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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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Modorov MV, Kleshcheva AA, Osintseva KR, Tkachenko IV, Sevost’yanov MY, Zezin NN. The Use of KASP Technology to Study Associations of Single Nucleotide Polymorphisms in the GPAD4, CCL3, DGKG, PPARGC1A, STAT1, and TLR4 Genes with Milk Production in Cattle. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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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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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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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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Jacinto JGP, Häfliger IM, Borel N, Zanolari P, Drögemüller C, Veiga IMB. Clinicopathological and Genomic Characterization of a Simmental Calf with Generalized Bovine Juvenile Angiomatosis. Animals (Basel) 2021; 11:ani11030624. [PMID: 33652974 PMCID: PMC7996833 DOI: 10.3390/ani11030624] [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: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Vascular anomalies represent a heterogeneous group of rare disorders encompassing both vascular malformations and tumors, which can be congenital or arise shortly after birth. They often pose a diagnostic challenge in human and veterinary medicine, and the referring nomenclature is equivocal. Bovine juvenile angiomatosis (BJA), a clinical condition belonging to this group of disorders, encompasses vascular malformations and tumors arising in calves. Usually, such vascular anomalies are not further investigated on a molecular genetic level, mainly because of a lack of resources and diagnostic tools, as well as the low value and short lifespan of the affected animals. Here we report the clinical, pathological, immunohistochemical, and genetic features of a Simmental calf that displayed multiple cutaneous, subcutaneous, and visceral vascular hamartomas compatible with a generalized form of BJA. Whole-genome sequencing identified six coding variants, including four heterozygous variants in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes, which occurred only in the BJA-affected calf and were absent in the global control cohort of more than 4500 cattle. Assuming a germline mutation as etiology, one of these variants might be responsible for the vascular malformations identified in this calf. Abstract Bovine juvenile angiomatosis (BJA) comprises a group of single or multiple proliferative vascular anomalies in the skin and viscera of affected calves. The purpose of this study was to characterize the clinicopathological phenotype of a 1.5-month-old Simmental calf with multiple cutaneous, subcutaneous, and visceral vascular hamartomas, which were compatible with a generalized form of BJA, and to identify genetic cause for this phenotype by whole-genome sequencing (WGS). The calf was referred to the clinics as a result of its failure to thrive and the presence of multiple cutaneous and subcutaneous nodules, some of which bled abundantly following spontaneous rupture. Gross pathology revealed similar lesions at the inner thoracic wall, diaphragm, mediastinum, pericardium, inner abdominal wall, and mesentery. Histologically, variably sized cavities lined by a single layer of plump cells and supported by a loose stroma with occasional acute hemorrhage were observed. Determined by immunochemistry, the plump cells lining the cavities displayed a strong cytoplasmic signal for PECAM-1, von Willebrand factor, and vimentin. WGS revealed six private protein-changing variants affecting different genes present in the calf and absent in more than 4500 control genomes. Assuming a spontaneous de novo mutation event, one of the identified variants found in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes may represent a possible candidate pathogenic variant for this rare form of vascular malformation.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano Emilia (BO), Italy;
- 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;
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
| | - Patrik Zanolari
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
- Correspondence: ; Tel.: +41-31-631-2529
| | - Inês M. B. Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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Sasaki S, Miki Y, Ibi T, Wakaguri H, Yoshida Y, Sugimoto Y, Suzuki Y. A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle. BMC Genomics 2021; 22:107. [PMID: 33549039 PMCID: PMC7866702 DOI: 10.1186/s12864-021-07415-6] [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: 07/01/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, whereas genetic factors affecting the susceptibility of calves to death are not well known. To identify variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait with a threshold model and performed a genome-wide copy number variation (CNV) association study on calf mortality. RESULTS We identified a 44-kb deleted-type CNV ranging from 103,317,687 to 103,361,802 bp on chromosome 5, which was associated with the mortality of 1-180-day-old calves. The CNV harbored C1RL, a pseudogene, and an IncRNA localized in the C1R and C1S gene cluster, which is a component of the classical complement activation pathway for immune complexes for infectious pathogens. The average complement activity in CNVR_221 homozygotes at postnatal day 7 was significantly lower than that of wild-type animals and heterozygotes. The frequency of the risk allele in dead calves suffering from diarrhea and pneumonia and in healthy cows was 0.35 and 0.28, respectively (odds ratio = 2.2, P = 0.016), suggesting that CNVR_221 was associated with the mortality of Japanese Black calves suffering from an infectious disease. CONCLUSIONS This study identified a deleted-type CNV associated with the mortality of 1-180-day-old calves. The complement activity in CNVR_221 homozygotes was significantly lower than that in heterozygotes and wild type animals. The frequency of the risk allele was higher in dead calves suffering from an infectious disease than in healthy cows. These results suggest that the existence of CNVR_221 in calves could be attributed to a reduction in complement activity, which in turn leads to susceptibility to infections. Thus, the risk allele could serve as a useful marker to reduce the mortality of infected Japanese Black calves.
