J, Thaller G, Leeb T, Rieder S. Imputation of sequence level genotypes in the Franches-Montagnes horse breed. Genet Sel Evol 2014; 46:63. [PMID: 25927638 PMCID: PMC4180851 DOI: 10.1186/s12711-014-0063-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 09/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population. Increased densities of typed markers are advantageous for genome-wide association studies (GWAS) and genomic predictions. METHODS We obtained genotypes for 54 602 SNPs (single nucleotide polymorphisms) in 1077 Franches-Montagnes (FM) horses and Illumina paired-end whole-genome sequencing data for 30 FM horses and 14 Warmblood horses. After variant calling, the sequence-derived SNP genotypes (~13 million SNPs) were used for genotype imputation with the software programs Beagle, Impute2 and FImpute. RESULTS The mean imputation accuracy of FM horses using Impute2 was 92.0%. Imputation accuracy using Beagle and FImpute was 74.3% and 77.2%, respectively. In addition, for Impute2 we determined the imputation accuracy of all individual horses in the validation population, which ranged from 85.7% to 99.8%. The subsequent inclusion of Warmblood sequence data further increased the correlation between true and imputed genotypes for most horses, especially for horses with a high level of admixture. The final imputation accuracy of the horses ranged from 91.2% to 99.5%. CONCLUSIONS Using Impute2, the imputation accuracy was higher than 91% for all horses in the validation population, which indicates that direct imputation of 50k SNP-chip data to sequence level genotypes is feasible in the FM population. The individual imputation accuracy depended mainly on the applied software and the level of admixture.
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Affiliation(s)
- Mirjam Frischknecht
- Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. .,Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. .,Graduate School for Cellular and Molecular Biology, University of Bern, 3012, Bern, Switzerland.
| | - Markus Neuditschko
- Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.
| | - Stefan Rieder
- Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. .,Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.
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Khatkar M, Randhawa I, Raadsma H. Meta-assembly of genomic regions and variants associated with female reproductive efficiency in cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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