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van den Berg I, Nguyen TV, Nguyen TTT, Pryce JE, Nieuwhof GJ, MacLeod IM. Imputation accuracy and carrier frequency of deleterious recessive defects in Australian dairy cattle. J Dairy Sci 2024:S0022-0302(24)00968-8. [PMID: 38945256 DOI: 10.3168/jds.2024-24780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Widespread genotyping has enabled the identification of putative recessive mutations that affect fertility through early embryonic fetal loss, or compromise neonate or calf viability. The use of artificial insemination in the global dairy population can rapidly spread these harmful mutations, and testing for multiple mutations can become relatively expensive if not all tests are available on the same SNP panel. However, it is possible to provide heifer and cow predicted carrier status to farmers at no additional cost if the animals are genotyped with a standard SNP panel. Additionally, for defects where the causal mutation is unknown, but a haplotype of markers has been associated with the defect, the carrier status can be predicted based on that haplotype. The aims of this study were 3-fold: 1) to determine the accuracy of imputation of putative causal mutations for recessive deleterious conditions in Australian dairy cattle, 2) to impute carrier status for known recessive deleterious conditions in all genotyped Australian Holstein, Jersey and Red breed cows, and 3) to determine the changes in carrier frequencies across time for these recessive deleterious mutations. We used the F1 statistic, combining precision and recall, to assess the accuracy of carrier status prediction. We showed that known deleterious mutations can be accurately imputed in Australian Holstein and Jersey cattle that are not directly genotyped for the causal mutation, with F1 ranging between 0.88 and 0.99. For recessive deleterious conditions not included on the standard Australian SNP panel, carrier status could be predicted using a marker haplotype, with F1 ranging from 0.91 to 0.92. Most putative causals and haplotypes were either stable with a low carrier percentage or had a declining carrier percentage. However, several recessive mutations showed a relatively high or increasing percentage, highlighting the importance of detecting carriers to reduce the number of at risk matings. Furthermore, the high carrier percentage of the recently identified Bovine Lymphocyte Intestinal Retention Defect (BLIRD) mutation emphasizes the importance of detection of novel mutations.
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Affiliation(s)
- I van den Berg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
| | - T V Nguyen
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - T T T Nguyen
- DataGene, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - J E Pryce
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - G J Nieuwhof
- DataGene, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - I M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
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Zhou B, Yu H, Xue Y, Li M, Zhang C, Yu B. The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis. Nat Commun 2024; 15:2399. [PMID: 38493158 PMCID: PMC10944506 DOI: 10.1038/s41467-024-46676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
MicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy of DNA-dependent RNA polymerases at MIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient pri-miRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with the 20 S proteasome and PRP4KA, facilitating SE phosphorylation by PRP4KA, and subsequent non-functional SE degradation by the 20 S proteasome. These data reveal that CWC15 ensures optimal miRNA biogenesis by maintaining proper SE levels and by modulating pri-miRNA levels. Taken together, this study uncovers the role of a conserved splicing-related protein in miRNA biogenesis.
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Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Yong Xue
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA.
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA.
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Sudhakar A, Nayee N, Saha S, Donthula SK, Poojara HV, Gohil T, Patel AC, Maurya BK. Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 2023; 55:399. [PMID: 37940810 DOI: 10.1007/s11250-023-03798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
Fertility is an important trait associated with reproductive performance and animal welfare concern. Lethal alleles affect fertility through early embryonic death, abortions, and stillbirth depending on the genetic expression of the allele. Holstein Friesian and Jersey are two major Bos taurus breeds used widely for increasing milk yield along with purebreds of Bos indicus breeds like Gir, Kankrej, Sahiwal, and Tharparkar. In the present study, prevalence of lethal mutants in crossbred Holstein Friesian (CBHF, n = 2435), crossbred Jersey (CBJY, n = 2874), Gir (n = 3288), Kankrej (n = 593), Sahiwal (n = 965), and Tharparkar (n = 18) were studied. Heterozygous carrier animals were identified for bovine leukocyte adhesion deficiency (BLAD), Citrullinemia, complex vertebral malformation (CVM), Brachyspina, Holstein Haplotype 1 (HH1), Holstein Haplotype 3 (HH3),Holstein Haplotype 4 (HH4) and Jersey Haplotype 1 (JH1). Breed purity analysis confirmed inheritance of Bos taurus genes contributing to the presence of lethal mutant alleles like BLAD, Citrullinemia, HH1, and JH1 in apparently phenotypic Bos indicus animals. Screening and elimination of heterozygous carrier bulls/cows is essential to control fertility loss associated with lethal alleles.
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Affiliation(s)
- A Sudhakar
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India.
| | - Nilesh Nayee
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Sujit Saha
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | | | - Hardik V Poojara
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Tejas Gohil
- Sabarmati Ashram Gaushala ( Genomics lab), Anand, 388001, Gujarat, India
| | - Aashish C Patel
- College of Veterinary Science and Animal Husbandry, KU, Anand, 388001, Gujarat, India
| | - Brijesh K Maurya
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
- NDDB CALF Ltd., Anand, 388001, Gujarat, India
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Branda-Sica A, Artigas R, de Torres E, Kinley E, Nicolini P, Federici MT, Llambí S. Monitoring of recessive defects associated with low reproductive performance in dairy cattle in Uruguay. Open Vet J 2023; 13:1290-1298. [PMID: 38027404 PMCID: PMC10658014 DOI: 10.5455/ovj.2023.v13.i10.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023] Open
Abstract
Background Most dairy cattle breeds originate show an average generational inbreeding rate of 1%, which favors the occurrence of recessive defects associated with low reproductive performance. Aim The objective of this study was to monitor recessive defects associated with low reproductive performance in dairy cattle. Methods To monitor bulls carrying the Holstein Friesian haplotype (HH) 1, HH3, and HH4 haplotypes, we analyzed the records of 3,028 national and imported Holstein Friesian bulls from the 2021 updated sires' catalog published by "Evaluaciones Genéticas Lecheras"; and to determine the presence of these mentioned haplotypes, as well as Jersey haplotype (JH) 1 and complex vertebral malformation (CVM), were genotype with the GeneTitan® 2,500 single nucleotide polymorphism (SNP) bovine chip, estimate their frequencies and evaluate their impact on the fertility of 100 Holstein Friesian cows and 70 Holstein Friesian-Jersey crosses belonging to an experimental dairy. Results From a total of 1,468 (48.5%) bulls with genetic information from the sires' catalog for HH1 and 1,471 (48.6%) for HH3 and HH4, we found 90 (6.1%) carriers for HH1, 60 (4.1%) for HH3, and 6 (0.4%) for HH4, respectively. By genotyping with the chip, we calculated the herd frequency of the mutant alleles and herd prevalence of carriers for HH1 and CVM as q = 0.003 and 0.022; 0.59% and 4.3% (call rate >0.99), respectively. No mutant alleles were found for HH3, HH4, and JH1 in the analyzed population. We examined reproductive data by observing the presence of CVM and HH1 mutant alleles in repeat cows with an average of four services to achieve pregnancy. Conclusion This study demonstrated the presence of recessive defects associated with low reproductive performance in the analyzed population, which can affect the health and productivity of dairy cattle. Therefore, cows and bulls should be closely monitored through genetic testing to lower the incidence of recessive defects in dairy cattle.
