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Wang J, Gao G, Wang D. Developing AAV-delivered nonsense suppressor tRNAs for neurological disorders. Neurotherapeutics 2024; 21:e00391. [PMID: 38959711 PMCID: PMC11269797 DOI: 10.1016/j.neurot.2024.e00391] [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: 02/14/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Adeno-associated virus (AAV)-based gene therapy is a clinical stage therapeutic modality for neurological disorders. A common genetic defect in myriad monogenic neurological disorders is nonsense mutations that account for about 11% of all human pathogenic mutations. Stop codon readthrough by suppressor transfer RNA (sup-tRNA) has long been sought as a potential gene therapy approach to target nonsense mutations, but hindered by inefficient in vivo delivery. The rapid advances in AAV delivery technology have not only powered gene therapy development but also enabled in vivo preclinical assessment of a range of nucleic acid therapeutics, such as sup-tRNA. Compared with conventional AAV gene therapy that delivers a transgene to produce therapeutic proteins, AAV-delivered sup-tRNA has several advantages, such as small gene sizes and operating within the endogenous gene expression regulation, which are important considerations for treating some neurological disorders. This review will first examine sup-tRNA designs and delivery by AAV vectors. We will then analyze how AAV-delivered sup-tRNA can potentially address some neurological disorders that are challenging to conventional gene therapy, followed by discussing available mouse models of neurological diseases for in vivo preclinical testing. Potential challenges for AAV-delivered sup-tRNA to achieve therapeutic efficacy and safety will also be discussed.
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Affiliation(s)
- Jiaming Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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Boussaha M, Boulling A, Wolgust V, Bourgeois-Brunel L, Michot P, Grohs C, Gaiani N, Grivaud PY, Leclerc H, Danchin-Burge C, Vilotte M, Rivière J, Boichard D, Gourreau JM, Capitan A. Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle. Genet Sel Evol 2023; 55:40. [PMID: 37308849 DOI: 10.1186/s12711-023-00814-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Inherited epidermolysis bullosa (EB) is a group of painful and life-threatening genetic disorders that are characterized by mechanically induced blistering of the skin and mucous membranes. Congenital skin fragility resembling EB was recently reported in three Charolais calves born in two distinct herds from unaffected parents. Phenotypic and genetic analyses were carried out to describe this condition and its molecular etiology. RESULTS Genealogical, pathological and histological investigations confirmed the diagnosis of recessive EB. However, the affected calves showed milder clinical signs compared to another form of EB, which was previously reported in the same breed and is caused by a homozygous deletion of the ITGB4 gene. Homozygosity mapping followed by analysis of the whole-genome sequences of two cases and 5031 control individuals enabled us to prioritize a splice donor site of ITGA6 (c.2160 + 1G > T; Chr2 g.24112740C > A) as the most compelling candidate variant. This substitution showed a perfect genotype-phenotype correlation in the two affected pedigrees and was found to segregate only in Charolais, and at a very low frequency (f = 1.6 × 10-4) after genotyping 186,154 animals from 15 breeds. Finally, RT-PCR analyses revealed increased retention of introns 14 and 15 of the ITGA6 gene in a heterozygous mutant cow compared with a matched control. The mutant mRNA is predicted to cause a frameshift (ITGA6 p.I657Mfs1) that affects the assembly of the integrin α6β4 dimer and its correct anchoring to the cell membrane. This dimer is a key component of the hemidesmosome anchoring complex, which ensures the attachment of basal epithelial cells to the basal membrane. Based on these elements, we arrived at a diagnosis of junctional EB. CONCLUSIONS We report a rare example of partial phenocopies observed in the same breed and due to mutations that affect two members of the same protein dimer, and provide the first evidence of an ITGA6 mutation that causes EB in livestock species.
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Affiliation(s)
- Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Arnaud Boulling
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Valérie Wolgust
- Unité de Pathologie du Bétail, Ecole Nationale Vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | | | - Pauline Michot
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Eliance, 75012, Paris, France
- Herd Book Charolais, 58470, Magny-Cours, France
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Nicolas Gaiani
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Pierre-Yves Grivaud
- Cabinet Vétérinaire des Monts du Charolais, 71220, Saint Bonnet de Joux, France
| | - Hélène Leclerc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Eliance, 75012, Paris, France
| | | | - Marthe Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Julie Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS, 78350, Jouy-en-Josas, France
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Marie Gourreau
- Unité de Pathologie du Bétail, Ecole Nationale Vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Aurélien Capitan
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
- Eliance, 75012, Paris, France.
