51
|
Raszek MM, Guan LL, Plastow GS. Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases. Front Genet 2016; 7:30. [PMID: 27014337 PMCID: PMC4780072 DOI: 10.3389/fgene.2016.00030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/18/2016] [Indexed: 12/15/2022] Open
Abstract
Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.
Collapse
Affiliation(s)
- Mikolaj M Raszek
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Le L Guan
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| |
Collapse
|
52
|
Ortega MS, Denicol AC, Cole JB, Null DJ, Hansen PJ. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows. Anim Genet 2016; 47:288-97. [DOI: 10.1111/age.12420] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Affiliation(s)
- M. S. Ortega
- Department of Animal Sciences; D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute; University of Florida; Gainesville FL USA
| | - A. C. Denicol
- Department of Animal Sciences; D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute; University of Florida; Gainesville FL USA
| | - J. B. Cole
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; United States Department of Agriculture; Beltsville MD USA
| | - D. J. Null
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; United States Department of Agriculture; Beltsville MD USA
| | - P. J. Hansen
- Department of Animal Sciences; D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute; University of Florida; Gainesville FL USA
| |
Collapse
|
53
|
Attia S, Katila T, Andersson M. The Effect of Sperm Morphology and Sire Fertility on Calving Rate of Finnish Ayrshire AI Bulls. Reprod Domest Anim 2015; 51:54-8. [PMID: 26660630 DOI: 10.1111/rda.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/31/2015] [Indexed: 11/27/2022]
Abstract
Good-quality semen is a prerequisite for successful and profitable artificial insemination (AI) of modern dairy cattle. Fertility of the bulls is evaluated with andrological examinations and semen analyses, such as morphology. However, little attention has been paid to the inheritance of bull fertility. In this study, we correlated sperm morphology, birth year and station of 695 AI bulls with calving rate (CR). Sperm morphology was clearly associated with CR underlining the usefulness of morphological examination in the assessment of fertility. The correlation between the proportion of normal spermatozoa and CR was significant (p < 0.001). No significant differences were detected between stations or birth years. We also compared the CR of 695 AI bulls with the CR of their 27 sires to study the inheritance of fertility. Sire's CR did not correlate with the CR of the sons (p = 0.218). This result indicates that at least when sires of acceptable CR are used to produce sons for use in AI the inheritance of CR is not significantly correlated.
Collapse
Affiliation(s)
- S Attia
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - T Katila
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - M Andersson
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| |
Collapse
|
54
|
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.
Collapse
Affiliation(s)
- John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| |
Collapse
|
55
|
Williams JL, Hall SJ, Del Corvo M, Ballingall KT, Colli L, Ajmone Marsan P, Biscarini F. Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity. Anim Genet 2015; 47:19-27. [DOI: 10.1111/age.12376] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Williams
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - S. J.G. Hall
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - M. Del Corvo
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - K. T. Ballingall
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik Midlothian EH26 0PZ UK
| | - L. Colli
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - P. Ajmone Marsan
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - F. Biscarini
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| |
Collapse
|
56
|
Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D. Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds. PLoS One 2015; 10:e0135931. [PMID: 26317361 PMCID: PMC4552564 DOI: 10.1371/journal.pone.0135931] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022] Open
Abstract
High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
Collapse
Affiliation(s)
- Mekki Boussaha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- * E-mail:
| | - Diane Esquerré
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Johanna Barbieri
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anis Djari
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Rabia Letaief
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Gérald Salin
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Frédéric Escudié
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Roulet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Sébastien Fritz
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- Union Nationale des Coopératives Agricoles d’Elevage et d’Insémination Animale, Paris, France
| | - Franck Samson
- INRA, UR1077, Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Maria Bernard
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Didier Boichard
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Dominique Rocha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| |
Collapse
|
57
|
Capitan A, Michot P, Baur A, Saintilan R, Hozé C, Valour D, Guillaume F, Boichon D, Barbat A, Boichard D, Schibler L, Fritz S. Genetic tools to improve reproduction traits in dairy cattle. Reprod Fertil Dev 2015; 27:14-21. [PMID: 25472040 DOI: 10.1071/rd14379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fertility is a major concern in the dairy cattle industry and has been the subject of numerous studies over the past 20 years. Surprisingly, most of these studies focused on rough female phenotypes and, despite their important role in reproductive success, male- and embryo-related traits have been poorly investigated. In recent years, the rapid and important evolution of technologies in genetic research has led to the development of genomic selection. The generalisation of this method in combination with the achievements of the AI industry have led to the constitution of large databases of genotyping and sequencing data, as well as refined phenotypes and pedigree records. These resources offer unprecedented opportunities in terms of fundamental and applied research. Here we present five such examples with a focus on reproduction-related traits: (1) detection of quantitative trait loci (QTL) for male fertility and semen quality traits; (2) detection of QTL for refined phenotypes associated with female fertility; (3) identification of recessive embryonic lethal mutations by depletion of homozygous haplotypes; (4) identification of recessive embryonic lethal mutations by mining whole-genome sequencing data; and (5) the contribution of high-density single nucleotide polymorphism chips, whole-genome sequencing and imputation to increasing the power of QTL detection methods and to the identification of causal variants.