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Affiliation(s)
- Andrea Branda-Sica
- Instituto Nacional de Investigación Agropecuaria, Sistema Ganadero Extensivo—Salud Animal, Canelones, Uruguay
| | - Rody Artigas
- Facultad de Veterinaria, Unidad Académica de Genética y Mejora Animal, Universidad de la República, Montevideo, Uruguay
| | - Elena de Torres
- Facultad de Veterinaria, Campo Experimental N°2, Universidad de la República, San José, Uruguay
| | - Evangelina Kinley
- Facultad de Veterinaria, Campo Experimental N°2, Universidad de la República, San José, Uruguay
| | - Paula Nicolini
- Centro Universitario de Tacuarembó, Instituto Superior de la Carne, Universidad de la República, Tacuarembó, Uruguay
| | - María Teresa Federici
- Instituto Nacional de Investigación Agropecuaria, Sistema Ganadero Extensivo—Salud Animal, Canelones, Uruguay
| | - Silvia Llambí
- Facultad de Veterinaria, Unidad Académica de Genética y Mejora Animal, Universidad de la República, Montevideo, Uruguay
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Id-Lahoucine S, Casellas J, Suárez-Vega A, Fonseca PAS, Schenkel FS, Sargolzaei M, Cánovas A. Unravelling transmission ratio distortion across the bovine genome: identification of candidate regions for reproduction defects. BMC Genomics 2023; 24:383. [PMID: 37422635 DOI: 10.1186/s12864-023-09455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Biological mechanisms affecting gametogenesis, embryo development and postnatal viability have the potential to alter Mendelian inheritance expectations resulting in observable transmission ratio distortion (TRD). Although the discovery of TRD cases have been around for a long time, the current widespread and growing use of DNA technologies in the livestock industry provides a valuable resource of large genomic data with parent-offspring genotyped trios, enabling the implementation of TRD approach. In this research, the objective is to investigate TRD using SNP-by-SNP and sliding windows approaches on 441,802 genotyped Holstein cattle and 132,991 (or 47,910 phased) autosomal SNPs. RESULTS The TRD was characterized using allelic and genotypic parameterizations. Across the whole genome a total of 604 chromosomal regions showed strong significant TRD. Most (85%) of the regions presented an allelic TRD pattern with an under-representation (reduced viability) of carrier (heterozygous) offspring or with the complete or quasi-complete absence (lethality) for homozygous individuals. On the other hand, the remaining regions with genotypic TRD patterns exhibited the classical recessive inheritance or either an excess or deficiency of heterozygote offspring. Among them, the number of most relevant novel regions with strong allelic and recessive TRD patterns were 10 and 5, respectively. In addition, functional analyses revealed candidate genes regulating key biological processes associated with embryonic development and survival, DNA repair and meiotic processes, among others, providing additional biological evidence of TRD findings. CONCLUSIONS Our results revealed the importance of implementing different TRD parameterizations to capture all types of distortions and to determine the corresponding inheritance pattern. Novel candidate genomic regions containing lethal alleles and genes with functional and biological consequences on fertility and pre- and post-natal viability were also identified, providing opportunities for improving breeding success in cattle.
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Affiliation(s)
- Samir Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joaquim Casellas
- Departament de Ciència Animal I Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Aroa Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Pablo A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Select Sires, Inc, Plain City, OH, 43064, USA
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Schmidt PI, Mota LFM, Fonseca LFS, Dos Santos Silva DB, Frezarim GB, Arikawa LM, de Abreu Santos DJ, Magalhães AFB, Cole JB, Carvalheiro R, de Oliveira HN, Null DJ, VanRaden P, Ma L, de Albuquerque LG. Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Sci Rep 2023; 13:10399. [PMID: 37369809 DOI: 10.1038/s41598-023-37586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.
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Affiliation(s)
- Patrícia Iana Schmidt
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Danielly Beraldo Dos Santos Silva
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Leonardo Machestropa Arikawa
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jordan de Abreu Santos
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - John Bruce Cole
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Roberto Carvalheiro
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Henrique Nunes de Oliveira
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jacob Null
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Paul VanRaden
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, 20742, USA
| | - Lucia Galvão de Albuquerque
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
- National Council for Scientific and Technological Development (CNPq), Brasília, Brazil.
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Tomihara K, Tanaka S, Katsuma S, Shimada T, Kobayashi J, Kiuchi T. Recessive embryonic lethal mutations uncovered in heterozygous condition in silkworm semiconsomic strains. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 155:103933. [PMID: 36931352 DOI: 10.1016/j.ibmb.2023.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 05/10/2023]
Abstract
In this study, we found two embryonic lethal mutations, t04 lethal (l-t04) and m04 lethal (l-m04), in semiconsomic strains T04 and M04, respectively. In these semiconsomic strains, the entire diploid genome, except for one chromosome 4 of the wild silkworm Bombyx mandarina, is substituted with chromosomes of the domesticated silkworm B. mori, and l-t04 and l-m04 mutations are located on B. mandarina-derived chromosome 4. To clarify the cause of the lethalities and the genes responsible for these mutations, positional cloning and CRISPR/Cas9 mediated knockout screening were performed. Finally, genetic complementation tests identified the mutations responsible for the l-t04 and l-m04 as the Bombyx homolog of imaginal discs arrested (Bmida) and TATA box binding protein-associated factor 5 (BmTaf5), respectively. Lethal stages of each knockout mutant indicated the importance of these genes in B. mori late embryogenesis. The lethal mutations responsible for l-t04 and l-m04 were not found in parental strains or wild B. mandarina collected from 39 distinct locations in Japan, indicating that both mutations were independently introduced during or after the development of the semiconsomic strains. We conclude that the recessive embryonic lethality in the T04 and M04 strains is due to deleterious mutations produced in B. mandarina-derived chromosome 4.
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Affiliation(s)
- Kenta Tomihara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Saori Tanaka
- Department of Biological and Environmental Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toru Shimada
- Department of Life Science, Faculty of Science/Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, 171-8588, Japan
| | - Jun Kobayashi
- Department of Biological and Environmental Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Potapova NA. Nonsense Mutations in Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:400-412. [PMID: 35790376 DOI: 10.1134/s0006297922050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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9
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Ben Braiek M, Moreno-Romieux C, Allain C, Bardou P, Bordes A, Debat F, Drögemüller C, Plisson-Petit F, Portes D, Sarry J, Tadi N, Woloszyn F, Fabre S. A Nonsense Variant in CCDC65 Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep. Genes (Basel) 2021; 13:genes13010045. [PMID: 35052387 PMCID: PMC8774411 DOI: 10.3390/genes13010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
We recently demonstrated that the Lacaune deficient homozygous haplotype 6 (LDHH6) potentially hosts a recessive perinatal lethal mutation in Lacaune dairy sheep mapped on OAR3. In the present study, we have analyzed the whole-genome sequences of two Lacaune ram heterozygous carriers of LDHH6. After variant calling and filtering against the variants of 86 non-carrier rams, we have identified a single nucleotide variant (SNV) in the two LDHH6 carriers whose variant allele induced a premature stop codon (p.Glu111*) in the Coiled-Coil Domain Containing 65 (CCDC65) gene. CCDC65 is involved in the assembly of the nexin-dynein regulatory complex for the formation of microtubules in ciliated cells. In order to identify the phenotype in homozygous sheep, we generated at-risk matings (n = 17) between rams and ewes heterozygous for the candidate variant in CCDC65. A total of 16 lambs were born alive with five genotyped as homozygous carriers. The homozygous lambs suffered from respiratory problems, and four of them died within the first month of life. At necropsy, we observed a broad hepatization of lung lobes possibly induced by infectious pneumonia. The management of this lethal recessive allele (frequency of 0.06) through reasoned mating in the Lacaune sheep selection schemes could reduce lamb mortality by 2%.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Charlotte Allain
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Philippe Bardou
- Sigenae, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 31326 Castanet-Tolosan, France;
| | - Arnaud Bordes
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Frédéric Debat
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Florence Plisson-Petit
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - David Portes
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Julien Sarry
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Némuel Tadi
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Stéphane Fabre
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
- Correspondence:
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10
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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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11
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Häfliger IM, Seefried FR, Spengeler M, Drögemüller C. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 2021; 53:95. [PMID: 34915862 PMCID: PMC8675516 DOI: 10.1186/s12711-021-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00686-3.
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Affiliation(s)
- Irene M Häfliger
- 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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12
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Häfliger IM, Seefried FR, Drögemüller C. Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland. Animals (Basel) 2021; 11:3535. [PMID: 34944310 PMCID: PMC8698008 DOI: 10.3390/ani11123535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
We herein report the result of a large-scale reverse genetic screen in the Swiss Simmental population, a local dual-purpose cattle breed. We aimed to detect possible recessively inherited variants affecting protein-coding genes, as such deleterious variants can impair fertility and rearing success significantly. We used 115,000 phased SNP data of almost 10 thousand cattle with pedigree data. This revealed evidence for 11 genomic regions of 1.17 Mb on average, with haplotypes (SH1 to SH11) showing a significant depletion in homozygosity and an allele frequency between 3.2 and 10.6%. For the proposed haplotypes, it was unfortunately not possible to evaluate associations with fertility traits as no corresponding data were available. For each haplotype region, possible candidate genes were listed based on their known function in development and disease. Subsequent mining of single-nucleotide variants and short indels in the genomes of 23 sequenced haplotype carriers allowed us to identify three perfectly linked candidate causative protein-changing variants: a SH5-related DIS3:p.Ile678fs loss-of-function variant, a SH8-related CYP2B6:p.Ile313Asn missense variant, and a SH9-related NUBPL:p.Ser143Tyr missense variant. None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.