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Ahmad SF, Singh A, Gangwar M, Kumar S, Dutt T, Kumar A. Haplotype-based association study of production and reproduction traits in multigenerational Vrindavani population. Gene 2023; 867:147365. [PMID: 36918047 DOI: 10.1016/j.gene.2023.147365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations.
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Affiliation(s)
- Sheikh Firdous Ahmad
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Akansha Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Munish Gangwar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subodh Kumar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Amit Kumar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Ivanenko AV, Evtushenko NA, Gurskaya NG. Genome Editing in Therapy of Genodermatoses. Mol Biol 2022. [DOI: 10.1134/s0026893322060085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Guan X, Zhao S, Xiang W, Jin H, Chen N, Lei C, Jia Y, Xu L. Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing. BIOLOGY 2022; 11:biology11091327. [PMID: 36138806 PMCID: PMC9495734 DOI: 10.3390/biology11091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/07/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary To protect the genetic resources of Chinese native cattle breeds, we investigated the genetic structure, genetic diversity and genetic signature from artificial or natural selection by sequencing 32 bovine genomes from the breeding farm of the Dabieshan population. We discovered that the ancestral contributions of Dabieshan originated from Chinese indicine and East Asian taurine on the autosomal genome, which had abundant genomic diversity. Some candidate genes associated with fertility, feed efficiency, fat deposition, immune response, heat resistance and the coat color were identified by a selective sweep. The SNPs data were based on genomics, which could establish a foundation for breed amelioration and support conservation for indigenous cattle breeds. Abstract Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.
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Affiliation(s)
- Xiwen Guan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Shuanping Zhao
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Weixuan Xiang
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Hai Jin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yutang Jia
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lei Xu
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence: ; Tel.: +86-153-7547-2704
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Widmer S, Seefried FR, von Rohr P, Häfliger IM, Spengeler M, Drögemüller C. Associated regions for multiple birth in Brown Swiss and Original Braunvieh cattle on chromosomes 15 and 11. Anim Genet 2022; 53:557-569. [PMID: 35748198 PMCID: PMC9539900 DOI: 10.1111/age.13229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/30/2022]
Abstract
Twin and multiple births have negative effects on the performance and health of cows and calves. To decipher the genetic architecture of this trait in the two Swiss Brown Swiss cattle populations, we performed various association analyses based on de-regressed breeding values. Genome-wide association analyses were executed using ~600 K imputed SNPs for the maternal multiple birth trait in ~3500 Original Braunvieh and ~7800 Brown Swiss animals. Significantly associated QTL were observed on different chromosomes for both breeds. We have identified on chromosome 11 a QTL that explains ~6% of the total genetic variance of the maternal multiple birth trait in Original Braunvieh. For the Brown Swiss breed, we have discovered a QTL on chromosome 15 that accounts for ~4% of the total genetic variance. For Original Braunvieh, subsequent haplotype analysis revealed a 90-kb window on chromosome 11 at 88 Mb, where a likely regulatory region is located close to the ID2 gene. In Brown Swiss, a 130-kb window at 75 Mb on chromosome 15 was identified. Analysis of whole-genome sequence data using linkage-disequilibrium estimation revealed possible causal variants for the identified QTL. A presumably regulatory variant in the non-coding 5' region of the ID2 gene was strongly associated with the haplotype for Original Braunvieh. In Brown Swiss, an intron variant in PRDM11, one 3' UTR variant in SYT13 and three intergenic variants 5' upstream of SYT13 were identified as candidate variants for the trait multiple birth maternal. In this study, we report for the first time QTL for the trait of multiple births in Original Braunvieh and Brown Swiss cattle. Moreover, our findings are another step towards a better understanding of the complex genetic architecture of this polygenic trait.