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Affiliation(s)
- Shinji Sasaki
- University of the Ryukyus, Faculty of Agriculture, 1 Senbaru, Nishihara, Nakagami-gun, Okinawa, 903-0213, Japan. .,United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Youko Miki
- Hokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Asago, Hyogo, Japan
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
| | - Hiroyuki Wakaguri
- Department of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Yuichi Yoshida
- Hokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Asago, Hyogo, Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Yushima, Bunkyouku, Tokyo, 113-0034, Japan
| | - Yutaka Suzuki
- Department 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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Ren P, Deng F, Chen S, Ran J, Li J, Yin L, Wang Y, Yin H, Zhu Q, Liu Y. Whole-genome resequencing reveals loci with allelic transmission ratio distortion in F 1 chicken population. Mol Genet Genomics 2021; 296:331-339. [PMID: 33404883 DOI: 10.1007/s00438-020-01744-z] [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: 08/20/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022]
Abstract
Allelic transmission ratio distortion (TRD) is the significant deviation from the expected ratio under Mendelian inheritance theory, which may be resulted from multiple disrupted biological processes, including germline selection, meiotic drive, gametic competition, imprint error, and embryo lethality. However, it is less known that whether or what extent the allelic TRD is present in farm animals. In this study, whole-genome resequencing technology was applied to reveal TRD loci in chicken by constructing a full-sib F1 hybrid population. Through the whole-genome resequencing data of two parents (30 ×) and 38 offspring (5 ×), we detected a total of 2850 TRD SNPs (p-adj < 0.05) located within 400 genes showing TRD, and all of them were unevenly distributed on macrochromosomes and microchromosomes. Our findings suggested that TRD in the chicken chromosome 16 might play an important role in chicken immunity and disease resistance and the MYH1F with significant TRD and allele-specific expression could play a key role in the fast muscle development. In addition, functional enrichment analyses revealed that many genes (e.g., TGFBR2, TGFBR3, NOTCH1, and NCOA1) with TRD were found in the significantly enriched biological process and InterPro terms in relation to embryonic lethality and germline selection. Our results suggested that TRD is considerably prevalent in the chicken genome and has functional implications.
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Affiliation(s)
- Peng Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Feilong Deng
- Special Key Laboratory of Microbial Resources and Drug Development, Zunyi Medical University, Zunyi, 563000, China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jinshan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China. .,Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, 211 Huiming Road, Wenjiang, Sichuan, 611130, China.
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Zinovieva NA, Dotsev AV, Sermyagin AA, Deniskova TE, Abdelmanova AS, Kharzinova VR, Sölkner J, Reyer H, Wimmers K, Brem G. Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis. PLoS One 2020; 15:e0242200. [PMID: 33196682 PMCID: PMC7668599 DOI: 10.1371/journal.pone.0242200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.