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Affiliation(s)
- Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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13
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Liu X, Pan X, Chen D, Yin C, Peng J, Shi W, Qi L, Wang R, Zhao W, Zhang Z, Yang J, Peng YL. Prp19-associated splicing factor Cwf15 regulates fungal virulence and development in the rice blast fungus. Environ Microbiol 2021; 23:5901-5916. [PMID: 34056823 DOI: 10.1111/1462-2920.15616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
The splicing factor Cwf15 is an essential component of the Prp19-associated component of the spliceosome and regulates intron splicing in several model species, including yeasts and human cells. However, the roles of Cwf15 remain unexplored in plant pathogenic fungi. Here, we report that MoCWF15 in the rice blast fungus Magnaporthe oryzae is non-essential to viability and important to fungal virulence, growth and conidiation. MoCwf15 contains a putative nuclear localization signal (NLS) and is localized into the nucleus. The NLS sequence but not the predicted phosphorylation site or two sumoylation sites was essential for the biological functions of MoCwf15. Importantly, MoCwf15 physically interacted with the Prp19-associated splicing factors MoCwf4, MoSsa1 and MoCyp1, and negatively regulated protein accumulations of MoCyp1 and MoCwf4. Furthermore, with the deletion of MoCWF15, aberrant intron splicing occurred in near 400 genes, 20 of which were important to the fungal development and virulence. Taken together, MoCWF15 regulates fungal growth and infection-related development by modulating the intron splicing efficiency of a subset of genes in the rice blast fungus.
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Affiliation(s)
- Xinsen Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiao Pan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Deng Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Changfa Yin
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Junbo Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Shi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Linlu Qi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ruijin Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Yang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
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14
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Identification of homozygous haplotypes carrying putative recessive lethal mutations that compromise fertility traits in French Lacaune dairy sheep. Genet Sel Evol 2021; 53:41. [PMID: 33932977 PMCID: PMC8088666 DOI: 10.1186/s12711-021-00634-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background Homozygous recessive deleterious mutations can cause embryo/fetal or neonatal lethality, or genetic defects that affect female fertility and animal welfare. In livestock populations under selection, the frequency of such lethal mutations may increase due to inbreeding, genetic drift, and/or the positive pleiotropic effects of heterozygous carriers on selected traits. Results By scanning the genome of 19,102 Lacaune sheep using 50 k single nucleotide polymorphism (SNP) phased genotypes and pedigree data, we identified 11 Lacaune deficient homozygous haplotypes (LDHH1 to LDHH11) showing a highly significant deficit of homozygous animals ranging from 79 to 100%. These haplotypes located on chromosomes 3, 4, 13, 17 and 18, spanned regions from 1.2 to 3.0 Mb long with a frequency of heterozygous carriers between 3.7 and 12.1%. When we compared at-risk matings (between carrier rams and daughters of carrier rams) and safe matings, seven of the 11 haplotypes were associated with a significant alteration of two fertility traits, a reduced success of artificial insemination (LDHH1, 2, 8 and 9), and/or an increased stillbirth rate (LDHH3, 6, 8, 9, and 10). The 11 haplotypes were also tested for a putative selective advantage of heterozygous carrier rams based on their daughter yield deviation for six dairy traits (milk, fat and protein yields, fat and protein contents and lactation somatic cell score). LDHH1, 3, 4, 5, 7, 9 and 11 were associated with positive effects on at least one selected dairy trait, in particular milk yield. For each haplotype, the most probable candidate genes were identified based on their roles in lethality of mouse knock-out models and in mammalian genetic disorders. Conclusions Based on a reverse genetic strategy, we identified at least 11 haplotypes with homozygous deficiency segregating in French Lacaune dairy sheep. This strategy represents a first tool to limit at-risk matings in the Lacaune dairy selection scheme. We assume that most of the identified LDHH are in strong linkage disequilibrium with a recessive lethal mutation that affects embryonic or juvenile survival in sheep but is yet to be identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00634-1.
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15
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Sasaki S, Watanabe T, Ibi T, Hasegawa K, Sakamoto Y, Moriwaki S, Kurogi K, Ogino A, Yasumori T, Wakaguri H, Muraki E, Miki Y, Yoshida Y, Inoue Y, Tabuchi I, Iwao K, Arishima T, Kawashima K, Watanabe M, Sugano S, Sugimoto Y, Suzuki Y. Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle. Sci Rep 2021; 11:6687. [PMID: 33758295 PMCID: PMC7988166 DOI: 10.1038/s41598-021-86225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Intensive use of a few elite sires has increased the risk of the manifestation of deleterious recessive traits in cattle. Substantial genotyping data gathered using single-nucleotide polymorphism (SNP) arrays have identified the haplotypes with homozygous deficiency, which may compromise survival. We developed Japanese Black cattle haplotypes (JBHs) using SNP array data (4843 individuals) and identified deleterious recessive haplotypes using exome sequencing of 517 sires. We identified seven JBHs with homozygous deficiency. JBH_10 and JBH_17 were associated with the resuming of estrus after artificial insemination, indicating that these haplotypes carried deleterious mutations affecting embryonic survival. The exome data of 517 Japanese Black sires revealed that AC_000165.1:g.85341291C>G of IARS in JBH_8_2, AC_000174.1:g.74743512G>T of CDC45 in JBH_17, and a copy variation region (CNVR_27) of CLDN16 in JBH_1_1 and JBH_1_2 were the candidate mutations. A novel variant AC_000174.1:g.74743512G>T of CDC45 in JBH_17 was located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing. Mating between heterozygotes of JBH_17 indicated that homozygotes carrying the risk allele died around the blastocyst stage. Analysis of frequency of the CDC45 risk allele revealed that its carriers were widespread throughout the tested Japanese Black cattle population. Our approach can effectively manage the inheritance of recessive risk alleles in a breeding population.
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Affiliation(s)
- Shinji Sasaki
- grid.267625.20000 0001 0685 5104Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami-gun, Okinawa, 903-0213 Japan ,grid.258333.c0000 0001 1167 1801United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065 Japan
| | - Toshio Watanabe
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Takayuki Ibi
- grid.261356.50000 0001 1302 4472Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530 Japan
| | - Kiyotoshi Hasegawa
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Yoichi Sakamoto
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Shunsuke Moriwaki
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Kazuhito Kurogi
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Atsushi Ogino
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Takanori Yasumori
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Hiroyuki Wakaguri
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Eiji Muraki
- Hida Beef Cattle Research Department, Gifu Prefectural Livestock Research Institute, Makigadou, Kiomi, Takayama, Gifu 506-0101 Japan
| | - Youko Miki
- Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Hokubu Agricultural Technology Institute, Asago, Hyogo 669-5254 Japan
| | - Yuichi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Hokubu Agricultural Technology Institute, Asago, Hyogo 669-5254 Japan
| | - Yoshinobu Inoue
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Ichiro Tabuchi
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Ken Iwao
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Taichi Arishima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima 899-8212 Japan
| | - Keisuke Kawashima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima 899-8212 Japan
| | - Manabu Watanabe
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Sumio Sugano
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Yushima, Bunkyouku, Tokyo 113-0034 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
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16
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Kumar A, Gupta ID, Mohan G, M R V, D RK, S J, Kataria RS, Niranjan SK. Alternate PCR assays for screening of JH1 mutation associated with embryonic death in Jersey cattle. Mol Cell Probes 2020; 55:101688. [PMID: 33279530 DOI: 10.1016/j.mcp.2020.101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Jersey haplotype (JH) 1, a stop-gain lethal mutation in the CWC15 gene, causes embryonic losses in Jersey cattle. Two PCR based assays using Amplification Refractory Mutation System (T-ARMS-PCR) and restriction fragment length polymorphism (PCR-RFLP) were developed for screening of the JH1 in cattle. During the screening, seven among 30 Indian Jersey bulls were identified as carriers of the mutant JH1 allele, the first time in the country. These PCR assays are economical, rapid and accurate; and can be used separately or in combination for screening and cross-validation of the JH1 carriers in Jersey cattle.
