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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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Hao X, Liang A, Plastow G, Zhang C, Wang Z, Liu J, Salzano A, Gasparrini B, Campanile G, Zhang S, Yang L. An Integrative Genomic Prediction Approach for Predicting Buffalo Milk Traits by Incorporating Related Cattle QTLs. Genes (Basel) 2022; 13:genes13081430. [PMID: 36011341 PMCID: PMC9408041 DOI: 10.3390/genes13081430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Background: The 90K Axiom Buffalo SNP Array is expected to improve and speed up various genomic analyses for the buffalo (Bubalus bubalis). Genomic prediction is an effective approach in animal breeding to improve selection and reduce costs. As buffalo genome research is lagging behind that of the cow and production records are also limited, genomic prediction performance will be relatively poor. To improve the genomic prediction in buffalo, we introduced a new approach (pGBLUP) for genomic prediction of six buffalo milk traits by incorporating QTL information from the cattle milk traits in order to help improve the prediction performance for buffalo. Results: In simulations, the pGBLUP could outperform BayesR and the GBLUP if the prior biological information (i.e., the known causal loci) was appropriate; otherwise, it performed slightly worse than BayesR and equal to or better than the GBLUP. In real data, the heritability of the buffalo genomic region corresponding to the cattle milk trait QTLs was enriched (fold of enrichment > 1) in four buffalo milk traits (FY270, MY270, PY270, and PM) when the EBV was used as the response variable. The DEBV as the response variable yielded more reliable genomic predictions than the traditional EBV, as has been shown by previous research. The performance of the three approaches (GBLUP, BayesR, and pGBLUP) did not vary greatly in this study, probably due to the limited sample size, incomplete prior biological information, and less artificial selection in buffalo. Conclusions: To our knowledge, this study is the first to apply genomic prediction to buffalo by incorporating prior biological information. The genomic prediction of buffalo traits can be further improved with a larger sample size, higher-density SNP chips, and more precise prior biological information.
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Affiliation(s)
- Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence: (X.H.); (L.Y.)
| | - Aixin Liang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Graham Plastow
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada
| | - Chunyan Zhang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada
| | - Zhiquan Wang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada
| | - Jiajia Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Angela Salzano
- Department of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, 80137 Naples, Italy
| | - Bianca Gasparrini
- Department of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, 80137 Naples, Italy
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, 80137 Naples, Italy
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.H.); (L.Y.)
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3
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SNPRBb: economically important trait specific SNP resources of buffalo (Bubalus bubalis). CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01210-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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4
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species. G3-GENES GENOMES GENETICS 2020; 10:2327-2343. [PMID: 32434754 PMCID: PMC7341147 DOI: 10.1534/g3.120.401090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes.
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6
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Zhang Y, Colli L, Barker JSF. Asian water buffalo: domestication, history and genetics. Anim Genet 2020; 51:177-191. [PMID: 31967365 DOI: 10.1111/age.12911] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000-7000 years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.
