www.illumina.com/agriculture

PAG 2012

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 BallroomRefreshments will be provided.

Unraveling Green GenomesTodd Michael, Ph.D. Head, The Genome Analysis Center Monsanto

Applications of Next-Generation Sequencing: From Genes to GenomesGary Schroth, Ph.D. Distinguished Scientist Illumina, Inc.

Characterization of Transgene Insertion Sites via Amplicon SequencingMary BeattyResearch Scientist Pioneer Hi-Bred

Applied Genomics for Genetic Improvement: Paving the Way for Biological DiscoveryTad 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 PresentationsScientists 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 DeMoSProgram No. Title Primary organization

C13The 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

WoRKSHoPSProgram No. Title Primary organization

W008 Improving the maize genome via GBS (genotyping by sequencing) Cornell University

W014extent 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

W033From 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

W034Rapid development of molecular resources for a freshwater mussel, Villosa lienosa (Bivalvia: Unionidae) using a RNA-Seq-based approach

Auburn University

W035Creation 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

W038RNA-Seq analysis of differentially expressed genes in channel catfish after Flavobacterium columnare challenge

Auburn University

W041Identification 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 ProjectCenter 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

W064Design 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

W100Uncovering 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 allocationeMBRAPA–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

W137Genetic determinism and candidate genes for flowering date—A phenological trait highly affected by climate change in Sweet Cherry

INRA

W144Performance of Illumina and Affymetrix Bovine high density genotyping platforms in Holsteins and Jerseys

Department of Animal Science, University of California, Davis

W145Differential 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

W153Goat 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 expressionCSIRo Livestock Industries, on behalf of the International Sheep Genomics Consortium

W157Whole 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 updateGenome Center, University of California, Davis

W189 The Sunflower genome and its evolution University of British Columbia, Vancouver

W190 Genomic resourses in Cynara cardunculusDIVAPRA - 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

W281The 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 SpruceNorwegian 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

W296Comparative genomics of 15 tropical Fagaceae species using shallow Illumina sequencing and a reference-free approach

Chinese Academy of Sciences

W300Association 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

W315A 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

W442Transcriptome of common Bean (Phaseolus vulgaris) through RNA-seq: Nodulation, symbiotic nitrogen fixation, transcription factors

Centro de Ciencias Genomicas-Universidad Nacional Autónoma de México, Cuernavaca

W448High resolution TranSNiPtomics: Gene expression and SNP detection in high throughput and high resolution by “Massive Analysis of cDNA ends” (MACe)

GenXPro-GmbH

W469Development 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

W530Chilling 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

W588Search 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

W628The 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 relativesIBqM/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

PoSTeRSProgram No. Title Primary organization

P0001 ARK-Genomics Centre for Comparative and Functional GenomicsThe Roslin Institute, University of edinburgh

P0007enhancing 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 updatePennsylvania State University, University Park

P0020An 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

P0022Reference-guided de novo genome assembly of the Indica Type Rice Variety IR 64 using short-read sequencing

International Rice Research Institute

P0026Gene 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

P0029Whole 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

P0042Unraveling Chickpea transcriptome for gene discovery and marker development using next generation sequencing technologies

National Institute of Plant Genome Research

P0043Using 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 unifloraLaboratory of Genomes and Plant Population, Center of Biotechnology, Federal University of Rio Grande do Sul

P0050Genome 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)

P0051Identification 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 genomesRutgers University, Waksman Institute of Microbiology

P0061RNA-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 transcriptomeInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University

P0070Resequencing 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 sequenceIRTA, 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

P0082Whole-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)

P0085Challenges 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 fragariaeSchool of Agricultural, Forest, and environmental Sciences, Clemson University

P0089De 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 abilityState 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 SheepAgResearch Ltd. Invermay Agricultural Centre

P0126 Transcriptome sequencing of Water Buffalo embryos Parco Tecnologico Padano

P0127Transcript 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

P0130The 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

P0170Using 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)

P0192Characterising 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

P0201A 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 SunflowerDepartment 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 qualityCollege of Life Sciences and Biotechnology, Korea University

P0211 Genomic evaluation for litter size in Canadian Yorkshire pigs Canadian Centre for Swine Improvement Inc.

P0213An 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

P0227Developing 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 cropsInstitute for Agricultural and Fisheries Research (ILVo)

P0251 Developing a high-throughput SNP genotyping workflow to support breeding applications in Rice International Rice Research Institute

P0262Isolation of Rice genes involved in important agronomic traits using whole genome resequencing

Iwate Biotechnology Research Center

P0274Identification of candidate genes in Rice for resistance to Sheath Blight Disease by whole genome sequencing

Louisiana State University Agricultural Center, Baton Rouge

P0295Characterizing 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

P0315Discovery 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

P0346Structural 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

P0359A 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

P0386Identification 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 libraryLeibniz 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

P0418Development and evaluation of a high-density Illumina Infinium iSelect BeadChip SoySNP50K

USDA-ARS, Soybean Genomics and Improvement Lab

P0432Genome-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 TomatoBoyce Thompson Institute for Plant Research