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Affiliation(s)
- Anshuman Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Govind Mohan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vineeth M R
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Ravi Kumar D
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Jayakumar S
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
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17
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Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep 2020; 10:13336. [PMID: 32770129 PMCID: PMC7415139 DOI: 10.1038/s41598-020-70324-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Cameron H Lee
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Yingjing Miao
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Steffen Lau
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | | | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany.
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A genome-wide scan for candidate lethal variants in Thoroughbred horses. Sci Rep 2020; 10:13153. [PMID: 32753654 PMCID: PMC7403398 DOI: 10.1038/s41598-020-68946-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3'UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.
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19
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Huson HJ, Sonstegard TS, Godfrey J, Hambrook D, Wolfe C, Wiggans G, Blackburn H, VanTassell CP. A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle. Front Genet 2020; 11:366. [PMID: 32362912 PMCID: PMC7181675 DOI: 10.3389/fgene.2020.00366] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/25/2020] [Indexed: 11/15/2022] Open
Abstract
For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in 2008. This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from 1964 to 2004 and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 Guernsey cattle derived from the Island of Guernsey and 71 Holstein cattle served as reference populations for genetic comparison. Cattle were genotyped on the Illumina BovineHD Beadchip producing 777,962 SNPs spanning the genome. Principal component analysis revealed population stratification within breed reflective of individual animal’s continental origin. When compared to Holstein and Guernsey, all Jersey clustered together by breed. The Jersey breed demonstrated increased inbreeding in comparison to Holstein or Guernsey with slightly higher estimates of inbreeding coefficients and identity-by-descent. The Island and United States Jersey have relatively similar, yet statistically different inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jersey were identified using genome-wide homozygosity association and marker-based FST that provided population informative single-nucleotide polymorphism (SNPs). Biological significance of the homozygosity association results identified multiple genes on chromosomes 5, 24, and 27, involved in immune function and cellular processes. Overall, genomic variation was identified between the Island and non-Island Jersey cattle producing population informative SNPs and differing runs of homozygosity (ROH) over immune regulation and metabolic genes. Results on inbreeding measures and ROH may reflect varying effective population size or differential selection with grazing systems promoting natural selection for traits such as parasite resistance, whereas confinement systems demonstrate a more intensive artificial selection. More broadly, differences in breed formation, particularly between the two Channel Island breeds, likely contributed to the variation in ROH and inbreeding. This research provides a reference for the Jersey breed based on the genetic foundation of the Island cattle as compared to the intensively selected United States cattle, and identifies regions of the genome for future investigation of immune regulation and metabolic processes.
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Affiliation(s)
- Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | | | - James Godfrey
- Royal Jersey Agricultural & Horticultural Society, Trinity, Jersey, United Kingdom
| | - David Hambrook
- Royal Jersey Agricultural & Horticultural Society, Trinity, Jersey, United Kingdom
| | - Cari Wolfe
- American Jersey Cattle Association, Reynoldsburg, OH, United States
| | - George Wiggans
- Council on Dairy Cattle Breeding, Bowie, MD, United States
| | - Harvey Blackburn
- National Animal Germplasm Program, USDA-ARS, Fort Collins, CO, United States
| | - Curtis P VanTassell
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, United States
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20
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Wu X, Mesbah-Uddin M, Guldbrandtsen B, Lund MS, Sahana G. Novel haplotypes responsible for prenatal death in Nordic Red and Danish Jersey cattle. J Dairy Sci 2020; 103:4570-4578. [PMID: 32197842 DOI: 10.3168/jds.2019-17831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/27/2020] [Indexed: 01/04/2023]
Abstract
Haplotypes that are common in a population but not observed as homotypes in living animals may harbor lethal alleles that compromise embryo survival. In this study, we searched for homozygous-deficient haplotypes in the genomes of 19,309 Nordic Red Dairy (RDC) and 4,291 Danish Jersey (JER) cattle genotyped using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). For statistically significant deficient haplotypes, we evaluated the effect on nonreturn rate in at-risk matings (mating between carrier bull and daughter of carrier sire) versus not-at-risk matings (mating between noncarrier bull and daughter of noncarrier sire). Next, we analyzed whole-genome sequence variants from the 1000 Bull Genomes Project to identify putative causal variants underlying these haplotypes. In RDC, we identified 3 homozygous-deficient regions (HDR) that overlapped with known recessive lethal mutations: a 662-kb deletion on chromosome 12 in RDC [Online Mendelian Inheritance in Animals (OMIA) 001901-9913), a missense mutation in TUBD1, g.11063520T>C, in Braunvieh cattle (OMIA 001939-9913), and a 525-kb deletion on chromosome 23 in RDC (OMIA 001991-9913)]. In addition, we identified 15 novel HDR and their tag haplotypes for the underlying causative variants. The tag haplotype located between 39.2 and 40.3 Mbp on chromosome 18 had a negative effect on nonreturn rate in at-risk mating, confirming embryonic lethality. In Danish Jersey, we identified 12 novel HDR and their tag haplotypes for underlying causative variants. For 3 of these 12 tag haplotypes, insemination records of at-risk mating showed a negative effect on nonreturn rate, confirming the association with early embryonic mortality. Cattle that had both genotype and whole-genome sequence data were analyzed to detect the causative variants underlying each tag haplotype. However, none of the functional variants or deletions showed concordance with carrier status of the novel tag haplotypes. Carrier status of these detected haplotypes can be used to select bulls to reduce the frequencies of lethal alleles in the population and to avoid at-risk matings.
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Affiliation(s)
- Xiaoping Wu
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830 Tjele, Denmark.
| | - Md Mesbah-Uddin
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830 Tjele, Denmark; Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830 Tjele, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830 Tjele, Denmark.
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Jagannathan V, Drögemüller C, Leeb T. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 2019; 50:695-704. [PMID: 31486122 PMCID: PMC6842318 DOI: 10.1111/age.12834] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/16/2022]
Abstract
The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Wu X, Mesbah-Uddin M, Guldbrandtsen B, Lund MS, Sahana G. Haplotypes responsible for early embryonic lethality detected in Nordic Holsteins. J Dairy Sci 2019; 102:11116-11123. [PMID: 31548059 DOI: 10.3168/jds.2019-16651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/09/2019] [Indexed: 12/13/2022]
Abstract
Widespread use of a limited number of elite sires in dairy cattle breeding increases the risk of some deleterious allelic variants spreading in the population. Genomic data are being used to detect relatively common (frequency >1%) haplotypes that never occur in the homozygous state in live animals. Such haplotypes likely include recessive lethal or semilethal alleles. The aim of this study was to detect such haplotypes in the Nordic Holstein population and to identify causal genetic factors underlying these haplotypes. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) genotypes for 26,312 Nordic Holstein animals were phased to construct haplotypes. Haplotypes that are common in the population but never observed as homozygous were identified. Two such haplotypes overlapped with previously identified recessive lethal mutations in Holsteins-namely, structural maintenance of chromosomes 2 (HH3) and brachyspina. In addition, we identified 9 novel putative recessive lethal-carrying haplotypes, with 26 to 36 homozygous individuals expected among the genotyped animals but only 0 to 3 homozygotes observed. For 2 out of 9 homozygous-deficient haplotypes, insemination records of at-risk mating (carrier bull with daughter of carrier sire) showed reduced insemination success compared with not-at-risk mating (noncarrier bull with daughter of noncarrier sire), supporting early embryonic mortality. To detect the causative variant underlying each homozygous-deficient haplotype, data from the 1000 Bull Genome Project were used. However, no variants or deletions identified in the chromosome regions covered by the haplotypes showed concordance with haplotype carrier status. The carrier status of detected haplotypes could be used to select bulls to reduce the frequency of the latent lethal mutations in the population. If desired, at-risk matings could be avoided.