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Affiliation(s)
- Sarah Widmer
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | | | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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Hiltpold M, Janett F, Mapel XM, Kadri NK, Fang ZH, Schwarzenbacher H, Seefried FR, Spengeler M, Witschi U, Pausch H. A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities. Genet Sel Evol 2022; 54:18. [PMID: 35255804 PMCID: PMC8900305 DOI: 10.1186/s12711-022-00710-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/17/2022] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
Semen quality and insemination success are monitored in artificial insemination bulls to ensure high male fertility rates. Only ejaculates that fulfill minimum quality requirements are processed and eventually used for artificial inseminations. We examined 70,990 ejaculates from 1343 Brown Swiss bulls to identify bulls from which all ejaculates were rejected due to low semen quality. This procedure identified a bull that produced 12 ejaculates with an aberrantly small number of sperm (0.2 ± 0.2 × 109 sperm per mL) which were mostly immotile due to multiple morphological abnormalities.
Results
The genome of this bull was sequenced at a 12× coverage to investigate a possible genetic cause. Comparing the sequence variant genotypes of this bull with those from 397 fertile bulls revealed a 1-bp deletion in the coding sequence of the QRICH2 gene which encodes the glutamine rich 2 protein, as a compelling candidate causal variant. This 1-bp deletion causes a frameshift in translation and a premature termination codon (ENSBTAP00000018337.1:p.Cys1644AlafsTer52). The analysis of testis transcriptomes from 76 bulls showed that the transcript with the premature termination codon is subject to nonsense-mediated mRNA decay. The 1-bp deletion resides in a 675-kb haplotype that includes 181 single nucleotide polymorphisms (SNPs) from the Illumina BovineHD Bead chip. This haplotype segregates at a frequency of 5% in the Brown Swiss cattle population. Our analysis also identified another bull that carried the 1-bp deletion in the homozygous state. Semen analyses from the second bull confirmed low sperm concentration and immotile sperm with multiple morphological abnormalities that primarily affect the sperm flagellum and, to a lesser extent, the sperm head.
Conclusions
A recessive loss-of-function allele of the bovine QRICH2 gene likely causes low sperm concentration and immotile sperm with multiple morphological abnormalities. Routine sperm analyses unambiguously identify homozygous bulls for this allele. A direct gene test can be implemented to monitor the frequency of the undesired allele in cattle populations.
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Nosková A, Hiltpold M, Janett F, Echtermann T, Fang ZH, Sidler X, Selige C, Hofer A, Neuenschwander S, Pausch H. Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing. Genetics 2021; 217:6041611. [PMID: 33724408 DOI: 10.1093/genetics/iyaa033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Maya Hiltpold
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Fredi Janett
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Echtermann
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Xaver Sidler
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Stefan Neuenschwander
- Animal Genetics, Institute of Agricultural Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
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Widmer S, Seefried FR, von Rohr P, Häfliger IM, Spengeler M, Drögemüller C. A major QTL at the LHCGR/FSHR locus for multiple birth in Holstein cattle. Genet Sel Evol 2021; 53:57. [PMID: 34217202 PMCID: PMC8255007 DOI: 10.1186/s12711-021-00650-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Twin and multiple births are rare in cattle and have a negative impact on the performance and health of cows and calves. Therefore, selection against multiple birth would be desirable in dairy cattle breeds such as Holstein. We applied different methods to decipher the genetic architecture of this trait using de-regressed breeding values for maternal multiple birth of ~ 2500 Holstein individuals to perform genome-wide association analyses using ~ 600 K imputed single nucleotide polymorphisms (SNPs). RESULTS In the population studied, we found no significant genetic trend over time of the estimated breeding values for multiple birth, which indicates that this trait has not been selected for in the past. In addition to several suggestive non-significant quantitative trait loci (QTL) on different chromosomes, we identified a major QTL on chromosome 11 for maternal multiple birth that explains ~ 16% of the total genetic variance. Using a haplotype-based approach, this QTL was fine-mapped to a 70-kb window on chromosome 11 between 31.00 and 31.07 Mb that harbors two functional candidate genes (LHCGR and FSHR). Analysis of whole-genome sequence data by linkage-disequilibrium estimation revealed a regulatory variant in the 5'-region of LHCGR as a possible candidate causal variant for the identified major QTL. Furthermore, the identified haplotype showed significant effects on stillbirth and days to first service. CONCLUSIONS QTL detection and subsequent identification of causal variants in livestock species remain challenging in spite of the availability of large-scale genotype and phenotype data. Here, we report for the first time a major QTL for multiple birth in Holstein cattle and provide evidence for a linked variant in the non-coding region of a functional candidate gene. This discovery, which is a first step towards the understanding of the genetic architecture of this polygenic trait, opens the path for future selection against this undesirable trait, and thus contributes to increased animal health and welfare.
