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PAG 2012 www.illumina.com/agriculture Illumina Technology Workshop Discover. Develop. Deploy. In Any Species. On Any Scale. Tuesday, January 17 3:50 p.m. – 6:00 p.m. Golden West Ballroom Refreshments will be provided. Unraveling Green Genomes Todd Michael, Ph.D. Head, The Genome Analysis Center Monsanto Applications of Next-Generation Sequencing: From Genes to Genomes Gary Schroth, Ph.D. Distinguished Scientist Illumina, Inc. Characterization of Transgene Insertion Sites via Amplicon Sequencing Mary Beatty Research Scientist Pioneer Hi-Bred Applied Genomics for Genetic Improvement: Paving the Way for Biological Discovery Tad S. Sonstegard, Ph.D. Research Geneticist USDA, ARS Beltsville Visit Illumina at Booth #211 to see a live demo of the MiSeq® personal sequencer. Learn more at www.illumina.com/MiSeq Illumina Customer Presentations Scientists worldwide are discovering that Illumina provides the industry’s best solutions for cutting-edge genetics research. Below is a list of workshops and posters at the Plant & Animal Genomes XX Conference that present results from studies using Illumina products. Visit these presentations and ask the presenters about their experience using Illumina. Computer Demos Program No. Title Primary Organization C13 The rice annotation project database: Update for a new genome assembly (Os-Nipponbare-Reference-IRGSP-1.0) National Institute of Agrobiological Sciences C28 MAPHiTS: an efficient workflow for SNP detection URGI–INRA de Versailles WorKshops Program No. Title Primary Organization W008 Improving the maize genome via GBS (genotyping by sequencing) Cornell University W014 Extent and characterization of the Arabidopsis defense transcriptome regulated at the transcript isoform level North Carolina State University, Raleigh W016 Transcriptome diversity through alternative and antisense polyadenylation Miami University W018 Genome-wide methylation analysis of chicken primordial germ cells North Carolina State University, Raleigh W021 Feed efficiency in cattle: An epigenetic perspective University of Missouri, Columbia W033 From SNP discovery to SNP associations: Using next-generation sequencing and custom arrays to create a high density genetic linkage map for the Silver Lipped Pearl Oyster, Pinctada maxima Centre for Sustainable Fisheries and Aquaculture, James Cook University W034 Rapid development of molecular resources for a freshwater mussel, Villosa lienosa (Bivalvia: Unionidae) using a RNA-Seq-based approach Auburn University W035 Creation of a genomic resource and quantitative trait loci detection in Pacific Whiteleg Shrimp Litopenaeus vannamei for selective breeding applications Centre for Sustainable Fisheries and Aquaculture, James Cook University W038 RNA-Seq analysis of differentially expressed genes in channel catfish after Flavobacterium columnare challenge Auburn University W041 Identification Of differentially expressed miRNAs potentially associated with egg quality in Rainbow Trout (Oncorhynchus mykiss) West Virginia University, Morgantown W043 Towards the complete genome: Progress of Common Carp Genome Project Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences W044 An EST/RNAseq library and first-generation linkage map for Sablefish (Anoplopoma fimbria) University of Victoria W045 New in-depth Rainbow Trout transcriptome reference and digital atlas of gene expression West Virginia University, Morgantown W064 Design of an Illumina Infinium 6K SNPchip for genotyping two large Avocado mapping populations USDA-ARS SHRS W068 The sequence of the Banana (Musa acuminata) genome CIRAD W073 Sequences of 14,600 gene-bearing minimal tiling path BACs of Morex Barley University of California, Riverside W081 An efficient pipeline for sequence based variant detection in commercial Chicken lines Georg-August-University, Göttingen W088 Efficient assembly of large genomes from short reads University of Maryland, College Park W097 B. napus genome sequence URGV-INRA W099 Comparative and population genomics in the Brassicaceae University of Toronto W100 Uncovering the ancestral blocks reveals the hexaploid genome of the emerging biofuel crop, Camelina sativa Agriculture and Agri-Food Canada W111 Efficient whole genome assembly of mammalian genomes from short reads University of Maryland, College Park W112 Status of the Buffalo genome Università della Tuscia W113 The Buffalo transcriptome Parco Tecnologico Padano W114 SNP discovery across Buffalo breeds USDA-ARS-ANRI-BFGL W120 Comparative transcriptome analysis of Eucalyptus genotypes that differ in carbon allocation