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Affiliation(s)
- Y Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - L Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - J S F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
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7
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Zou C, Karn A, Reisch B, Nguyen A, Sun Y, Bao Y, Campbell MS, Church D, Williams S, Xu X, Ledbetter CA, Patel S, Fennell A, Glaubitz JC, Clark M, Ware D, Londo JP, Sun Q, Cadle-Davidson L. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun 2020; 11:413. [PMID: 31964885 PMCID: PMC6972940 DOI: 10.1038/s41467-019-14280-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Bruce Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Allen Nguyen
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yongming Sun
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yun Bao
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | | | | | | | - Xia Xu
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Craig A Ledbetter
- USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA
| | - Sagar Patel
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Jeffrey C Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Jason P Londo
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
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8
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Laodim T, Elzo MA, Koonawootrittriron S, Suwanasopee T, Jattawa D. Identification of SNP markers associated with milk and fat yields in multibreed dairy cattle using two genetic group structures. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis. Mamm Genome 2017; 28:520-527. [PMID: 28864882 DOI: 10.1007/s00335-017-9714-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/27/2017] [Indexed: 10/18/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis: (MAP) causes a contagious chronic infection results in Johne's disease in a wide range of animal species, including cattle. Several genome-wide association studies (GWAS) have been carried out to identify loci putatively associated with MAP susceptibility by testing each marker separately and identifying SNPs that show a significant association with the phenotype, while SNP with modest effects are usually ignored. The objective of this study was to identify modest-effect genes associated with MAP susceptibility using a pathway-based approach. The Illumina BovineSNP50 BeadChip was used to genotype 966 Holstein cows, 483 positive and 483 negative for antibody response to MAP, data were then analyzed using novel SNP-based Gene Set Enrichment Analysis (GSEA-SNP) and validated with Adaptive Rank Truncated Product methodology. An allele-based test was carried out to estimate the statistical association for each marker with the phenotype, subsequently SNPs were mapped to the closest genes, considering for each gene the single variant with the highest value within a window of 50 kb, then pathway-statistics were tested using the GSEA-SNP method. The GO biological process "embryogenesis and morphogenesis" was most highly associated with antibody response to MAP. Within this pathway, five genes code for proteins which play a role in the immune defense relevant to response to bacterial infection. The immune response genes identified would not have been considered using a standard GWAS, thus demonstrating that the pathway approach can extend the interpretation of genome-wide association analyses and identify additional candidate genes for target traits.
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10
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Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel. Animal 2017; 12:464-471. [PMID: 28735584 DOI: 10.1017/s1751731117001719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo's milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10-5 and 2.0×10-7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.
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11
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El-Halawany N, Abdel-Shafy H, Shawky AEMA, Abdel-Latif MA, Al-Tohamy AF, Abd El-Moneim OM. Genome-wide association study for milk production in Egyptian buffalo. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.01.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.07.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Ivy JA, Putnam AS, Navarro AY, Gurr J, Ryder OA. Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs. J Hered 2016; 107:403-12. [PMID: 27208150 DOI: 10.1093/jhered/esw029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/22/2016] [Indexed: 12/24/2022] Open
Abstract
Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P << 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.
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Affiliation(s)
- Jamie A Ivy
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Andrea S Putnam
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Asako Y Navarro
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Jessica Gurr
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Oliver A Ryder
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
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14
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Zhang L, Zhou X, Michal JJ, Ding B, Li R, Jiang Z. Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations. Int J Biol Sci 2014; 10:236-44. [PMID: 24644423 PMCID: PMC3957079 DOI: 10.7150/ijbs.7744] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/16/2014] [Indexed: 12/23/2022] Open
Abstract
Birth weight is an economically important trait in pig production because it directly impacts piglet growth and survival rate. In the present study, we performed a genome wide survey of candidate genes and pathways associated with individual birth weight (IBW) using the Illumina PorcineSNP60 BeadChip on 24 high (HEBV) and 24 low estimated breeding value (LEBV) animals. These animals were selected from a reference population of 522 individuals produced by three sires and six dam lines, which were crossbreds with multiple breeds. After quality-control, 43,257 SNPs (single nucleotide polymorphisms), including 42,243 autosomal SNPs and 1,014 SNPs on chromosome X, were used in the data analysis. A total of 27 differentially selected regions (DSRs), including 1 on Sus scrofa chromosome 1 (SSC1), 1 on SSC4, 2 on SSC5, 4 on SSC6, 2 on SSC7, 5 on SSC8, 3 on SSC9, 1 on SSC14, 3 on SSC18, and 5 on SSCX, were identified to show the genome wide separations between the HEBV and LEBV groups for IBW in piglets. A DSR with the most number of significant SNPs (including 7 top 0.1% and 31 top 5% SNPs) was located on SSC6, while another DSR with the largest genetic differences in FST was found on SSC18. These regions harbor known functionally important genes involved in growth and development, such as TNFRSF9 (tumor necrosis factor receptor superfamily member 9), CA6 (carbonic anhydrase VI) and MDFIC (MyoD family inhibitor domain containing). A DSR rich in imprinting genes appeared on SSC9, which included PEG10 (paternally expressed 10), SGCE (sarcoglycan, epsilon), PPP1R9A (protein phosphatase 1, regulatory subunit 9A) and ASB4 (ankyrin repeat and SOCS box containing 4). More importantly, our present study provided evidence to support six quantitative trait loci (QTL) regions for pig birth weight, six QTL regions for average birth weight (ABW) and three QTL regions for litter birth weight (LBW) reported previously by other groups. Furthermore, gene ontology analysis with 183 genes harbored in these 27 DSRs suggested that protein, metal, ion and ATP binding, viral process and innate immune response present important pathways for deciphering their roles in fetal growth or development. Overall, our study provides useful information on candidate genes and pathways for regulating birth weight in piglets, thus improving our understanding of the genetic mechanisms involved in porcine embryonic or fetal development.
