1
|
Costes V, Sellem E, Marthey S, Hoze C, Bonnet A, Schibler L, Kiefer H, Jaffrezic F. Multi-omics data integration for the identification of biomarkers for bull fertility. PLoS One 2024; 19:e0298623. [PMID: 38394258 PMCID: PMC10890740 DOI: 10.1371/journal.pone.0298623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Bull fertility is an important economic trait, and the use of subfertile semen for artificial insemination decreases the global efficiency of the breeding sector. Although the analysis of semen functional parameters can help to identify infertile bulls, no tools are currently available to enable precise predictions and prevent the commercialization of subfertile semen. Because male fertility is a multifactorial phenotype that is dependent on genetic, epigenetic, physiological and environmental factors, we hypothesized that an integrative analysis might help to refine our knowledge and understanding of bull fertility. We combined -omics data (genotypes, sperm DNA methylation at CpGs and sperm small non-coding RNAs) and semen parameters measured on a large cohort of 98 Montbéliarde bulls with contrasting fertility levels. Multiple Factor Analysis was conducted to study the links between the datasets and fertility. Four methodologies were then considered to identify the features linked to bull fertility variation: Logistic Lasso, Random Forest, Gradient Boosting and Neural Networks. Finally, the features selected by these methods were annotated in terms of genes, to conduct functional enrichment analyses. The less relevant features in -omics data were filtered out, and MFA was run on the remaining 12,006 features, including the 11 semen parameters and a balanced proportion of each type of-omics data. The results showed that unlike the semen parameters studied the-omics datasets were related to fertility. Biomarkers related to bull fertility were selected using the four methodologies mentioned above. The most contributory CpGs, SNPs and miRNAs targeted genes were all found to be involved in development. Interestingly, fragments derived from ribosomal RNAs were overrepresented among the selected features, suggesting roles in male fertility. These markers could be used in the future to identify subfertile bulls in order to increase the global efficiency of the breeding sector.
Collapse
Affiliation(s)
- Valentin Costes
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
| | - Eli Sellem
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
| | - Sylvain Marthey
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Chris Hoze
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
| | - Aurélie Bonnet
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
| | | | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Florence Jaffrezic
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
| |
Collapse
|
2
|
Reding JJ, van der Westhuizen RR, Berry DP, van Marle-Köster E. Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle. BMC Genomics 2023; 24:480. [PMID: 37620802 PMCID: PMC10464233 DOI: 10.1186/s12864-023-09518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/14/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models. RESULTS Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability's of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation. CONCLUSIONS This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.
Collapse
Affiliation(s)
- Jason J Reding
- Department of Animal Sciences, University of Pretoria, Hatfield, 0028, South Africa.
| | | | - Donagh P Berry
- Department of Animal Sciences, University of Pretoria, Hatfield, 0028, South Africa
- Teagasc - The Irish Agriculture and Food Development Authority, Moorepark, Fermoy, Cork, Ireland
| | | |
Collapse
|
3
|
Tahir MS, Porto-Neto LR, Reverter-Gomez T, Olasege BS, Sajid MR, Wockner KB, Tan AWL, Fortes MRS. Utility of multi-omics data to inform genomic prediction of heifer fertility traits. J Anim Sci 2022; 100:skac340. [PMID: 36239447 PMCID: PMC9733504 DOI: 10.1093/jas/skac340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
Biologically informed single nucleotide polymorphisms (SNPs) impact genomic prediction accuracy of the target traits. Our previous genomics, proteomics, and transcriptomics work identified candidate genes related to puberty and fertility in Brahman heifers. We aimed to test this biological information for capturing heritability and predicting heifer fertility traits in another breed i.e., Tropical Composite. The SNP from the identified genes including 10 kilobases (kb) region on either side were selected as biologically informed SNP set. The SNP from the rest of the Bos taurus genes including 10-kb region on either side were selected as biologically uninformed SNP set. Bovine high-density (HD) complete SNP set (628,323 SNP) was used as a control. Two populations-Tropical Composites (N = 1331) and Brahman (N = 2310)-had records for three traits: pregnancy after first mating season (PREG1, binary), first conception score (FCS, score 1 to 3), and rebreeding score (REB, score 1 to 3.5). Using the best linear unbiased prediction method, effectiveness of each SNP set to predict the traits was tested in two scenarios: a 5-fold cross-validation within Tropical Composites using biological information from Brahman studies, and application of prediction equations from one breed to the other. The accuracy of prediction was calculated as the correlation between genomic estimated breeding values and adjusted phenotypes. Results show that biologically informed SNP set estimated heritabilities not significantly better than the control HD complete SNP set in Tropical Composites; however, it captured all the observed genetic variance in PREG1 and FCS when modeled together with the biologically uninformed SNP set. In 5-fold cross-validation within Tropical Composites, the biologically informed SNP set performed marginally better (statistically insignificant) in terms of prediction accuracies (PREG1: 0.20, FCS: 0.13, and REB: 0.12) as compared to HD complete SNP set (PREG1: 0.17, FCS: 0.10, and REB: 0.11), and biologically uninformed SNP set (PREG1: 0.16, FCS: 0.10, and REB: 0.11). Across-breed use of prediction equations still remained a challenge: accuracies by all SNP sets dropped to around zero for all traits. The performance of biologically informed SNP was not significantly better than other sets in Tropical Composites. However, results indicate that biological information obtained from Brahman was successful to predict the fertility traits in Tropical Composite population.
Collapse
Affiliation(s)
- Muhammad S Tahir
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Toni Reverter-Gomez
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Babatunde S Olasege
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Mirza R Sajid
- Department of Statistics, University of Gujrat, 50700 Punjab, Pakistan
| | - Kimberley B Wockner
- Queensland Department of Agriculture and Fisheries, Brisbane 4072, QLD, Australia
| | - Andre W L Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| |
Collapse
|
4
|
Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras. Animals (Basel) 2022; 12:ani12162128. [PMID: 36009718 PMCID: PMC9405194 DOI: 10.3390/ani12162128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary This article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones. Abstract In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.
Collapse
|
5
|
Álvarez Cecco P, Rogberg Muñoz A, Balbi M, Bonamy M, Munilla S, Forneris NS, Peral García P, Cantet RJC, Giovambattista G, Fernández ME. Genome-wide scan for signatures of selection in the Brangus cattle genome. J Anim Breed Genet 2022; 139:679-694. [PMID: 35866697 DOI: 10.1111/jbg.12733] [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: 11/05/2021] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
Brangus is a composite cattle breed developed with the objective of combining the advantages of Angus and Zebuine breeds (Brahman, mainly) in tropical climates. The aim of this work was to estimate breed composition both genome-wide and locally, at the chromosome level, and to uncover genomic regions evidencing positive selection in the Argentinean Brangus population/nucleus. To do so, we analysed marker data from 478 animals, including Brangus, Angus and Brahman. Average breed composition was 35.0% ± 9.6% of Brahman, lower than expected according to the theoretical fractions deduced by the usual cross-breeding practice in this breed. Local ancestry analysis evidenced that breed composition varies between chromosomes, ranging from 19.6% for BTA26 to 56.1% for BTA5. Using approaches based on allelic frequencies and linkage disequilibrium, genomic regions with putative selection signatures were identified in several chromosomes (BTA1, BTA5, BTA6 and BTA14). These regions harbour genes involved in horn development, growth, lipid metabolism, reproduction and immune response. We argue that the overlapping of a chromosome segment originated in one of the parental breeds and over-represented in the sample with the location of a signature of selection constitutes evidence of a selection process that has occurred in the breed since its take off in the 1950s. In this regard, our results could contribute to the understanding of the genetic mechanisms involved in cross-bred cattle adaptation and productivity in tropical environments.