EMBRAPA–Brazilian Agricultural Research Corporation, Embrapa Forestry W123 Identification, analysis and mapping of SNP markers in Theobroma cacao USDA-ARS W124 A core set of SNPs for Cacao genotyping USDA-ARS SHRS W126 Construction of genomic library of Theobroma cacao using genotyping by sequencing (GBS) Cocoa Research Institute of Ghana W136 GWAS data sharing University of Sydney W137 Genetic determinism and candidate genes for flowering date—A phenological trait highly affected by climate change in Sweet Cherry INRA W144 Performance of Illumina and Affymetrix Bovine high density genotyping platforms in Holsteins and Jerseys Department of Animal Science, University of California, Davis W145 Differential gene expression detected via transcriptome sequencing in Angus steers differing for feed efficiency University of Missouri, Columbia W151 Genome-wide association study of entropion eyelid in multiple breeds in Sheep USDA-ARS W153 Goat genome assembly, availability of an international 50K SNP chip and RH panel: An update of the International Goat Genome Consortium projects INRA W158 Sheep Genome Project: Gap filling and unbalanced allelic expression CSIRO Livestock Industries, on behalf of the International Sheep Genomics Consortium W157 Whole genome sequencing for variant detection, disease gene identification and an HD SNP chip for Sheep CSIRO Livestock Industries W164 Transcriptome of Ponkan mandarin (Citrus reticulata Blanco) in the early infection of Xylella fastidiosa Centro de Citricultura Sylvio Moreiral W179 Overview of the genotyping-by-sequencing technology and its applications In diverse organisms Cornell University W185 Targeted analysis of polyploid Wheat genome by exon capture Kansas State University, Manhattan W188 Lettuce genome update Genome Center, University of California, Davis W189 The Sunflower genome and its evolution University of British Columbia, Vancouver W190 Genomic resourses in Cynara cardunculus DIVAPRA - Plant Genetics and Breeding, University of Turin W202 SNP-based genotyping in Lentil: Linking sequence information with phenotypes University of Saskatchewan W217 High-throughput sequencing makes TILLING more fun University of California, Davis W259 Cribbing: A compulsive behavior and its genetic component University of Sydney W262 Genome-wide across and within breed association studies in Horses University of Veterinary Medicine Hannover W281 The repetitive DNA of conifers–lessons from the Norway Spruce (Picea abies) genome and resequencing of 5 other conifers Science for Life Laboratory/Karolinska Institute W282 Differential transcriptomes during forming of epigenetic memory In Norway Spruce Norwegian Forest and Landscape Institute W288 Exploring the megagenome of Pine by targeted resequencing University of Florida, Gainesville W291 The genome of Aspen (Populus tremula)–the most complex genome sequenced to date? Umeå Plant Science Centre, Dept of Plant Physiology, Umeå University W296 Comparative genomics of 15 tropical Fagaceae species using shallow Illumina sequencing and a reference-free approach Chinese Academy of Sciences W300 Association genetics of traits underlying secondary cell wall chemistry and ultrastructure in Populus trichocarpa University of British Columbia W313 RosBREED: Infinium SNP genotyping in Prunus Clemson University W314 Genomic tools enhance power and precision of Hazelnut breeding Oregon State University, Corvallis W315 A draft assembly and analysis of the highly heterozygous diploid Red Raspberry genome (Rubus idaeus cv. Heritage) Cornell University, Geneva, NY W317 Genome-wide SNP detection, validation, and development of an 8K SNP array for Apple Plant and Food Research W320 Genome sequencing and resource development for European Hazelnut cultivars Oregon State University, Corvallis W323 Finding function in complex crop genomes University of Queensland W332 Studying functional genomics with next-generation sequencing Illumina W333 Routine digital methylation profiling of population cohorts with bisulfite padlock probes University of California, San Diego W355 Applications of genome sequencing for Peanut improvement University of California, Davis Genome Center W361 Identification of SNP haplotypes and prospects of association mapping in Watermelon Gus R. Douglass Institute and Department of Biology, West Virginia State University W363 Germplasm management in the post-genomics era—A case study with Lettuce USDA- ARS W426 Physical map and shotgun sequence of the Aegilops tauschii genome University of California, Davis W427 Towards a reference sequence of the Bread Wheat chromosome 3B INRA GDEC W439 