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UW-Madison ANSCI 361 - Introduction to Genomic Selection

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ANSCI 361 1st Edition Lecture 2Outline of Last Lecture I.EuropeII.Vision of Europe for food production towards 2050 (Horizon 2020)III.Biotechnology and food production in EUIV.Cloning/GMOsOutline of Current Lecture I. Genomic testinga. SNPsb. Elite breedingc. Commercial Farmsd. Imputatione. Phenotyping femalesII. SummaryCurrent LectureThe bovine genome: 30 pairs of chromosomes, 3 billion base pairsGenotype: Genetic constitution of an individual organismHaplotype: A set of DNA variations, or polymorphisms, that tend to be inherited together. Can refer to a combo of alleles or to a set of single nucleotide polymorphisms (SNPs) found on the same chromosome.SNP Chips: Automated and inexpensive genotyping. Many other, low, medium and high-density chips are now available.“AA” is Code 0, “AT” is Code 1, and “TT” is Code 2Estimating SNP Effects: Slope of line indicated estimated SNP effect, which is the change in PTA protein per extra copy of given SNP allele.Genomic PTA (GPTA) for a young calf: Reference population (made up of older animals) + Calf with genotype = Estimated SNP Effects (Height of dot indicated expected gain in PTA milk from inheriting one extra copy of the favorable SNP allele)Genomics for Elite Breeding Stock:These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute. Genomic data have been used in routine genetic evaluations of US dairy cattle since January 2009 GPTA for a bull calf is nearly as accurate as the PTA for an older bull with dozens of daughters GPTA for a heifer calf is more accurate than the PTA of an older cow with several lactation records Hundreds of genome-tested young bulls are being marketed to dairy farmers Most females are marketed using genomic dataGenomics for Commercial Farms: Routine genomic testing of heifer calves as potential herd replacements requires an inexpensive DNA test A chip with a smaller number of selected SNPs might deliver most of the benefit for a fraction of the price Applications may include: parentage discovery, culling low-merit replacement heifers, screening potentially marketable animals, or mating programsGenotype Imputation: Aoccdring to rscheearch at Cmabrigde Uinervtisy, it deosn’t mttaer in what odrer the ltteers in a wrod are, the olny iprmoetnt tnihg is taht the frist and lsat ltteer be at the rghit pclae. The rset can be a toatl mses and you can sitll raed it wouthit a porbelm. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe.-Your brain does this after learning a language.-Imputation algorithms do this after learning what haplotypes are present among cows and bulls of the same breed that have been tested with a more expensive chip.Strategies for phenotyping females: Test the whole herd Test potentially elite animals for marketing Test potentially inferior animals for culling Test animals that are “on the bubble”Summary: Genomic testing has revolutionized selection programs in most food animal species Species with high-value animals, long generation interval, and accurate EBV for referenceanimals (such as dairy cattle) get the greatest benefit Genotype imputation allows inexpensive genomic testing of females on commercial farms Accuracy of genomic predictions is good enough to rank animals, but it is far from perfect  Additional genetic and management applications of genomic information have yet to be


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