Collapse
Affiliation(s)
- Paulo Álvarez Cecco
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marianela Balbi
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martín Bonamy
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sebastián Munilla
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Soledad Forneris
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pilar Peral García
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Rodolfo Juan Carlos Cantet
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guillermo Giovambattista
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Elena Fernández
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| |
Collapse
|
6
|
Chen SY, Schenkel FS, Melo ALP, Oliveira HR, Pedrosa VB, Araujo AC, Melka MG, Brito LF. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics 2022; 23:331. [PMID: 35484513 PMCID: PMC9052698 DOI: 10.1186/s12864-022-08555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08555-z.
Collapse
Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ana L P Melo
- Department of Reproduction and Animal Evaluation, Rural Federal University of Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI, 54022, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA. .,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
7
|
Komatsu M, Mannen H, Taniguchi M, Oshima K. Expression and differential posttranscriptional regulation of the elongation factor 1 alpha 1 gene in endometrial caruncle and intercaruncle of Japanese Black cattle at early and mid-gestation stages. Anim Sci J 2022; 93:e13746. [PMID: 35791676 DOI: 10.1111/asj.13746] [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: 01/01/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
The elongation factor 1 alpha 1 (EEF1A1), an isoform of EEF1A, is one of the most abundant cytoplasmic proteins and an important component of the translational machinery. We investigated the relative expression, alternative polyadenylation (APA), and changes in poly(A) tail length of EEF1A1 mRNA in the endometrial caruncle (CAR) and intercaruncle (ICAR) at early and mid-gestation in Japanese Black cattle. The relative EEF1A1 mRNA expression levels in the CAR were the highest on Gestation day 20 and were significantly decreased at mid-gestation. The expression levels in the ICAR were significantly higher than those in the CAR, and the gestation stage had no significant impact. Four different EEF1A1 transcripts with distinct 3' untranslated regions (UTRs) (proximal and distal types) and poly(A) tails (medium and short types) of different lengths were identified. The EEF1A1 mRNAs with distal 3' UTR and medium-length poly(A) tails were specific from the CAR of uterus horn at early gestation. RNA-sequencing data analyses revealed that the HSF1, MZF1, E47, SRF, GATA2, GATA3, GATA6, HNF-3 beta (FOXA2), CPSF1, and Ataxin-2 genes might affect the EEF1A1 gene expression or poly(A) length.
Collapse
Affiliation(s)
- Masanori Komatsu
- Komatsu Laboratory of Computational Biology for Domestic Animals, Ryugasaki, Japan.,Division of Tear-Round Grazing Research, Western Region Agricultural Research Center, NARO, Oda, Japan
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masaaki Taniguchi
- Division of Animal Breeding and Reproduction Research, Institute of Livestock and Grassland Science, National Agriculture Food Research Organization (NARO), Tsukuba, Japan
| | - Kazunaga Oshima
- Division of Tear-Round Grazing Research, Western Region Agricultural Research Center, NARO, Oda, Japan
| |
Collapse
|
8
|
Haile-Mariam M, Pryce JE. Use of insemination data for joint evaluation of male and female fertility in predominantly seasonal-calving dairy herds. J Dairy Sci 2021; 104:11807-11819. [PMID: 34419266 DOI: 10.3168/jds.2020-20006] [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: 12/07/2020] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
Conception in dairy cattle is influenced by the fertility of the cow and the bull and their interaction. Despite genetic selection for female fertility in many countries, selection for male fertility is largely not practiced. The primary objective of this study was to quantify variation in male and female fertility using insemination data from predominantly seasonal-calving herds. Nonreturn rate (NRR) was derived by coding each insemination as successful (1) or failed (0) based on a minimum of at least 25 d. The NRR was treated as a trait of the bull with semen (male fertility) and the cow that is mated (female fertility). The data (805,463 cows that mated to 5,776 bulls) were used to estimate parameters using either models that only included bulls with mating data or models that fitted the genetic and permanent environmental (PE) effects of bulls and cows simultaneously. We also evaluated whether fitting genetic and PE effects of bulls as one term is better for ranking bulls based on NRR compared with a model that ignored genetic effect. The age of cows that were mated, age of the bulls with semen data, season of mating, breed of cow that mated, inbreeding of cows and bulls, and days from calving to mating date were found to have a significant effect on NRR. Only about 3% of the total variance was explained by the random effects in the model, despite fitting the genetic and PE effects of the bull and cow. The 2 components of fertility (male and fertility) were not correlated. The heritability of male fertility was low (0.001 to 0.008), and that of female fertility was also low (~0.016). The highest heritability estimate for male fertility was obtained from the model that fitted the additive genetic relationship matrix and PE component of the bull as one term. When this model was used to calculate bull solutions, the difference between bulls with at least 100 inseminations was up to 19.2% units (-9.6 to 9.6%). Bull solutions from this model were compared with bull solutions that were predicted fitting bull effects ignoring pedigree. Bull solutions that were obtained considering pedigree had (1) the highest accuracy of prediction when early insemination was used to predict yet-to-be observed insemination data of bulls, and (2) improved model stability (i.e., a higher correlation between bull solutions from 2 randomly split herds) compared with the model which fitted bull with no pedigree. For practical purposes, the model that fitted genetic and PE effect as one term can provide more accurate semen fertility values for bulls than the model without genetic effect. To conclude, insemination data from predominantly seasonal-calving herds can be used to quantify variability between bulls for male fertility, which makes their ranking on NRR feasible. Potentially this information can be used for monitoring bulls and can supplement efforts to improve herd fertility by avoiding or minimizing the use of semen from subfertile bulls.
Collapse
Affiliation(s)
- Mekonnen Haile-Mariam
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
| | - J E Pryce
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083 Australia
| |
Collapse
|
9
|
Sweett H, Fonseca PAS, Suárez-Vega A, Livernois A, Miglior F, Cánovas A. Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle. Sci Rep 2020; 10:20102. [PMID: 33208801 PMCID: PMC7676258 DOI: 10.1038/s41598-020-75758-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Fertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.
Collapse
Affiliation(s)
- H Sweett
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - P A S Fonseca
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Livernois
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
10
|
Silva R, Espigolan R, Berton M, Stafuzza N, Santos F, Negreiros M, Schuchmann R, Rodriguez J, Lôbo R, Banchero G, Pereira A, Bergmann J, Baldi F. Genetic parameters and genomic regions associated with calving ease in primiparous Nellore heifers. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
11
|
Gororo E, Makuza SM, Chidzwondo F, Chatiza FP. Variation in sperm cryosurvival is not modified by replacing the cryoprotectant glycerol with ethylene glycol in bulls. Reprod Domest Anim 2020; 55:1210-1218. [PMID: 32628298 DOI: 10.1111/rda.13766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/29/2020] [Indexed: 01/17/2023]
Abstract
Breed and sire differences in sperm cryosurvival have been noted, with negative implications for sperm cryobanking and assisted reproduction programmes. This study hypothesized that these differences could be modified by using lower molecular weight cryoprotectants. Therefore, the effect of replacing glycerol (GLY) with ethylene glycol (EG) on differential cryosurvival of semen from two Sanga cattle breeds (Mashona vs. Tuli) was determined. Three to five ejaculates were collected from each of ten bulls (3-8 years) by electro-ejaculation, diluted in three Tris-egg yolk extenders (Triladyl® , 7% GLY-based and 7% EG-based) and evaluated for sperm motility, viability and morphology at three time periods (fresh - 0 hr, pre-freeze - 4 hr and post-thaw). Tuli bulls produced larger (11.8 ± 0.31 ml vs. 8.5 ± 0.38 ml) and more concentrated ejaculates of lower fresh semen quality. Breeds differed across time for motility and morphology, but not viability. Mashona bull semen had significantly higher motility and normal morphology values at each sampling time. Bulls classified as poor freezers had lower concentration (0.70 ± 0.09 × 109 sperm/ml vs. 1.37 ± 0.10 × 109 sperm/ml), sperm motility index (SMI, 35.0 ± 3.4 % vs. 67.8 ± 2.1 %) and viability (69.7 ± 1.1 % vs. 75.7 ± 1.0 %) compared to good freezers. Maintenance of semen quality by GLY and EG did not differ between breeds, poor and good freezers, or age groups. The interaction breed by extender across time did not reach statistical significance for all variables. The study revealed that bull and breed variation in sperm quality and cryosurvival is not modified by replacing GLY with EG, suggesting that cryostress tolerance of sperm may be under control of mechanisms other than differential response to GLY cytotoxicity.