Genomic diversity and sequence-based association analyses in Medicago truncatula University of Minnesota, Saint Paul W442 Transcriptome of common Bean (Phaseolus vulgaris) through RNA-seq: Nodulation, symbiotic nitrogen fixation, transcription factors Centro de Ciencias GenomicasUniversidad Nacional Autónoma de México, Cuernavaca W448 High resolution TranSNiPtomics: Gene expression and SNP detection in high throughput and high resolution by “Massive Analysis of cDNA Ends” (MACE) GenXPro-GmbH W469 Development of a high-density SNP genotyping panel as a community resource for genetic analysis in Oat USDA-ARS W474 Sequencing and genotyping in a complex genome: Current status and future possibilities Illumina W475 Identification of fertility restorers for S Male-Sterile Maize: Beyond PPRs University of Florida, Gainesville W512 Assembly of huge plant genomes from WGS data University of Maryland, College Park W528 Population genomics of vegetative phenology in Populus West Virginia University, Morgantown W530 Chilling requirement and bloom date in Peach: Genetic and genomic approaches for deciphering a complex gene network Clemson University W539 The Potato Aphid transcriptome and salivary secretome University of California, Riverside W588 Search for genomic footprints of divergent selection from whole genome sequencing of four experimental lines of Broiler Chickens Department of Animal and Food Sciences, University of Delaware, Newark W627 Genomes to genes: Comparative genomic analysis in Prunoideae Washington State University, Pullman W628 The Potato genome sequencing project 2 years on: Comparison of strategies with related projects and perspectives for the future of the world’s 3rd food crop Wageningen-UR W629 Just genes–well mostly: Genomic enrichment for Sugarcane genic regions The University of Queensland W644 Sequencing and comparison of the genomes of Petunia inflata and Petunia axillaris Northern Illinois University W646 Towards completion of the genome that makes Hot Pepper Seoul National University W659 Towards early-stage chilling tolerance for European energy sorghum Justus-Liebig University Giessen, Department of Plant Breeding W680 Re-sequencing and hybrid assembly strategy of two nematode resistant Beta vulgaris translocation lines Christian Albrechts University of Kiel W686 Genomic and epigenetic characterization of Sugarcane hybrids and wild relatives IBqM/Universidade Federal do Rio de Janeiro W694 Whole genome re-sequencing of Pigs and Wild Boar reveals unexpected signatures in variation related to biogeography, domestication, and hybridization Wageningen University, Animal Breeding and Genomics Centre W695 Identification of QTLs and genes related to immune response to Poly (I:C) stimulation in a Duroc-Erhualian F2 Pig population Huazhong Agricultural University W696 Genome-wide association of a novel Porcine stress-syndrome to dystrophin USDA-ARS, USMARC W718 Sequencing the obligate Oomycete plant pathogen, Bremia lactucae University of California, Davis Genome Center W720 Genome sequence for the Apicomplexan Sarcosystis neurona University of Georgia, Institute of Bioinformatics, Center for Tropical and Emerging Global Diseases & Department of Genetics posters Program No. Title Primary Organization P0001 ARK-Genomics Centre for Comparative and Functional Genomics The Roslin Institute, University of Edinburgh P0007 Enhancing whole genome, transcriptome and metagenomic sequencing with next-generation sequencing platforms University of Illinois W. M. Keck Center, Urbana P0009 Repeat reduction in Illumina libraries prior to sequencing using duplex-specific nuclease University of California, Davis Genome Center P0010 Rapid and efficient methods for preparing rRNA-depleted and directional Plant RNA-Seq libraries Epicentre (an Illumina® company) P0014 Resequencing in a mapping population Southern Illinois University Carbondale P0015 Exploring the genome diversity of Mycorrhizal Fungi–A JGI Sequencing Project update Pennsylvania State University, University Park P0020 An evolutionary aspect for two subspecies of Oryza sativa and three wild accessions of Oryza rufipogon Mitsubishi Space Software Co., Ltd. P0021 Analysis of the Oryza nivara genome Institute of Plant Biology, National Taiwan University P0022 Reference-guided de novo genome assembly of the Indica Type Rice Variety IR 64 using short-read sequencing International Rice Research Institute P0026 Gene content, loss, conservation and genetic variation among Triticum aestivum group 7 chromosomes Australian Centre for Plant Functional Genomics P0027 Sequence-ready, physical maps of chromosomes 