1. Library preparation (with barcodes specific to adapters), 2. Sequencing the fragments, 3. Imaging and sequencing to detect nucleotides, 4. Base calling.

1. DNA extraction, 2. PCR amplification, 3. Gel electrophoresis, 4. Sanger sequencing.

1. Protein isolation, 2. Western blotting, 3. Antibody staining, 4. Imaging.

1. Cell lysis, 2. RNA extraction, 3. cDNA synthesis, 4. Microarray analysis.

Short read: strength with high number of reads per experiment. Long read: strength with high number of bases per read.

Short read: strength with high number of bases per read. Long read: strength with high number of reads per experiment.

Short read: used for protein sequencing. Long read: used for carbohydrate sequencing.

Short read: produces longer sequences. Long read: produces shorter sequences.

A fixed position on a chromosome, like the position of a gene or a marker.

A type of cell found in the liver.

A process of DNA replication.

A chemical that signals cell division.

Enzyme by which cells replicate themselves, producing two identical copies.

Transports amino acids to ribosomes during protein synthesis.

Breaks down glucose to release energy.

Synthesizes ribosomal RNA in the nucleolus.

Chromatin into chromosomes (attach to spindle fibers by centromeres).

Chromosomes line up at the cell equator.

Sister chromatids are pulled apart to opposite poles.

The cell divides into two identical daughter cells.

Classic Sanger: Incorporate labeled primers, electrophoresis, PCR verification, sequencing a mixture of fragments, labeled base calling long or short. Classic dideoxy: Incorporate dideoxy method, combine DNA & digest with restriction enzymes and a subset of fragments is eluted and spotted onto a microarray slide. DNA from each sample is then used to create a fluorescent signal.

Classic Sanger: Uses only dideoxy nucleotides, no electrophoresis, and does not require labeled primers. Classic dideoxy: Uses only labeled primers and does not involve restriction enzymes.

Classic Sanger: Involves microarray slides and fluorescent signals for detection. Classic dideoxy: Uses PCR verification and does not require labeled base calling.

Classic Sanger: Uses restriction enzymes and microarray slides. Classic dideoxy: Involves only electrophoresis and PCR verification.

A set of overlapping DNA segments that together represent a consensus region of DNA.

A type of protein found in cell membranes.

A chemical used to stain chromosomes.

A process of breaking down RNA molecules.

Chromosomes line up.

The cell divides into two.

DNA is replicated.

The nuclear membrane reforms.

Sister chromatids pulled off opposite poles.

Chromosomes line up at the cell equator.

Nuclear envelope reforms around chromosomes.

DNA replicates in the nucleus.

Nuclear envelope reforms and chromosomes unfold and are in two new cells.

Chromosomes line up in the middle of the cell.

Spindle fibers attach to centromeres and pull chromatids apart.

DNA replicates and the cell grows.

A 3 base sequence in mRNA that codes for an amino acid (AUG common start codon).

A type of protein found in the cell membrane.

A segment of DNA that codes for a carbohydrate.

A molecule that transports oxygen in the blood.

Part of a gene that stays in the final mRNA (meaning it gets translated).

A type of enzyme that breaks down DNA.

A region of DNA that is always removed during RNA processing.

A molecule that carries amino acids to the ribosome.

Non-coding regions spliced out of mRNA.

Coding regions translated into protein.

A type of enzyme involved in DNA replication.

A molecule that carries amino acids to the ribosome.

A group of interbreeding individuals that share a common set of genes.

A collection of different species living in the same area.

A group of organisms that do not reproduce.

A set of genes found only in plants.

Random changes in allele frequencies (especially in small populations). Can lead to alleles loss or fixation, increases population differentiation.

A process where organisms acquire traits from their environment and pass them to offspring.

The movement of genes between populations through migration.

A type of natural selection that favors the average phenotype in a population.

Non-random association of alleles at different loci.

Loss of genetic material during replication.

Random mutation of DNA sequences.

Equal distribution of alleles in a population.

A 3 base sequence in mRNA that codes for an amino acid.

A single base in DNA that codes for a protein.

A 5 base sequence in tRNA that codes for a carbohydrate.

A 2 base sequence in mRNA that codes for a lipid.

Exon: part of a gene that stays in the final mRNA (gets translated). Intron: non-coding region spliced out of mRNA.

Exon: non-coding region spliced out of mRNA. Intron: part of a gene that stays in the final mRNA (gets translated).

Exon: a type of enzyme. Intron: a type of protein.

Exon: found only in prokaryotes. Intron: found only in eukaryotes.

Genetic drift.

Mutation.

Migration.

Natural selection.

Migration (gene flow) homogenizes populations, reduces FST (differentiation), introduces new alleles, breaks up local adaptation.

Migration increases genetic drift and leads to complete isolation of populations.

Migration causes populations to become more genetically distinct and increases FST.

Migration eliminates all genetic variation within populations.