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Affiliation(s)
- Lifan Zhang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA. ; 2. College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiang Zhou
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA
| | - Jennifer J Michal
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA
| | - Bo Ding
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA
| | - Rui Li
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA. ; 2. College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Jiang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA
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Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, Ding B, Dodson MV, El-Halawany NK, Lewis GS, Jiang Z. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep. PLoS One 2013; 8:e65942. [PMID: 23762451 PMCID: PMC3677876 DOI: 10.1371/journal.pone.0065942] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/30/2013] [Indexed: 11/18/2022] Open
Abstract
Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of FST, significant genetic differentiation appeared between Suffolk and Rambouillet (FST = 0.1621), while Rambouillet and Targhee had the closest relationship (FST = 0.0681). A scan of the genome revealed 45 and 41 differentially selected regions (DSRs) between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.
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Affiliation(s)
- Lifan Zhang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michelle R. Mousel
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Xiaolin Wu
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Bo Ding
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael V. Dodson
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Nermin K. El-Halawany
- Cell Biology Department, Division of Genetic Engineering and Biotechnology, National Research Center, Dokki, Gueza, Egypt
| | - Gregory S. Lewis
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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16
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Cochran SD, Cole JB, Null DJ, Hansen PJ. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genet 2013; 14:49. [PMID: 23759029 PMCID: PMC3686577 DOI: 10.1186/1471-2156-14-49] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/23/2013] [Indexed: 11/22/2022] Open
Abstract
Background Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ −2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed. Results A total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion SNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for understanding the physiology of reproduction. Given the large number of SNPs associated with DPR that were not negatively associated with production traits, it should be possible to select for DPR without compromising production.
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Affiliation(s)
- Sarah D Cochran
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
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17
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Rodrigues JB, Araújo S, Guedes-Pinto H, San Roman F, Viegas C, Bastos E. Analysis of new Matrilin-1 gene variants in a case-control study related to dental malocclusions in Equus asinus. Gene 2013; 522:70-4. [PMID: 23558247 DOI: 10.1016/j.gene.2013.03.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/08/2013] [Accepted: 03/15/2013] [Indexed: 10/27/2022]
Abstract
Prognathism and brachygnathism are craniofacial deformities that severely affect the health of human and vertebrates, such as donkeys. The multifactorial etiology of this disease makes the genetic analysis a powerful tool for its understanding and prevention of spreading these deformities. This study aims to contribute to the characterization of the genetic basis of prognathism and brachygnathism in donkeys, using the Zamorano-Leonés donkey, an endangered Spanish breed, as a model. Matrilin-1 (MATN1) polymorphisms have been previously described as markers for mandibular prognathism in Korean and Japanese human populations. Genetic variations in MATN1 gene were sought, in order to verify its association in a case-control study, including 30 donkeys presenting brachygnathism, 30 donkeys presenting prognathism and 30 donkeys with normal occlusion phenotypes. One genetic variation (g503G > A) located in an intronic region of MATN1 gene was identified and characterized. Statistically significant differences were detected between the control group and prognathism cases, but no statistical significant results were found between the control group and the brachygnathism cases. These results support evidence for an important role of MATN1 on prognathism in the analyzed population with MATN1 genetic variation - 503G>A - having a protective effect. Further studies should be developed in order to understand the whole role of MATN1 and the mechanisms affected by its genetic variations.