Collapse
Affiliation(s)
- A Capitan
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - P Michot
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - A Baur
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - R Saintilan
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - C Hozé
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - D Valour
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - F Guillaume
- EVOLUTION, 69 rue de la Motte Brûlon, 35706 Rennes, France
| | - D Boichon
- MIDATEST, Les Nauzes, 81580 Soual, France
| | - A Barbat
- INRA (Institut National de la Recherche Agronomique), UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - D Boichard
- INRA (Institut National de la Recherche Agronomique), UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - L Schibler
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - S Fritz
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| |
Collapse
|
58
|
Zhang Y, Guo G, Huang H, Lu L, Wang L, Fang L, Liu L, Wang Y, Zhang S. Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay. J Vet Diagn Invest 2015; 27:596-9. [DOI: 10.1177/1040638715589362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene.
Collapse
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Gang Guo
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Hetian Huang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Lu Lu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Lijie Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Lingzhao Fang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Lin Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, China Agricultural University, Beijing, China (Y Zhang, Huang, Lu, L Wang, Fang, Y Wang, S Zhang)
- Beijing Shounong Xumu Fazhan Co Ltd., Beijing, China (Guo, Liu)
| |
Collapse
|
59
|
Kim ES, Sonstegard TS, Van Tassell CP, Wiggans G, Rothschild MF. The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection. PLoS One 2015; 10:e0129967. [PMID: 26154171 PMCID: PMC4496098 DOI: 10.1371/journal.pone.0129967] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 05/14/2015] [Indexed: 11/19/2022] Open
Abstract
Inbreeding is often an inevitable outcome of strong directional artificial selection but on average it reduces population fitness with increased frequency of recessive deleterious alleles. Runs of homozygosity (ROH) representing genomic autozygosity that occur from mating between selected and genomically related individuals may be able to reveal the regions affecting fitness. To examine the influence of genomic autozygosity on fitness, we used a genome-wide association test to evaluate potential negative correlations between ROH and daughter pregnancy rate (DPR) or somatic cell score (SCS) in US Jersey cattle. In addition, relationships between changes of local ROH and inbreeding coefficients (F) were assessed to locate genomic regions with increased inbreeding. Despite finding some decreases in fertility associated with incremental increases in F, most emerging local ROH were not significantly associated with DPR or SCS. Furthermore, the analyses of ROH could be approximated with the most frequent haplotype(s), including the associations of ROH and F or traits. The analysis of the most frequent haplotype revealed that associations of ROH and fertility could be accounted for by the additive genetic effect on the trait. Thus, we suggest that a change of autozygosity is more likely to demonstrate footprints of selected haplotypes for production rather than highlight the possible increased local autozygosity of a recessive detrimental allele resulting from the mating between closely related animals in Jersey cattle.