Single Nucleotide Polymorphism

Simple Nucleotide Pairing

Single Nitrogenous Protein

Sequence Nucleotide Pattern

A) Physical linkage on a chromosome

B) Random mating

C) Genetic drift

D) Population admixture

$$p^2 + 2pq + q^2 = 1$$

$$p^2 - 2pq + q^2 = 1$$

$$p^2 + pq + q^2 = 1$$

$$p^2 + 2pq - q^2 = 1$$

Genetic differentiation between subpopulations

Mutation rate within a population

Average lifespan of individuals

Rate of gene flow between species

The probability that two alleles at a locus are identical by descent.

The number of alleles present in a population.

The rate of mutation at a specific gene locus.

The frequency of dominant alleles in a population.

Compare observed and expected genotype counts.

Measure allele frequencies over time.

Sequence the entire genome of individuals.

Use PCR to amplify DNA segments.

Deviation from the neutral frequency spectrum in nucleotide sequences.

The rate of protein synthesis in cells.

The presence of specific amino acids in proteins.

The length of introns in eukaryotic genes.

Genetic variance among populations for quantitative traits.

The mutation rate in a population.

The average lifespan of individuals in a population.

The frequency of dominant alleles in a gene pool.

Genetic differentiation among individuals relative to the total population.

The mutation rate within a single gene.

The average lifespan of individuals in a population.

The rate of migration between different species.

Fst is based on allele frequencies. 0=0, 1=1 based on molecular distances (shows just presence or absence).

Fst is based on chromosome number. 0=0, 1=1 based on gene expression levels.

Fst is based on protein structure. 0=0, 1=1 based on amino acid sequences.

Fst is based on cell morphology. 0=0, 1=1 based on physical appearance.

Estimates posterior probability of parameters by combining likelihood from the data and prior information.

Estimates only the mean of the observed data.

Estimates the mode of the prior distribution only.

Estimates the variance of the likelihood function only.

The probability of the observed data, given the model.

The prior probability of the model.

The variance of the data.

The number of parameters in the model.

ML gives a single value; Bayesian gives a distribution.

ML gives a distribution; Bayesian gives a single value.

Both give only single values.

Both give only distributions.

Identity by state; two individuals have the same allele, regardless of where it came from.

Identical base sequence; two DNA sequences are exactly the same.

Inherited by selection; a trait passed down due to selective breeding.

Immuno-biological status; the immune condition of an individual.

Distance between populations, useful to link families as groups.

A measure of mutation rate in a single gene.

A method to calculate allele frequency in an individual.

A technique for sequencing mitochondrial DNA.

LD decay may be less accurate because sparse markers and LD may vary by region.

LD decay refers to the increase in genetic diversity over time.

LD decay is the process of increasing linkage disequilibrium between loci.

LD decay is the method of amplifying DNA sequences in a laboratory.

Find local haplotypes; diversity is highest where populations are usually the center of origin.

It shows that all populations have equal diversity.

It indicates that genetic diversity is lowest at the center of origin.

It proves that haplotypes are randomly distributed across all regions.

Selective sweeps are identified by reduced neutral diversity and rapid increase in frequency due to positive selection.

Selective sweeps are identified by increased mutation rates and stable allele frequencies.

Selective sweeps are identified by high genetic diversity and slow changes in allele frequency.

Selective sweeps are identified by random genetic drift and decreased recombination rates.

It allows calculation of 'allele frequency' at subsequent times as the 'frequency of the contribution of a specific ancestor to the modern gene pool'.

It helps in determining the exact age of an individual.

It is used to predict weather patterns.

It is necessary for identifying plant species.

Maximize genetic gain by combining multiple traits and correlations to maximize genetic gain.

Minimize the number of traits considered in breeding programs.

Select individuals based solely on physical appearance.

Reduce the genetic diversity within a population.

Maximize gain in some traits while holding other constant.

Select only one trait for improvement.

Restrict the number of individuals selected.

Limit selection to a specific environment.

GxE refers to genotype by environment interaction.

GxE refers to gene expression only.

GxE refers to genetic exchange.

GxE refers to general environmental factors.

Statistical model that analyzes different performance across multiple environments and captures GxE interaction.

A type of soil nutrient analysis method used in agriculture.

A genetic engineering technique for improving crop yield.

A weather forecasting model for predicting rainfall patterns.

Field book genotype and environment values (raw log).

A type of fertilizer used in agriculture.

A software for weather prediction.

A method for DNA sequencing.

Can't use raw; need multiple environments. Should only use environments if types of data and variance in weather are available for each year.

Raw data from a single environment is sufficient for AMMI analysis.

AMMI and GxE analysis require only genotype data, not environment data.

You can use any data structure as long as it includes plant height measurements.

Genotype performance across environments by regressing values on the environmental mean.

The rate of mutation in a single genotype over time.

The correlation between genotype and phenotype within a single environment.

The effect of fertilizer on crop yield regardless of genotype.

How much variation in a trait is due to genetic differences and how predictable the trait is.

The process by which traits are acquired during an organism's lifetime.

The ability of an organism to adapt to environmental changes.