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Affiliation(s)
- Xiaoping Wu
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark.
| | - Md Mesbah-Uddin
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark; Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
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Upperman LR, Kinghorn BP, MacNeil MD, Van Eenennaam AL. Management of lethal recessive alleles in beef cattle through the use of mate selection software. Genet Sel Evol 2019; 51:36. [PMID: 31382878 PMCID: PMC6683482 DOI: 10.1186/s12711-019-0477-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Recessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions. METHODS Two beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0-100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping. RESULTS With full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring (aa) as compared to indiscriminate selection against carrier parents (Aa). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses. CONCLUSIONS Genotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding.
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Affiliation(s)
- Lindsay R. Upperman
- Department of Animal Science, University of California, Davis, CA 95616 USA
- Present Address: Department of Animal Science, University of Nebraska, Lincoln, NE 68583 USA
| | - Brian P. Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - Michael D. MacNeil
- Delta G, Miles City, MT 59301 USA
- University of the Free State, Bloemfontein, 9300 South Africa
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24
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Mesbah-Uddin M, Hoze C, Michot P, Barbat A, Lefebvre R, Boussaha M, Sahana G, Fritz S, Boichard D, Capitan A. A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle. J Dairy Sci 2019; 102:6340-6356. [DOI: 10.3168/jds.2018-16100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/15/2019] [Indexed: 12/12/2022]
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Johnsson M, Gaynor RC, Jenko J, Gorjanc G, de Koning DJ, Hickey JM. Removal of alleles by genome editing (RAGE) against deleterious load. Genet Sel Evol 2019; 51:14. [PMID: 30995904 PMCID: PMC6472060 DOI: 10.1186/s12711-019-0456-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 04/01/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing it. Deleterious variants can be identified by bioinformatics screening methods that use sequence conservation and biological prior information about protein function. However, once deleterious variants have been identified, how can they be used in breeding? RESULTS We simulated a closed animal breeding population that is subject to both natural selection against deleterious load and artificial selection for a quantitative trait representing the breeding goal. Deleterious load was polygenic and was due to either codominant or recessive variants. We compared strategies for removal of deleterious alleles by genome editing (RAGE) to selection against carriers. When deleterious variants were codominant, the best strategy for prioritizing variants was to prioritize low-frequency variants. When deleterious variants were recessive, the best strategy was to prioritize variants with an intermediate frequency. Selection against carriers was inefficient when variants were codominant, but comparable to editing one variant per sire when variants were recessive. CONCLUSIONS Genome editing of deleterious alleles reduces deleterious load, but requires the simultaneous editing of multiple deleterious variants in the same sire to be effective when deleterious variants are recessive. In the short term, selection against carriers is a possible alternative to genome editing when variants are recessive. Our results suggest that, in the future, there is the potential to use RAGE against deleterious load in animal breeding.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - R. Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - John M. Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
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Guarini AR, Sargolzaei M, Brito LF, Kroezen V, Lourenco DAL, Baes CF, Miglior F, Cole JB, Schenkel FS. Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. J Dairy Sci 2019; 102:5315-5322. [PMID: 30954262 DOI: 10.3168/jds.2018-15366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/18/2019] [Indexed: 11/19/2022]
Abstract
The effects of 2 deleterious recessive haplotypes on reproduction performance of Ayrshire cattle, Ayrshire Haplotype 1 (AH1) and Ayrshire Haplotype 2 (AH2), were investigated in Canadian Ayrshire cattle. We calculated their phenotypic effects on stillbirth (SB) rate and 56-d nonreturn rate (NRR) by estimating the interaction of service sire carrier status with maternal grandsire carrier status using the official Canadian evaluation models for those 2 traits. The interaction term included 9 subclasses for the 3 possible statuses of each bull: haplotype carrier, noncarrier, or not genotyped. For AH1, 394 carriers and 1,433 noncarriers were available, whereas 313 carriers and 1,543 noncarriers were available for the AH2 haplotype. The number of matings considered for SB was 34,312 for heifers (first parity) and 115,935 for cows (later parities). For NRR, 49,479 matings for heifers and 160,528 for cows were used to estimate the haplotype effects. We observed a negative effect of AH1 on SB rates, which was 2.0% higher for matings of AH1-carrier sires to dams that had an AH1-carrier sire; this effect was found for both heifers and cows. However, AH1 had small, generally nonsignificant effects on NRR. The AH2 haplotype had a substantial negative effect on NRR, with 5.1% more heifers and 4.0% more cows returning to service, but the effects on SB rates were inconsistent and mostly small effects. Our results validate the harmful effects of AH1 and AH2 on reproduction traits in the Canadian Ayrshire population. This information will be of great interest for the dairy industry, allowing producers to make mating decisions that would reduce reproductive losses.
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Affiliation(s)
- A R Guarini
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Select Sires Inc., Plain City, OH 43064
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - V Kroezen
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Canadian Dairy Network, Guelph, Ontario N1K 1E5, Canada
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Services, USDA, Beltsville, MD 20705
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Ma L, Cole J, Da Y, VanRaden P. Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits. J Dairy Sci 2019; 102:3735-3743. [DOI: 10.3168/jds.2018-15269] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022]
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Baes CF, Makanjuola BO, Miglior F, Marras G, Howard JT, Fleming A, Maltecca C. Symposium review: The genomic architecture of inbreeding: How homozygosity affects health and performance. J Dairy Sci 2019; 102:2807-2817. [DOI: 10.3168/jds.2018-15520] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/21/2018] [Indexed: 11/19/2022]
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Bach À. Effects of nutrition and genetics on fertility in dairy cows. Reprod Fertil Dev 2019; 31:40-54. [DOI: 10.1071/rd18364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Optimal reproductive function in dairy cattle is mandatory to maximise profits. Dairy production has progressively improved milk yields, but, until recently, the trend in reproductive performance has been the opposite. Nutrition, genetics, and epigenetics are important aspects affecting the reproductive performance of dairy cows. In terms of nutrition, the field has commonly fed high-energy diets to dairy cows during the 3 weeks before calving in an attempt to minimise postpartum metabolic upsets. However, in the recent years it has become clear that feeding high-energy diets during the dry period, especially as calving approaches, may be detrimental to cow health, or at least unnecessary because cows, at that time, have low energy requirements and sufficient intake capacity. After calving, dairy cows commonly experience a period of negative energy balance (NEB) characterised by low blood glucose and high non-esterified fatty acid (NEFA) concentrations. This has both direct and indirect effects on oocyte quality and survival. When oocytes are forced to depend highly on the use of energy resources derived from body reserves, mainly NEFA, their development is compromised due to a modification in mitochondrial β-oxidation. Furthermore, the indirect effect of NEB on reproduction is mediated by a hormonal (both metabolic and reproductive) environment. Some authors have attempted to overcome the NEB by providing the oocyte with external sources of energy via dietary fat. Conversely, fertility is affected by a large number of genes, each with small individual effects, and thus it is unlikely that the decline in reproductive function has been directly caused by genetic selection for milk yield per se. It is more likely that the decline is the consequence of a combination of homeorhetic mechanisms (giving priority to milk over other functions) and increased metabolic pressure (due to a shortage of nutrients) with increasing milk yields. Nevertheless, genetics is an important component of reproductive efficiency, and the incorporation of genomic information is allowing the detection of genetic defects, degree of inbreeding and specific single nucleotide polymorphisms directly associated with reproduction, providing pivotal information for genetic selection programs. Furthermore, focusing on improving bull fertility in gene selection programs may represent an interesting opportunity. Conversely, the reproductive function of a given cow depends on the interaction between her genetic background and her environment, which ultimately modulates gene expression. Among the mechanisms modulating gene expression, microRNAs (miRNAs) and epigenetics seem to be most relevant. Several miRNAs have been described to play active roles in both ovarian and testicular function, and epigenetic effects have been described as a consequence of the nutrient supply and hormonal signals to which the offspring was exposed at specific stages during development. For example, there are differences in the epigenome of cows born to heifers and those born to cows, and this epigenome seems to be sensitive to the availability of methyl donor compounds of the dam. Lastly, recent studies in other species have shown the relevance of paternal epigenetic marks, but this aspect has been, until now, largely overlooked in dairy cattle.