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Affiliation(s)
- Natalia Anatolievna Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- * E-mail:
| | - Arsen Vladimirovich Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexander Alexandrovich Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Tatiana Evgenievna Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexandra Sergeevna Abdelmanova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Veronika Ruslanovna Kharzinova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine [VMU], Vienna, Austria
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10
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Molecular Evolution, Neurodevelopmental Roles and Clinical Significance of HECT-Type UBE3 E3 Ubiquitin Ligases. Cells 2020; 9:cells9112455. [PMID: 33182779 PMCID: PMC7697756 DOI: 10.3390/cells9112455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination belongs to the best characterized pathways of protein degradation in the cell; however, our current knowledge on its physiological consequences is just the tip of an iceberg. The divergence of enzymatic executors of ubiquitination led to some 600–700 E3 ubiquitin ligases embedded in the human genome. Notably, mutations in around 13% of these genes are causative of severe neurological diseases. Despite this, molecular and cellular context of ubiquitination remains poorly characterized, especially in the developing brain. In this review article, we summarize recent findings on brain-expressed HECT-type E3 UBE3 ligases and their murine orthologues, comprising Angelman syndrome UBE3A, Kaufman oculocerebrofacial syndrome UBE3B and autism spectrum disorder-associated UBE3C. We summarize evolutionary emergence of three UBE3 genes, the biochemistry of UBE3 enzymes, their biology and clinical relevance in brain disorders. Particularly, we highlight that uninterrupted action of UBE3 ligases is a sine qua non for cortical circuit assembly and higher cognitive functions of the neocortex.
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11
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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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12
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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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13
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Xu Q, Wu Z, Zeng X, An X. Identification and Expression Profiling of Chemosensory Genes in Hermetia illucens via a Transcriptomic Analysis. Front Physiol 2020; 11:720. [PMID: 32655421 PMCID: PMC7325966 DOI: 10.3389/fphys.2020.00720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/29/2020] [Indexed: 02/03/2023] Open
Abstract
The black soldier fly, Hermetia illucens, is a cosmopolitan insect of the family Stratiomyidae (Diptera). Chemosensory genes encode proteins involved directly in the detection of odorants. In this study, we sequenced the antennal transcriptome of H. illucens adults to identify chemosensory genes. Putative unigenes encoding 27 odorant binding proteins (OBPs), five chemosensory proteins (CSPs), 70 odorant receptors (ORs), 25 ionotropic receptors (IRs), 10 gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) were identified. Tissue-specific expression profiles of the identified OBPs, CSPs and SNMPs were investigated using RT-PCR. Eight OBPs (HillOBP1-2, 9, 11-14, and 17), one CSP (HillCSP5) and one SNMP (HillSNMP1) were predominantly expressed in antennae. Further real-time quantitative PCR analyses revealed that the antennae-enriched unigenes also exhibited significant differences in expression between males and females. Among the sex-biased unigenes, six ORs showed female-biased expression, suggesting that these genes might participate in female-specific behaviors such as oviposition site searching. Sixteen ORs and two OBPs showed male-biased expression, indicating that they may play key roles in the detection of female sex pheromones. Our study is the first attempt to delineate the molecular basis of chemoreception in H. illucens. Our data provide useful information for comparative studies on the differentiation and evolution of Dipteran chemosensory gene families.
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Affiliation(s)
- Qiyun Xu
- Guangdong Engineering Research Center for Insect Behavior Regulation, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zhongzhen Wu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinnian Zeng
- Guangdong Engineering Research Center for Insect Behavior Regulation, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xincheng An
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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14
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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: 132] [Impact Index Per Article: 26.4] [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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15
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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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16
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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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17
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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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18
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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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19
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Kariminejad A, Ajeawung NF, Bozorgmehr B, Dionne-Laporte A, Molidperee S, Najafi K, Gibbs RA, Lee BH, Hennekam RC, Campeau PM. Kaufman oculo-cerebro-facial syndrome in a child with small and absent terminal phalanges and absent nails. J Hum Genet 2016; 62:465-471. [PMID: 28003643 PMCID: PMC5370204 DOI: 10.1038/jhg.2016.151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 01/25/2023]
Abstract
Background Kaufman oculo-cerebro-facial syndrome (KOS) is caused by recessive UBE3B mutations and presents with microcephaly, ocular abnormalities, distinctive facial morphology, low cholesterol levels and intellectual disability. We describe a child with microcephaly, brachycephaly, hearing loss, ptosis, blepharophimosis, hypertelorism, cleft palate, multiple renal cysts, absent nails, small or absent terminal phalanges, absent speech and intellectual disability. Syndromes which were initially considered include DOORS syndrome, Coffin-Siris syndrome and Dubowitz syndrome. Methods Clinical investigations coupled with, karyotype analysis, array-CGH, exome and Sanger sequencing were performed to characterize the condition in this child. Results Sanger sequencing was negative for the DOORS syndrome gene TBC1D24 but exome sequencing identified a homozygous deletion in UBE3B (NM_183415:c.3139_3141del, p.1047_1047del) located within the terminal portion of the HECT domain. This finding coupled with the presence of characteristic features such as brachycephaly, ptosis, blepharophimosis, hypertelorism, short palpebral fissures, cleft palate and developmental delay, allowed us to make a diagnosis of KOS. Conclusion Our findings highlight the importance of considering KOS as a differential diagnosis for patients under evaluation for DOORS syndrome and expand the phenotype of KOS to include small or absent terminal phalanges, nails, and the presence of hallux varus and multicystic dysplastic kidneys.