Collapse
Affiliation(s)
- Eddington Gororo
- Germplasm and Reproductive Technology Laboratory, Department of Animal Production & Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Stanley Marshal Makuza
- School of Agricultural Sciences & Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Fungayi Primrose Chatiza
- Germplasm and Reproductive Technology Laboratory, Department of Animal Production & Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
Gross N, Peñagaricano F, Khatib H. Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility. Anim Genet 2020; 51:502-510. [PMID: 32323873 DOI: 10.1111/age.12941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
Predicting bull fertility prior to breeding is a current challenge for the dairy industry. The use of molecular biomarkers has been previously assessed. However, the integration of this information has not been performed to extract biologically relevant markers. The goal of this study was to integrate DNA methylation data with previously published RNA-sequencing results in order to identify candidate markers for sire fertility. A total of 1765 differentially methylated cytosines were found between high- and low-fertility sires. Ten genes associated with 11 differentially methylated cytosines were found in a previous study of gene expression between high- and low-fertility sires. Additionally, two of these genes code for proteins found exclusively in bull seminal plasma. Collectively, our results reveal 10 genes that could be used in the future as a panel for predicting bull fertility.
Collapse
Affiliation(s)
- Nicole Gross
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
| |
Collapse
|
14
|
Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers. Sci Rep 2020; 10:6481. [PMID: 32296097 PMCID: PMC7160148 DOI: 10.1038/s41598-020-63516-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/01/2020] [Indexed: 01/11/2023] Open
Abstract
Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production. This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers’ adaptation to a wide range of environments. Genome-wide association studies through the reaction norm model were carried out to identify genomic regions associated with AFC in Nellore heifers, raised under different environmental conditions (EC). The SNP effects for AFC were estimated in three EC levels (Low, Medium, and High, corresponding to average contemporary group effects on yearling body weight equal to 159.40, 228.6 and 297.6 kg, respectively), which unraveled shared and unique genomic regions for AFC in Low, Medium, and High EC levels, that varied according to the genetic correlation between AFC in different EC levels. The significant genomic regions harbored key genes that might play an important biological role in controlling hormone signaling and metabolism. Shared genomic regions among EC levels were identified on BTA 2 and 14, harboring candidate genes associated with energy metabolism (IGFBP2, IGFBP5, SHOX, SMARCAL1, LYN, RPS20, MOS, PLAG1, CHCD7, and SDR16C6). Gene set enrichment analyses identified important biological functions related to growth, hormone levels affecting female fertility, physiological processes involved in female pregnancy, gamete generation, ovulation cycle, and age at puberty. The genomic regions highlighted differences in the physiological processes linked to AFC in different EC levels and metabolic processes that support complex interactions between the gonadotropic axes and sexual precocity in Nellore heifers.
Collapse
|
15
|
Bedhane M, van der Werf J, Gondro C, Duijvesteijn N, Lim D, Park B, Park MN, Hee RS, Clark S. Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data. Front Genet 2019; 10:1235. [PMID: 31850078 PMCID: PMC6895209 DOI: 10.3389/fgene.2019.01235] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/06/2019] [Indexed: 01/28/2023] Open
Abstract
The discovery of single nucleotide polymorphisms (SNP) and the subsequent genotyping of large numbers of animals have enabled large-scale analyses to begin to understand the biological processes that underpin variation in animal populations. In beef cattle, genome-wide association studies using genotype arrays have revealed many quantitative trait loci (QTL) for various production traits such as growth, efficiency and meat quality. Most studies regarding meat quality have focused on marbling, which is a key trait associated with meat eating quality. However, other important traits like meat color, texture and fat color have not commonly been studied. Developments in genome sequencing technologies provide new opportunities to identify regions associated with these traits more precisely. The objective of this study was to estimate variance components and identify significant variants underpinning variation in meat quality traits using imputed whole genome sequence data. Phenotypic and genomic data from 2,110 Hanwoo cattle were used. The estimated heritabilities for the studied traits were 0.01, 0.16, 0.31, and 0.49 for fat color, meat color, meat texture and marbling score, respectively. Marbling score and meat texture were highly correlated. The genome-wide association study revealed 107 significant SNPs located on 14 selected chromosomes (one QTL region per selected chromosome). Four QTL regions were identified on BTA2, 12, 16, and 24 for marbling score and two QTL regions were found for meat texture trait on BTA12 and 29. Similarly, three QTL regions were identified for meat color on BTA2, 14 and 24 and five QTL regions for fat color on BTA7, 10, 12, 16, and 21. Candidate genes were identified for all traits, and their potential influence on the given trait was discussed. The significant SNP will be an important inclusion into commercial genotyping arrays to select new breeding animals more accurately.
Collapse
Affiliation(s)
- Mohammed Bedhane
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Julius van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Cedric Gondro
- College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Naomi Duijvesteijn
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
| | - Byoungho Park
- Animal Genetic Improvement Division, National Institute of Animal Science, Rural Development Administration, Seonghwan, South Korea
| | - Mi Na Park
- Animal Genetic Improvement Division, National Institute of Animal Science, Rural Development Administration, Seonghwan, South Korea
| | - Roh Seung Hee
- Animal Genetic Improvement Division, National Institute of Animal Science, Rural Development Administration, Seonghwan, South Korea
| | - Samuel Clark
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| |
Collapse
|
16
|
Tahir MS, Nguyen LT, Schulz BL, Boe-Hansen GA, Thomas MG, Moore SS, Lau LY, Fortes MRS. Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers ( Bos indicus L.). Genes (Basel) 2019; 10:E923. [PMID: 31726744 PMCID: PMC6895798 DOI: 10.3390/genes10110923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.
Collapse
Affiliation(s)
- Muhammad S. Tahir
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Gry A. Boe-Hansen
- School of Veterinary Sciences, University of Queensland, Brisbane 4343, Queensland, Australia;
| | - Milton G. Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO 80523, USA;
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Li Yieng Lau
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| |
Collapse
|
17
|
Fonseca PADS, dos Santos FC, Lam S, Suárez-Vega A, Miglior F, Schenkel FS, Diniz LDAF, Id-Lahoucine S, Carvalho MRS, Cánovas A. Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results. J Anim Sci 2018; 96:4978-4999. [PMID: 30304443 PMCID: PMC6276581 DOI: 10.1093/jas/sky382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022] Open
Abstract
Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of genes shared between different traits was observed, indicating a high impact of the population genetic structure and environmental effects. Several chromosomal regions were enriched for functional candidate genes associated with fertility traits. Moreover, multiple functional candidate genes were enriched for markers in a species-specific basis, taurine (Bos taurus) or indicine (Bos indicus). For the different candidate regions identified in the GWAS in the literature, functional candidate genes were detected as follows: B. Taurus chromosome X (BTX) (TEX11, IRAK, CDK16, ATP7A, ATRX, HDAC6, FMR1, L1CAM, MECP2, etc.), BTA17 (TRPV4 and DYNLL1), and BTA14 (MOS, FABP5, ZFPM2). These genes are responsible for regulating important metabolic pathways or biological processes associated with fertility, such as progression of spermatogenesis, control of ciliary activity, development of Sertoli cells, DNA integrity in spermatozoa, and homeostasis of testicular cells. This study represents the first systematic review on male fertility traits in cattle using a system biology approach to identify key candidate genes for these traits.