Collapse
Affiliation(s)
- Eui-Soo Kim
- Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Tad S. Sonstegard
- Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Curtis P. Van Tassell
- Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - George Wiggans
- Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|
60
|
Mészáros G, Boison SA, Pérez O'Brien AM, Ferenčaković M, Curik I, Da Silva MVB, Utsunomiya YT, Garcia JF, Sölkner J. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle. Front Genet 2015; 6:173. [PMID: 26074948 PMCID: PMC4443735 DOI: 10.3389/fgene.2015.00173] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/20/2015] [Indexed: 11/30/2022] Open
Abstract
Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.
Collapse
Affiliation(s)
- Gábor Mészáros
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Solomon A Boison
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | | | - Ino Curik
- Department of Animal Science, University of Zagreb Zagreb, Croatia
| | | | | | - Jose F Garcia
- UNESP-Universidade Estadual Paulista Jaboticabal, Brazil
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| |
Collapse
|
61
|
Pausch H, Schwarzenbacher H, Burgstaller J, Flisikowski K, Wurmser C, Jansen S, Jung S, Schnieke A, Wittek T, Fries R. Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle. BMC Genomics 2015; 16:312. [PMID: 25927203 PMCID: PMC4403906 DOI: 10.1186/s12864-015-1483-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/24/2015] [Indexed: 12/20/2022] Open
Abstract
Background Cattle breeding populations are susceptible to the propagation of recessive diseases. Individual sires generate tens of thousands of progeny via artificial insemination. The frequency of deleterious alleles carried by such sires may increase considerably within few generations. Deleterious alleles manifest themselves often by missing homozygosity resulting from embryonic/fetal, perinatal or juvenile lethality of homozygotes. Results A scan for homozygous haplotype deficiency in 25,544 Fleckvieh cattle uncovered four haplotypes affecting reproductive and rearing success. Exploiting whole-genome resequencing data from 263 animals facilitated to pinpoint putatively causal mutations in two of these haplotypes. A mutation causing an evolutionarily unlikely substitution in SUGT1 was perfectly associated with a haplotype compromising insemination success. The mutation was not found in homozygous state in 10,363 animals (P = 1.79 × 10−5) and is thus likely to cause lethality of homozygous embryos. A frameshift mutation in SLC2A2 encoding glucose transporter 2 (GLUT2) compromises calf survival. The mutation leads to premature termination of translation and activates cryptic splice sites resulting in multiple exon variants also with premature translation termination. The affected calves exhibit stunted growth, resembling the phenotypic appearance of Fanconi-Bickel syndrome in humans (OMIM 227810), which is also caused by mutations in SLC2A2. Conclusions Exploiting comprehensive genotype and sequence data enabled us to reveal two deleterious alleles in SLC2A2 and SUGT1 that compromise pre- and postnatal survival in homozygous state. Our results provide the basis for genome-assisted approaches to avoiding inadvertent carrier matings and to improving reproductive and rearing success in Fleckvieh cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1483-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hubert Pausch
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | | | - Johann Burgstaller
- Clinic for Ruminants, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
| | - Krzysztof Flisikowski
- Lehrstuhl fuer Biotechnologie der Nutztiere, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Christine Wurmser
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Sandra Jansen
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Simone Jung
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Angelika Schnieke
- Lehrstuhl fuer Biotechnologie der Nutztiere, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Thomas Wittek
- Clinic for Ruminants, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| |
Collapse
|
62
|
Biffani S, Dimauro C, Macciotta N, Rossoni A, Stella A, Biscarini F. Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis. Genet Sel Evol 2015; 47:4. [PMID: 25651874 PMCID: PMC4318450 DOI: 10.1186/s12711-015-0094-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
Background SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we present a procedure combining variable selection (i.e. the selection of predictive SNPs) and linear discriminant analysis for the identification of carriers of a haplotype on BTA19 (Bos taurus autosome 19) known to be associated with reduced cow fertility. A population of 3645 Brown Swiss cows and bulls genotyped with the 54K SNP-chip was available for the analysis. Results The overall error rate for the prediction of haplotype carriers was on average very low (∼≤1%). The error rate was found to depend on the number of SNPs in the model and their density around the region of the haplotype on BTA19. The minimum set of SNPs to still achieve accurate predictions was 5, with a total test error rate of 1.59. Conclusions The paper describes a procedure to accurately identify haplotype carriers from SNP genotypes in cattle populations. Very few misclassifications were observed, which indicates that this is a very reliable approach for potential applications in cattle breeding.