1D, 4D, and 6D of hexaploid Wheat Kansas State University, Manhattan P0029 Whole genome shotgun sequencing and assembly to access the gene rich portion of the genome of Lolium perenne L Teagasc P0030 De novo genome sequencing of perennial Ryegrass (Lolium perenne) Department of Molecular Biology and Genetics, Aarhus University P0032 A gene expression atlas of developing Oat seeds for enhancing nutritional composition USDA-ARS P0033 A whole genome reference sequence of Amborella University of Florida, Gainesville P0040 De novo assembly of the Carrot mitochondrial genome University of Wisconsin, Madison P0042 Unraveling Chickpea transcriptome for gene discovery and marker development using next generation sequencing technologies National Institute of Plant Genome Research P0043 Using genomic approaches to study an economic important Weedy Plant Conyza canadensis University of Tennessee, Knoxville P0044 Gossypium arboreum genome assembly using a sequence-based physical map National Center for Genome Resources P0049 Identification and characterization of microRNAs from Eugenia uniflora Laboratory of Genomes and Plant Population, Center of Biotechnology, Federal University of Rio Grande do Sul P0050 Genome size evolution in the genus Genlisea—From half of the A. thaliana genome to the twenty-fold Max Planck Institute for Plant Breeding Research (MPIPZ) P0051 Identification of rhizome-specific transcripts, putative TFs and SNPs in Ginger using next-generation sequencing technology Institute of Biological Chemistry, Washington State University, Pullman P0054 Alfalfa genome sequencing efforts: Strategies and progress Noble Foundation P0055 Next generation sequencing of Medicago truncatula plastid genomes Rutgers University, Waksman Institute of Microbiology P0061 RNA-seq reveals extensive diversity among Potato genomes and functional complexity of organ and transgene specific defense mechanisms against the Late Blight Pathogen (Phytopthora infestans) Department of Plant Pathology, University of Minnesota P0062 Transcriptome characterization for genome annotation and functional genomics In Pyrus spp Nanjing Agricultural University P0064 Comparative genomic analysis in Prunoideae Washington State University, Pullman P0067 Sequencing and analysis of the Rotylenchulus reniformis transcriptome Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University P0070 Resequencing of recombination inbred line populations reveals the landscape of SNP distribution and recombination patterns in Soybean University of Missouri, Columbia P0071 Towards a first draft of the octoploid Strawberry genome sequence IRTA, Centre for Research in Agricultural Genomics P0078 Branching out–Expanding the sequencing of the mammalian tree Broad Institute P0080 Variation detection in the Bos taurus genome using novel in-solution exome capture Cofactor Genomics P0082 Whole-genome sequencing identifies multiple protein function affecting variants within QTL regions for pulmonary hypertension syndrome in Chicken Wageningen University, Animal Breeding and Genomics Centre P0083 Analysing the Buffalo genome Parco Tecnologico Padano P0084 Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) National Center for Genome Resources (NCGR) P0085 Challenges and opportunities for improving the Atlantic Cod genome assembly and annotation University of Oslo P0086 De novo transcriptome assembly of the plant-parasitic nematode Aphelenchoides fragariae School of Agricultural, Forest, and Environmental Sciences, Clemson University P0089 De novo assembly of Campylobacter fetus subspecies and biovars genomes reveal unique features in pathogenecity islands Centre for Comparative Genomics, Murdoch University P0104 Validation of VERSA Mini NGLP for automated library preparation with the Illumina platform Aurora Biomed P0106 Automation of library preparation for high-resolution ChIP-seq profiling University of California, Davis P0112 Long-span, mate-pair pNGS-FOS libraries and applications Lucigen Corporation P0114 Sequences of 14,600 gene-bearing minimal tiling path BACs of Morex Barley University of California, Riverside P0117 Global allele-specific expression reveals the molecular basis of general combining ability State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University P0121 Using Sequenom to study gene expression and gene loss in natural and synthetic polyploid generations (Tragopogon, Asteraceae) University of Florida, Gainesville P0124 Identification of differentially expressed microRNAs associated with PRRSV infection North Carolina State University, Raleigh P0125 Genotyping-by-sequencing (GBS) in