1
|
O'Connor RE, Fonseka G, Frodsham R, Archibald AL, Lawrie M, Walling GA, Griffin DK. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Anim Genet 2017; 48:395-403. [PMID: 28497848 PMCID: PMC5518436 DOI: 10.1111/age.12548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 12/02/2022]
Abstract
Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy (reduced litter size) in domestic animals such as pigs. With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc. are considerable. There is therefore a need for novel tools to facilitate rapid, cost-effective chromosome translocation screening. This has previously been achieved by standard karyotype analysis; however, this approach relies on a significant level of expertise and is limited in its ability to identify subtle, cryptic translocations. To address this problem, we developed a novel device and protocol for translocation screening using subtelomeric probes and fluorescence in situ hybridisation. Probes were designed using BACs (bacterial artificial chromosomes) from the subtelomeric region of the short (p-arm) and long (q-arm) of each porcine chromosome. They were directly labelled with FITC or Texas Red (p-arm and q-arm respectively) prior to application of a 'Multiprobe' device, thereby enabling simultaneous detection of each individual porcine chromosome on a single slide. Initial experiments designed to isolate BACs in subtelomeric regions led to the discovery of a series of incorrectly mapped regions in the porcine genome assembly (from a total of 82 BACs, only 45 BACs mapped correctly). Our work therefore highlights the importance of accurate physical mapping of newly sequenced genomes. The system herein described allows for robust and comprehensive analysis of the porcine karyotype, an adjunct to classical cytogenetics that provides a valuable tool to expedite efficient, cost effective food production.
Collapse
Affiliation(s)
- R. E. O'Connor
- School of BiosciencesUniversity of KentCanterburyCT2 7AFUK
| | | | | | - A. L. Archibald
- The Roslin InstituteR(D)SVSUniversity of EdinburghDivision of Genetics and GenomicsEaster BushMidlothianEH25 9RGUK
| | - M. Lawrie
- Cytocell LtdNewmarket RoadCambridgeUK
| | - G. A. Walling
- JSR GeneticsSouthburnDriffieldNorth HumbersideYO25 9EDUK
| | - D. K. Griffin
- School of BiosciencesUniversity of KentCanterburyCT2 7AFUK
| |
Collapse
|
2
|
Bruce IJ. Novel and Improved Nanomaterials, Chemistries and Apparatus for Nanobiotechnology: the NACBO Project. Nanomedicine (Lond) 2011; 6:187-93. [DOI: 10.2217/nnm.10.155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article outlines the nature and activities of the recently completed EU Framework Programme 6 Integrated Project, Novel and Improved Nanomaterials, Chemistries and Apparatus for Nanobiotechnology (NACBO). This project was designed to yield new nanomaterials, surface activation and synthetic nucleic acid chemistries, procedures and hardware for applications in forensics and diagnostics. It provides details on the project’s structure and partnership along with its principal objectives and successes in terms of publications and commercial exploitation.
Collapse
Affiliation(s)
- Ian James Bruce
- Nanobiotechnology Research Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| |
Collapse
|
3
|
Skinner BM, Robertson LBW, Tempest HG, Langley EJ, Ioannou D, Fowler KE, Crooijmans RPMA, Hall AD, Griffin DK, Völker M. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics 2009; 10:357. [PMID: 19656363 PMCID: PMC2907691 DOI: 10.1186/1471-2164-10-357] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 08/05/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu. RESULTS We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey. CONCLUSION Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies.
Collapse
Affiliation(s)
| | - Lindsay BW Robertson
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- Institute of Cancer Research, Belmont, Surrey, SM2 5NG, UK
| | - Helen G Tempest
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- Bridge Genoma, 1 St Thomas Street, London Bridge, London, SE1 9RY, UK
| | | | - Dimitris Ioannou
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Katie E Fowler
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Richard PMA Crooijmans
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The Netherlands
| | - Anthony D Hall
- Cherry Valley Ltd, Rothwell, Market Rasen, Lincolnshire, LN7 6BJ, UK
| | - Darren K Griffin
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin Völker
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| |
Collapse
|