Collapse
Affiliation(s)
| | | | | | | | | | - Filippo Biscarini
- Department of Bioinformatics, PTP, Via Einstein - Loc, Cascina Codazza, Lodi 26900, Italy.
| |
Collapse
|
63
|
Egger-Danner C, Cole JB, Pryce JE, Gengler N, Heringstad B, Bradley A, Stock KF. Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits. Animal 2015; 9:191-207. [PMID: 25387784 PMCID: PMC4299537 DOI: 10.1017/s1751731114002614] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 09/11/2014] [Indexed: 12/26/2022] Open
Abstract
For several decades, breeding goals in dairy cattle focussed on increased milk production. However, many functional traits have negative genetic correlations with milk yield, and reductions in genetic merit for health and fitness have been observed. Herd management has been challenged to compensate for these effects and to balance fertility, udder health and metabolic diseases against increased production to maximize profit without compromising welfare. Functional traits, such as direct information on cow health, have also become more important because of growing concern about animal well-being and consumer demands for healthy and natural products. There are major concerns about the impact of drugs used in veterinary medicine on the spread of antibiotic-resistant strains of bacteria that can negatively impact human health. Sustainability and efficiency are also increasingly important because of the growing competition for high-quality, plant-based sources of energy and protein. Disruptions to global environments because of climate change may encourage yet more emphasis on these traits. To be successful, it is vital that there be a balance between the effort required for data recording and subsequent benefits. The motivation of farmers and other stakeholders involved in documentation and recording is essential to ensure good data quality. To keep labour costs reasonable, existing data sources should be used as much as possible. Examples include the use of milk composition data to provide additional information about the metabolic status or energy balance of the animals. Recent advances in the use of mid-infrared spectroscopy to measure milk have shown considerable promise, and may provide cost-effective alternative phenotypes for difficult or expensive-to-measure traits, such as feed efficiency. There are other valuable data sources in countries that have compulsory documentation of veterinary treatments and drug use. Additional sources of data outside of the farm include, for example, slaughter houses (meat composition and quality) and veterinary labs (specific pathogens, viral loads). At the farm level, many data are available from automated and semi-automated milking and management systems. Electronic devices measuring physiological status or activity parameters can be used to predict events such as oestrus, and also behavioural traits. Challenges concerning the predictive biology of indicator traits or standardization need to be solved. To develop effective selection programmes for new traits, the development of large databases is necessary so that high-reliability breeding values can be estimated. For expensive-to-record traits, extensive phenotyping in combination with genotyping of females is a possibility.
Collapse
Affiliation(s)
- C. Egger-Danner
- ZuchtData EDV-Dienstleistungen GmbH, Dresdner Str.
89/19, A-1200 Vienna, Austria
| | - J. B. Cole
- Animal Genomics and Improvement Laboratory,
ARS, USDA, 10300 Baltimore
Avenue, Beltsville, MD 20705-2350,
USA
| | - J. E. Pryce
- Department of Environment and Primary Industries, La
Trobe University, Agribio, 5 Ring
Road, Bundoora, Victoria 3083,
Australia
| | - N. Gengler
- University of Liège, Gembloux Agro-Bio Tech
(GxABT), Animal Science Unit, Passage des
Déportés 2, B-5030 Gembloux, Belgium
| | - B. Heringstad
- Department of Animal and Aquacultural Sciences,
Norwegian University of Life Sciences, PO Box
5003, N-1432 Ås, Norway
| | - A. Bradley
- Quality Milk Management Services Ltd, Cedar
Barn, Easton Hill, Easton,
Wells, Somerset, BA5
1EY, UK
- University of Nottingham, School of Veterinary
Medicine and Science, Sutton Bonington Campus,
Sutton Bonington, Leicestershire,
LE12 5RD, UK
| | - K. F. Stock
- Vereinigte Informationssysteme Tierhaltung w.V. (vit),
Heideweg 1, D-27283 Verden,
Germany
| |
Collapse
|
64
|
Valour D, Michot P, Eozenou C, Lefebvre R, Bonnet A, Capitan A, Uzbekova S, Sellem E, Ponsart C, Schibler L. Dairy cattle reproduction is a tightly regulated genetic process: Highlights on genes, pathways, and biological processes. Anim Front 2015. [DOI: 10.2527/af.2015-0006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- D. Valour
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - P. Michot