Sheep AgResearch Ltd. Invermay Agricultural Centre P0126 Transcriptome sequencing of Water Buffalo embryos Parco Tecnologico Padano P0127 Transcript profiling differentiates healthy control, sub-clinical and clinical Johne's Disease in Dairy Cattle National Center for Genome Resources P0129 SNP-calling in the Zebrafish Mutation Project Wellcome Trust Sanger Institute P0130 The Zebrafish Mutation Project: Systematic genome-wide identification of knockout alleles in the Zebrafish using whole exome enrichment and Illumina sequencing Wellcome Trust Sanger Institute P0133 New NEBNext reagents and adaptors for NGS library preparation New England Biolabs P0137 Phylogenomics of organelles using Illumina sequence data University of Missouri, Columbia P0150 Genotyping-by-sequencing for mapping phenotypic traits in T. cacao Stanford University P0170 Using multiplexed massively parallel sequencing to aid genetic conservation and restoration in Port-Orford-cedar USDA Forest Service P0182 Mass genotyping by sequencing technology Eureka Genomics P0184 Application of random sequence-based genotyping (rSBG) in crops KeyGene P0189 SNP mining in the genome of Barley Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) P0192 Characterising genetic variation in Lolium perenne breeding populations using a genotype by sequencing approach Department of Molecular Biology and Genetics, Aarhus University P0199 Genome-wide SNP development and validation for Allotetraploid Gossypium Texas A&M University P0201 A 1536-plex Oil Palm SNP set for genetic mapping and identification of markers associated with Oil Palm fruit colour Malaysian Palm Oil Board P0202 High-density SNP mapping on Peach (Prunus persica L. Batsch) populations University of California, Davis P0203 Genome-wide assessment of SNPs in Peanut using Illumina (Solexa) sequencing Texas Tech University P0205 High density genetic mapping of Sunflower Department of Plant Biology, University of Georgia P0206 The genetics of branching in Sunflower University of Georgia, Athens P0207 Association genetics in cultivated Sunflower University of Georgia, Athens P0208 High-density SNP analysis of cultivated Tomato (Solanum lycopersicum L.) The Ohio State University/OARDC, Wooster P0209 Effects of the Porcine 384-SNP assay system using selected SNPs for meat quality College of Life Sciences and Biotechnology, Korea University P0211 Genomic evaluation for litter size in Canadian Yorkshire pigs Canadian Centre for Swine Improvement Inc. P0213 An approach for genome-wide characterization of nsSNPs using the Illumina BovineHD SNPchip Universidad Autónoma de Baja California P0225 Genomic studies of the Coconut (Cocos nucifera L.) The Australian National University P0227 Developing market-class specific indel markers from next generation sequence data in Phaseolus vulgaris Genomics and Bioinformatics Program, North Dakota State University, Fargo P0239 A pipeline for transcriptome assembly and SNP identification in highly heterozygous crops Institute for Agricultural and Fisheries Research (ILVO) P0251 Developing a high-throughput SNP genotyping workflow to support breeding applications in Rice International Rice Research Institute P0262 Isolation of Rice genes involved in important agronomic traits using whole genome resequencing Iwate Biotechnology Research Center P0274 Identification of candidate genes in Rice for resistance to Sheath Blight Disease by whole genome sequencing Louisiana State University Agricultural Center, Baton Rouge P0295 Characterizing the effects of down-regulating the GPC genes on the Wheat transcriptome during monocarpic senescence in Wheat University of California, Davis P0309 Mining high water and nitrogen use efficient Wheat (T. aestivum L.) genotypes in the USDA-ARS National Small Grains Collection University of Idaho P0315 Discovery of Puccinia striiformis f.sp. tritici effectors by whole genome resequencing and comparative genomics John Innes Centre P0332 Genetic dissection of the domestication syndrome in tetraploid Wheat University of California, Davis P0338 Development of chromosome genomics in wild relatives of Wheat (Aegilops spp.) Institute of Experimental Botany P0346 Structural and temporal variation in the genetic diversity of a European collection of Barley cultivars and utility for association mapping of quantitative traits CRA–Genomics Research Centre P0353 Annotation of miRNAs from developing Sseeds in Avena sativa University of North Carolina, Charlotte P0359 A large Maize SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome TraitGenetics GmbH P0378 RNA-Seq in Puccinia melanocephala susceptible