P0480Genome-wide SNP discovery from de novo assemblies of Pepper (Capsicum annuum) transcriptomes

Seed Biotechnology Center, University of California, Davis

P0483Development 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

P0488Deep re-sequencing of Apricot genome toward genome-wide association analysis in Stone Fruit species

Clemson University

P0491Simultaneous mapping and candidate gene identification in Peach via sequencing of pooled genomes (Pnomes)

USDA-ARS

P0492Application 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 CherryPennsylvania 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

P0542An integrated approach to Cattle epigenomics: Genome-wide methylome and histone modification profiling

Dept. for Innovation in Biological, Agro-food and Forest systems, University of Tuscia

P0543 High throughput SNP discovery in the Bovine lactome by RNA sequencingDepartment of Animal Science, University of California, Davis

P0550 Validation of Bovine selective sweeps using high resolution SNP data University of Missouri, Columbia

P0552Comparison 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 CattleDepartment of Animal Sciences, University of Wisconsin, Madison

P0559A 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

P0562Large-scale identification of the causative genetic variants influencing traits of economic interest in French Dairy breeds

Animal Genetics and Integrative Biology

P0564Polymorphisms in positional candidate genes on BTA3 and BTA13 affect carcass quality in Hanwoo Cattle

Chungbuk National University

P0565A 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 tissuesDept. 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

P0578The use of a 50K SNP array for identifying genomic regions associated with a range of traits in Rambouillet Sheep

Utah State University, Logan

P0581Validation 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

P0586A region on ovine chromosome 2 is associated with brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS) in Merino Sheep

University of Sydney

P0587A 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

P0598Insight 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 genomeInstitut National de la Recherche Agronomique

P0617Pig Genome 10.2 annotation and gene prediction using mRNA and microRNA sequencing evidence

Aarhus University, Department of Molecular Biology and Genetics

P0623efficiency of heterologous capture for targeted resequencing of the major histocompatibility complex in Suidae and Tayassuidae

INRA, UMR GABI

P0633Associations 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 TaintThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of edinburgh

P0648A 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

P0651Candidate 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

P0657Comprehensive annotation of the transcriptome of Channel Catfish (Ictalurus punctatus) by paired-end RNA-Seq

Auburn University

P0659RNA-Seq analysis of differentially expressed genes in Channel Catfish after Flavobacterium columnare challenge

Auburn University

P0661Identification 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

P0665Identification 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 fishesColumbia River Intertribal Fish Commission

P0668Identification of 2 novel interleukin 1 beta family genes in Japanese flounder  Paralichthys olivaceus

Tokyo University of Marine Science and Technology

P0671Identification 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 LDIVAPRA Plant Genetics and Breeding, University of Turin

P0690 High density SSR- and SNP-based genetic maps of Flax University of Mantioba, Winnipeg

P0695Quick 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

P0710Detection of single nucleotide variation in Polar, Black and Brown Bears using a next generation sequencing approach

Department of Animal Science, University of California, Davis

P0713Comparative 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

P0726The 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

P0807De 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

P0819Monitoring 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)

P0822Investigating 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 cessationSchool of Agricultural, Forest & environmental Sciences, Clemson University

P0835 Using RNASeq to profile Soybean seed development from fertilization to maturity University of Illinois, Urbana

P0838endogenous 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

P0868effects 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

P0937Gene 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-sequencingNational Academy of Agricultural Science, RDA

P0966 Updates in GDR, the genome database for Rosaceae Washington State University, Pullman

P0982 PAVe: Integrated transcript analysisUniversity of Arizona/Bio5 Institute, Tucson

P0985A new statistical method for gene discovery from large-scale gene expression data with next-generation sequencing technology

Meiji University

P0989Improving draft genome assemblies using next-gen data with gap-filling and scaffolding assembly tools

Human Genome Sequencing Center, Baylor College of Medicine

P0990extensive 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 sequencingMax 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

P1024De novo assembly and annotation of a Dinoflagellate transcriptome from 2nd generation sequencing technology

University of Maryland, College Park

CSPro WorkshopsBGI

Next-Gen Sequencing for Enhanced Agricultural Breeding

Monday, January 16 6:10 p.m. – 8:20 p.m.

Pacific Salon I

Illumina CSPro® Partners at PAG

GeneSeek Inc.

Next Generation Genomic Solutions for Agribusiness

Tuesday, January 17 1:30 p.m. – 3:40 p.m.

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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. Illumina CSPro certification provides a competitive advantage for service providers and ensures that customers who use Illumina CSPro services receive the industry-leading data quality and service they have come to expect from Illumina.

Learn more at www.illumina.com/CSPro

© 2012 Illumina, Inc. All rights reserved.Illumina, illuminaDx, BaseSpace, BeadArray, BeadXpress, cBot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium, iSelect, MiSeq, Nextera, Sentrix, SeqMonitor, Solexa, TruSeq, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registered trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners. Pub No. 070-2011-035 Current as of 09 January 2012

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