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - C. Eozenou
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - R. Lefebvre
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - A. Bonnet
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| | - A. Capitan
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - S. Uzbekova
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352 Jouy en Josas, France
| | - E. Sellem
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - C. Ponsart
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| | - L. Schibler
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| |
Collapse
|
65
|
Ponsart C, Le Bourhis D, Knijn H, Fritz S, Guyader-Joly C, Otter T, Lacaze S, Charreaux F, Schibler L, Dupassieux D, Mullaart E. Reproductive technologies and genomic selection in dairy cattle. Reprod Fertil Dev 2014; 26:12-21. [PMID: 24305173 DOI: 10.1071/rd13328] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genomic tools are now available for most livestock species and are used routinely for genomic selection (GS) in cattle. One of the most important developments resulting from the introduction of genomic testing for dairy cattle is the application of reasonably priced low-density single nucleotide polymorphism technology in the selection of females. In this context, combining genome testing and reproductive biotechnologies in young heifers enables new strategies to generate replacement and elite females in a given period of time. Moreover, multiple markers have been detected in biopsies of preimplantation stage embryos, thus paving the way to develop new strategies based on preimplantation diagnosis and the genetic screening of embryos. Based on recent advances in GS, the present review focuses on new possibilities inherent in reproductive technologies used for commercial purposes and in genetic schemes, possible side effects and beneficial impacts on reproductive efficiency. A particular focus is on the different steps allowing embryo genotyping, including embryo micromanipulation, DNA production and quality assessment.
Collapse
Affiliation(s)
- C Ponsart
- UNCEIA Research and Development, 13 rue Jouet, 94704 Maisons Alfort, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
66
|
|
67
|
Efficiency of haplotype-based methods to fine-map QTLs and embryonic lethal variants affecting fertility: Illustration with a deletion segregating in Nordic Red cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
68
|
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]
|
69
|
Robert C, Fuentes-Utrilla P, Troup K, Loecherbach J, Turner F, Talbot R, Archibald AL, Mileham A, Deeb N, Hume DA, Watson M. Design and development of exome capture sequencing for the domestic pig (Sus scrofa). BMC Genomics 2014; 15:550. [PMID: 24988888 PMCID: PMC4099480 DOI: 10.1186/1471-2164-15-550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig. Results We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels. Conclusions We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.
| |
Collapse
|
70
|
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PLoS One 2014; 9:e92769. [PMID: 24667746 PMCID: PMC3965462 DOI: 10.1371/journal.pone.0092769] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/26/2014] [Indexed: 01/13/2023] Open
Abstract
The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP) genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo development contained within three of these haplotypes (Brown Swiss haplotype 1 and Holstein haplotypes 2 and 3) by combining exome capture with next generation sequencing. Of the 68,476,640 sequence variations (SV) identified, only 1,311 genome-wide SNP were concordant with the haplotype status of 21 sequenced carriers. Validation genotyping of 36 candidate SNP identified only 1 variant that was concordant to Holstein haplotype 3 (HH3), while no variants located within the refined intervals for HH2 or BH1 were concordant. The variant strictly associated with HH3 is a non-synonymous SNP (T/C) within exon 24 of the Structural Maintenance of Chromosomes 2 (SMC2) on Chromosome 8 at position 95,410,507 (UMD3.1). This polymorphism changes amino acid 1135 from phenylalanine to serine and causes a non-neutral, non-tolerated, and evolutionarily unlikely substitution within the NTPase domain of the encoded protein. Because only exome capture sequencing was used, we could not rule out the possibility that the true causative mutation for HH3 might lie in a non-exonic genomic location. Given the essential role of SMC2 in DNA repair, chromosome condensation and segregation during cell division, our findings strongly support the non-synonymous SNP (T/C) in SMC2 as the likely causative mutation. The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array.