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Affiliation(s)
| | | | - Bita Bozorgmehr
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Sirinart Molidperee
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Kimia Najafi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
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20
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Braganza A, Li J, Zeng X, Yates NA, Dey NB, Andrews J, Clark J, Zamani L, Wang XH, St Croix C, O'Sullivan R, Garcia-Exposito L, Brodsky JL, Sobol RW. UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase. J Biol Chem 2016; 292:2470-2484. [PMID: 28003368 DOI: 10.1074/jbc.m116.766824] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
Recent genome-wide studies found that patients with hypotonia, developmental delay, intellectual disability, congenital anomalies, characteristic facial dysmorphic features, and low cholesterol levels suffer from Kaufman oculocerebrofacial syndrome (KOS, also reported as blepharophimosis-ptosis-intellectual disability syndrome). The primary cause of KOS is autosomal recessive mutations in the gene UBE3B However, to date, there are no studies that have determined the cellular or enzymatic function of UBE3B. Here, we report that UBE3B is a mitochondrion-associated protein with homologous to the E6-AP Cterminus (HECT) E3 ubiquitin ligase activity. Mutating the catalytic cysteine (C1036A) or deleting the entire HECT domain (amino acids 758-1068) results in loss of UBE3B's ubiquitylation activity. Knockdown of UBE3B in human cells induces changes in mitochondrial morphology and physiology, a decrease in mitochondrial volume, and a severe suppression of cellular proliferation. We also discovered that UBE3B interacts with calmodulin via its N-terminal isoleucine-glutamine (IQ) motif. Deletion of the IQ motif (amino acids 29-58) results in loss of calmodulin binding and a significant increase in the in vitro ubiquitylation activity of UBE3B. In addition, we found that changes in calcium levels in vitro disrupt the calmodulin-UBE3B interaction. These studies demonstrate that UBE3B is an E3 ubiquitin ligase and reveal that the enzyme is regulated by calmodulin. Furthermore, the modulation of UBE3B via calmodulin and calcium implicates a role for calcium signaling in mitochondrial protein ubiquitylation, protein turnover, and disease.
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Affiliation(s)
- Andrea Braganza
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jianfeng Li
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, School of the Health Sciences, and
| | - Nathan A Yates
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,Biomedical Mass Spectrometry Center, School of the Health Sciences, and.,the Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and
| | - Nupur B Dey
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Joel Andrews
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Jennifer Clark
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Leila Zamani
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xiao-Hong Wang
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Claudette St Croix
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Roderick O'Sullivan
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Laura Garcia-Exposito
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jeffrey L Brodsky
- the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Robert W Sobol
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, .,the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
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21
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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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Schwarzenbacher H, Burgstaller J, Seefried FR, Wurmser C, Hilbe M, Jung S, Fuerst C, Dinhopl N, Weissenböck H, Fuerst-Waltl B, Dolezal M, Winkler R, Grueter O, Bleul U, Wittek T, Fries R, Pausch H. A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle. BMC Genomics 2016; 17:400. [PMID: 27225349 PMCID: PMC4880872 DOI: 10.1186/s12864-016-2742-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/14/2016] [Indexed: 12/04/2022] Open
Abstract