The total number of genes present in a population.

H2 = Vg / Vp

H2 = Vp / Vg

H2 = Ve / Vp

H2 = Vg / Ve

General combining ability

Genetic cross analysis

Growth control agent

Gene cluster arrangement

Specific combining ability

Single cross analysis

Seed coat analysis

Standard crop assessment

High h2 = due to additive genetic selection will work; Low h2 = due to non-additive genetic influences so selecting parents won’t reliably pass on traits.

High h2 = due to environmental factors only; Low h2 = due to strong genetic inheritance.

High h2 = traits are not heritable; Low h2 = traits are always passed on.

High h2 = due to mutation rates; Low h2 = due to stable genes.

h2 = Va / Vp

h2 = Vd / Vp

h2 = Ve / Vp

h2 = Vp / Va

Response to selection depends on the heritability of a trait and the selection differential.

It predicts the mutation rate in a population.

It measures the genetic drift in small populations.

It calculates the rate of gene flow between populations.

ΔG = (Selection intensity × h2 × σp) / L

ΔG = (Selection intensity × h2 × σg) / L

ΔG = (Selection intensity × h × σp) / L

ΔG = (Selection intensity × h2 × σp) × L

Recombinant Inbred Line

Random Insertion Locus

Repetitive Intergenic Linker

Regulatory Intron Loop

Great for stable trait mapping

Increases genetic diversity in a population

Reduces the need for any genetic analysis

Ensures all offspring are genetically identical

Backcross Inbred Line

Bacterial Insertion Locus

Base Inheritance Level

Binary Integration Link

Mapping population with more recurrent genome

Increasing mutation rates in a population

Producing genetically identical individuals

Preserving endangered species

Best line/parent selected

A random group of individuals

The oldest generation

A genetically modified organism

Best linear unbiased prediction; used to estimate breeding values and genotype data

Basic linkage unit protocol; used for DNA sequencing

Binary linear unit process; used for gene editing

Biological linkage update program; used for protein synthesis

Genomic best linear unbiased prediction; uses all SNP markers to estimate genomic breeding values by shrinking marker effects to avoid overfitting.

Genetic baseline linear unbiased prediction; uses only significant SNP markers for trait selection.

Generalized breeding linear unbiased prediction; estimates phenotypic values without using SNP markers.

Genomic best likelihood unbiased prediction; uses SNP markers but does not shrink marker effects.

Applies a penalty to large marker effects

Removes all genetic markers from analysis

Predicts only dominant traits

Increases the variance of marker effects

Minor allele frequency

Maximum allele frequency

Major allele factor

Molecular analysis factor

Polymorphism information content

Protein interaction complex

Primary inheritance code

Polymerase initiation complex

A SNP with the same genotype in all samples (e.g., all samples as AA)

A SNP with multiple genotypes in all samples

A SNP that causes a change in protein function

A SNP that is only found in one individual

The number of copies of a specific allele in an individual at a given locus

The process of measuring gene expression levels in a cell

The total number of genes present on a chromosome

The frequency of an allele in a population

Customarily regularly interspaced short palindromic repeats; used for genome editing

A method for protein synthesis in mitochondria

A technique for increasing cell membrane permeability

A process for DNA replication in prokaryotes

Turns the endonuclease (nuc) with RNA and an enzyme that cuts DNA at a specific sequence allowing for precise editing

Binds to mRNA to prevent translation of proteins

Acts as a signaling molecule in cell communication

Synthesizes new strands of RNA from a DNA template

Inducing mutations in DNA of radiation or mutagenic chemicals to create novel traits

Crossing two different species to produce hybrids

Selecting plants with desirable traits over generations

Grafting two plants together to combine characteristics

Locating a broad region of the genome linked to a QTL

Identifying the exact nucleotide sequence of a gene

Mapping the entire genome at single-base resolution

Determining the function of a specific protein

Narrowing down mapping regions to fewer genes or candidates

Identifying the entire genome sequence of an organism

Studying the physical appearance of an organism

Measuring gene expression levels in different tissues

Filling in missing genotype data or predicting untyped SNPs using known SNPs and patterns of LD

The process of amplifying DNA using PCR

The removal of introns from pre-mRNA

The sequencing of the entire genome

Quantitative Trait Locus; region of the genome that is statistically associated with variation in a quantitative trait

Quantitative Transcription Level; a gene that controls all traits in an organism

Quality Trait Linkage; a process of linking genes to traits qualitatively

Quantum Trait Locus; a region of the genome responsible for binary traits

Logarithm of odds; a measure of how likely it is that a marker is linked to a trait

Level of DNA; a measure of DNA concentration in a sample

Loss of dominance; a measure of gene suppression

Length of DNA; a measure of chromosome size

Reads are aligned to a reference genome, and variants like SNPs are called by comparing reads to that reference.

Reads are aligned to each other without using any reference genome.

Reference-based alignment refers to aligning protein sequences only.

It is a method where only the reference genome is sequenced, not the reads.