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Affiliation(s)
- Sarah Widmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | | | - 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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Hiltpold M, Kadri NK, Janett F, Witschi U, Schmitz-Hsu F, Pausch H. Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population. BMC Genomics 2021; 22:225. [PMID: 33784962 PMCID: PMC8010996 DOI: 10.1186/s12864-021-07523-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cattle are ideally suited to investigate the genetics of male fertility. Semen from individual bulls is used for thousands of artificial inseminations for which the fertilization success is monitored. Results from the breeding soundness examination and repeated observations of semen quality complement the fertility evaluation for each bull. RESULTS In a cohort of 3881 Brown Swiss bulls that had genotypes at 683,609 SNPs, we reveal four novel recessive QTL for male fertility on BTA1, 18, 25, and 26 using haplotype-based association testing. A QTL for bull fertility on BTA1 is also associated with sperm head shape anomalies. All other QTL are not associated with any of the semen quality traits investigated. We perform complementary fine-mapping approaches using publicly available transcriptomes as well as whole-genome sequencing data of 125 Brown Swiss bulls to reveal candidate causal variants. We show that missense or nonsense variants in SPATA16, VWA3A, ENSBTAG00000006717 and ENSBTAG00000019919 are in linkage disequilibrium with the QTL. Using whole-genome sequence data, we detect strong association (P = 4.83 × 10- 12) of a missense variant (p.Ile193Met) in SPATA16 with male fertility. However, non-coding variants exhibit stronger association at all QTL suggesting that variants in regulatory regions contribute to variation in bull fertility. CONCLUSION Our findings in a dairy cattle population provide evidence that recessive variants may contribute substantially to quantitative variation in male fertility in mammals. Detecting causal variants that underpin variation in male fertility remains difficult because the most strongly associated variants reside in poorly annotated non-coding regions.
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Affiliation(s)
- Maya Hiltpold
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland.
| | - Naveen Kumar Kadri
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
| | - Fredi Janett
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | | | | | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
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Mehrotra A, Bhushan B, Kumar A, Panigrahi M, A K, Singh A, Tiwari AK, Pausch H, Dutt T, Mishra BP. A 1.6 Mb region on SSC2 is associated with antibody response to classical swine fever vaccination in a mixed pig population. Anim Biotechnol 2021; 33:1128-1133. [PMID: 33451274 DOI: 10.1080/10495398.2021.1873145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Classical Swine Fever (CSF) is a contagious viral disease of pigs which is endemic in several parts of the world, including India. Prophylactic vaccination using live attenuated vaccine is the preferred method of control. However, there is significant inter-individual variation in the antibody response to vaccination. In this study, we measured the E2 antibody blocking percentage after 21 days of CSF vaccination in a mixed pig population consisting of Landrace, indigenous Ghurrah pigs, and their crossbreds. A Genome Wide Association Study (GWAS) carried out using single-SNP and haplotype based methods detected a 1.6 Mb region on SSC2 (28.92-30.52 Mb) as significantly associated with antibody response to CSF vaccination. The significant region and 1 Mb flanking sequences encompass 3 genes - EIF3M, DNAJC24 and ARL14EP, which code for proteins involved in Pestivirus replication and host immune response system. Our results combined with previous studies on immune response of pigs present this region as a suitable candidate for future functional investigations.
