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Proceedings of the 36Th International Conference on Animal Genetics

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Proceedings of the 36Th International Conference on Animal Genetics Bioinformatics · Comparative Genomics · Computational Biology Epigenetics · Functional Genomics · Genome Diversity · Geno Genome Sequencing · Immunogenetics · Integrative Geno · Microbiomics · Population Genomics · Systems Biolog Genetic Markers and Selection · Genetics and Dis Gene Editing · Bioinformatics · Comparative Computational Biology · Epigenetics · Fun Genome Diversity · Genome Sequeng Integrative Genomics · Microbiom Population Genomics · Syste Genetic Markers and Sel Genetics and Disease Gene Editing · Bi O’Brien Centre for Science Bioinformati and O’Reilly Hall, University College Dublin, Dublin, Ireland ABSTRACTMINI PROGRAMME BOOK www.isag.us/2017 PB #ISAG2017 1 @isagofficial #ISAG2017 #ISAG2017 Contents ORAL PRESENTATIONS 1 Animal Forensic Genetics Workshop 1 Applied Genetics and Genomics in Other Species of Economic Importance 3 Domestic Animal Sequencing and Annotation 5 Genome Edited Animals 8 Horse Genetics and Genomics 9 Avian Genetics and Genomics 12 Comparative MHC Genetics: Populations and Polymorphism 16 Equine Genetics and Thoroughbred Parentage Testing Workshop 19 Genetics of Immune Response and Disease Resistance 20 ISAG-FAO Genetic Diversity 24 Ruminant Genetics and Genomics 28 Animal Epigenetics 31 Cattle Molecular Markers and Parentage Testing 33 Companion Animal Genetics and Genomics 34 Microbiomes 37 Pig Genetics and Genomics 40 Novel, Groundbreaking Research/Methodology Presentation 44 Applied Genetics of Companion Animals 44 Applied Sheep and Goat Genetics 45 Comparative and Functional Genomics 47 Genetics and Genomics of Aquaculture Species 50 Livestock Genomics for Developing Countries 53 POSTER PRESENTATIONS 56 Animal Epigenetics 56 Animal Forensic Genetics 61 Applied Genetics and Genomics in Other Species of Economic Importance 61 Avian Genetics and Genomics 64 Cattle Molecular Markers and Parentage Testing 75 Companion Animal Genetics and Genomics 81 Comparative MHC Genetics: Populations and Polymorphism 87 Domestic Animal Sequencing and Annotation 90 Equine Genetics and Thoroughbred Parentage Testing: 94 Genetics of Immune Response and Disease Resistance 95 Genome Edited Animals 107 Horse Genetics and Genomics 108 ISAG-FAO Genetic Diversity 121 Microbiomes 125 Pig Genetics and Genomics 127 Ruminant Genetics and Genomics 143 Applied Genetics of Companion Animals 167 Applied Sheep and Goat Genetics 169 Comparative and Functional Genomics 177 Gene Function 186 Genetics and Genomics of Aquaculture Species 189 Livestock Genomics for Developing Countries 193 Author Index 199 Key Word Index 212 ORAL PRESENTATIONS Animal Forensic Genetics Workshop 1 De novo genome assembly of Agapornis roseicollis and SNP panel, selected in a previous study was evaluated on different SNP discovery for parentage verification. H. van der Zwan*1, R. biological matrices. The main sources of genomic DNA are periph- van der Sluis1, and C. Visser2, 1North-West University, Potchefst- eral blood leukocytes, semen, hair follicles and tissues but sampling room, North-West, South Africa; 2University of Pretoria, Pretoria, requires specialised staff and the animals may be subject to stress, Gauteng, South Africa. influencing negatively welfare, health and productivity. A valid and cheaper alternative of genomic source can be the milk somatic cells The African parakeet Agapornis, or lovebirds, are globally (from 2 × 104 to 2 × 105 cells per millilitre of milk). In details, bred as pets. The main breeding selection criterion is plumage col- DNA from 50 semen, 30 meat, 30 hair and 30 milk samples were oration. Birds with rare coloration and their heterozygous offspring collected. DNA from 140 samples was processed by TaqMan PCR (with wildtype coloration) are sold at a premium. Currently, there and scanning array on the Open Array platform, the genotypes were is no genetic test inferring parentage of the heterozygous offspring, generated by SNP Genotyping and TaqMan Genotyper software. nor has the genes or mutations linked to colour variation been iden- Allele frequencies for each SNP were determined by direct count- tified. The aim of this study was to discover SNPs to develop a SNP- ing. A software developed ‘ad hoc’ (PAF), was used to estimate the based parentage verification test for A. roseicollis by sequencing, levels of genetic variability: expected heterozygosity (He) values assembling and annotating its de novo genome. One young male ranging from 0.47 to 0.50 with medium value of 0.46, observed was selected and its genome sequenced at 100x coverage on the Il- heterozygosity (Ho) ranging from 0,38 to 0,60 and medium value lumina HiSeq platform. The size of the genome was 1.1Gbp and 15 of 0,48. Probability of identity (PI) was calculated for the 32 SNPs 045 genes were identified. This is comparable to other bird species and it was equal to 8.40 × 10−14 The 32 SNPs assay described in this such as the budgerigar (Melopsittacus undulates). The genomes of study represents a valid and useful tool for DNA-based traceability the male’s parents were sequenced at 30x coverage on the same employed in different applied research projects and in the major platform. The parents’ reads were mapped to the offspring’s ref- commercial cattle products. erence genome using the Burrow-Wheeler aligner. Making use of the command line Linux-based program Genome Analysis Toolkit Key Words: cattle, single nucleotide polymorphisms, product (GATK), variants were discovered using the HaplotypeCaller mod- traceability ule. Approximately 1.2 million raw SNPs were discovered for the mother and 800 000 for the father. Since it is a non-model organ- 4 The population and landscape genetics of the European ism, hard filtering parameters had to be applied to first extract SNPs badger (Meles meles) in Ireland. A. Allen*1, J. Guerrero2, A. By- and then indels from the raw SNP set. SNPs discovered in indels 1,3 1 1 1 4 5 were discarded. These SNPs were further filtered to include only rne , J. Lavery , E. Presho , G. Kelly , E. Courcier , J. O’Keefe , 6 7 8 1 variants where both parents were heterozygous at that locus indi- U. Fogarty , D. O’Meara , G. Wilson , D. Ensing , C. McCor- 1 9 1,3 1 cating heterozygosity from all grandparents. This resulted in a total mick , R. Biek , R. Skuce , Agri Food and Biosciences Institute, 2 of 614 700 SNPs after all the filters were applied. SNPs not com- Belfast, Northern Ireland; CEFE-CNRS, Centre D’Ecologie 3 plying with Mendelian inheritance patterns between the parents and Fonctionelle et Evolutie, Montpelier, France; School of Biolog- offspring were rejected. Where SNPs was located less than 100bp ical Sciences, Queen’s University Belfast, Belfast, Northern Ire- apart only the SNP with the highest quality score was included. A land; 4Department of Agriculture, Environment and Rural Affairs, panel of the top 400 SNPs was selected based on the quality scores Belfast, Northern Ireland; 5Department of Agriculture Food and obtained during the GATK analyses. This panel will form the foun- the Marine, Dublin, Ireland; 6Irish Equine Centre, Johnstown, dation for the development of a commercial parentage verification Republic of Ireland; 7Waterford Institute of Technology, Waterford, test for lovebirds. Ireland; 8Animal and Plant Health Agency (APHA), Stonehouse, Gloucestershire, England; 9University of Glasgow, Glasgow, Key Words: lovebird, avian genomics, bioinformatics, de novo Scotland. genome assembly, genomic selection The European badger (Meles meles) is an important member of the fauna of Britain and Ireland, not least because it acts as a 3 Effectiveness of SNPs genotyping assay as a tool for wildlife reservoir for bovine tuberculosis. Genetic structure of the 1 genetic traceability of cattle production chain. A. Pozzi* , C. species is expected to have been influenced by anthropogenic ac- 1 1 1 2 1 Previtali , R. Capoferri , S. Arabi , A. Galli , and G. Bongioni , tivities and also landscape-level effects. The relative contribution 1 Istituto Sperimentale Italiano L. Spallanzani, Rivolta d’Adda, of both factors is debated, but will conceivably have implications Cremona, Italy; 2Centro di ricerca per le produzioni foraggere e for both wildlife and disease management. Recent Europe-wide sur- lattiero-casearie CREA, Lodi, Italy. veys of genetic diversity have suggested human-aided introduction In the last years the concern of consumer about food safe- of badgers into Ireland. These studies have not, however, indexed ty is increased, so in the European Union great value is placed island-wide diversity of the species, nor comprehensively attempt- on accurate and safe animal identification; breeding plan, disease ed to detail demographic and geographic factors which shaped the monitoring, and food safety depend heavily on conventional ani- extant population. Herein, we detail the most comprehensive popu- mal identification. For this reason, the protection of the integrity of lation and landscape genetic study of the badger in Ireland to date. these programs from fraud or accidental errors is necessary. Genetic Our data demonstrate that north-eastern and south-eastern counties traceability is presented here as a way to further enhance conven- of Ireland contain a badger sub-population genetically similar to tional traceability; it represents a powerful tool to verify the identity its British contemporaries. Approximate Bayesian computation of animal products during every step of the cattle production chain. suggests this sub-population arose in Ireland ~250–3500 years ago From the molecular point of view, Single Nucleotide
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