PPT-Fine-mapping of QTL using high-density SNP genotypes

Illumina genotyping arrays BovineSNP50 54001 SNPs version 1 54609 SNPs version 2 BovineHD 777962 SNPs BovineLD 6909 SNPs Allows for additional SNPs eg GeneSeek Genomic Profiler. . in . the . Legume . Genomics Community. January 11. th. , 2015. Tripal. Workshop. Ethy Cannon. Iowa State University. A case study of . Tripal. /Chado. A description of two . Tripal. modules our groups are developing. Matt Spangler. University of Nebraska-Lincoln. Imputation. Imputation creates data that were not actually collected . I. mputation allows us to retain observations that would otherwise be left out of an analysis. By Sharon Creech. Pictures by Harry Bliss. principal. The head of a school. The . principal. . of Bridge City Intermediate is a woman . named Dr. . Fountain. . . Soared. To rise or fly high in the air.. Jeff Barrett. Challenges to GWAS?. Data quality control . No common, single SNP main effects (all epistasis or rare variants or …). Sample size too small to detect effects. Computational . burden. Multiple . analysis. SNP/genomic signature. Clinical sampling. Personalized chemotherapy. Personalized Targeted therapy. Personalized RNA therapy. Personalized radiation therapy. drugs. Targeted molecules. s. iRNA. Welcome to . PolyMarker. !. http://polymarker.tgac.ac.uk/. How to use Biomart to find SNP markers www.wheat-training.com. Options:. Design your own primers. Download pre-designed primers for SNP data. {in the classical twin design}. Slide acknowledgements (fonts all over the place and inconsistent color coding): . Manuel . Ferreira. , . Pak Sham. , . Shaun Purcell. , . Sarah Medland. , . and . Sophie . Dairy Cattle. 9 million cows in US. Attempt to have a calf born every year. Replaced after 2 or 3 years of milking. Bred via AI. Bull semen collected several times/week. Diluted and frozen. Popular bulls have 10,000+ progeny. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring . 2018. Anthony Gitter. gitter@biostat.wisc.edu. These slides, excluding third-party material, are licensed under . CC BY-NC 4.0. . by Mark Craven, Colin Dewey, and Anthony Gitter. these tools may offer educators as yet unrealised and potentially complementary functions to aid The over-riding aim of all mapping tools is similar. If students can represent or manipulate a complex 1. Be Safe. Vaccinations . -. . recommended. . b) Gloves. . – wear gloves during sampling, discard gloves inside cooler.. d. ) Field. Gear. . Hepatitis A&B. Tetanus. c. ) Hand. Sanitizer. Baud, A. et al. . Rat Genome Sequencing and Mapping Consortium. Presented by Alex . Gileta. Hailing from the Palmer Lab. Nature Genetics .  . 45. , . . 767–775 (2013). Genetic Variation and Complex Traits. Research Geneticist, USDA-ARS. Sugarbeet & Potato Res Unit. Fargo, ND 58102. 03. 01. 2023. Single nucleotide polymorphism (SNP). Introduction. Widely spread in the genome. High density. Genetic diversity . Dr.. Danny Arends. Northumbria University, Sept 2022. danny.arends@northumbria.ac.uk. About me. QTL mapping in 3 slides. LMM-MQM time series mapping. Linear mixed models & Multiple QTL mapping. More statistical power through modelling of time series .