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Affiliation(s)
- Arnav Mehrotra
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Karthikeyan A
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Akansha Singh
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Ashok K Tiwari
- Biological Standardization Division, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Triveni Dutt
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bishnu P Mishra
- Animal Biotechnology, ICAR - Indian Veterinary Research Institute, Bareilly, UP, India
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12
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Nosková A, Wurmser C, Crysnanto D, Sironen A, Uimari P, Fries R, Andersson M, Pausch H. Deletion of porcine BOLL is associated with defective acrosomes and subfertility in Yorkshire boars. Anim Genet 2020; 51:945-949. [PMID: 32975846 DOI: 10.1111/age.12998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 12/30/2022]
Abstract
A recessive sperm defect of Yorkshire boars was detected more than a decade ago. Affected boars produce ejaculates that contain spermatozoa with defective acrosomes, resulting in low fertility. The acrosome defect was mapped to porcine chromosome 15 but the causal mutation has not been identified. We re-analyzed microarray-derived genotypes of affected boars and confirmed that the acrosome defect maps to a 12.24 Mb segment of porcine chromosome 15. To detect the mutation causing defective acrosomes, we sequenced the genomes of two affected and three unaffected boars to an average coverage of 11-fold. Read depth analysis revealed a 55 kb deletion that is associated with the acrosome defect. The deletion encompasses the BOLL gene encoding the boule homolog, an RNA binding protein which is an evolutionarily conserved member of the DAZ (Deleted in AZoospermia) gene family. Lack of BOLL expression causes spermatogenic arrest and sperm maturation failure in many species. Boars that carry the deletion in the homozygous state produce sperm but their acrosomes are defective, suggesting that lack of porcine BOLL compromises acrosome formation. Our findings warrant further research to investigate the role of BOLL during spermatogenesis and sperm maturation in pigs.
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Affiliation(s)
- A Nosková
- Animal Genomics, ETH Zürich, Eschikon 27, Lindau, 8315, Switzerland
| | - C Wurmser
- Chair of Animal Breeding, TU München, Liesel-Beckmann-Str. 1, Freising, 85354, Germany
| | - D Crysnanto
- Animal Genomics, ETH Zürich, Eschikon 27, Lindau, 8315, Switzerland
| | - A Sironen
- Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland
| | - P Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - R Fries
- Chair of Animal Breeding, TU München, Liesel-Beckmann-Str. 1, Freising, 85354, Germany
| | - M Andersson
- Department of Production Animal Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - H Pausch
- Animal Genomics, ETH Zürich, Eschikon 27, Lindau, 8315, Switzerland
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13
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Fang ZH, Nosková A, Crysnanto D, Neuenschwander S, Vögeli P, Pausch H. A 63-bp insertion in exon 2 of the porcine KIF21A gene is associated with arthrogryposis multiplex congenita. Anim Genet 2020; 51:820-823. [PMID: 32686171 DOI: 10.1111/age.12984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 12/30/2022]
Abstract
A recessive form of arthrogryposis multiplex congenita (AMC) was detected 20 years ago in the Swiss Large White (SLW) pig population. A diagnostic marker test enabled the identification of carrier animals, but the underlying causal mutation remains unknown. To identify the mutation underlying AMC, we collected SNP chip genotyping data for 11 affected piglets and 23 healthy pigs. Association testing using 47 829 SNPs confirmed that AMC maps to SSC5 (P = 9.4 × 10-13 ). Subsequent autozygosity mapping revealed a common 6.06 Mb region (from 66 757 970 to 72 815 151 bp) of extended homozygosity in 11 piglets affected by AMC. Using WGS data, we detected a 63-bp insertion compatible with the recessive inheritance of AMC in the second exon of KIF21A gene encoding Kinesin Family Member 21A. The 63-bp insertion is predicted to introduce a premature stop codon in KIF21A gene (p.Val41_Phe42insTer) that truncates 1614 amino acids (~97%) from the protein. We found that this deleterious allele still segregates at a frequency of 0.1% in the SLW pig population. Carrier animals can now be detected unambiguously and excluded from breeding.
