Genomics Exam 1: Mohammed Cal Poly

What is the difference between genetics and genomics?

genetics focuses on a specific gene while genomics focuses on genomes as a whole.

What are the impacts of genomics on genetic change improvement?

Genetic rates doubled, meaning that selection and breeding efficiency have significantly increased, leading to enhanced traits in crops and livestock.

What are the applications of genomics in common dairy cattle operations?

genetic condition or disorder detections, improving the accuracy of genomic selection, parentage testing

Parentage testing in genomics

Determining the ancestry or lineage of a genetic line for better genetic selection

The Dairy Industry and genomics

sees genomics as an extension of genetics not as a replacement

What is genomics used in the dairy industry for?

enhance breeding decisions, improve animal health, and optimize production efficiency.

Genetics is the study of

heredity, how different traits are inherited or transmitted from generation to generation

Genetic Evaluation Source of Information

pedigree + phenotypes + one gene/few mutations

What sources of information is used for “Selective Breeding”

pedigree + phenotypes + one gene/few mutations

What is the calculated value for “selective breeding”

the “Estimated Breeding Value (EBV)

What point in life must selective breeding evaluation be done and why?

Post mortem due to phenotypic traits looked at like marbling, carcass quality, etc.

Genomic Evaluation System uses…

DNA genotype + phenotypes

What is the value calculated through the genetic evaluation system?

genomic breeding value (GBV)

Whats different about the processes of Genomic Evaluation System and Selective Breeding

Genomic Evaluation System relies on DNA information to predict breeding value, while Selective Breeding focuses on observable phenotypic traits for animal selection. Also, you can do GES without killing animal.

What are the applications of the genomic testing like 23&Me

ancestry, health risks, and trait links

What happens to DNA data of millions as 23&Me files for bankruptcy?

The DNA data may be destroyed or sold to pay creditors, impacting user privacy and access to personal genetic information.

What happened behind the decline of 23&Me

risk factor and predictions were apart of the accuracy values, the accuracy of prediction of the test was unclear

Animal Genomics Equivalent of Human Health DNA Testing

screening for haplotypes, genetic recessives (lethal defects), and calculating GBV for health and disease resistance

Animal Equivalent of Human Trait Testing

Genomic Selection using GBV’s for production traits like milk yield, growth rate, and meat quality

Animal Genomics Equivalent of Human Ancestry Testing

monitoring and managing genetic diversity, pedigree verification, and avoiding inbreeding

Role of recessive carrier screening in animal populations

to identify animals carrying undesirable or lethal recessive alleles to prevent mating pairs that cause genetic disorders

Haplotype

a set of DNA variations or alleles that tend to be inherited together from a single parent

Genomic Selection

a form of marker-assisted selection where genetic markers across the entire genome are used to predict breeding values

Allele

one of two or more versions of a gene that can exist at a specific locus in an organism's genome.

List the problems or downfall of animal DNA testing

• Limited reference population not only for ancestry purposes but also for different breeds, purebreds, etc.

• Variability in accuracy across different companies

to calculate the GBV you need

phenotype and genotype

to know breed composition you need

genotypes

What determines the accuracy of prediction for genomic testing

the GBV & breed composition’s relationship with the companies reference population

What are the factors affecting the accuracy of prediction using GBV and breed comp with a company?

# of animals in the reference population, # of breeds in the reference population, # of markers (SNAP)

What is the main objective of structural genomics in livestock?

Focuses on mapping, sequencing, and analyzing physical genome structures to apply genetic insights across animal breeding, health, and management.

What is QTL Mapping, and what tools are used for it?

QTL mapping identifies specific regions on chromosomes linked to polygenic traits (like growth rate or milk yield) using tools like Genome-Wide Association Studies (GWAS) and candidate gene analysis.

What does QTL mapping stand for?

Quantitative Trait Loci (QTL)

What is Genomic Selection?

Selecting breeding animals based on estimated breeding values calculated from genome-wide marker panels (like SNPs) rather than solely relying on physical traits or pedigree history.

How is structural genomics used in parentage verification and traceability?

DNA profiling verifies biological parents, tracks individual animals, and confirms meat/product origin throughout the supply chain.

What role does genomics play in managing haplotypes and genetic recessives?

It identifies blocks of inherited genes (haplotypes) to detect harmful or lethal recessive mutations and eliminate them from breeding lines.

How does structural genomics assist with heterosis (hybrid vigor)?

