2-Mercaptoethanol: Used in plant DNA extraction. Is a strong reducing agent and removes polyphenols like tannin from interacting with the DNA.

2X CTAB Buffer: A detergent that breaks up and dissolves the lipid membranes of the cells. Chemically alters the proteins and polysaccharides so that they don't interact with DNA.

5M potassium acetate: Removes proteins from the DNA. Also used as a salt for the ethanol precipitation of DNA.

20% (w/v) sodium dodecyl sulfate: Aids in lysing of the cells for DNA extraction.

70% ethanol: Removes salts and other water-soluble impurities from the DNA pellet.

Absolute isopropanol: Causes the DNA to precipitate out of solution.

Agarose: Used to make the gel. Separates DNA fragments.

Alkaline soil conditions: Soil with a higher pH.

Amplification: Increases the number of DNA fragments into millions of copies.

Cosegregation: Transmission of two or more linked genes on a chromosome to the same daughter cell, leading to the inheritance of these genes together.

Digital pipettes: Adjustable pipettes that can measure small volumes.

DNA polymorphisms: Differences in DNA sequences.

dNTP: Stands for deoxynucleotide triphosphates. They are single units of DNA composed of a sugar, phosphate group and one of the bases A, T, C, will form the new DNA strands during PCR.

Doubled haploid: Cells that contains two identical homologous chromosomes (one chromosome from one parent that has been doubled).

Epistasis: When the expression of one gene depends on the presence of one or more genes.

F1: The first generation produced by a cross between parents that are homozygous for the trait. The F1 generation will be heterozygous (one dominant gene, one recessive gene).

GelGreen DNA stain: Stain for detecting double-stranded DNA in agarose gels. Less hazardous alternative to ethidium bromide.

Gel Loading Dye: Helps to weigh down the DNA solution in the gel wells. It also helps to monitor the progress of the DNA as it moves through the gel.

Genotype: The genetic makeup of an organism.

Homoeotic mutation: Mutation in a gene that causes the development of specific structures.

Hooded: Phenotype resulting from Kap (from German “kapuze" meaning hood). Creates a morphological hood by placing extra palea on the distal end of the lemma followed by rudimentary florets with inverse polarities.

Introns: Non-coding sequence of RNA removed from a transcript before translating to a protein.

Kap gene: Gene that encodes the hooded phenotype.

Lks2 epistasis of the Kap gene: In plants homozygous for the recessive allele at lks2, the expression of hooded phenotype is masked. This results in the expression of a short, rather than hooded, phenotype. The use of the nomenclature “Lks2/_" or “Kap/_“ indicates that the plant has at least one copy of the dominant allele, but we might not know from the data provided if the plant is homozygous dominant (Lks2/Lks2 or Kap/Kap) vs heterozygous (Lks2/lks2 or Kap/kap).

Master Mix: Contains salts, magnesium, dNTPs, and optimized reaction buffer, all ingredients to perform a PCR. The magnesium is needed for the enzyme polymerase to function properly. The salt and buffer are needed for appropriate pH. dNTPs are single unit nucleotides that will be the “building blocks" for new DNA strands.

Molecular Grade Water: Certified to be contamination-free.

Oregon Wolfe Barley (OWB) doubled haploid seed: Barley seed of the genetically and phenotypically diverse OWB population.

Phenotype: The observed properties or outward appearance of a trait. The physical expression of the genes possessed by an organism.

Polymerase chain reaction (PCR): Method of amplifying or copying DNA fragments. Begins with a trace template (genomic DNA in this module) and produces exponentially large amounts of a specific piece of DNA.

Polymorphic: When two or more clearly different phenotypes exist in the same species population.

DNA polymorphisms: Variation in DNA sequences among individuals, groups, or populations. This could be a single base pair change, many base pairs, insertions or deletions, or repeated sequences.

Primers: Used to determine the DNA fragment to be amplified by PCR. Serves as starting points for DNA synthesis. They are short pieces of single-stranded DNA that are complementary to the target sequence.

Restriction enzyme digest: Enzymes isolated from bacteria that recognize specific sequences and DNA.

Sickle Cell Disorder: Hereditary blood disorder, characterized by red blood cells that are a rigid, sickle shape. This decreases the cells' flexibility and can cause complications.

Size fractionate: The separation of DNA fragments by size.

Supernatant: Liquid lying above a solid after precipitation and centrifugation. (Image created in BioRender.com)

Taq DNA Polymerase: A DNA polymerase that can withstand the high temperatures required to synthesize a new DNA strand from a template.

Tay-Sachs Disorder: A recessive genetic disorder that causes progressive deterioration of nerves. It begins around six months of age and usually results in death at an early age.

TBE Buffer: Commonly used in electrophoresis. Provides ions to carry the current and maintains a relatively constant pH. Made of Tris, Boric Acid, and EDTA.

TE Buffer: Commonly used buffer solution that makes DNA or RNA soluble, while protecting it from degradation.

Thermal cycler: Machine that rapidly heats and cools for PCR reactions. The thermal cycler (also known as a thermocycler, PCR machine or DNA amplifier) is a laboratory apparatus most commonly used to amplify segments of DNA via the polymerase chain reaction (PCR).

Vortex: A machine that agitates a solution vigorously.

Vrs1 gene: Gene that causes either a two-rowed spike (dominant allele) or a six-rowed (recessive allele).

​​Overview​​Experiment 1​​Experiment 2​​Experiment 3​​​
​iTAG Instructor’s Planning Resources​​Appendix​

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