and resistant Sugarcane USDA-ARS P0386 Identification of key genes involved in cell death and defense responses to pathogens in Arabidopsis using next generation sequencing strategy and the lesion mimic mutant vad1 CNRS-INRA P0390 Genetic diversity in C genome diploid Brassicas University of Warwick P0392 SNP analysis in Brassica napus University of Queensland P0393 Mutation detection in Brassica napus using Illumina sequencing National Research Council, Saskatoon P0394 PCR-based screening platform for an Oilseed Rape BAC library Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) P0398 High density SNP consensus map a useful tool for Rapeseed genomic Biogemma P0410 Curating the Medicago truncatula genome J. Craig Venter Institute P0418 Development and evaluation of a high-density Illumina Infinium iSelect BeadChip SoySNP50K USDA-ARS, Soybean Genomics and Improvement Lab P0432 Genome-wide transcriptional analysis of five-foliate leaf mutant and wild type Soybean isolines University of Illinois, Urbana P0455 Improvement of information and material resources of Lotus japonicus Kazusa DNA Research Institute P0467 The transcriptome of Tomato (S. lycopersicum) Italian Agency for New Technologies Energy & Sustainable Development P0468 Comparative genomics of Solanum galapagense, a wild relative of Tomato Boyce Thompson Institute for Plant Research P0480 Genome-wide SNP discovery from de novo assemblies of Pepper (Capsicum annuum) transcriptomes Seed Biotechnology Center, University of California, Davis P0483 Development of a saturated linkage map for Apple using a high-throughput GoldenGate SNP platform Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana-Champaign P0488 Deep re-sequencing of Apricot genome toward genome-wide association analysis in Stone Fruit species Clemson University P0491 Simultaneous mapping and candidate gene identification in Peach via sequencing of pooled genomes (Pnomes) USDA-ARS P0492 Application of high throughput genotyping techniques in Peach germplasm and breeding lines within the FruitBreedomics Project IRTA-Consortium CSIC-IRTA-UAB-UB. Centre of Research in Agricultural Genomics (CRAG) P0494 Sequence analysis of 16 ethylene-related genes in “Stony Hard” Peach using NGS data CRA–Fruit Tree Research Center P0504 Introns and exons in Citrus genome Centro de Citricultura Sylvio Moreira, IAC P0511 Prunus mume draft genome Beijing Forestry University P0514 Genome-wide gene diversity of two Pinus species University of Florida, Gainesville P0515 Transcriptome dynamics in the dormancy-spring growth transition of Douglas Fir Needles US Forest Service P0519 Genomic resources for Black Cherry Pennsylvania State University, University Park P0520 The Chinese Chestnut (Castanea Mollissima) Genome Project Pennsylvania State University P0522 Generation of a Eucalyptus globulus reference genome and gene catalogue GYDLE P0542 An integrated approach to Cattle epigenomics: Genome-wide methylome and histone modification profiling Dept. for Innovation in Biological, Agrofood and Forest systems, University of Tuscia P0543 High throughput SNP discovery in the Bovine lactome by RNA sequencing Department of Animal Science, University of California, Davis P0550 Validation of Bovine selective sweeps using high resolution SNP data University of Missouri, Columbia P0552 Comparison of different bayesian methods for QTL mapping in Hereford Beef Cattle using 1 Mb Windows Iowa State University, Ames P0553 Utilising information from heterogeneous SNP panels for genome analysis in Dairy Cattle University of Sydney P0556 Genome-wide association analysis of Paratuberculosis susceptibility in US Jersey Cattle Department of Animal Sciences, University of Wisconsin, Madison P0559 A mutation in Hephaestin-Like 1 (HEPHL1) is responsible for hypotrichosis in Belted Galloway Cattle University of Illinois, Urbana P0560 SNP array based identification of copy number variants in Italian Brown Swiss Cattle Università degli Studi di Milano P0561 Hunting for the weaver causative mutation in Brown Swiss Cattle BFGL, ARS-USDA P0562 Large-scale identification of the causative genetic variants influencing traits of economic interest in French Dairy breeds Animal Genetics and Integrative Biology P0564 Polymorphisms in positional candidate genes on BTA3 and BTA13 affect carcass quality in Hanwoo Cattle Chungbuk National University P0565 A whole genome association study to detect SNPs for growth and carcass qualtiy traits in Korean native cattle, Hanwoo Yeungnam University P0567 A genome wide association analysis for carcass traits in Beef Cattle University of Illinois, Urbana P0569 