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Affiliation(s)
- João B Rodrigues
- Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, Quinta de Prados, P.O. Box 1013, 5001-801 Vila Real, Portugal.
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18
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Senn H, Ogden R, Cezard T, Gharbi K, Iqbal Z, Johnson E, Kamps-Hughes N, Rosell F, McEwing R. Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data. Mol Ecol 2013; 22:3141-50. [DOI: 10.1111/mec.12242] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/21/2012] [Accepted: 01/05/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Helen Senn
- WildGenes Laboratory; Royal Zoological Society of Scotland; Edinburgh, EH12 6TS UK
| | - Rob Ogden
- WildGenes Laboratory; Royal Zoological Society of Scotland; Edinburgh, EH12 6TS UK
| | - Timothee Cezard
- The GenePool; School of Biological Sciences; The University of Edinburgh; Edinburgh, EH9 3JT UK
| | - Karim Gharbi
- The GenePool; School of Biological Sciences; The University of Edinburgh; Edinburgh, EH9 3JT UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics; University of Oxford, OX3 7BN; Oxford UK
| | - Eric Johnson
- The Institute of Molecular Biology; 297 Klamath Hall, 1229 University of Oregon; Eugene OR 97403-1229 USA
| | - Nick Kamps-Hughes
- The Institute of Molecular Biology; 297 Klamath Hall, 1229 University of Oregon; Eugene OR 97403-1229 USA
| | - Frank Rosell
- Department of Environmental and Health Studies; Faculty of Arts and Sciences; Telemark University College; 3800 Bø i Telemark Norway
| | - Ross McEwing
- WildGenes Laboratory; Royal Zoological Society of Scotland; Edinburgh, EH12 6TS UK
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Hayashida K, Abe T, Weir W, Nakao R, Ito K, Kajino K, Suzuki Y, Jongejan F, Geysen D, Sugimoto C. Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent. DNA Res 2013; 20:209-20. [PMID: 23404454 PMCID: PMC3686427 DOI: 10.1093/dnares/dst003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa. We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains (Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains. Comparison with the reference Muguga genome sequence revealed 34 814–121 545 single nucleotide polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic trees were constructed with selected informative SNPs that allowed the investigation of possible complex recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (non-synonymous substitutions per non-synonymous site divided by synonymous substitutions per synonymous site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates. This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with prediction of possible past recombination events, providing insight into the migration, diversification, and evolution of this parasite species in the African continent.
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Affiliation(s)
- Kyoko Hayashida
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo-shi, Hokkaido 001-0020, Japan
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20
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Sonstegard TS, Cole JB, VanRaden PM, Van Tassell CP, Null DJ, Schroeder SG, Bickhart D, McClure MC. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One 2013; 8:e54872. [PMID: 23349982 PMCID: PMC3551820 DOI: 10.1371/journal.pone.0054872] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/17/2012] [Indexed: 12/22/2022] Open
Abstract
With the recent advent of genomic tools for cattle, several recessive conditions affecting fertility have been identified and selected against, such as deficiency of uridine monophosphate synthase, complex vertebral malformation, and brachyspina. The current report refines the location of a recessive haplotype affecting fertility in Jersey cattle using crossover haplotypes, discovers the causative mutation using whole genome sequencing, and examines the gene's role in embryo loss. In an attempt to identify unknown recessive lethal alleles in the current dairy population, a search using deep Mendelian sampling of 5,288 Jersey cattle was conducted for high-frequency haplotypes that have a deficit of homozygotes at the population level. This search led to the discovery of a putative recessive lethal in Jersey cattle on Bos taurus autosome 15. The haplotype, denoted JH1, was associated with reduced fertility, and further investigation identified one highly-influential Jersey bull as the putative source ancestor. By combining SNP analysis of whole-genome sequences aligned to the JH1 interval and subsequent SNP validation a nonsense mutation in CWC15 was identified as the likely causative mutation underlying the fertility phenotype. No homozygous recessive individuals were found in 749 genotyped animals, whereas all known carriers and carrier haplotypes possessed one copy of the mutant allele. This newly identified lethal has been responsible for a substantial number of spontaneous abortions in Jersey dairy cattle throughout the past half-century. With the mutation identified, selection against the deleterious allele in breeding schemes will aid in reducing the incidence of this defect in the population. These results also show that carrier status can be imputed with high accuracy. Whole-genome resequencing proved to be a powerful strategy to rapidly identify a previously mapped deleterious mutation in a known carrier of a recessive lethal allele.