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Affiliation(s)
- Z-H Fang
- Animal Genomics, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
| | - A Nosková
- Animal Genomics, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
| | - D Crysnanto
- Animal Genomics, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
| | - S Neuenschwander
- Animal Genetics unit, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
| | - P Vögeli
- Animal Genetics unit, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
| | - H Pausch
- Animal Genomics, Institute of Agricultural Science, D-USYS, ETH Zürich, Zürich, 8092, Switzerland
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14
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Maciak S, Sawicka D, Sadowska A, Prokopiuk S, Buczyńska S, Bartoszewicz M, Niklińska G, Konarzewski M, Car H. Low basal metabolic rate as a risk factor for development of insulin resistance and type 2 diabetes. BMJ Open Diabetes Res Care 2020; 8:8/1/e001381. [PMID: 32690630 PMCID: PMC7373309 DOI: 10.1136/bmjdrc-2020-001381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Identification of physiological factors influencing susceptibility to insulin resistance and type 2 diabetes (T2D) remains an important challenge for biology and medicine. Numerous studies reported energy expenditures as one of those components directly linked to T2D, with noticeable increase of basal metabolic rate (BMR) associated with the progression of insulin resistance. Conversely, the putative link between genetic, rather than phenotypic, determination of BMR and predisposition to development of T2D remains little studied. In particular, low BMR may constitute a considerable risk factor predisposing to development of T2D. RESEARCH DESIGN AND METHODS We analyzed the development of insulin resistance and T2D in 20-week-old male laboratory mice originating from three independent genetic line types. Two of those lines were subjected to divergent, non-replicated selection towards high or low body mass-corrected BMR. The third line type was non-selected and consisted of randomly bred animals serving as an outgroup (reference) to the selected line types. To induce insulin resistance, mice were fed for 8 weeks with a high fat diet; the T2D was induced by injection with a single dose of streptozotocin and further promotion with high fat diet. As markers for insulin resistance and T2D advancement, we followed the changes in body mass, fasting blood glucose, insulin level, lipid profile and mTOR expression. RESULTS We found BMR-associated differentiation in standard diabetic indexes between studied metabolic lines. In particular, mice with low BMR were characterized by faster body mass gain, blood glucose gain and deterioration in lipid profile. In contrast, high BMR mice were characterized by markedly higher expression of the mTOR, which may be associated with much slower development of T2D. CONCLUSIONS Our study suggests that genetically determined low BMR makeup involves metabolism-specific pathways increasing the risk of development of insulin resistance and T2D.
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Affiliation(s)
| | - Diana Sawicka
- Faculty of Health Sciences, Medical University of Bialystok, Bialystok, Poland
| | - Anna Sadowska
- Faculty of Health Sciences, Medical University of Bialystok, Bialystok, Poland
| | - Sławomir Prokopiuk
- Faculty of Health Sciences, Medical University of Bialystok, Bialystok, Poland
- Faculty of Health Sciences, Lomza State University of Applied Sciences, Lomza, Poland
| | | | | | - Gabriela Niklińska
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | | | - Halina Car
- Faculty of Health Sciences, Medical University of Bialystok, Bialystok, Poland
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15
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Hiltpold M, Niu G, Kadri NK, Crysnanto D, Fang ZH, Spengeler M, Schmitz-Hsu F, Fuerst C, Schwarzenbacher H, Seefried FR, Seehusen F, Witschi U, Schnieke A, Fries R, Bollwein H, Flisikowski K, Pausch H. Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility. PLoS Genet 2020; 16:e1008804. [PMID: 32407316 PMCID: PMC7252675 DOI: 10.1371/journal.pgen.1008804] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/27/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10−27), head (P = 2.0 x 10−44) and tail anomalies (P = 7.2 x 10−49) and insemination success (P = 9.9 x 10−13). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10−32) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle. In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.
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Affiliation(s)
| | - Guanglin Niu
- Livestock Biotechnology, TU München, Freising, Germany
| | | | | | - Zih-Hua Fang
- Animal Genomics, ETH Zürich, Lindau, Switzerland
| | | | | | | | | | | | - Frauke Seehusen
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | | | | | - Ruedi Fries
- Animal Breeding, TU München, Freising, Germany
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, University of Zurich, Zürich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, Switzerland
- * E-mail:
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16
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Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics 2020; 21:27. [PMID: 31914939 PMCID: PMC6950892 DOI: 10.1186/s12864-020-6446-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich, Switzerland.