Collapse
|
71
|
Pausch H, Kölle S, Wurmser C, Schwarzenbacher H, Emmerling R, Jansen S, Trottmann M, Fuerst C, Götz KU, Fries R. A nonsense mutation in TMEM95 encoding a nondescript transmembrane protein causes idiopathic male subfertility in cattle. PLoS Genet 2014; 10:e1004044. [PMID: 24391514 PMCID: PMC3879157 DOI: 10.1371/journal.pgen.1004044] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022] Open
Abstract
Genetic variants underlying reduced male reproductive performance have been identified in humans and model organisms, most of them compromising semen quality. Occasionally, male fertility is severely compromised although semen analysis remains without any apparent pathological findings (i.e., idiopathic subfertility). Artificial insemination (AI) in most cattle populations requires close examination of all ejaculates before insemination. Although anomalous ejaculates are rejected, insemination success varies considerably among AI bulls. In an attempt to identify genetic causes of such variation, we undertook a genome-wide association study (GWAS). Imputed genotypes of 652,856 SNPs were available for 7962 AI bulls of the Fleckvieh (FV) population. Male reproductive ability (MRA) was assessed based on 15.3 million artificial inseminations. The GWAS uncovered a strong association signal on bovine chromosome 19 (P = 4.08×10−59). Subsequent autozygosity mapping revealed a common 1386 kb segment of extended homozygosity in 40 bulls with exceptionally poor reproductive performance. Only 1.7% of 35,671 inseminations with semen samples of those bulls were successful. None of the bulls with normal reproductive performance was homozygous, indicating recessive inheritance. Exploiting whole-genome re-sequencing data of 43 animals revealed a candidate causal nonsense mutation (rs378652941, c.483C>A, p.Cys161X) in the transmembrane protein 95 encoding gene TMEM95 which was subsequently validated in 1990 AI bulls. Immunohistochemical investigations evidenced that TMEM95 is located at the surface of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. These findings imply that integrity of TMEM95 is required for an undisturbed fertilisation. Our results demonstrate that deficiency of TMEM95 severely compromises male reproductive performance in cattle and reveal for the first time a phenotypic effect associated with genomic variation in TMEM95. Impaired male fertility is a prevalent condition in many species and is often explained by aberrant semen quality. In some cases, male fertility is severely compromised although semen quality is without any apparent pathological findings (i.e., idiopathic male subfertility). The genetic mechanisms underlying idiopathic male subfertility often remain unexplained. In the present paper, we report a recessively inherited variant of idiopathic male subfertility in a cattle population. We use 650,000 genome-wide SNP markers genotyped in >7900 artificial insemination bulls to pinpoint the underlying genomic region. We take advantage of whole-genome re-sequencing data of 43 animals to identify a causal loss-of-function mutation in TMEM95 encoding a nondescript transmembrane protein. We demonstrate that transmembrane protein 95 is located at the plasma membrane of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. Our results indicate that integrity of transmembrane protein 95 is required for an undisturbed fertilisation. This is the first report to reveal a phenotypic effect associated with genomic variation in TMEM95 in any organism.
Collapse
Affiliation(s)
- Hubert Pausch
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, Germany
- * E-mail:
| | - Sabine Kölle
- Department of Urology, University of Munich, Munich, Germany
| | - Christine Wurmser
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, Germany
| | | | - Reiner Emmerling
- Institut fuer Tierzucht, Bayerische Landesanstalt für Landwirtschaft, Poing, Germany
| | - Sandra Jansen
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, Germany
| | | | | | - Kay-Uwe Götz
- Institut fuer Tierzucht, Bayerische Landesanstalt für Landwirtschaft, Poing, Germany
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, Germany
| |
Collapse
|
72
|
Kadri NK, Sahana G, Charlier C, Iso-Touru T, Guldbrandtsen B, Karim L, Nielsen US, Panitz F, Aamand GP, Schulman N, Georges M, Vilkki J, Lund MS, Druet T. A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock. PLoS Genet 2014; 10:e1004049. [PMID: 24391517 PMCID: PMC3879169 DOI: 10.1371/journal.pgen.1004049] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/04/2013] [Indexed: 12/02/2022] Open
Abstract
In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated. We report the identification of a large deletion encompassing four genes and the demonstration of its negative effect on fertility in Nordic Red dairy cattle. We show that this deletion is recessively lethal (homozygous embryos die) and therefore, when carrier cows are mated to carrier bulls, there is a high risk of embryonic mortality. As a result, chances of insemination failure are higher for such matings. Surprisingly, despite its negative effect, the deletion is frequent in Nordic Red cattle. We show that this high frequency may be a consequence of the fact that the deletion is associated with increased milk production and therefore selected for. Due to increased levels of inbreeding resulting from the widespread use of artificial insemination, such recessive lethal alleles may account for a non-negligible fraction of the reduction in fertility observed in cattle.