Collapse
Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Stephanie Lam
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Aroa Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Samir Id-Lahoucine
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
18
|
Naderi S, Bohlouli M, Yin T, König S. Genomic breeding values, SNP effects and gene identification for disease traits in cow training sets. Anim Genet 2018; 49:178-192. [PMID: 29624705 DOI: 10.1111/age.12661] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Holstein Friesian cow training sets were created according to disease incidences. The different datasets were used to investigate the impact of random forest (RF) and genomic BLUP (GBLUP) methodology on genomic prediction accuracies. In addition, for further verifications of some specific scenarios, single-step genomic BLUP was applied. Disease traits included the overall trait categories of (i) claw disorders, (ii) clinical mastitis and (iii) infertility from 80 741 first lactation Holstein cows kept in 58 large-scale herds. A subset of 6744 cows was genotyped (50K SNP panel). Response variables for all scenarios were de-regressed proofs (DRPs) and pre-corrected phenotypes (PCPs). Initially, all sick cows were allocated to the testing set, and healthy cows represented the training set. For the ongoing cow allocation schemes, the number of sick cows in the training set increased stepwise by moving 10% of the sick cows from the testing to the training set in each step. The size of training and testing sets was kept constant by replacing the same number of cows in the testing set with (randomly selected) healthy cows from the training set. For both the RF and GBLUP methods, prediction accuracies were larger for DRPs compared to PCPs. For PCPs as a response variable, the largest prediction accuracies were observed when the disease incidences in training sets reflected the disease incidence in the whole population. A further increase in prediction accuracies for some selected cow allocation schemes (i.e. larger prediction accuracies compared to corresponding scenarios with RF or GBLUB) was achieved via single-step GBLUP applications. Correlations between genome-wide association study SNP effects and RF importance criteria for single SNPs were in a moderate range, from 0.42 to 0.57, when considering SNPs from all chromosomes or from specific chromosome segments. RF identified significant SNPs close to potential positional candidate genes: GAS1, GPAT3 and CYP2R1 for clinical mastitis; SPINK5 and SLC26A2 for laminitis; and FGF12 for endometritis.
Collapse
Affiliation(s)
- S Naderi
- Institute of Animal Breeding and Genetics, University of Gießen, Ludwigstr. 21b, 35390, Gießen, Germany
| | - M Bohlouli
- Institute of Animal Breeding and Genetics, University of Gießen, Ludwigstr. 21b, 35390, Gießen, Germany
| | - T Yin
- Institute of Animal Breeding and Genetics, University of Gießen, Ludwigstr. 21b, 35390, Gießen, Germany
| | - S König
- Institute of Animal Breeding and Genetics, University of Gießen, Ludwigstr. 21b, 35390, Gießen, Germany
| |
Collapse
|
19
|
Abstract
Fertility is one of the most economically important traits in both beef and dairy cattle production; however, only female fertility is typically subjected to selection. Male and female fertility have only a small positive genetic correlation which is likely due to the existence of a relatively small number of genetic variants within each breed that cause embryonic and developmental losses. Genomic tools have been developed that allow the identification of lethal recessive loci based upon marker haplotypes. Selection against haplotypes harbouring lethal alleles in conjunction with selection to improve female fertility will result in an improvement in male fertility. Genomic selection has resulted in a two to fourfold increase in the rate of genetic improvement of most dairy traits in US Holstein cattle, including female fertility. Considering the rapidly increasing rate of adoption of high-throughput single nucleotide polymorphism genotyping in both the US dairy and beef industries, genomic selection should be the most effective of all currently available approaches to improve male fertility. However, male fertility phenotypes are not routinely recorded in natural service mating systems and when artificial insemination is used, semen doses may be titrated to lower post-thaw progressively motile sperm numbers for high-merit and high-demand bulls. Standardization of sperm dosages across bull studs for semen distributed from young bulls would allow the capture of sire conception rate phenotypes for young bulls that could be used to generate predictions of genetic merit for male fertility in both males and females. These data would allow genomic selection to be implemented for male fertility in addition to female fertility within the US dairy industry. While the rate of use of artificial insemination is much lower within the US beef industry, the adoption of sexed semen in the dairy industry has allowed dairy herds to select cows from which heifer replacements are produced and cows that are used to produce terminal crossbred bull calves sired by beef breed bulls. Capture of sire conception rate phenotypes in dairy herds utilizing sexed semen will contribute data enabling genomic selection for male fertility in beef cattle breeds. As the commercial sector of the beef industry increasingly adopts fixed-time artificial insemination, sire conception rate phenotypes can be captured to facilitate the development of estimates of genetic merit for male fertility within US beef breeds.
Collapse
|
20
|
Tiezzi F, Arceo ME, Cole JB, Maltecca C. Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle. BMC Genet 2018; 19:20. [PMID: 29609562 PMCID: PMC5880070 DOI: 10.1186/s12863-018-0606-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions. Results Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models. Conclusions Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data. Electronic supplementary material The online version of this article (10.1186/s12863-018-0606-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Maria E Arceo
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, 27705, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
| |
Collapse
|
21
|
Dickinson SE, Griffin BA, Elmore MF, Kriese-Anderson L, Elmore JB, Dyce PW, Rodning SP, Biase FH. Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential. BMC Genomics 2018; 19:129. [PMID: 29426285 PMCID: PMC5807776 DOI: 10.1186/s12864-018-4505-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022] Open
Abstract
Background Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection for fertility is challenging. Beef cattle operations leverage estrous synchronization in combination with artificial insemination (AI) to breed heifers and benefit from an early and uniform calving season. A couple of weeks following AI, heifers are exposed to bulls for an opportunity to become pregnant by natural breeding (NB), but they may also not become pregnant during this time period. Focusing on beef heifers, in their first breeding season, we hypothesized that: a- at the time of AI, the transcriptome of peripheral white blood cells (PWBC) differs between heifers that become pregnant to AI and heifers that become pregnant late in the breeding season by NB or do not become pregnant during the breeding season; and b- the ratio of transcript abundance between genes in PWBC classifies heifers according to pregnancy by AI, NB, or failure to become pregnant. Results We generated RNA-sequencing data from 23 heifers from two locations (A: six AI-pregnant and five NB-pregnant; and B: six AI-pregnant and six non-pregnant). After filtering out lowly expressed genes, we quantified transcript abundance for 12,538 genes. The comparison of gene expression levels between AI-pregnant and NB-pregnant heifers yielded 18 differentially expressed genes (DEGs) (ADAM20, ALDH5A1, ANG, BOLA-DQB, DMBT1, FCER1A, GSTM3, KIR3DL1, LOC107131247, LOC618633, LYZ, MNS1, P2RY12, PPP1R1B, SIGLEC14, TPPP, TTLL1, UGT8, eFDR≤0.02). The comparison of gene expression levels between AI-pregnant and non-pregnant heifers yielded six DEGs (ALAS2, CNKSR3, LOC522763, SAXO2, TAC3, TFF2, eFDR≤0.05). We calculated the ratio of expression levels between all gene pairs and assessed their potential to classify samples according to experimental groups. Considering all samples, relative expression from two gene pairs correctly classified 10 out of 12 AI-pregnant heifers (P = 0.0028) separately from the other 11 heifers (NB-pregnant, or non-pregnant). Conclusion The transcriptome profile in PWBC, at the time of AI, is associated with the fertility potential of beef heifers. Transcript levels of specific genes may be further explored as potential classifiers, and thus selection tools, of heifer fertility. Electronic supplementary material The online version of this article (10.1186/s12864-018-4505-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarah E Dickinson
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Brock A Griffin
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Michelle F Elmore
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Lisa Kriese-Anderson
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | | | - Paul W Dyce
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Soren P Rodning
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Fernando H Biase
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.