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31
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Xie X, Yang Y, Ren Q, Ding X, Bao P, Yan B, Yan X, Han J, Yan P, Qiu Q. Accumulation of deleterious mutations in the domestic yak genome. Anim Genet 2018; 49:384-392. [DOI: 10.1111/age.12703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2018] [Indexed: 12/19/2022]
Affiliation(s)
- X. Xie
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Y. Yang
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Q. Ren
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - P. Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - B. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - J. Han
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - P. Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - Q. Qiu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
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Fritz S, Hoze C, Rebours E, Barbat A, Bizard M, Chamberlain A, Escouflaire C, Vander Jagt C, Boussaha M, Grohs C, Allais-Bonnet A, Philippe M, Vallée A, Amigues Y, Hayes BJ, Boichard D, Capitan A. An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. J Dairy Sci 2018; 101:6220-6231. [DOI: 10.3168/jds.2017-14119] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/05/2018] [Indexed: 01/25/2023]
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Hoff JL, Decker JE, Schnabel RD, Taylor JF. Candidate lethal haplotypes and causal mutations in Angus cattle. BMC Genomics 2017; 18:799. [PMID: 29047335 PMCID: PMC5648474 DOI: 10.1186/s12864-017-4196-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/08/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population. RESULTS Seven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes. CONCLUSIONS Selective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.
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Affiliation(s)
- Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Michot P, Fritz S, Barbat A, Boussaha M, Deloche MC, Grohs C, Hoze C, Le Berre L, Le Bourhis D, Desnoes O, Salvetti P, Schibler L, Boichard D, Capitan A. A missense mutation in PFAS (phosphoribosylformylglycinamidine synthase) is likely causal for embryonic lethality associated with the MH1 haplotype in Montbéliarde dairy cattle. J Dairy Sci 2017; 100:8176-8187. [DOI: 10.3168/jds.2017-12579] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/21/2017] [Indexed: 01/09/2023]
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Weller JI, Ezra E, Ron M. Invited review: A perspective on the future of genomic selection in dairy cattle. J Dairy Sci 2017; 100:8633-8644. [PMID: 28843692 DOI: 10.3168/jds.2017-12879] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022]
Abstract
Genomic evaluation has been successfully implemented in the United States, Canada, Great Britain, Ireland, New Zealand, Australia, France, the Netherlands, Germany, and the Scandinavian countries. Adoption of this technology in the major dairy producing countries has led to significant changes in the worldwide dairy industry. Gradual elimination of the progeny test system has led to a reduction in the number of sires with daughter records and fewer genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Although genomic selection has been successful in increasing rates of genetic gain, we still know very little about the genetic architecture of quantitative variation. Apparently, a very large number of genes affect nearly all economic traits, in accordance with the infinitesimal model for quantitative traits. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and on environmentally friendly production with reduced waste and gas emission. Genetic variance for economic traits is maintained by the increase in frequency of rare alleles, new mutations, and changes in selection goals and management. Thus, it is unlikely that a selection plateau will be reached in the near future.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel.
| | - E Ezra
- Israeli Cattle Breeders Association, Caesarea Industrial Park 3088900, Israel
| | - M Ron
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
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Howard DM, Pong-Wong R, Knap PW, Woolliams JA. Use of haplotypes to identify regions harbouring lethal recessive variants in pigs. Genet Sel Evol 2017; 49:57. [PMID: 28709397 PMCID: PMC5512953 DOI: 10.1186/s12711-017-0332-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
Background Lethal recessive genetic variants are maintained at relatively low frequencies in a population in the heterozygous state, but by definition are fatal and therefore unobserved in the homozygous state. Since haplotypes allow the tagging of rare and untyped genetic variants, they have potential for studying lethal recessive variants. In this study, we used a large commercial population to identify putative lethal recessive haplotypes that impact either the total number born (TNB) or the number born alive (NBA) as a proportion of the total number born (NBA/TNB). We also compared the use of haplotypes with a single nucleotide polymorphism (SNP)-by-SNP approach and examined the benefits of using additional haplotypes imputed from low-density genotype data for the detection of lethal recessive variants. Candidate haplotypes were identified using population-wide haplotype frequencies and within-family analyses. These candidate haplotypes were subsequently assessed for putative lethal recessive effects on TNB and NBA/TNB by comparing carrier-to-carrier matings with carrier-to-non-carrier matings. Results Using both medium-density and imputed low-density genotype data six regions were identified as containing putative lethal recessive haplotypes that had an effect on TNB. It is likely that these regions were related to at least four putative lethal recessive variants, each located on a different chromosome. Evidence for putative lethal recessive effects on TNB was found on chromosomes 1, 6, 10 and 14 using haplotypes. Using haplotypes from individuals genotyped only at medium-density or a SNP-by-SNP approach did not detect any lethal recessive effects. No lethal recessive haplotypes or SNPs were detected that had an effect on NBA/TNB. Conclusions We show that the use of haplotypes from combining medium-density and imputed low-density genotype data is superior for the identification of lethal recessive variants compared to both a SNP-by-SNP approach and to the use of only medium-density data. We developed a formal statistical framework that provided sufficient power to detect lethal recessive variants in species, which produce large full-sib families, while reducing false positive or type I errors. Applying this framework results in improvements in reproductive performance by purging lethal recessive alleles from a population in a timely and cost-effective manner. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0332-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David M Howard
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK.
| | - Ricardo Pong-Wong
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK
| | - Pieter W Knap
- Genus-PIC, Ratsteich 31, 24837, Schleswig, Germany.,Genus PLC, 100 Bluegrass Commons Blvd, Suite 2200, Hendersonville, TN, 37075, USA
| | - John A Woolliams
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK
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37
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Ferenčaković M, Sölkner J, Kapš M, Curik I. Genome-wide mapping and estimation of inbreeding depression of semen quality traits in a cattle population. J Dairy Sci 2017; 100:4721-4730. [PMID: 28434751 DOI: 10.3168/jds.2016-12164] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/27/2017] [Indexed: 11/19/2022]
Abstract
Inbreeding depression is known to affect quantitative traits such as male fertility and sperm quality, but the genetic basis for these associations is poorly understood. Most studies have been limited to examining how pedigree- or marker-derived genome-wide autozygosity is associated with quantitative phenotypes. In this study, we analyzed possible associations of genetic features of inbreeding depression with percentage of live spermatozoa and total number of spermatozoa in 19,720 ejaculates obtained from 554 Austrian Fleckvieh bulls during routine artificial insemination programs. Genome-wide inbreeding depression was estimated and genomic regions contributing to inbreeding depression were mapped. Inbreeding depression did affect total number of spermatozoa, and such depression was predicted by pedigree-based inbreeding levels and genome-wide inbreeding levels based on runs of homozygosity (ROH). Genome-wide inbreeding depression did not seem to affect percentage of live spermatozoa. A model incorporating genetic effects of the bull, environmental factors, and additive genetic and ROH status effects of individual single-nucleotide polymorphisms revealed genomic regions significantly associated with ROH status for total number of spermatozoa (4 regions) or percentage of live spermatozoa (5 regions). All but one region contains genes related to spermatogenesis and sperm morphology. These genomic regions contain genes affecting sperm morphogenesis and efficacy. The results highlight that next-generation sequencing may help explain some of the genetic factors contributing to inbreeding depression of sperm quality traits in Fleckvieh bulls.
