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Dementieva NV, Dysin AP, Shcherbakov YS, Nikitkina EV, Musidray AA, Petrova AV, Mitrofanova OV, Plemyashov KV, Azovtseva AI, Griffin DK, Romanov MN. Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study. Animals (Basel) 2024; 14:251. [PMID: 38254422 PMCID: PMC10812825 DOI: 10.3390/ani14020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Elena V. Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem A. Musidray
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Anna V. Petrova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Kirill V. Plemyashov
- Federal State Budgetary Educational Institution of Higher Education “St. Petersburg State University of Veterinary Medicine”, 196084 St. Petersburg, Russia;
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
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Seabury CM, Smith JL, Wilson ML, Bhattarai E, Santos JEP, Chebel RC, Galvão KN, Schuenemann GM, Bicalho RC, Gilbert RO, Rodriguez-Zas SL, Rosa G, Thatcher WW, Pinedo PJ. Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins. G3 (BETHESDA, MD.) 2023; 13:jkad043. [PMID: 36848195 PMCID: PMC10468724 DOI: 10.1093/g3journal/jkad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/18/2022] [Accepted: 12/20/2022] [Indexed: 03/01/2023]
Abstract
Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination (AI) with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein cows and produce genomic heritability estimates. Moreover, we use genomic best linear unbiased prediction (GBLUP) to investigate the potential utility of the RI by performing genomic predictions with cross validation. Notably, genomic heritability estimates for the U.S. Holstein RI were moderate (h2 = 0.1654 ± 0.0317-0.2550 ± 0.0348), while single and multi-locus GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29, including the known QTL for the daughter pregnancy rate (DPR) and cow conception rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR) QTL (59 Mb). Positional candidate genes for the detected QTL included male and female fertility loci (i.e. spermatogenesis and oogenesis), meiotic and mitotic regulators, and genes associated with immune response, milk yield, enhanced pregnancy rates, and the reproductive longevity pathway. Based on the proportion of the phenotypic variance explained (PVE), all detected QTL (n = 13; P ≤ 5e - 05) were estimated to have moderate (1.0% < PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted probability of pregnancy. Genomic prediction using GBLUP with cross validation (k = 3) produced mean predictive abilities (0.1692-0.2301) and mean genomic prediction accuracies (0.4119-0.4557) that were similar to bovine health and production traits previously investigated.
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Affiliation(s)
- Christopher M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Johanna L Smith
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Eric Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Jose E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Ricardo C Chebel
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Gustavo M Schuenemann
- Department of Veterinary Preventative Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Rob O Gilbert
- Department of Clinical Sciences, School of Veterinary Medicine, Ross University, St. Kitts, West Indies, KN
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL 61801, USA
| | - Guilherme Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - William W Thatcher
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Pablo J Pinedo
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80521, USA
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Mukherjee A, Gali J, Kar I, Datta S, Roy M, Acharya AP, Patra AK. Candidate genes and proteins regulating bull semen quality: a review. Trop Anim Health Prod 2023; 55:212. [PMID: 37208528 DOI: 10.1007/s11250-023-03617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Poor semen profile reflected by suboptimum fertility statistics is a concern in bulls reared for breeding purpose. A critical review of research on candidate genes and proteins associated with semen quality traits will be useful to understand the progress of molecular marker development for bull semen quality traits. Here, we have tabulated and classified candidate genes and proteins associated with bull semen quality based on a literature survey. A total of 175 candidate genes are associated with semen quality traits in various breeds of cattle. Several studies using candidate gene approach have identified 26 genes carrying a total of 44 single nucleotide polymorphisms. Furthermore, nine genome-wide association studies (GWASes) have identified 150 candidate genes using bovine single nucleotide polymorphisms (SNP) chips. Three genes, namely membrane-associated ring-CH-type finger 1 (MARCH1), platelet-derived growth factor receptor beta, and phosphodiesterase type 1, were identified commonly in two GWASes, which, especially MARCH1, are required to explore their regulatory roles in bull semen quality in in-depth studies. With the advancement of high-throughput-omic technologies, more candidate genes associated with bull semen quality may be identified in the future. Therefore, the functional significance of candidate genes and proteins need to be delved further into future investigations to augment bull semen quality.
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Affiliation(s)
- Ayan Mukherjee
- Department of Veterinary Biotechnology, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Jaganmohanarao Gali
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Indrajit Kar
- Department of Avian Science, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Sanjoy Datta
- Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Manoranjan Roy
- Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Aditya Pratap Acharya
- Department of Veterinary Biotechnology, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Amlan Kumar Patra
- Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India.
- American Institute for Goat Research, Langston University, Langston, Oklahoma, USA.
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Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle. Front Genet 2021; 12:699422. [PMID: 34306039 PMCID: PMC8299338 DOI: 10.3389/fgene.2021.699422] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. Result De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. Conclusion The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
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Affiliation(s)
- Satish Kumar Illa
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sabyasachi Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sapna Nath
- Artificial Breeding Research Center, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Anupama Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
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Krivoruchko AY, Yatsyk OA, Safaryan EY. Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed. Vavilovskii Zhurnal Genet Selektsii 2020; 24:836-843. [PMID: 35087996 PMCID: PMC8763718 DOI: 10.18699/vj20.681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study
of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class.
The aim of this study was to identify new candidate genes for economically valuable traits based on the search for
single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals
belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6,
10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the
region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation
Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex
of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA,
EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and
DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development
of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can
influence the formation of exterior features and productive qualities of sheep. However, further research is needed
to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.
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Affiliation(s)
- A. Y. Krivoruchko
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - O. A. Yatsyk
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - E. Y. Safaryan
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
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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.
