Introduction to Genomics

What is genetics?

• The study of heredity: how traits are inherited or transmitted from generation to generation

• It often focuses on one gene, one mutation, or a small number of genes

What is genomics?

• The study of all of an organism's genes, or its genome

• It examines information across the genome rather than only one or a few loci

What information is used in a traditional genetic evaluation?

• Pedigree information

• Phenotypes

• One gene or a few mutations

• All used to help support selective breeding decisions

  • Considered simpler than genomics since it uses simpler designs, models, and laboratory techniques.

What is a major use of traditional genetic evaluation in animal breeding?

It is used in selective breeding; pedigree and performance records help identify animals likely to transmit desirable traits.

Why can genomics be especially useful for complex traits?

Genomics can help study complex traits that are difficult to measure, have low heritability, or are expressed late in life. Genome-wide information can improve prediction when phenotype data alone are limited. Often requires:

• Advanced data-analysis and statistical methods

• High-performance computing

• Sophisticated laboratory instruments (i.e. sequencing platforms)

What does DNA or genomic testing mean?

• It means using DNA-based information to generate a genetic or genomic profile.

• The profile can inform ancestry, health-related risk, traits, or breeding decisions.

Why is prediction accuracy a key factor in a genomic test?

• A genomic test is useful only to the extent that its predictions are accurate

• An inaccurate prediction can lead to poor health, management, or breeding decisions.

What is a limitation of many direct-to-consumer DNA tests?

• They are direct-to-consumer tests rather than clinical predictive gene-panel tests, and they may lack therapeutic prediction

• A DNA result does not automatically provide a clinical diagnosis or treatment plan.

What are three broad applications of human DNA testing, and how does each relate to animal populations?

Health, traits, and ancestry

• Ancestry → genetic diversity

  • Ancestry-related information helps describe population relationships and genetic diversity.

• Traits → genomic selection and GBVs

  • In animals, GBVs are used to predict breeding merit/value

• Health → haplotypes, genetic recessives, and GBVs

  • These genomic tools can help manage inherited health risks

What is genomic selection?

AKA genomic breeding value (GBV).

• Uses genome-wide genetic information to predict an animal's genetic merit (value)

• It supports selection before all traits can be directly measured

What is a customized marker panel?

A selected set of DNA markers designed for a particular purpose or population. It can make targeted genomic testing more efficient.

What is QTL mapping used for?

QTL, or a quantitative trait locus, mapping is used to identify genomic regions associated with variation in a measurable performance trait. It helps connect genotype with phenotype.

How are GWAS and candidate-gene approaches related to QTL mapping?

• They’re approaches used to identify genetic variants or regions associated with traits.

• GWAS scans broadly across the genome

• A candidate-gene approach tests biologically plausible genes.

What is biomarker development in genomics?

Identifies measurable genomic indicators (SNPs, CNVs, structural variants, etc.) that are associated with a biological state or trait, like a disease. They can support prediction, diagnosis, or selection.

What is heterosis?

Heterosis, AKA hybrid vigor, is a biological phenomenon in which the crossbred offspring shows improved performance (stronger, healthier, superior traits) compared to both of its parent lines. Genomics can help study and use genetic differences between populations.

What is the purpose of traceability and parentage verification?

They use genetic information to verify an animal's identity, origin, or parentage that can support breeding records, product traceability, and management.

Why are haplotypes and genetic recessives important in animal genomics?

They help identify inherited chromosome segments and manage the risk of recessive disorders. Carriers may be healthy but can produce affected offspring under certain matings.

• Haplotypes are groups of gene variants or SNPs on one chromosome that are inherited together from one parent

• Genetic recessive traits are gene variants that only cause a trait or condition when an individual inherits two copies (one from each parent)

Why is genetic diversity an important genomic application?

Genetic diversity helps maintain variation within populations and reduces the risks associated with excessive relatedness.

• Diversity supports long-term population health and adaptability.

Name the applications of structural genomics.

Genomics has both research and applied breeding uses.