| |
Collapse
|
22
|
Laissue P, Lakhal B, Vatin M, Batista F, Burgio G, Mercier E, Santos ED, Buffat C, Sierra-Diaz DC, Renault G, Montagutelli X, Salmon J, Monget P, Veitia RA, Méhats C, Fellous M, Gris JC, Cocquet J, Vaiman D. Association of FOXD1 variants with adverse pregnancy outcomes in mice and humans. Open Biol 2017; 6:rsob.160109. [PMID: 27805902 PMCID: PMC5090055 DOI: 10.1098/rsob.160109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/25/2016] [Indexed: 01/29/2023] Open
Abstract
Recurrent spontaneous abortion (RSA) is a common cause of infertility, but previous attempts at identifying RSA causative genes have been relatively unsuccessful. Such failure to describe RSA aetiological genes might be explained by the fact that reproductive phenotypes should be considered as quantitative traits resulting from the intricate interaction of numerous genetic, epigenetic and environmental factors. Here, we studied an interspecific recombinant congenic strain (IRCS) of Mus musculus from the C57BL6/J strain of mice harbouring an approximate 5 Mb DNA fragment from chromosome 13 from Mus spretus mice (66H-MMU13 strain), with a high rate of embryonic resorption (ER). Transcriptome analyses of endometrial and placental tissues from these mice showed a deregulation of many genes associated with the coagulation and inflammatory response pathways. Bioinformatics approaches led us to select Foxd1 as a candidate gene potentially related to ER and RSA. Sequencing analysis of Foxd1 in the 66H-MMU13 strain, and in 556 women affected by RSA and 271 controls revealed non-synonymous sequence variants. In vitro assays revealed that some led to perturbations in FOXD1 transactivation properties on promoters of genes having key roles during implantation/placentation, suggesting a role of this gene in mammalian implantation processes.
Collapse
Affiliation(s)
- Paul Laissue
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France.,Centro de Investigación en Genética y Genómica-CIGGUR, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Besma Lakhal
- Department of Cytogenetics and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Magalie Vatin
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | - Frank Batista
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Gaëtan Burgio
- Institut Pasteur, Unité de Génétique des Mammifères, Paris, France.,Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, 131 Garran Road, Canberra 2601, Australian Capital Territory, Australia
| | - Eric Mercier
- Department of Haematology, University Hospital, Nîmes. Faculty of Pharmacy and Research Team EA 2992, University of Montpellier, Montpellier, France
| | - Esther Dos Santos
- GIG-EA 7404, Université de Versailles-Saint Quentin en Yvelines, Unité de Formation et de Recherche des Sciences de la Santé Simone Veil, 78180 Montigny-le-Bretonneux, France.,Service de Biologie Médicale, Centre Hospitalier de Poissy-Saint-Germain, 78300 Poissy, France
| | - Christophe Buffat
- Centre National de la Recherche Scientifique UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, Marseille, France
| | - Diana Carolina Sierra-Diaz
- Centro de Investigación en Genética y Genómica-CIGGUR, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Gilles Renault
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | | | - Jane Salmon
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Philippe Monget
- INRA-CNRS, Université de Tours-Haras Nationaux, IFR 135, 37380 Nouzilly, France
| | - Reiner A Veitia
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | - Céline Méhats
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | - Marc Fellous
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | - Jean-Christophe Gris
- Department of Haematology, University Hospital, Nîmes. Faculty of Pharmacy and Research Team EA 2992, University of Montpellier, Montpellier, France
| | - Julie Cocquet
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.,Inserm, U1016 Paris, France
| | - Daniel Vaiman
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France .,Inserm, U1016 Paris, France
| |
Collapse
|
23
|
Arishima T, Sasaki S, Isobe T, Ikebata Y, Shimbara S, Ikeda S, Kawashima K, Suzuki Y, Watanabe M, Sugano S, Mizoshita K, Sugimoto Y. Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle. BMC Genet 2017; 18:103. [PMID: 29212449 PMCID: PMC5719641 DOI: 10.1186/s12863-017-0573-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022] Open
Abstract
Background Repeat breeding, which is defined as cattle failure to conceive after three or more inseminations in the absence of clinical abnormalities, is a substantial problem in cattle breeding. To identify maternal genetic variants of repeat breeding in Japanese Black cattle, we selected 29 repeat-breeding heifers that failed to conceive following embryo transfer (ET) and conducted a genome-wide association study (GWAS) using the traits. Results We found that a single-nucleotide polymorphism (SNP; g.92,377,635A > G) in the upstream region of the FOXP3 gene on the X chromosome was highly associated with repeat breeding and failure to conceive following ET (P = 1.51 × 10−14). FOXP3 is a master gene for differentiation of regulatory T (Treg) cells that function in pregnancy maintenance. Reporter assay results revealed that the activity of the FOXP3 promoter was lower in reporter constructs with the risk-allele than in those with the non-risk-allele by approximately 0.68 fold. These findings suggest that the variant in the upstream region of FOXP3 with the risk-allele decreased FOXP3 transcription, which in turn, could reduce the number of maternal Treg cells and lead to infertility. The frequency of the risk-allele in repeat-breeding heifers is more than that in cows, suggesting that the risk-allele could be associated with infertility in repeat-breeding heifers. Conclusions This GWAS identified a maternal variant in the upstream region of FOXP3 that was associated with infertility in repeat-breeding Japanese Black cattle that failed to conceive using ET. The variant affected the level of FOXP3 mRNA expression. Thus, the results suggest that the risk-allele could serve as a useful marker to reduce and eliminate animals with inferior fertility in Japanese Black cattle. Electronic supplementary material The online version of this article (10.1186/s12863-017-0573-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Taichi Arishima
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Shinji Sasaki
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan. .,Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
| | - Tomohiro Isobe
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Yoshihisa Ikebata
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Shinichi Shimbara
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Shogo Ikeda
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Keisuke Kawashima
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, 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
| | - Manabu Watanabe
- Department of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Kazunori Mizoshita
- Kagoshima prefectural Cattle Breeding Development Institute, Osumi, So, Kagoshima, 899-8212, Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan
| |
Collapse
|
24
|
Signer-Hasler H, Burren A, Neuditschko M, Frischknecht M, Garrick D, Stricker C, Gredler B, Bapst B, Flury C. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol 2017; 49:83. [PMID: 29115934 PMCID: PMC5674839 DOI: 10.1186/s12711-017-0358-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 10/26/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). RESULTS The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH: 0.027), OB (F ROH: 0.029), and SI (F ROH: 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH: 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. CONCLUSIONS The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.