Deep mRNA sequencing for transcriptome profiling of skeletal muscle tissues Dept. of Ecology and Biology, University of Tuscia P0576 Development and characterisation of a low density (5K) Illumina Ovine SNP chip AgResearch P0577 Development of a SNP panel for parentage assignment in Sheep CSIRO Livestock Industries P0578 The use of a 50K SNP array for identifying genomic regions associated with a range of traits in Rambouillet Sheep Utah State University, Logan P0581 Validation of a low density SNP panel for breed certification testing in Brazilian Sheep (Ovis aries) breeds as a tool for flock genetic management EMBRAPA Recursos Geneticos e Biotecnologia P0586 A region on ovine chromosome 2 is associated with brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS) in Merino Sheep University of Sydney P0587 A heritable AGTPBP1 missense mutation is responsible for a lower motor neuron disease in Romney Sheep Iowa State University, Ames P0589 Ovine GM1-gangliosidosis is caused by a mutation in GLB1 University of Illinois, Urbana P0591 Mapping the dark eye patching gene in Churra and Ojalada Spanish Sheep breeds Universidad de Leon P0598 Insight into human directed selection through comparison of gene expression patterns between modern and heritage Chicken lines University of Delaware, Newark P0612 Spleen transcriptome response to aflatoxin in the domestic Turkey University of Minnesota, St. Paul P0614 Sequencing radiation hybrids for genome assembly: Example of the Duck genome Institut National de la Recherche Agronomique P0617 Pig Genome 10.2 annotation and gene prediction using mRNA and microRNA sequencing evidence Aarhus University, Department of Molecular Biology and Genetics P0623 Efficiency of heterologous capture for targeted resequencing of the major histocompatibility complex in Suidae and Tayassuidae INRA, UMR GABI P0633 Associations between multiple single nucleotide polymorphisms (SNPs) in 33 candidate genes and meat quality traits in commercial Pigs University of Alberta, Edmonton P0634 GWAS and beyond: Unravelling complex genomic variation in Boar Taint The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh P0648 A genome-wide association study identifies locus for eye color variation in Puerto Rican Paso Fino Horses University of Tampa P0650 Genome wide association of sarcoid tumors in Horses Cornell University P0651 Candidate gene evaluation of Equine neuroaxonal dystrophy based on genome-wide association analysis University of California, Davis P0652 Genetic determinants in Equine cervical stenotic myelopathy University of Kentucky, Lexington P0654 Towards the complete genome: Progress of Common Carp Genome Project Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences P0657 Comprehensive annotation of the transcriptome of Channel Catfish (Ictalurus punctatus) by paired-end RNA-Seq Auburn University P0659 RNA-Seq analysis of differentially expressed genes in Channel Catfish after Flavobacterium columnare challenge Auburn University P0661 Identification of genes associated with heat tolerance in Catfish exposed to chronic thermal stress using RNA-Seq Auburn University P0663 New in-depth Rainbow Trout transcriptome reference and digital atlas of gene expression West Virginia University, Morgantown P0665 Identification of differentially expressed miRNAs potentially associated with egg quality in Rainbow Trout (Oncorhynchus mykiss) West Virginia University, Morgantown P0667 RAD sequencing applications in three species of Columbia River fishes Columbia River Intertribal Fish Commission P0668 Identification of 2 novel interleukin 1 beta family genes in Japanese flounder Paralichthys olivaceus Tokyo University of Marine Science and Technology P0671 Identification of quantitative trait loci associated with caviar yield and ovarian adiposity in White Sturgeon (Acipenser transmontanus) University of California, Davis P0679 Sequencing Brachypodium insertional mutants using TDNA-Seq USDA P0689 Markers development and linkage analysis in Cynara cardunculus L DIVAPRA Plant Genetics and Breeding, University of Turin P0690 High density SSR- and SNP-based genetic maps of Flax University of Mantioba, Winnipeg P0695 Quick determination of chloroplast whole genome of Magnolia kobus DC., a deciduous Magnolia, using Solexa/Illumina technology Teragen Co. P0700 A sequence-based physical map of the Sunflower (Helianthus annuus L.) genome University Of British Columbia, Vancouver P0710 Detection of single nucleotide variation in Polar, Black and Brown Bears using a next generation sequencing approach Department of Animal Science, University of California, Davis