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17
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Iso-Touru T, Wurmser C, Venhoranta H, Hiltpold M, Savolainen T, Sironen A, Fischer K, Flisikowski K, Fries R, Vicente-Carrillo A, Alvarez-Rodriguez M, Nagy S, Mutikainen M, Peippo J, Taponen J, Sahana G, Guldbrandtsen B, Simonen H, Rodriguez-Martinez H, Andersson M, Pausch H. A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle. BMC Genomics 2019; 20:286. [PMID: 30975085 PMCID: PMC6460654 DOI: 10.1186/s12864-019-5628-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/20/2019] [Indexed: 01/10/2023] Open
Abstract
Background Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of artificial insemination bulls. Two young Nordic Red bulls delivered sperm with low progressive motility (i.e., asthenospermia) during a semen collection period of more than four months. The bulls were related through a common ancestor on both their paternal and maternal ancestry. Thus, a recessive mode of inheritance of asthenospermia was suspected. Results Both bulls were genotyped at 54,001 SNPs using the Illumina BovineSNP50 Bead chip. A scan for autozygosity revealed that they were identical by descent for a 2.98 Mb segment located on bovine chromosome 25. This haplotype was not found in the homozygous state in 8557 fertile bulls although five homozygous haplotype carriers were expected (P = 0.018). Whole genome-sequencing uncovered that both asthenospermic bulls were homozygous for a mutation that disrupts a canonical 5′ splice donor site of CCDC189 encoding the coiled-coil domain containing protein 189. Transcription analysis showed that the derived allele activates a cryptic splice site resulting in a frameshift and premature termination of translation. The mutated CCDC189 protein is truncated by more than 40%, thus lacking the flagellar C1a complex subunit C1a-32 that is supposed to modulate the physiological movement of the sperm flagella. The mutant allele occurs at a frequency of 2.5% in Nordic Red cattle. Conclusions Our study in cattle uncovered that CCDC189 is required for physiological movement of sperm flagella thus enabling active progression of spermatozoa and fertilization. A direct gene test may be implemented to monitor the asthenospermia-associated allele and prevent the birth of homozygous bulls that are infertile. Our results have been integrated in the Online Mendelian Inheritance in Animals (OMIA) database (https://omia.org/OMIA002167/9913/). Electronic supplementary material The online version of this article (10.1186/s12864-019-5628-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Terhi Iso-Touru
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Christine Wurmser
- Chair of Animal Breeding, Technische Universität München, 85354, Freising-Weihenstephan, Germany
| | | | - Maya Hiltpold
- Animal Genomics, ETH Zurich, 8001, Zurich, Switzerland
| | | | - Anu Sironen
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Konrad Fischer
- Chair of Livestock Biotechnology, Technische Universität München, 85354, Freising-Weihenstephan, Germany
| | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Technische Universität München, 85354, Freising-Weihenstephan, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, 85354, Freising-Weihenstephan, Germany
| | | | - Manuel Alvarez-Rodriguez
- Department of Clinical and Experimental Medicine, Linköping University, 58183, Linköping, Sweden
| | | | - Mervi Mutikainen
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | | | - Goutam Sahana
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | | | | | | | - Hubert Pausch
- Animal Genomics, ETH Zurich, 8001, Zurich, Switzerland.
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18
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Czech B, Frąszczak M, Mielczarek M, Szyda J. Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes. PLoS One 2018; 13:e0198419. [PMID: 29856873 PMCID: PMC5983434 DOI: 10.1371/journal.pone.0198419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 05/19/2018] [Indexed: 12/04/2022] Open
Abstract
In Bos taurus the universality of the reference genome is biased towards genetic variation represented by only two related individuals representing the same Hereford breed. Therefore, results of genetic analyses based on this reference may not be reliable. The 1000 Bull Genomes resource allows for identification of breed-specific polymorphisms and for the construction of breed-specific reference genomes. Whole-genome sequences or 936 bulls allowed us to construct seven breed specific reference genomes of Bos taurus for Angus, Brown Swiss, Fleckvieh, Hereford, Jersey, Limousin and Simmental. In order to identify breed-specific variants all detected SNPs were filtered within-breed to satisfy criteria of the number of missing genotypes not higher than 7% and the alternative allele frequency equal to unity. The highest number of breed-specific SNPs was identified for Jersey (130,070) and the lowest—for the Simmental breed (197). Such breed-specific polymorphisms were annotated to coding regions overlapping with 78 genes in Angus, 140 in Brown Swiss, 132 in Fleckvieh, 100 in Hereford, 643 in Jersey, 10 in Limousin and no genes in Simmental. For most of the breeds, the majority of breed-specific variants from coding regions was synonymous. However, most of Fleckvieh-specific and Hereford-specific polymorphisms were missense mutations. Since the identified variants are characteristic for the analysed breeds, they form the basis of phenotypic differences observed between them, which result from different breeding programmes. Breed-specific reference genomes can enhance the accuracy of SNP driven inferences such as Genome-wide Association Studies or SNP genotype imputation.
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Affiliation(s)
- Bartosz Czech
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Magdalena Frąszczak
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Magda Mielczarek
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
- Institute of Animal Breeding, Balice, Poland
| | - Joanna Szyda
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
- Institute of Animal Breeding, Balice, Poland
- * E-mail:
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