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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.
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Michailidou S, Tsangaris GT, Tzora A, Skoufos I, Banos G, Argiriou A, Arsenos G. Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds. PLoS One 2019; 14:e0226179. [PMID: 31830089 PMCID: PMC6907847 DOI: 10.1371/journal.pone.0226179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/21/2019] [Indexed: 12/02/2022] Open
Abstract
Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.
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Affiliation(s)
- S. Michailidou
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
- * E-mail:
| | - G. Th. Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - A. Tzora
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - I. Skoufos
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - G. Banos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland's Rural College and The Roslin Institute University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - A. Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
| | - G. Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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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.
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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
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Sarakul M, Elzo MA, Koonawootrittriron S, Suwanasopee T, Jattawa D, Laodim T. Characterization of biological pathways associated with semen traits in the Thai multibreed dairy population. Anim Reprod Sci 2018; 197:324-334. [PMID: 30213568 DOI: 10.1016/j.anireprosci.2018.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
Abstract
The objective of this research was to characterize biological pathways associated with semen volume (VOL), number of sperm (NS), and sperm motility (MOT) of dairy bulls in the Thai multibreed dairy population. Phenotypes for VOL (n = 13,535), NS (n = 12,773), and MOT (n = 12,660) came from 131 bulls of the Dairy Farming Promotion Organization of Thailand. Genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNP) from 72 animals. The SNP variances for VOL, NS, and MOT were estimated using a three-trait genomic-polygenic repeatability model. Fixed effects were contemporary group, ejaculate order, age of bull, ambient temperature, and heterosis. Random effects were animal additive genetic, permanent environmental, and residual. Individual SNP explaining at least 0.001% of the total genetic variance for each trait were selected to identify associated genes in the NCBI database (UMD Bos taurus 3.1 assembly) using the R package Map2NCBI. A set of 1,999 NCBI genes associated with all three semen traits was utilized for the pathway analysis conducted with the ClueGO plugin of Cytoscape using information from the Kyoto Encyclopedia of Genes and Genomes database. The pathway analysis revealed seven significant biological pathways involving 127 genes that explained 1.04% of the genetic variance for VOL, NS, and MOT. These genes were known to affect cell structure, motility, migration, proliferation, differentiation, survival, apoptosis, signal transduction, oxytocin release, calcium channel, neural development, and immune system functions related to sperm morphology and physiology during spermatogenesis.
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Affiliation(s)
- Mattaneeya Sarakul
- Department of Animal Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Mauricio A Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | | | | | - Danai Jattawa
- Department of Animal Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thawee Laodim
- Department of Animal Science, Kasetsart University, Bangkok, 10900, Thailand
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Borowska A, Szwaczkowski T, Kamiński S, Hering DM, Kordan W, Lecewicz M. Identification of genome regions determining semen quality in Holstein-Friesian bulls using information theory. Anim Reprod Sci 2018; 192:206-215. [PMID: 29572044 DOI: 10.1016/j.anireprosci.2018.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/16/2018] [Accepted: 03/09/2018] [Indexed: 10/17/2022]
Abstract
Use of information theory can be an alternative statistical approach to detect genome regions and candidate genes that are associated with livestock traits. The aim of this study was to verify the validity of the SNPs effects on some semen quality variables of bulls using entropy analysis. Records from 288 Holstein-Friesian bulls from one AI station were included. The following semen quality variables were analyzed: CASA kinematic variables of sperm (total motility, average path velocity, straight line velocity, curvilinear velocity, amplitude of lateral head displacement, beat cross frequency, straightness, linearity), sperm membrane integrity (plazmolema, mitochondrial function), sperm ATP content. Molecular data included 48,192 SNPs. After filtering (call rate = 0.95 and MAF = 0.05), 34,794 SNPs were included in the entropy analysis. The entropy and conditional entropy were estimated for each SNP. Conditional entropy quantifies the remaining uncertainty about values of the variable with the knowledge of SNP. The most informative SNPs for each variable were determined. The computations were performed using the R statistical package. A majority of the loci had relatively small contributions. The most informative SNPs for all variables were mainly located on chromosomes: 3, 4, 5 and 16. The results from the study indicate that important genome regions and candidate genes that determine semen quality variables in bulls are located on a number of chromosomes. Some detected clusters of SNPs were located in RNA (U6 and 5S_rRNA) for all the variables for which analysis occurred. Associations between PARK2 as well GALNT13 genes and some semen characteristics were also detected.
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Affiliation(s)
- Alicja Borowska
- Division of Horse Breeding, Poznan University of Life Sciences, Wolynska st. 33, 60-637 Poznan, Poland
| | - Tomasz Szwaczkowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska st. 33, 60-637 Poznan, Poland.
| | - Stanisław Kamiński
- Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, M. Oczapowski st. 5, 10-718 Olsztyn, Poland
| | - Dorota M Hering
- Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, M. Oczapowski st. 5, 10-718 Olsztyn, Poland
| | - Władysław Kordan
- Department of Animal Biochemistry and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowski st. 5, 10-718 Olsztyn, Poland
| | - Marek Lecewicz
- Department of Animal Biochemistry and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowski st. 5, 10-718 Olsztyn, Poland
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11
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Alyethodi RR, Deb R, Alex R, Kumar S, Singh U, Tyagi S, Mandal D, Raja T, Das A, Sharma S, Sengar GS, Singh R, Prakash B. Molecular markers, BM1500 and UMN2008, are associated with post-thaw motility of bull sperm. Anim Reprod Sci 2016; 174:143-149. [DOI: 10.1016/j.anireprosci.2016.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 02/07/2023]
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