Beef Genomics Glossary

Alleles Alternate forms of genes. Two copies of each gene occur in animal and each copy can have the same or different effects on a trait.
Allele frequency The frequency with which a particular allele appears in a population.
Animal breeding The practical application of genetic analysis for development of lines of domestic animals suited to human purposes.
Animal ID The unique identification of an animal.
Base population A group of animals with unknown parents in genetic evaluations, whose EBV’s are set to zero, or other group of animals with EBV’s set to zero (e.g. those born in a particular year).
Breed Animals with a common origin and selection history. Animals within a breed have characteristics that distinguish them from other breeds or groups of animals within that same species. Examples are the Hereford, Holstein, and Kerry breeds.
Breeding value The transmissible genetic merit of an individual, or the value of that individual as a parent.
Contemporary group A contemporary group may comprise of animals of the same breed, sex, and age range kept under the same or at least similar management conditions.
DNA (Deoxyribonucleic acid) The chemical compound that stores, within each cell, genetic information unique to an individual.  DNA is made of 4 bases: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).  These bases are often referred to by their abbreviations: A, C, G, and T.

The cattle genome is made of 3 billion base pairs that are spread over 29 autosomes, the mitochondria, and the sex chromosomes (X and Y).  Each animal has a unique DNA sequence which control and influence all phenotypes of the individual.
DNA extraction The process of removing DNA from a tissue sample so that the DNA can be used for genotyping.  While DNA is present in all tissues some are better than others for DNA extraction.  This is why hair roots, ear punches, and AI semen straws are often used for genotyping livestock.
Dominant When only one copy of an allele is needed to produce the phenotype. An example of this is the poll allele.  If an animal has one or two copies of the poll allele the animal will be polled (have no horns).  Only if the animal has no copies of the poll allele can it have horns.
Ear punch Tissue sample for DNA extraction.  For the Beef Genomic Scheme this is the preferred sample and taken via the supplied button tag.  Apply the button tag as described in the information included with it (essentially the same as other ear tags).  The ear sample is captured in the metal punch and when the punch+ear sample is put into the supplied tube the enclosed liquid helps to preserve the tissue sample until DNA extraction.
Environmental variance The portion of phenotypic variance that is controlled or influenced by an animal’s environment.
EBV Estimated breeding value.  An estimate of an animal’s genetic merit for a given trait. An animal’s EBV values are twice its EPD value. 
EPD Expected Progeny Difference.  This is essentially how different an animal’s progeny will be from its breed average.  It can be thought of the amount of genetic merit that an animal can pass on to its offspring.  If a bull’s birth weight EPD is +5 then on average his progeny would weigh 5 kg more than the breed average.
Gene A DNA section that codes for a protein that has a function in the individual and can influence and individuals phenotype.
Gene interactions The collaboration of several different genes in the production a phenotype.  Most traits that have a range, such as height or marbling, are affected by such gene interactions.
Genetic defect A genetic defect is a disease, disorder, or other undesirable phenotype caused by a specific DNA sequence.  The defect can be recessive or dominant and is inheritable.
Genetic evaluation The prediction of breeding values.
Genetic proofs The breeding value of an animal as determined by a recognised genetic evaluation procedure.
Genetic variance The portion of phenotypic variance that is controlled or influenced by genes.
Genetic markers A genetic marker is an allele, DNA marker or cytogenetic marker used as a probe to keep track of an individual, a tissue, a cell, a nucleus, a chromosome, or a gene.
Genotype An animal’s genetic makeup.  Usually refers to the data obtained from specific genetic markers.  As animals can have two alleles present at a genetic marker (say an P or p allele) three genotypes are possible for each marker.   For example, at the polled/horned locus in cattle, two common alleles are P ( the dominant allele preventing growth of horns) and p (the recessive allele allowing horn growth). The three possible genotypes are PP (homozygous dominant), Pp (heterozygous or carrier), and pp (homozygous recessive).
Genotyping The process of determining an animal’s genetic make-up by examining specific parts of its DNA.  Often specific microsatellites or SNP are used for genotyping. 
Hair root Tissue sample type for DNA extraction.  It is best if the samples are taken from the hair on a cow’s tail switch (bottom of tail).  These are some of the largest hair roots on a cow and therefore contain lots of DNA.  It is recommended that you grasp the hair shaft close to the tail and pull slowly to reduce the chance of the hair shaft breaking.  Please ensure that the hair roots are dry and clean before placing them in a supplied hair card or plastic bag.
IDB
chip		 Custom designed International Beef and Dairy SNP chip assay that was designed to be highly informative in all Irish and the major European cattle breeds. It provides genotypes on >17,000 SNP and the data from it can be used for Parentage testing, Genomic evaluations, and determining an animal’s status for multiple genetic diseases.
Measured traits The trait (phenotype) recorded on the animal.
Microsatellites A region of the genome where the same sequence of base pairs is repeated several times, end to end.  Traditionally used in the cattle industry for pedigree verification.
Parentage/Pedigree verification The validation or exclusion of an animal’s sire and dam relationships via genetic markers.  As each parent on passes on 1 allele from each genetic marker to its offspring the animals’ genotypes can be used to identify their offspring or pedigree errors.  For instance if an animal has a genotype of AA we can exclude any animal with a BB genotype as the potential parent of the animal.  This is because a BB genotype animal can only pass on a B allele to its offspring, so it offspring will have a AB or BB genotype depending if the other parent passed on an A or B allele.
Pedigree A list of an individual’s ancestors, usually only the three to five closest generations. Pedigree information is used to establish genetic relationships among individuals to use in genetic evaluations.
Phenotype The set of observable characteristics of an animal. For example it’s coat colour, height, rib eye size, or birth weight.
Polygenic A phenotype trait that is controlled by many genes and their interactions.
Progeny The young, or offspring, of an animal.
Progeny test The evaluation procedure of generating the breeding value of an animal based on the performance of its progeny.
Recessive When o copies of the same allele must be present to produce the phenotype.  An example is red coat colour in Angus cattle.  If a cow has only one copy of the red coat colour allele it will have a black coat.  If the cow has two copies of the red coat colour allele it will have a red coat.
Sex limited traits Phenotypic traits that are expressed in only one sex, such as milk production.
SNP Single Nucleotide Polymorphism (SNP).  A variation in an animal’s DNA sequence at a single DNA base.  SNP are located throughout the genome and occur about once every 300 base pairs.  Approximately 10.3 million SNP have been identified in cattle.