• QTL mapping

• Genomic selection

• Genetic diversity

• Traceability and parentage verification

• Customized marker panels

• Biomarker development

• Haplotypes and genetic recessives

• Heterosis

• Understanding biology

What is meant by the phrase from genome to phenome, and why is it considered a prediction problem?

It means connecting genomic information to observable, high-dimensional phenotypic information.

• The central challenge is using genomic data to predict biological performance

• Genomicists aim to use DNA info + other data to predict traits and performance

Why does the lecture say that phenotype is king?

Phenotypes remain essential because they are the observable outcomes that genomics ultimately aims to explain or predict. Genomic predictions are only useful when tied to meaningful performance data.

What sources of information characterized animal breeding in the 1950s, 2010s, and 2020s?

• 1950s: Pedigree and performance records; selection relied primarily on family relationships and observed traits

• 2010s: DNA, pedigree, and performance were combined; genomic information added predictive power to traditional records.

• 2020s: Omics data, sensor data, pedigree, and performance are combined. Modern prediction can integrate multiple biological and environmental data streams.

What does the term omics mean?

Omics refers to the comprehensive study of biological molecules (omes) within an organism.

• Genomics → epigenomics → transcriptomics → proteomics → metabolomics.

• These layers connect genetic information to molecular function and phenotype.

What is a genome?

The complete set of genetic material, or all genes, of an organism. Genomics studies this complete genetic content.

What is a proteome?

The entire set of proteins expressed by a genome, cell, tissue, or organism. Proteins are functional products whose expression can vary by cell type and condition.

What is a transcriptome?

The complete set of RNA transcripts in a single cell or tissue. It reflects which genes are being transcribed under particular conditions.

What is a metabolome?

The complete set of small-molecule metabolites found within a biological organism. Metabolites provide a snapshot of biochemical activity.

What is a metagenome?

The collective genetic material of a community of microorganisms. It is useful for studying microbial communities without isolating every organism.

What is metatranscriptomics?

Examines the collective RNA transcripts of a microbial community. It indicates which microbial genes are actively being expressed.

What is a phenome?

The acquisition of high-dimensional phenotypic data on an organism. It represents comprehensive observable trait information.

Match each ome to its main molecule type.

• Genome: genetic material

• Transcriptome: RNA transcripts

• Proteome: proteins

• Metabolome: small-molecule metabolites

• Metagenome: collective genetic material of microorganisms

• Phenome: high-dimensional phenotype data

Why are phenotype records still necessary when genomic data are available?

They measure actual performance and provide the outcomes needed to train and validate genomic predictions. DNA alone does not replace measurement of traits.

What does the equation P = G + E + GxE represent?

It represents phenotype as the combined result of genotype, environment, and genotype-by-environment interaction because observable performance is not determined by genes alone.

In the equation P = G + E + GxE, what does each variable mean?

• P: phenotype; the observable trait or level of performance

• G: genotype; an organism's genetic contribution to the trait.

• E: environment; conditions that can influence an animal's observed performance.

• GxE: genotype-by-environment interaction; different genotypes can respond differently to the same environment.

Why did Robert Bakewell's work matter to animal breeding?

He introduced systematic recording of performance. Measurement makes it possible to identify and improve desirable traits through selection.

What is a genetic relationship?

• The proportion of alleles two animals share because of family membership or a common ancestor

• More specifically, it reflects alleles that are identical by descent

• Relatives resemble one another because they inherit DNA from common ancestors.

What is a pedigree?

• A recorded chart or table of an animal's ancestry, lineage, and descent

• It provides the genetic and record information on the individual animal and its ancestors

What is a common ancestor?

• An ancestor shared by two or more individuals, contributing to their allelic similarity

• A common ancestor of both parents can also cause inbreeding in their offspring.

What does identical by descent (IBD) mean?

• Alleles are shared because they were directly inherited from a recent/common ancestor.

  • Example: full sibling shared the same allele from a grandparent

• IBD is the basis of pedigree relationship and inbreeding coefficients.

What does identical by state (IBS) mean?

• Alleles have the same state but may not have come from a common ancestor

  • Example: two unrelated people having the same allele due to evolutionary pressures

• Similarity can occur coincidentally or through independent mutation.