P0713 Comparative analysis of the Marmoset (Callithrix jacchus) genome, an initial report of a highly unusual new world primate Human Genome Sequencing Center, Baylor College of Medicine P0714 Bodyweight: Genetic aspects in an experimental Cat population University of Sydney P0726 The Camelina sativa Genome Project: An emerging stress-tolerant biofuel seed crop in the Brassicaeae Pennsylvania State University, University Park P0727 Cassava genome from ancestor to cultivar Institute of Tropical Biosciences & Biotechnology, CATAS P0743 Quantitative genetic analysis of wood chemistry and biomass traits in Sunflower University of Georgia, Athens P0793 An improved rRNA removal process for RNA-Seq library preparation Epicentre (an Illumina comapny) P0797 Expression differences in six Puccinia triticina races and their effect on Wheat USDA-ARS P0807 De novo hybrid transcriptome assembly and RNA-Seq analysis of Switchgrass crowns and rhizomes USDA-ARS P0808 Expression analysis of endophyte-infected and endophyte-free Tall Fescue USDA-ARS P0819 Monitoring expression profiling of a set of abiotic and biotic stress responsive candidate genes in Chickpea (Cicer arietinum L.) through qRT-PCR International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) P0822 Investigating the novel sesquiterpene biosynthesis pathway in Copaifera officinalis, ‘the Diesel Tree,' through next-generation de novo transcriptome sequencing and functional genomics University of Tennessee, Knoxville P0825 Investigation of suberin biosynthesis using Cotton fibers National Center for Genome Resources P0829 Quantitative differential gene expression in Peach during short-day induced growth cessation School of Agricultural, Forest & Environmental Sciences, Clemson University P0835 Using RNASeq to profile Soybean seed development from fertilization to maturity University of Illinois, Urbana P0838 Endogenous siRNAs that silence chalcone synthase result in pigment pattern formation on seed coats in Glycine max University of Illinois, Urbana P0839 Identification of differentially expressed genes in Fiskeby III under ozone stress conditions University of North Carolina, Charlotte P0844 Transcriptome response to acute thermal stress in juvenile Chinook Salmon University of California, Davis P0860 Functional genomics of nitrogen metabolism in Maize kernels grown in culture University of Illinois, Urbana-Champaign P0863 Mapping cell fate decisions that occur during Soybean defense responses Mississippi State University P0868 Effects of nitrogen fertilization on global xylem transcript profiling of Eucalyptus urophylla x grandis evaluated by RNA-seq technology UNICAMP P0874 Discovery and characterization of conserved and novel miRNAs of leaf, root and fiber of Cotton Auburn University P0916 Systems approach to the understanding of metabolic diversity in Melon Agricultural Research Organization P0925 The extent of LD in the domestic Cat Felis catus University of California, Davis P0937 Gene expression and SNP detection in high throughput and high resolution by “Massive Analysis of cDNA Ends” (MACE) GenXPro-GmbH P0953 The Triticeae toolbox (T3): Containing keys to unlock the Triticeae genome and phenome USDA-ARS-WRRC P0957 BraMRs: A novel Brassica rapa miRNA database based on small RNA deep-sequencing National Academy of Agricultural Science, RDA P0966 Updates in GDR, the genome database for Rosaceae Washington State University, Pullman P0982 PAVE: Integrated transcript analysis University of Arizona/Bio5 Institute, Tucson P0985 A new statistical method for gene discovery from large-scale gene expression data with next-generation sequencing technology Meiji University P0989 Improving draft genome assemblies using next-gen data with gap-filling and scaffolding assembly tools Human Genome Sequencing Center, Baylor College of Medicine P0990 Extensive analysis of parameter tuning effects in a de novo assembly pipeline based on short reads Keio University P1015 Efficient de novo computation of ultra-high density genetic maps from RAD marker sequencing Max Planck Institute for Developmental Biology P1022 Accuracy of imputed 50k genotypes from 3k and 6k chips in Dairy Cattle breeds using FImpute University of Guelph P1024 De novo assembly and annotation of a Dinoflagellate transcriptome from 2nd generation sequencing technology University of Maryland, College Park Illumina CSPro Partners at PAG ® The Illumina Certified Service Provider (CSPro) program is a collaborative service partnership dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications. 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