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Genetics I

Role of Genetic Material (phenotypes) genetic material > transcription and translation > proteins and regulatory factors > cell function > phenotype
Role of Genetic Material (genotypes) genetic material > replication and division > genetic material
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
Principles of Heredity Parent genes (homo/heter), gene interactions (recessive, dominant, epistasis), Mendel's principles, gene or allelic frequency
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
Key Equation Change in BV/T = accuracy * selection intensity * genetic variation / generation interval Tells a herd's response to selection
Accuracy Strength of relationship between true BV and their predictions for a trait
Selection Intensity Measures how choosey breeders are in deciding which individuals are selected
Genetic Variation Variation of BV, not easy to change
Generation Interval Amount of time required to replace on generation with the next, parents age when offspring are born
Decrease L Tradeoff Decrease R
Increase R Tradeoff Decrease I
Increase I Tradeoff Increase L
Increase R Proper contemporary groups, adjust records, use all information for PTA
Increase I Select only on economic traits, test all animals, maximize reproductive rate
Increase GV Hard, avoid inbreeding
Decrease L Breed animals early, turn generations rapidly, avoid unnecessary progeny testing
Animal Model P = environmental effects + genetic effects + residual effects (mom)
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
Reliablility Degree of confidence in PTA estimate, relies on parent/relative reliability, number of records (cows), number of herds daughters in (sires)
EPD Estimated Progeny Difference = PTA = 1/2 BV
BLUP Best linear unbiased predictor, used to develop predicted transmitting ability for genetic evaluations - replaced progeny tests
Large Scale Genetic Evaluations Progeny/performance test, nucleus breeding schemes, sire summaries/proofs
Progeny/Performance Tests ADV: accurate, DADV: long L and expensive, wrong bulls tested
Nucleus Breeding Schemes Village herds, shared animals with best genetics
Sire Summaries Combine genetic information from BLUP and progeny data
Dairy Management Inc Created to increase sales and demand for dairy products
National Dairy Council Established to protect the dairy industry image
Dairy Checkoff Promotion of dairy products, new product development, nutrition education
National Dairy Herd Information Association Promotes accuracy, credibility, uniformity
Dairy Records Management Systems Provide dairy management information and products to east coast
Animal Genomics and Improvement Laboratory Research
Council on Dairy Cattle Breeding Genetic and genomic evaluations
CDCB info goes to Purebred breed associations, AI industry, genomic testing companies
SNP Genotyping Measurement of genetic variations of SNPs between animals
Uses of SNP Chips Identity testing, QTL to determine if SNP contributes to trait, GWAS
Synonymous Substitution No AA change, may still impact funciton
Non Synonymous Substitution AA change of protein, lead to disease Missense: protein change vs Nonsense: premature stop codon
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
Net Merit Genetic index that simplifies the process of selecting service sires based on their genetic merit for a combination of economically important traits
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
Simply Inherited Trait Controlled by one gene or allele, BLAD (R), Polled (D)
Simple Traits Controlled by a few genes or alleles, QTL, high h, easy to measure and select for, milk yield, milk components
QTL Quantitive trait loci: stretches of DAN containing or linked to the genes that underlie a quantitive trait
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
Clinical Mastitis Phenotypically associated with SCS, PL, RU height, U depth, genetically correlated with SCS - distinct QTL vs SCS not
Johnes Disease GI diesease
Subjective Traits Low heritability, based on pre-established scoring or ranking system
Marker Assisted Selection Complex traits, genomics (SNP, microarray), epigenomics, proteomics, metabolomics, metagenomics
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
Proteomics Large scale study of proteins structure and function, MALDI matrix assisted laser desorption/ionization, mass spectrometry - footrot
Metabolomics Chemical processes involving metabolites, gas chromatography mass spectrometry - distinguish diet
Metagenomics Analysis of ALL species that impact a specific process, microbes in dairy cattle, DNA isolation through HiSeq, MiSeq, 16S ribosome
Phenomics Physical and biochemical traits, understand the way organism change in response to genetic mutation and environmental influences
Genetics Study of single genes and their role in the way traits or conditions are passed from one generation to the next
Genomics study of all parts of an organism's genes
Created by: 1138967652782105