Genetics I
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| Role of Genetic Material (phenotypes) | genetic material > transcription and translation > proteins and regulatory factors > cell function > phenotype
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| Role of Genetic Material (genotypes) | genetic material > replication and division > genetic material
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| Structure of a Gene | DNA: Promoter and enhancer (TATA), exon, intron, exon, intron, stop (UAA)
Exons for gene coding, separation promotes gene expression
RNA: only exons, no introns
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| Principles of Heredity | Parent genes (homo/heter), gene interactions (recessive, dominant, epistasis), Mendel's principles, gene or allelic frequency
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| Heritability | Proportion of differences in performance for a train that are attributable to differences in breeding value - degree of which offspring resemble their parents - 0.2 low, 0.4 high
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| Key Equation | Change in BV/T = accuracy * selection intensity * genetic variation / generation interval
Tells a herd's response to selection
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| Accuracy | Strength of relationship between true BV and their predictions for a trait
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| Selection Intensity | Measures how choosey breeders are in deciding which individuals are selected
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| Genetic Variation | Variation of BV, not easy to change
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| Generation Interval | Amount of time required to replace on generation with the next, parents age when offspring are born
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| Decrease L Tradeoff | Decrease R
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| Increase R Tradeoff | Decrease I
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| Increase I Tradeoff | Increase L
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| Increase R | Proper contemporary groups, adjust records, use all information for PTA
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| Increase I | Select only on economic traits, test all animals, maximize reproductive rate
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| Increase GV | Hard, avoid inbreeding
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| Decrease L | Breed animals early, turn generations rapidly, avoid unnecessary progeny testing
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| Animal Model | P = environmental effects + genetic effects + residual effects (mom)
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| PTA | Average genetic value for a certain trait that an animal transmits to its offspring, calculated through genetic merit of parent, performance of animal, distribution of records in offspring
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| Reliablility | Degree of confidence in PTA estimate, relies on parent/relative reliability, number of records (cows), number of herds daughters in (sires)
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| EPD | Estimated Progeny Difference = PTA = 1/2 BV
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| BLUP | Best linear unbiased predictor, used to develop predicted transmitting ability for genetic evaluations - replaced progeny tests
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| Large Scale Genetic Evaluations | Progeny/performance test, nucleus breeding schemes, sire summaries/proofs
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| Progeny/Performance Tests | ADV: accurate, DADV: long L and expensive, wrong bulls tested
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| Nucleus Breeding Schemes | Village herds, shared animals with best genetics
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| Sire Summaries | Combine genetic information from BLUP and progeny data
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| Dairy Management Inc | Created to increase sales and demand for dairy products
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| National Dairy Council | Established to protect the dairy industry image
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| Dairy Checkoff | Promotion of dairy products, new product development, nutrition education
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| National Dairy Herd Information Association | Promotes accuracy, credibility, uniformity
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| Dairy Records Management Systems | Provide dairy management information and products to east coast
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| Animal Genomics and Improvement Laboratory | Research
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| Council on Dairy Cattle Breeding | Genetic and genomic evaluations
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| CDCB info goes to | Purebred breed associations, AI industry, genomic testing companies
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| SNP Genotyping | Measurement of genetic variations of SNPs between animals
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| Uses of SNP Chips | Identity testing, QTL to determine if SNP contributes to trait, GWAS
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| Synonymous Substitution | No AA change, may still impact funciton
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| Non Synonymous Substitution | AA change of protein, lead to disease
Missense: protein change vs Nonsense: premature stop codon
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| DNA to Genomic Predictions | Discovery population of old bulls, genetically diverse with known daughter performance, connect DNA data with daughter performance, equations applied to all bulls - combine SNP effect estimates with PTA
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| Net Merit | Genetic index that simplifies the process of selecting service sires based on their genetic merit for a combination of economically important traits
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| How to use Net Merit | Pay attention to difference among animals instead of value, avoid initial selection for too many traits, heifers choose sires with calving ease
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| Simply Inherited Trait | Controlled by one gene or allele, BLAD (R), Polled (D)
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| Simple Traits | Controlled by a few genes or alleles, QTL, high h, easy to measure and select for, milk yield, milk components
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| QTL | Quantitive trait loci: stretches of DAN containing or linked to the genes that underlie a quantitive trait
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| Complex Traits | Trait affected by many genes, no single gene has an overriding influence, MARKER ASSISTED SELECTION, economically relevant but hard to select for or measure, mastitis and Johnes disease, feed efficiency and methane production, milk composition
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| Clinical Mastitis | Phenotypically associated with SCS, PL, RU height, U depth, genetically correlated with SCS - distinct QTL vs SCS not
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| Johnes Disease | GI diesease
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| Subjective Traits | Low heritability, based on pre-established scoring or ranking system
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| Marker Assisted Selection | Complex traits, genomics (SNP, microarray), epigenomics, proteomics, metabolomics, metagenomics
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| Epigenomics | Reversible modifications on DNA or histones that affect gene expression without modifying DNA sequence, DNA methylation and histone modification - histone and methylation assays, Chip-Chip and Chip-Seq
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| Proteomics | Large scale study of proteins structure and function, MALDI matrix assisted laser desorption/ionization, mass spectrometry - footrot
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| Metabolomics | Chemical processes involving metabolites, gas chromatography mass spectrometry - distinguish diet
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| Metagenomics | Analysis of ALL species that impact a specific process, microbes in dairy cattle, DNA isolation through HiSeq, MiSeq, 16S ribosome
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| Phenomics | Physical and biochemical traits, understand the way organism change in response to genetic mutation and environmental influences
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| Genetics | Study of single genes and their role in the way traits or conditions are passed from one generation to the next
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| Genomics | study of all parts of an organism's genes
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