It allows breeders to predict optimal crossbreeding combinations by measuring genetic distance to maximize performance advantages in crossbred offspring.

What is a customized marker panel?

A targeted set of specific DNA markers (SNPs) designed for cost-effective screening of specific traits, diseases, or breed markers in a specific population.

How does genomics contribute to biomarker development?

It identifies biological indicators (DNA/RNA variants) that predict disease risk, physiological status, or economic trait potential.

Why is genetic diversity monitored using genomic tools?

To track overall genome-wide variation within a herd or breed, prevent inbreeding depression, and preserve long-term population health.

Genomics helps

increase production, reduce losses, improve sustainability, identify GBV’s, pin point natural resistance

Phenotype

level of performance, the observed category of a measured trait

Genotypes BLANK phenotype of the animal

Genotypes predict the phenotype of the animal

What is the primary ultimate goal for a geneticist/genomicist according to this framework?

Moving from Genome to Phenome by predicting the observable traits or performance of an animal based on its genetic and biological data.

How has phenotype prediction evolved over the decades?

1950s: Pedigree + Performance

2010s: DNA + Pedigree + Performance

2020s: "Omics" + Sensors + Precision Phenotyping / Performance

What does "Phenotype is king!" mean in modern animal genomics?

Genomic data is only useful if paired with accurate, high-quality phenotyping (performance data); you cannot build effective prediction models without knowing the actual observable outcome.

Proteomics

The large-scale study of proteins, particularly their functions and structures. Proteomics aims to understand how proteins interact and contribute to biological processes.

Metabolomics

analysis of metabolites and biological molecules in biological samples to understand metabolic processes and their regulation.

Transcriptomics

analysis of gene expression (mRNA/RNA)

Meta Genomics & Meta Transcriptomics

analysis of microbial communities, ex: the gut microbiome

What modern technology complements "Omics" data in 2020s genomic predictions?

Sensors like wearable livestock monitors, automated milk meters, activity collars that continuously capture high-throughput performance and health data.

Define OMICs

the comprehensive study of biological molecules (the “omes”) within an organism like genomes, proteins, or metabolites.

Which OMICs disciplines are classified as “nucleic acid-based methods”?

Genomics (DNA), Epigenomics (epigenetic modifications to DNA/Chromatin), Transcriptomics (RNA expression)

Which OMICs disciplines are not classified as “nucleic acid-based methods”?

Proteomics (study of proteins) and metabolomics (study of metabolites)

What is the goal of integrating multi-omnics data?

Combining data across genomics, epigenomics, transcriptomics, proteomics, and metabolomics to gain a complete, systems-level understanding of an organism's biology and phenotype.

Define Metabolome

the complete set of small molecule metabolites found within a biological organism

Define proteome

the entire set of proteins expressed by a genome, cell, tissue, or organism at a specific time.

Define transcriptome

the complete set of RNA transcripts in a single cell or a tissue (population of cells)

Define metagenome

The collective genetic material (genome) of a community of microorganisms

Define Phenome

the attainment of high dimensional phenotypic data on an organism (complete set of physical and behavioral traits)

Define genome

The complete set of genetic material present in a cell or organism.

Why are phenotypes still considered "king" even with advanced genomic technology?

Because genomic prediction models require continuous, high-quality phenotypic (performance) data to establish reference populations, train evaluation algorithms, and maintain prediction accuracy across generations.

What is the main take-home message regarding recording animal performance vs. using genomics?

While genomics is critical for early selection and mapping, DNA data alone is useless without accurate performance recording (phenotyping) to ground and validate the genetic predictions.

How do genomics and phenotyping complement each other in modern animal breeding?

Genomics provides the molecular blueprints and tools for early prediction, while phenotypic measurements provide the ground-truth data needed to train, update, and refine those genetic predictions over time.

Who is known as the “Old Father of animal breeding”?

Robert Bakewell (1725-1795)

What major contribution did Robert Bakewell make to animal breeding?

He introduced systematic recording of performance in livestock

What principle attributed to William Thomson emphasizes the importance of performance recording?

"To measure is to know" and "If you cannot measure it, you cannot improve it"

Why are measurements and performance recording foundational to animal genomics?

Because you cannot select for, evaluate, or genetically improve traits that you do not systematically measure and record.

What is the fundamental quantitative genetics formula

P = G + E + G*E

What is genomics

Study of all an organism’s genes, the branch of molecular biology concerned with structure and function. evolution and mapping of genomes.

Is genomics a multidisciplinary field?