Collapse
Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Alexander Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Mirjam Frischknecht
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
- Qualitas AG, Zug, Switzerland
| | | | | | | | | | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| |
Collapse
|
25
|
Xia J, Fan H, Chang T, Xu L, Zhang W, Song Y, Zhu B, Zhang L, Gao X, Chen Y, Li J, Gao H. Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle. Sci Rep 2017; 7:42048. [PMID: 28169328 PMCID: PMC5294460 DOI: 10.1038/srep42048] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/06/2017] [Indexed: 12/26/2022] Open
Abstract
Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.
Collapse
Affiliation(s)
- Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Huizhong Fan
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Wengang Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yuxin Song
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| |
Collapse
|
26
|
Diskin MG, Waters SM, Parr MH, Kenny DA. Pregnancy losses in cattle: potential for improvement. Reprod Fertil Dev 2017; 28:83-93. [PMID: 27062877 DOI: 10.1071/rd15366] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
For heifers, beef and moderate-yielding dairy cows, it appears that the fertilisation rate generally lies between 90% and 100%. For high-producing dairy cows, there is a less substantive body of literature, but it would appear that the fertilisation rate is somewhat lower and possibly more variable. In cattle, the major component of embryo loss occurs in the first 16 days following breeding (Day 0), with emerging evidence of greater losses before Day 8 in high-producing dairy cows. In cattle, late embryo mortality causes serious economic losses because it is often recognised too late to rebreed females. Systemic concentrations of progesterone during both the cycle preceding and following insemination affect embryo survival, with evidence of either excessive or insufficient concentrations being negatively associated with survival rate. The application of direct progesterone supplementation or treatments to increase endogenous output of progesterone to increase embryo survival cannot be recommended at this time. Energy balance and dry matter intake during the first 4 weeks after calving are critically important in determining pregnancies per AI when cows are inseminated at 70-100 days after calving. Level of concentrate supplementation of cows at pasture during the breeding period has minimal effects on conception rates, although sudden reductions in dietary intake should be avoided. For all systems of milk production, more balanced breeding strategies with greater emphasis on fertility and feed intake and/or energy must be developed. There is genetic variability within the Holstein breed for fertility traits, which can be exploited. Genomic technology will not only provide scientists with an improved understanding of the underlying biological processes involved in fertilisation and the establishment of pregnancy, but also, in the future, could identify genes responsible for improved embryo survival. Such information could be incorporated into breeding objectives in order to increase the rate of genetic progress for embryo survival. In addition, there is a range of easily adoptable management factors, under producer control, that can either directly increase embryo survival or ameliorate the consequences of low embryo survival rates. The correction of minor deficits in several areas can have a substantial cumulative positive effect on herd reproductive performance.
Collapse
Affiliation(s)
- M G Diskin
- Teagasc, Animal and Grassland and Innovation Research Centre, Mellows Campus, Athenry, Co. Galway, H65 R718, Ireland
| | - S M Waters
- Teagasc, Animal and Grassland and Innovation Research Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - M H Parr
- Teagasc, Animal and Grassland and Innovation Research Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - D A Kenny
- Teagasc, Animal and Grassland and Innovation Research Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| |
Collapse
|
27
|
Puglisi R, Gaspa G, Balduzzi D, Severgnini A, Vanni R, Macciotta N, Galli A. Genomewide analysis of bull sperm quality and fertility traits. Reprod Domest Anim 2016; 51:840-3. [PMID: 27550832 DOI: 10.1111/rda.12747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/07/2016] [Indexed: 01/08/2023]
Abstract
Because the priority of AI industry is to identify subfertile bulls, a predictive model that allowed for the prediction of 91% bulls of low fertility was implemented based on seminological (motility) parameters and DNA status assessed both as DNA fragmentation index (DFI) and by TUNEL assay using sperm of 105 Holstein-Friesian bulls (four batches per bull) selected based on in vivo estimated relative conception rates (ERCR). Thereafter, sperm quality and male fertility traits of bulls were explored by GWAS using a high-density (777K) Illumina chip. After data editing, 85 bulls and 591,988 SNPs were retained for GWAS. Of 12 SNPs with false discovery rate <0.2, four SNPs located on BTA28 and BTA18 were significantly associated (LD-adjusted Bonferroni <0.05) with the non-compensatory sperm parameters DFI and TUNEL. Other SNPs of interest for potential association with TUNEL were found on BTA3, in the same chromosome where associations with non-compensatory in vivo bull fertility were already reported. Further suggestive SNPs for sperm membrane integrity were located on BTA28, the chromosome where QTL studies previously reported associations with sperm quality traits. Suggestive SNPs for ERCR were found on BTA18 in the vicinity of a site already associated with in vivo bull fertility. Additional SNPs associated with ERCR and sperm kinetic parameters were also identified. In contrast to other, but very few GWAS on fertility traits in bovine spermatozoa, which reported significant SNPs located on BTX, we have not identified SNPs of interest in this sexual chromosome.
Collapse
Affiliation(s)
- R Puglisi
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy.
| | - G Gaspa
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy
| | - D Balduzzi
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - A Severgnini
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - R Vanni
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - Npp Macciotta
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy
| | - A Galli
- CREA - Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| |
Collapse
|
28
|
Fertility management of bulls to improve beef cattle productivity. Theriogenology 2016; 86:397-405. [DOI: 10.1016/j.theriogenology.2016.04.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 02/18/2016] [Accepted: 03/14/2016] [Indexed: 01/18/2023]
|
29
|
Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle. BMC Genet 2016; 17:75. [PMID: 27287773 PMCID: PMC4901445 DOI: 10.1186/s12863-016-0386-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genomic regions affecting milk production, milk components and fertility traits in Canadian Holstein cattle, and to use these positions to identify genes and pathways that may influence these traits. RESULT Several QTL regions were detected for milk production (MILK), fat production (FAT), protein production (PROT) and fat and protein deviation (FATD, PROTD respectively). The identified QTL regions for production traits (including milk production) support previous findings and some overlap with genes with known relevant biological functions identified in earlier studies such as DGAT1 and CPSF1. A significant region on chromosome 21 overlapping with the gene FAM181A and not previous linked to fertility in dairy cattle was identified for the calving to first service interval and days open. A functional enrichment analysis of the GWAS results yielded GO terms consistent with the specific phenotypes tested, for example GO terms GO:0007595 (lactation) and GO:0043627 (response to estrogen) for milk production (MILK), GO:0051057 (positive regulation of small GTPase mediated signal transduction) for fat production (FAT), GO:0040019 (positive regulation of embryonic development) for first service to calving interval (CTFS) and GO:0043268 (positive regulation of potassium ion transport) for days open (DO). In other cases the connection between the enriched GO terms and the traits were less clear, for example GO:0003279 (cardiac septum development) for FAT and GO:0030903 (notochord development) for DO trait. CONCLUSION The chromosomal regions and enriched pathways identified in this study confirm several previous findings and highlight new regions and pathways that may contribute to variation in production or fertility traits in dairy cattle.
Collapse
|
30
|
Parker Gaddis KL, Null DJ, Cole JB. Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits. J Dairy Sci 2016; 99:6420-6435. [PMID: 27209127 DOI: 10.3168/jds.2015-10444] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 04/15/2016] [Indexed: 01/03/2023]
Abstract
The objective of this study was to identify single nucleotide polymorphisms and gene networks associated with 3 fertility traits in dairy cattle-daughter pregnancy rate, heifer conception rate, and cow conception rate-using different approaches. Deregressed predicted transmitting abilities were available for approximately 24,000 Holstein bulls and 36,000 Holstein cows sampled from the National Dairy Database with high-density genotypes. Of those, 1,732 bulls and 375 cows had been genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA). The remaining animals were genotyped with various chips of lower density that were imputed to high density. Univariate and trivariate genome-wide association studies (GWAS) with both medium- (60,671 markers) and high-density (312,614 markers) panels were performed for daughter pregnancy rate, heifer conception rate, and cow conception rate using GEMMA (version 0.94; http://www.xzlab.org/software.html). Analyses were conducted using bulls only, cows only, and a sample of both bulls and cows. The partial correlation and information theory algorithm was used to develop gene interaction networks. The most significant markers were further investigated to identify putatively associated genes. Little overlap in associated genes could be found between GWAS using different reference populations of bulls only, cows only, and combined bulls and cows. The partial correlation and information theory algorithm was able to identify several genes that were not identified by ordinary GWAS. The results obtained herein will aid in further dissecting the complex biology underlying fertility traits in dairy cattle, while also providing insight into the nuances of GWAS.