Background Haplotypes with reduced or missing homozygosity may harbor deleterious alleles that compromise juvenile survival. A scan for homozygous haplotype deficiency revealed a short segment on bovine chromosome 19 (Braunvieh haplotype 2, BH2) that was associated with high juvenile mortality in Braunvieh cattle. However, the molecular genetic underpinnings and the pathophysiology of BH2 remain to be elucidated. Results The frequency of BH2 was 6.5 % in 8,446 Braunvieh animals from the national bovine genome databases. Both perinatal and juvenile mortality of BH2 homozygous calves were higher than the average in Braunvieh cattle resulting in a depletion of BH2 homozygous adult animals (P = 9.3x10−12). The analysis of whole-genome sequence data from 54 Braunvieh animals uncovered a missense mutation in TUBD1 (rs383232842, p.H210R) that was compatible with recessive inheritance of BH2. The availability of sequence data of 236 animals from diverse bovine populations revealed that the missense mutation also segregated at a low frequency (1.7 %) in the Fleckvieh breed. A validation study in 37,314 Fleckvieh animals confirmed high juvenile mortality of homozygous calves (P = 2.2x10−15). Our findings show that the putative disease allele is located on an ancestral haplotype that segregates in Braunvieh and Fleckvieh cattle. To unravel the pathophysiology of BH2, six homozygous animals were examined at the animal clinic. Clinical and pathological findings revealed that homozygous calves suffered from chronic airway disease possibly resulting from defective cilia in the respiratory tract. Conclusions A missense mutation in TUBD1 is associated with high perinatal and juvenile mortality in Braunvieh and Fleckvieh cattle. The mutation is located on a common haplotype likely originating from an ancient ancestor of Braunvieh and Fleckvieh cattle. Our findings demonstrate for the first time that deleterious alleles may segregate across closed cattle breeds without recent admixture. Homozygous calves suffer from chronic airway disease resulting in poor growth performance and high juvenile mortality. The respiratory manifestations resemble key features of diseases resulting from impaired function of airway cilia. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2742-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Johann Burgstaller
- Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | | | - Christine Wurmser
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Monika Hilbe
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University Zurich, Zurich, 8057, Switzerland
| | - Simone Jung
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | | | - Nora Dinhopl
- Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Herbert Weissenböck
- Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Birgit Fuerst-Waltl
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marlies Dolezal
- Platform Bioinformatics and Statistics, University of Veterinary Medicine, Vienna, Austria
| | | | | | - Ulrich Bleul
- Clinic of Reproductive Medicine, Department of Farm Animals, Vetsuisse-Faculty, University Zurich, Zurich, 8057, Switzerland
| | - Thomas Wittek
- Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Hubert Pausch
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany.
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Hekman JP, Johnson JL, Kukekova AV. Transcriptome Analysis in Domesticated Species: Challenges and Strategies. Bioinform Biol Insights 2016; 9:21-31. [PMID: 26917953 PMCID: PMC4756862 DOI: 10.4137/bbi.s29334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 12/26/2015] [Indexed: 12/13/2022] Open
Abstract
Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.
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Affiliation(s)
- Jessica P. Hekman
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Jennifer L. Johnson
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Anna V. Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
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Attia S, Katila T, Andersson M. The Effect of Sperm Morphology and Sire Fertility on Calving Rate of Finnish Ayrshire AI Bulls. Reprod Domest Anim 2015; 51:54-8. [PMID: 26660630 DOI: 10.1111/rda.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/31/2015] [Indexed: 11/27/2022]
Abstract
Good-quality semen is a prerequisite for successful and profitable artificial insemination (AI) of modern dairy cattle. Fertility of the bulls is evaluated with andrological examinations and semen analyses, such as morphology. However, little attention has been paid to the inheritance of bull fertility. In this study, we correlated sperm morphology, birth year and station of 695 AI bulls with calving rate (CR). Sperm morphology was clearly associated with CR underlining the usefulness of morphological examination in the assessment of fertility. The correlation between the proportion of normal spermatozoa and CR was significant (p < 0.001). No significant differences were detected between stations or birth years. We also compared the CR of 695 AI bulls with the CR of their 27 sires to study the inheritance of fertility. Sire's CR did not correlate with the CR of the sons (p = 0.218). This result indicates that at least when sires of acceptable CR are used to produce sons for use in AI the inheritance of CR is not significantly correlated.
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Affiliation(s)
- S Attia
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - T Katila
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - M Andersson
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
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