Yes, genomics integrates biology, computer science, statistics, and engineering to analyze and interpret genetic data.

Genomics Sub Disciplines

Structural, functional, and comparative genomics

Structural Genomics

studying the physical nature of genomes, including the sequencing and mapping of genomes.

What is structural genomics based on…

DNA, not tissue-specific, though. Can be obtained from hair, saliva, skin, etc.

Short term application of genomics based on genotype only

Haplotypes and genetic disorders, parentage testing (Sire assignment), genetic diversity (genomic relationship & genomic inbreeding, breed composition)

Long term application of genomics based on genotype and phenotype

Enhancing breeding using genomic selection, QTL mapping, GBV

Functional Genomics

studying the expression and function of entire genome

Is Functional genomics tissue specific?

Yes, functional genomics can be tissue specific, as it studies gene expression and functions in various biological tissues to understand specific roles and interactions.

Where can you take a sample from for functional genomics testing?

liver, kidney, brain, muscle, etc.

Transcriptome in Functional Genomics

The transcriptome in functional genomics refers to the complete set of RNA transcripts produced by the genome at any given time, reflecting gene expression levels and patterns in specific tissues or conditions. IS TIME SENSITIVE

Comparative Genomics

comparing genomes of different species

What is the effect of comparative genomics across different species?

knowledge of gene structure and function in one species can be applicable in another

Factors that shape genomics

1. advances in sequencing technology and reduction in the cost of sequencing

2. availability of high performance computing (HPC facilities)

3. Focus shift from single gene to genome

4. Advances in data analytics approaches such as machine learning (ML)

What is genomics shaped by?

Genomics is shaped by technology, now also machines that provide high resolution snapshots of the world of nucleic acids (not just DNA)

Sanger DNA sequencing

A method for determining the sequence of nucleotides in DNA using dideoxynucleotides. (1977-1990s)

DNA Microarrays

• tech used to measure the expression levels of many genes simultaneously

• or to genotype multiple regions of a genome

• DNA microarrays consist of a small solid support to which DNA molecules are attached, allowing for hybridization with fluorescently labeled samples.

• mid 1990s

2nd Generation DNA sequencing

• Since 2007

• Allows for massively parallel sequencing

• Significantly increases throughput

• Reduces costs compared to previous methods

3rd Generation and single molecule DNA sequencing

• since 2010

• Set of sequencing technologies that enable the direct sequencing of single DNA molecules in real-time

• Providing long read lengths and quick turnaround times

• Enhanced capabilities for de novo genome assembly and improved structural variation detection

Illumina sequencing platforms

• widely used second-generation sequencing technologies

• utilize a sequencing-by-synthesis method

• Enabling high-throughput sequencing with short read lengths and high accuracy.

Nucleotide options

are the building blocks of DNA and RNA, consisting of adenine (A), thymine (T), cytosine (C), and guanine (G) for DNA; and for RNA, it's the same but replaces thymine with uracil (U).

Sanger DNA Sequencing method used

Capillary Electrophoresis is a method used in Sanger sequencing to separate DNA fragments based on size, allowing for the determination of the DNA sequence.

Illumina Sequencing method used

sequencing-by-synthesis technology to produce millions of short DNA reads simultaneously. It's known for its high throughput, accuracy, and applications in various genomic studies.

Nanopore sequencing method used

real-time, long-read sequencing of DNA or RNA molecules by measuring changes in ionic current as the nucleic acids pass through a nanopore.

PacBio-HiFi method used

SMRT, highly accurate long read sequencing

What is identified as the most challenging aspect of genomics?

Big data computation and analyses

What primary computational resources are required to handle massive genomic datasets?

High Performance Computing (HPC) Core Facilities and Cloud computing providers

What major cloud computing providers are commonly used for genomics data analysis?

Amazon Web Services (AWS), Google Cloud, Digital Ocean, and Microsoft Azure

Why is the steep drop in sequencing costs significant for animal genomics?

dramatic reduction in sequencing costs makes whole-genome sequencing and high-density genotyping financially feasible for large-scale livestock and population-level productions.

primary file format produced immediately after sequencing quality control for both DNA and RNA

FASTQ files, store raw sequence reads and their associated quality scores.

What step comes after reading/filtering raw reads in a genomic or transcriptomic workflow?

Alignment of reads to a reference genome, producing a BAM file.

In genomic data analysis, what process follows BAM file generation to detect genetic differences?

Variant Calling, which outputs a VCF (Variant Call Format) file