Collapse
Affiliation(s)
- K L Parker Gaddis
- Department of Animal Sciences, University of Florida, Gainesville 32611.
| | - D J Null
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| |
Collapse
|
31
|
Juma AR, Damdimopoulou PE, Grommen SVH, Van de Ven WJM, De Groef B. Emerging role of PLAG1 as a regulator of growth and reproduction. J Endocrinol 2016; 228:R45-56. [PMID: 26577933 DOI: 10.1530/joe-15-0449] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/17/2015] [Indexed: 12/15/2022]
Abstract
Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors along with PLAG-like 1 and PLAG-like 2. The PLAG1 gene is best known as an oncogene associated with certain types of cancer, most notably pleomorphic adenomas of the salivary gland. While the mechanisms of PLAG1-induced tumorigenesis are reasonably well understood, the role of PLAG1 in normal physiology is less clear. It is known that PLAG1 is involved in cell proliferation by directly regulating a wide array of target genes, including a number of growth factors such as insulin-like growth factor 2. This is likely to be a central mode of action for PLAG1 both in embryonic development and in cancer. The phenotype of Plag1 knockout mice suggests an important role for PLAG1 also in postnatal growth and reproduction, as PLAG1 deficiency causes growth retardation and reduced fertility. A role for PLAG1 in growth and reproduction is further corroborated by genome-wide association studies in humans and domestic animals in which polymorphisms in the PLAG1 genomic region are associated with body growth and reproductive traits. Here we review the current evidence for PLAG1 as a regulator of growth and fertility and discuss possible endocrine mechanisms involved.
Collapse
Affiliation(s)
- Almas R Juma
- Department of PhysiologyAnatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Clinical SciencesIntervention and Technology, Karolinska Institutet and Karolinska University Hospital, Huddinge, 141 86 Stockholm, SwedenDepartment of Human GeneticsKU Leuven, B-3000 Leuven, Belgium
| | - Pauliina E Damdimopoulou
- Department of PhysiologyAnatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Clinical SciencesIntervention and Technology, Karolinska Institutet and Karolinska University Hospital, Huddinge, 141 86 Stockholm, SwedenDepartment of Human GeneticsKU Leuven, B-3000 Leuven, Belgium
| | - Sylvia V H Grommen
- Department of PhysiologyAnatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Clinical SciencesIntervention and Technology, Karolinska Institutet and Karolinska University Hospital, Huddinge, 141 86 Stockholm, SwedenDepartment of Human GeneticsKU Leuven, B-3000 Leuven, Belgium
| | - Wim J M Van de Ven
- Department of PhysiologyAnatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Clinical SciencesIntervention and Technology, Karolinska Institutet and Karolinska University Hospital, Huddinge, 141 86 Stockholm, SwedenDepartment of Human GeneticsKU Leuven, B-3000 Leuven, Belgium
| | - Bert De Groef
- Department of PhysiologyAnatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Clinical SciencesIntervention and Technology, Karolinska Institutet and Karolinska University Hospital, Huddinge, 141 86 Stockholm, SwedenDepartment of Human GeneticsKU Leuven, B-3000 Leuven, Belgium
| |
Collapse
|
32
|
Sasaki S, Ibi T, Matsuhashi T, Takeda K, Ikeda S, Sugimoto M, Sugimoto Y. Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle. BMC Genet 2015; 16:123. [PMID: 26486459 PMCID: PMC4618343 DOI: 10.1186/s12863-015-0282-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/16/2015] [Indexed: 12/24/2022] Open
Abstract
Background Female fertility, a fundamental trait required for animal reproduction, has gradually declined in the last 2 decades in Japanese Black cattle. To identify associated genetic variants in Japanese Black cattle, we evaluated female fertility as a metric to describe the average inverse of the number of artificial inseminations required for conception from the first through the fourth parity (ANAI4) and conducted a genome-wide association study (GWAS) using 430 animals with extreme ANAI4 values from 10,399 animals. Results We found that 2 variants, namely a single-nucleotide polymorphisms (SNP; g.48476925C > T) and a 3-bp indel (g.48476943_48476946insGGC), in the upstream region of the activin receptor IIA gene (ACVR2A) were associated with ANAI4. ACVR2A transcripts from Japanese Black cattle of the Q haplotype, defined by the SNP and the 3-bp indel, with increased ANAI4 were 1.29–1.32-fold more abundant than q-derived transcripts. In agreement, reporter assay results revealed that the activity of the ACVR2A promoter was higher in reporter constructs with the Q haplotype than in those with the q haplotype by approximately 1.2 fold. Expression of exogenous ACVR2A induced dose-dependent increases of reporter activity from the follicle-stimulating hormone, beta polypeptide (FSHB) promoter in response to activin A in a pituitary gonadotrophic cell line. The findings suggested that sequence variations in the upstream region of ACVR2A with the Q haplotype increased ACVR2A transcription, which in turn induced FSHB expression. This association was replicated using a sample population size of 1,433 animals; the frequency of the Q haplotype was 0.39, and Q-to-q haplotype substitution resulted in an increase of 0.02 in terms of ANAI4. Conclusions This GWAS identified variants in the upstream region of ACVR2A, which were associated with female fertility in Japanese Black cattle. The variants affected the level of ACVR2A mRNA expression, which could lead to an allelic imbalance. This association was replicated with a sample population of 1,433 animals. Thus, the results suggest that the Q haplotype could serve as a useful marker to select Japanese Black cattle with superior female fertility. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0282-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shinji Sasaki
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.
| | - Tamako Matsuhashi
- Gifu Prefectural Livestock Research Institute, Kiyomi, Takayama, Gifu, 506-0101, Japan.
| | - Kenji Takeda
- Gifu Prefectural Livestock Research Institute, Kiyomi, Takayama, Gifu, 506-0101, Japan.
| | - Shogo Ikeda
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima, 899-8212, Japan.
| | - Mayumi Sugimoto
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
| |
Collapse
|
33
|
Sasaki S, Ibi T, Kojima T, Sugimoto Y. A genome-wide association study reveals a quantitative trait locus for days open on chromosome 2 in Japanese Black cattle. Anim Genet 2015; 47:102-5. [PMID: 26374166 DOI: 10.1111/age.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2015] [Indexed: 12/01/2022]
Abstract
Days open (DO), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome-wide association study with 33,303 single nucleotide polymorphisms (SNPs) using 459 animals with extreme DO values selected from a larger group of 15,488 animals. We identified a SNP on bovine chromosome 2 (BTA2) that was associated with DO. After imputation using phased haplotype data inferred from 586 812 SNPs of 1041 Japanese Black cattle, six SNPs associated with DO were located in an 8.5-kb region of high linkage disequilibrium on BTA2. These SNPs were located on the telomeric side at a distance of 177 kb from the parathyroid hormone 2 receptor (PTH2R) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced-DO allele (Q) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q-to-q allele substitution on DO was a decrease of 3.74 days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance.