Collapse
Affiliation(s)
- Naveen Kumar Kadri
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- * E-mail: (GS); (TD)
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Terhi Iso-Touru
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Frank Panitz
- Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Nina Schulman
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Johanna Vilkki
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail: (GS); (TD)
| |
Collapse
|
73
|
Abstract
The advent of AI has markedly improved the production potential of dairy cows in all systems of production and transformed the dairy industry in many countries. Unfortunately, for many years breeding objectives focused solely on milk production. This resulted in a major decline in genetic merit for fertility traits. In recent years, the underlying physiological mechanisms responsible for this decline have started to be unravelled. It is apparent that poor genetic merit for fertility traits is associated with multiple defects across a range of organs and tissues that are antagonistic to achieving satisfactory fertility performance. The principal defects include excessive mobilisation of body condition score, unfavourable metabolic status, delayed resumption of cyclicity, increased incidence of endometritis, dysfunctional oestrus expression and inadequate luteal phase progesterone concentrations. On a positive note, it is possible to identify sires that combine good milk production traits with good fertility traits. Sire genetic merit for daughter fertility traits is improving rapidly in the dairy breeds, including the Holstein. With advances in animal breeding, especially genomic technologies, to identify superior sires, genetic merit for fertility traits can be improved much more quickly than they initially declined.
Collapse
|
74
|
Van Eenennaam AL, Weigel KA, Young AE, Cleveland MA, Dekkers JCM. Applied animal genomics: results from the field. Annu Rev Anim Biosci 2013; 2:105-39. [PMID: 25384137 DOI: 10.1146/annurev-animal-022513-114119] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic selection (GS) is the use of statistical methods to estimate the genetic merit of a genotyped animal based on prediction equations derived from large ancestral populations with both phenotypes and genotypes. It has revolutionized the dairy cattle breeding industry and has been implemented with varying degrees of success in other animal breeding programs, including swine, poultry, and beef cattle. The findings of empirical field studies applying GS to the breeding sectors of these main animal protein industries are reviewed. Several translational considerations must be addressed before implementing GS in genetic improvement programs. These include determining and obtaining economically relevant phenotypes and determining the optimal size of the training population, cost-effective genotyping strategies, the practicality of field implementation, and the relative costs versus the benefits of the realized rate of genetic gain. GS may additionally change the optimal breeding scheme design, and studies that address this consideration are also reviewed briefly.
Collapse
|
75
|
Affiliation(s)
- Thomas E. Spencer
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| |
Collapse
|
76
|
Fritz S, Capitan A, Djari A, Rodriguez SC, Barbat A, Baur A, Grohs C, Weiss B, Boussaha M, Esquerré D, Klopp C, Rocha D, Boichard D. Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS One 2013; 8:e65550. [PMID: 23762392 PMCID: PMC3676330 DOI: 10.1371/journal.pone.0065550] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/25/2013] [Indexed: 11/23/2022] Open
Abstract
The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10(-4)) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.
Collapse
Affiliation(s)
- Sébastien Fritz
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Aurelien Capitan
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Anis Djari
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Sabrina C. Rodriguez
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Anne Barbat
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Aurélia Baur
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Bernard Weiss
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Mekki Boussaha
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Diane Esquerré
- INRA, GeT Genomics Facility, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Dominique Rocha
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Didier Boichard
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| |
Collapse
|