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Affiliation(s)
- Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetosimunska 25, 10000 Zagreb, Croatia
| | - Johann Sölkner
- University of Natural Resources and Life Sciences Vienna, Department of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria.
| | - Miroslav Kapš
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetosimunska 25, 10000 Zagreb, Croatia
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetosimunska 25, 10000 Zagreb, Croatia
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de Camargo GMF, Costa RB, de Albuquerque LG, Regitano LCA, Baldi F, Tonhati H. Polymorphisms in TOX and NCOA2 genes and their associations with reproductive traits in cattle. Reprod Fertil Dev 2017; 27:523-8. [PMID: 25482955 DOI: 10.1071/rd13360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/04/2014] [Indexed: 12/13/2022] Open
Abstract
Reproductive traits are an important component of the economic selection index for beef cattle in the tropics. Phenotypic expression of these traits occurs late because they are measured when the animals reach reproductive age. Association studies using high-density markers have been conducted to identify genes that influence certain traits. The identification of causal mutations in these genes permits the inclusion of these single nucleotide polymorphisms (SNPs) in customised DNA chips to increase efficiency and validity. Therefore, the aim of the present study was to detect causal mutations in the TOX and NCOA2 genes, previously identified by genome-wide association studies of zebu cattle. DNA was extracted from 385 Nellore females and polymorphisms were investigated by polymerase chain reaction sequencing. Five polymorphisms were detected in the NCOA2 gene and four in the TOX gene that were associated with reproductive traits. Analysis of variance showed that SNP 1718 in the NCOA2 gene was significant for early pregnancy probability (P=0.02) and age at first calving (P=0.03), and SNP 2038 in the same gene was significant for days to calving (P=0.03). Studies investigating polymorphisms in other regions of the gene and in other genes should be conducted to identify causal mutations.
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Affiliation(s)
- Gregório M F de Camargo
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, s/n, 14884-900, Jaboticabal-SP, Brazil
| | - Raphael B Costa
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, s/n, 14884-900, Jaboticabal-SP, Brazil
| | - Lucia G de Albuquerque
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, s/n, 14884-900, Jaboticabal-SP, Brazil
| | - Luciana C A Regitano
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Centro Pecuária Sudeste, Rodovia Washington Luiz, km 234, 13560-970, São Carlos-SP, Brazil
| | - Fernando Baldi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, s/n, 14884-900, Jaboticabal-SP, Brazil
| | - Humberto Tonhati
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, s/n, 14884-900, Jaboticabal-SP, Brazil
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39
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Ortega MS, Denicol AC, Cole JB, Null DJ, Taylor JF, Schnabel RD, Hansen PJ. Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows. J Dairy Sci 2017; 100:3725-3734. [PMID: 28259397 DOI: 10.3168/jds.2016-12260] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/07/2017] [Indexed: 11/19/2022]
Abstract
Many genetic markers related to health or production traits are not evaluated in populations independent of the discovery population or related to phenotype. Here we evaluated 68 single nucleotide polymorphisms (SNP) in candidate genes previously associated with genetic merit for fertility and production traits for association with phenotypic measurements of fertility in a population of Holstein cows that was selected based on predicted transmitting ability (PTA) for daughter pregnancy rate (DPR; high, ≥1, n = 989; low, ≤ -1.0, n = 1,285). Cows with a high PTA for DPR had higher pregnancy rate at first service, fewer services per conception, and fewer days open than cows with a low PTA for DPR. Of the 68 SNP, 11 were associated with pregnancy rate at first service, 16 with services per conception, and 19 with days open. Single nucleotide polymorphisms in 12 genes (BDH2, BSP3, CAST, CD2, CD14, FUT1, FYB, GCNT3, HSD17B7, IBSP, OCLN, and PCCB) had significant associations with 2 fertility traits, and SNP in 4 genes (CSPP1, FCER1G, PMM2, and TBC1D24) had significant associations with each of the 3 traits. Results from this experiment were compared with results from 2 earlier studies in which the SNP were associated with genetic estimates of fertility. One study involved the same animals as used here, and the other study was of an independent population of bulls. A total of 13 SNP associated with 1 or more phenotypic estimates of fertility were directionally associated with genetic estimates of fertility in the same cow population. Moreover, 14 SNP associated with reproductive phenotype were directionally associated with genetic estimates of fertility in the bull population. Nine SNP (located in BCAS, BSP3, CAST, FUT1, HSD17B7, OCLN, PCCB, PMM2, and TBC1D24) had a directional association with fertility in all 3 studies. Examination of the function of the genes with SNP associated with reproduction in more than one study indicates the importance of steroid hormones and immune function as determinants of reproductive function. All but 1 of the 68 evaluated SNP were variable in 11 breeds besides Holstein, indicating the potential effects of these SNP on reproductive function across breeds of cattle.
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Affiliation(s)
- M Sofia Ortega
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville 32611
| | - Anna C Denicol
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville 32611
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Daniel J Null
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia 65211
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia 65211; Informatics Institute, University of Missouri, Columbia 65211
| | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville 32611.
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40
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Ortega MS, Wohlgemuth S, Tribulo P, Siqueira LGB, Null DJ, Cole JB, Da Silva MV, Hansen PJ. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows†. Biol Reprod 2017; 96:652-663. [DOI: 10.1093/biolre/iox004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/31/2017] [Indexed: 11/12/2022] Open
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Sharma A, Cho Y, Choi BH, Chai HH, Park JE, Lim D. Limited representation of OMIA causative mutations for cattle in SNP databases. Anim Genet 2017; 48:369-370. [PMID: 28116762 DOI: 10.1111/age.12534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Aditi Sharma
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
| | - Yongmin Cho
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
| | - Han-Ha Chai
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
| | - Jong-Eun Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Korea
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Biscarini F, Schwarzenbacher H, Pausch H, Nicolazzi EL, Pirola Y, Biffani S. Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations. BMC Genomics 2016; 17:857. [PMID: 27809787 PMCID: PMC5093950 DOI: 10.1186/s12864-016-3218-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/26/2016] [Indexed: 01/09/2023] 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 mutations. 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 compared - through cross-validation- five classification models (Lasso-penalized logistic regression -Lasso, Support Vector Machines with either linear or radial kernel -SVML and SVMR, k-nearest neighbors -KNN, and multi-allelic gene prediction -MAG), for the identification of carriers of the TUBD1 recessive mutation on BTA19 (Bos taurus autosome 19), known to be associated with high calf mortality. A population of 3116 Fleckvieh and 392 Brown Swiss animals genotyped with the 54K SNP-chip was available for the analysis. RESULTS In general, the use of SNP genotypes proved to be very effective for the identification of mutation carriers. The best predictive models were Lasso, SVML and MAG, with an average error rate, respectively, of 0.2 %, 0.4 % and 0.6 % in Fleckvieh, and 1.2 %, 0.9 % and 1.7 % in Brown Swiss. For the three models, the false positive rate was, respectively, 0.1 %, 0.1 % and 0.2 % in Fleckvieh, and 3.0 %, 2.4 % and 1.6 % in Brown Swiss; the false negative rate was 4.4 %, 7.6 %1.0 % in Fleckvieh, and 0.0 %, 0.1% and 0.8 % in Brown Swiss. MAG appeared to be more robust to sample size reduction: with 25 % of the data, the average error rate was 0.7 % and 2.2 % in Fleckvieh and Brown Swiss, compared to 2.1 % and 5.5 % with Lasso, and 2.6 % and 12.0 % with SVML. CONCLUSIONS The use of SNP genotypes is a very effective and efficient technique for the identification of mutation carriers in cattle populations. Very few misclassifications were observed, overall and both in the carriers and non-carriers classes. This indicates that this is a very reliable approach for potential applications in cattle breeding.
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Affiliation(s)
- Filippo Biscarini
- Department of Bioinformatics and Biostatistics, PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | - Hubert Pausch
- Technische Universität München, Liesel-Beckmann-Straße 1, Freising-Weihenstephan, D-85354 Germany
| | - Ezequiel L. Nicolazzi
- Department of Bioinformatics and Biostatistics, PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Yuri Pirola
- DISCo, Università degli Studi di Milano-Bicocca, Viale Sarca 336, Milano, Italy
| | - Stefano Biffani
- Department of Bioinformatics and Biostatistics, PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, 26900 Italy
- IBBA-CNR, Via Einstein - Loc. Cascina Codazza, Lodi, 26900 Italy
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Charlier C, Li W, Harland C, Littlejohn M, Coppieters W, Creagh F, Davis S, Druet T, Faux P, Guillaume F, Karim L, Keehan M, Kadri NK, Tamma N, Spelman R, Georges M. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res 2016; 26:1333-1341. [PMID: 27646536 PMCID: PMC5052051 DOI: 10.1101/gr.207076.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/19/2016] [Indexed: 01/20/2023]
Abstract
We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.