Collapse
Affiliation(s)
- Shinji Sasaki
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
| | - Takatoshi Kojima
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan
| |
Collapse
|
34
|
Capitan A, Michot P, Baur A, Saintilan R, Hozé C, Valour D, Guillaume F, Boichon D, Barbat A, Boichard D, Schibler L, Fritz S. Genetic tools to improve reproduction traits in dairy cattle. Reprod Fertil Dev 2015; 27:14-21. [PMID: 25472040 DOI: 10.1071/rd14379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fertility is a major concern in the dairy cattle industry and has been the subject of numerous studies over the past 20 years. Surprisingly, most of these studies focused on rough female phenotypes and, despite their important role in reproductive success, male- and embryo-related traits have been poorly investigated. In recent years, the rapid and important evolution of technologies in genetic research has led to the development of genomic selection. The generalisation of this method in combination with the achievements of the AI industry have led to the constitution of large databases of genotyping and sequencing data, as well as refined phenotypes and pedigree records. These resources offer unprecedented opportunities in terms of fundamental and applied research. Here we present five such examples with a focus on reproduction-related traits: (1) detection of quantitative trait loci (QTL) for male fertility and semen quality traits; (2) detection of QTL for refined phenotypes associated with female fertility; (3) identification of recessive embryonic lethal mutations by depletion of homozygous haplotypes; (4) identification of recessive embryonic lethal mutations by mining whole-genome sequencing data; and (5) the contribution of high-density single nucleotide polymorphism chips, whole-genome sequencing and imputation to increasing the power of QTL detection methods and to the identification of causal variants.
Collapse
Affiliation(s)
- A Capitan
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - P Michot
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - A Baur
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - R Saintilan
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - C Hozé
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - D Valour
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - F Guillaume
- EVOLUTION, 69 rue de la Motte Brûlon, 35706 Rennes, France
| | - D Boichon
- MIDATEST, Les Nauzes, 81580 Soual, France
| | - A Barbat
- INRA (Institut National de la Recherche Agronomique), UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - D Boichard
- INRA (Institut National de la Recherche Agronomique), UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - L Schibler
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| | - S Fritz
- UNCEIA (Union Nationale des Coopératives d'Elevage et d'Insémination Animale), 149 rue de Bercy, 75012 Paris, France
| |
Collapse
|
35
|
Valour D, Michot P, Eozenou C, Lefebvre R, Bonnet A, Capitan A, Uzbekova S, Sellem E, Ponsart C, Schibler L. Dairy cattle reproduction is a tightly regulated genetic process: Highlights on genes, pathways, and biological processes. Anim Front 2015. [DOI: 10.2527/af.2015-0006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- D. Valour
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - P. Michot
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - C. Eozenou
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - R. Lefebvre
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - A. Bonnet
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| | - A. Capitan
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- UMR INRA 85-CNRS 7247-Université de Tours, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France
| | - S. Uzbekova
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352 Jouy en Josas, France
| | - E. Sellem
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
- INRA, UMR1198 Biologie du Développement et de la Reproduction, F-78350 Jouy en Josas, France
| | - C. Ponsart
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| | - L. Schibler
- UNCEIA, 149 rue de Bercy, 75012 Paris, France
| |
Collapse
|
36
|
Abstract
We investigated the effect of maternal sire on early pregnancy failure (between D0, day of insemination and D90) in their progeny during the first and second lactations (n=3508) in the Holstein breed. The estimated breeding value (EBV) for cow fertility of 12 bulls (reliability⩾0.95) was used to create the following three groups: low, medium and high EBV (EBV from -0.7 to 1 expressed as genetic standard deviation relative to the mean of the breed). In their daughters (93 to 516 per bull), progesterone measurement was carried out on the day of artificial insemination (AI; D0) to check whether the cows were in the follicular phase and on D18 to 25 to assess non-fertilisation-early embryonic mortality (NF-EEM). Late embryonic mortality (LEM) and early foetal death (FD) were determined by ultrasonography on D45 and D90 and by the return to oestrus after the first AI. Frequencies of NF-EEM, LEM, FD and pregnancy were 33.3%, 11.7%, 1.4% and 48.5% and incidences were 35.1, 19.0, 2.7 and 51.1, respectively. Sire EBV was significantly related to the incidences of pregnancy failure between D0 and D90, fertilisation failure-early embryonic mortality (FF-EEM) and LEM but not to the incidence of FD between D45 and D90 of pregnancy. The relative risk (RR) of FF-EEM was significantly higher (RR=1.2; P<0.05) for the progeny group of low EBV bulls when compared with high EBV bulls. The same effect was observed when comparing LEM of the progeny groups from the low EBV bulls to those from moderate and high EBV bulls (RR, respectively, of 1.3 and 1.4; P<005). The incidence of FF-EEM was significantly higher when cows were inseminated before 80 days postpartum compared with later, and for the extreme values of the difference between milk fat and protein content measured during the first 3 months of lactation. FF-EEM was also significantly related to the year of observation. The incidence of LEM was higher for the highest producing cows and was influenced by interaction between milk yield×lactation rank and milk yield×milk protein content. In conclusion, this study showed large differences in early pregnancy failure between progeny groups and highlights the interest of accurate characterisation of embryonic death in order to identify potential candidate genes for female fertility.
Collapse
|
37
|
Khatkar M, Randhawa I, Raadsma H. Meta-assembly of genomic regions and variants associated with female reproductive efficiency in cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
38
|
Reverter A, Henshall JM, McCulloch R, Sasazaki S, Hawken R, Lehnert SA. Numerical analysis of intensity signals resulting from genotyping pooled DNA samples in beef cattle and broiler chicken. J Anim Sci 2014; 92:1874-85. [PMID: 24663186 DOI: 10.2527/jas.2013-7133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pooled genomic DNA has been proposed as a cost-effective approach in genomewide association studies (GWAS). However, algorithms for genotype calling of biallelic SNP are not adequate with pooled DNA samples because they assume the presence of 2 fluorescent signals, 1 for each allele, and operate under the expectation that at most 2 copies of the variant allele can be found for any given SNP and DNA sample. We adapt analytical methodology from 2-channel gene expression microarray technology to SNP genotyping of pooled DNA samples. Using 5 datasets from beef cattle and broiler chicken of varying degrees of complexity in terms of design and phenotype, continuous and dichotomous, we show that both differential hybridization (M = green minus red intensity signal) and abundance (A = average of red and green intensities) provide useful information in the prediction of SNP allele frequencies. This is predominantly true when making inference about extreme SNP that are either nearly fixed or highly polymorphic. We propose the use of model-based clustering via mixtures of bivariate normal distributions as an optimal framework to capture the relationship between hybridization intensity and allele frequency from pooled DNA samples. The range of M and A values observed here are in agreement with those reported within the context of gene expression microarray and also with those from SNP array data within the context of analytical methodology for the identification of copy number variants. In particular, we confirm that highly polymorphic SNP yield a strong signal from both channels (red and green) while lowly or nonpolymorphic SNP yield a strong signal from 1 channel only. We further confirm that when the SNP allele frequencies are known, either because the individuals in the pools or from a closely related population are themselves genotyped, a multiple regression model with linear and quadratic components can be developed with high prediction accuracy. We conclude that when these approaches are applied to the estimation of allele frequencies, the resulting estimates allow for the development of cost-effective and reliable GWAS.
Collapse
Affiliation(s)
- A Reverter
- CSIRO Food Futures Flagship and CSIRO Animal, Food and Health Sciences, 306Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia
| | | | | | | | | | | |
Collapse
|