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Affiliation(s)
- Tad S. Sonstegard
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - John B. Cole
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
| | - Paul M. VanRaden
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Curtis P. Van Tassell
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Daniel J. Null
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Steven G. Schroeder
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Derek Bickhart
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Matthew C. McClure
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
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21
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Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study. Mol Biol Rep 2012; 40:743-50. [PMID: 23232712 DOI: 10.1007/s11033-012-1932-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
Cattle and water buffalo belong to the same subfamily Bovinae and share chromosome banding and gene order homology. In this study, we used genome-wide Illumina BovineSNP50 BeadChip to analyze 91 DNA samples from three breeds of water buffalo (Nili-Ravi, Murrah and their crossbred with local GuangXi buffalos in China), to demonstrate the genetic divergence between cattle and water buffalo through a large single nucleotide polymorphism (SNP) transferability study at the whole genome level, and performed association analysis of functional traits in water buffalo as well. A total of 40,766 (75.5 %) bovine SNPs were found in the water buffalo genome, but 49,936 (92.5 %) were with only one allele, and finally 935 were identified to be polymorphic and useful for association analysis in water buffalo. Therefore, the genome sequences of water buffalo and cattle shared a high level of homology but the polymorphic status of the bovine SNPs varied between these two species. The different patterns of mutations between species may associate with their phenotypic divergence due to genome evolution. Among 935 bovine SNPs, we identified a total of 9 and 7 SNPs significantly associated to fertility and milk production traits in water buffalo, respectively. However, more works in larger sample size are needed in future to verify these candidate SNPs for water buffalo.
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22
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Stafuzza NB, Abbey CA, Gill CA, Womack JE, Amaral MEJ. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. GENETICS AND MOLECULAR RESEARCH 2012; 11:3013-9. [PMID: 22653673 DOI: 10.4238/2012.may.22.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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23
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Kraus RHS, Kerstens HHD, van Hooft P, Megens HJ, Elmberg J, Tsvey A, Sartakov D, Soloviev SA, Crooijmans RPMA, Groenen MAM, Ydenberg RC, Prins HHT. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks. BMC Evol Biol 2012; 12:45. [PMID: 22462721 PMCID: PMC3364866 DOI: 10.1186/1471-2148-12-45] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 04/02/2012] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct. RESULTS We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years. CONCLUSIONS By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.
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Affiliation(s)
- Robert H S Kraus
- Resource Ecology Group, Wageningen University, 6700 AA Wageningen, The Netherlands.
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Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011; 52:413-35. [PMID: 21698376 PMCID: PMC3189340 DOI: 10.1007/s13353-011-0057-x] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 12/21/2022]
Abstract
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.
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Affiliation(s)
- Chandra Shekhar Pareek
- Laboratory of Functional Genomics, Institute of General and Molecular Biology, Nicolaus Copernicus University, Torun, Poland.
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Melka HD, Jeon EK, Kim SW, Han JB, Yoon DH, Kim KS. Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip. Genomics Inform 2011. [DOI: 10.5808/gi.2011.9.2.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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