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Affiliation(s)
- Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Wanbo Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, P.R. China
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Mathew Littlejohn
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Frances Creagh
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Steve Davis
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - François Guillaume
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Mike Keehan
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Richard Spelman
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
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Cole J, Null D, VanRaden P. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J Dairy Sci 2016; 99:7274-7288. [DOI: 10.3168/jds.2015-10777] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/31/2016] [Indexed: 11/19/2022]
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A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds. Genet Sel Evol 2016; 48:56. [PMID: 27510606 PMCID: PMC4980790 DOI: 10.1186/s12711-016-0232-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background Domestication and artificial selection have resulted in strong genetic drift, relaxation of purifying selection and accumulation of deleterious mutations. As a consequence, bovine breeds experience regular outbreaks of recessive genetic defects which might represent only the tip of the iceberg since their detection depends on the observation of affected animals with distinctive symptoms. Thus, recessive mutations resulting in embryonic mortality or in non-specific symptoms are likely to be missed. The increasing availability of whole-genome sequences has opened new research avenues such as reverse genetics for their investigation. Our aim was to characterize the genetic load of 15 European breeds using data from the 1000 bull genomes consortium and prove that widespread harmful mutations remain to be detected. Results We listed 2489 putative deleterious variants (in 1923 genes) segregating at a minimal frequency of 5 % in at least one of the breeds studied. Gene enrichment analysis showed major enrichment for genes related to nervous, visual and auditory systems, and moderate enrichment for genes related to cardiovascular and musculoskeletal systems. For verification purposes, we investigated the phenotypic consequences of a frameshift variant in the retinitis pigmentosa-1 gene segregating in several breeds and at a high frequency (27 %) in Normande cattle. As described in certain human patients, clinical and histological examination revealed that this mutation causes progressive degeneration of photoreceptors leading to complete blindness in homozygotes. We established that the deleterious allele was even more frequent in the Normande breed before 1975 (>40 %) and has been progressively counter-selected likely because of its associated negative effect on udder morphology. Finally, using identity-by-descent analysis we demonstrated that this mutation resulted from a unique ancestral event that dates back to ~2800 to 4000 years. Conclusions We provide a list of mutations that likely represent a substantial part of the genetic load of domestication in European cattle. We demonstrate that they accumulated non-randomly and that genes related to cognition and sensory functions are particularly affected. Finally, we describe an ancestral deleterious variant segregating in different breeds causing progressive retinal degeneration and irreversible blindness in adult animals. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0232-y) contains supplementary material, which is available to authorized users.
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Adams HA, Sonstegard TS, VanRaden PM, Null DJ, Van Tassell CP, Larkin DM, Lewin HA. Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle. J Dairy Sci 2016; 99:6693-6701. [DOI: 10.3168/jds.2015-10517] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/23/2016] [Indexed: 11/19/2022]
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Saleem S, Heuer C, Sun C, Kendall D, Moreno J, Vishwanath R. Technical note: The role of circulating low-density lipoprotein levels as a phenotypic marker for Holstein cholesterol deficiency in dairy cattle. J Dairy Sci 2016; 99:5545-5550. [PMID: 27108167 DOI: 10.3168/jds.2015-10805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/14/2016] [Indexed: 11/19/2022]
Abstract
With the recent discovery of a Holstein cholesterol deficiency (HCD) haplotype, the USDA has labeled many dairy animals as HCD carriers based on haplotype and pedigree analysis. We set out to investigate the effect of HCD status on various cholesterol transport molecules, namely low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides in both males and females. A genome-wide association study was also conducted to narrow down the genomic region correlated with varying LDL-C levels. In the study, 34 HCD carrier animals showed significantly lower cholesterol and LDL-C levels compared with their 34 closely related, non-HCD controls. The genome-wide association study based on 73 animals using 56,198 SNP markers revealed an association with chromosome 11 in the region of 66,218,925 to 66,946,746 bp. We also tested the effect of HCD status on sperm quality traits using fresh ejaculates and frozen-thawed semen samples, but did not find any discriminating effects. Our study has demonstrated the use of LDL-C as a key phenotypic marker for determining HCD status in dairy cattle and this is the first study that clearly shows a cause-effect relationship of the HCD haplotype on circulating LDL-C.
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Affiliation(s)
- S Saleem
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868
| | - C Heuer
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868
| | - C Sun
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868
| | - D Kendall
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868
| | - J Moreno
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868
| | - R Vishwanath
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX 77868.
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Schrimpf R, Gottschalk M, Metzger J, Martinsson G, Sieme H, Distl O. Screening of whole genome sequences identified high-impact variants for stallion fertility. BMC Genomics 2016; 17:288. [PMID: 27079378 PMCID: PMC4832559 DOI: 10.1186/s12864-016-2608-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/30/2016] [Indexed: 02/07/2023] Open
Abstract
Background Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Methods Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). Results We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant g.37455302G>A in NOTCH1 with the de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). For 9 high-impact variants within the genes CFTR, OVGP1, FBXO43, TSSK6, PKD1, FOXP1, TCP11, SPATA31E1 and NOTCH1 (g.37453246G>C) absence of the homozygous mutant genotype in the validation sample of all 337 fertile stallions was obvious. Therefore, these variants were considered as potentially deleterious factors for stallion fertility. Conclusions In conclusion, this study revealed 17 genetic variants with a predicted high damaging effect on protein structure and missing homozygous mutant genotype. The g.37455302G>A NOTCH1 variant was identified as a significant stallion fertility locus in Hanoverian stallions and further 9 candidate fertility loci with missing homozygous mutant genotypes were validated in a panel including 19 horse breeds. To our knowledge this is the first study in horses using next generation sequencing data to uncover strong candidate factors for stallion fertility. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2608-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahel Schrimpf
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
| | - Maren Gottschalk
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
| | - Gunilla Martinsson
- State Stud Celle of Lower Saxony, Spörckenstraße 10, 29221, Celle, Germany
| | - Harald Sieme
- Clinic for Horses, Unit for Reproduction Medicine, University of Veterinary Medicine Hannover, Bünteweg 15, 30559, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany.
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Bickhart DM, Hutchison JL, Null DJ, VanRaden PM, Cole JB. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. J Dairy Sci 2016; 99:5526-5534. [PMID: 27085415 DOI: 10.3168/jds.2015-10347] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/23/2015] [Indexed: 11/19/2022]
Abstract
Many studies leverage targeted whole-genome sequencing (WGS) experiments to identify rare and causal variants within populations. As a natural consequence of their experimental design, many of these surveys tend to sequence redundant haplotype segments due to their high frequency in the base population, and the variants discovered within sequencing data are difficult to phase. We propose a new algorithm, called inverse weight selection (IWS), that preferentially selects individuals based on the cumulative presence of rare frequency haplotypes to maximize the efficiency of WGS surveys. To test the efficacy of this method, we used genotype data from 112,113 registered Holstein bulls derived from the US national dairy database. We demonstrate that IWS is at least 6.8% more efficient than previously published methods in selecting the least number of individuals required to sequence all haplotype segments ≥4% frequency in the US Holstein population. We also suggest that future surveys focus on sequencing homozygous haplotype segments as a first pass to achieve a 50% reduction in cost with an added benefit of phasing variant calls efficiently. Together, this new selection algorithm and experimental design suggestion significantly reduce the overall cost of variant discovery through WGS experiments, making surveys for causal variants influencing disease and production even more efficient.
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Affiliation(s)
- D M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
| | - J L Hutchison
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - D J Null
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
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Lim D, Strucken EM, Choi BH, Chai HH, Cho YM, Jang GW, Kim TH, Gondro C, Lee SH. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea. PLoS One 2016; 11:e0151324. [PMID: 27023061 PMCID: PMC4811422 DOI: 10.1371/journal.pone.0151324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 02/26/2016] [Indexed: 01/01/2023] Open
Abstract
Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.
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Affiliation(s)
- Dajeong Lim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Eva M. Strucken
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Bong Hwan Choi
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Han Ha Chai
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Yong Min Cho
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Gul Won Jang
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Tae-Hun Kim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305–764, Republic of Korea
- * E-mail:
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