Breeding Terms Glossary

 

Term Meaning Description
Allele A variant of a specific gene.  A specific version or variation of a gene. I.E. Most genes have several different forms known as Alleles.
ASR Supplementary Register "A" First stage or generation in the progress from a non-registered / non-pedigree animal towards becoming fully accepted into a herdbook, or "full pedigree".  To be accepted into the ASR, an animal must be at least 50% pure / having known parentage of the relevant breed. 
Base Year Genetic Base Year Refers to the year in which the mean PTA of 5 year old cows is used as  zero value in current genetic evaluations. E.G. PTA 2010 is calculated from cows born in 2005.
BSR Supplementary Register "B" Second stage or generation in the progress from a non-registered / non-pedigree animal towards becoming fully accepted into a herdbook, or "full pedigree".  The offspring of an ASR animal may be accepted into BSR section of the herdbook if at least 75% pure in the relevant breed.
Bull Selector Breeding Toolbox application allowing bulls to be identified to meet specified breeding criteria.

A free to use Breeding Toolbox application that allows bulls to be identified from the 2000-odd whole of market choices, that match a herd owner's chosen, totally flexible breeding criteria. Also used as key component of the wider WebMate application.
BV  Breeding Value A statistical measure of the breeding worth of an animal.
CDN Canadian Dairy Network A Canadian organisation employing a team of geneticists and other researchers, specialising in the genetic evaluations of dairy cattle. Based in Guelph, Ontario. Originally created to service a number of Canadian based DHI cooperatives and breed societies. Contracted by Holstein UK to derive the genetic merit for Type traits for all UK based Holstein & Friesian animals.
Chromosome A piece of DNA Cattle have 30 pairs of Chromosomes (i.e. 60 in total). Half of each Chromosome is passed onto offspring through sperm/eggs. But not always the same half.
ClassAct  A Breeding Toolbox data interrogation tool. A Breeding Toolbox utility that permits a herd owner to interrogate and analyse their animal's Classification results.
Classification Type Classification The process of assessment of phenotypes for conformation traits on UK cows and bulls. Over 25 traits and criteria are assessed at each inspection, most on a 9-point linear scale, plus several more farm environment and animal "defect" criteria. The collected data being used by herd owners to select appropriate matings to breed the next generation and when aggregated with data from other herds and animals, to perform genetic evaluations for Type.
Classifiers CDI employees who "classify" animals according to conformation critera. A team of professional people specialising in the assessment of both dairy and beef cattle conformation traits according to a series of carefully defined, internationally agreed criteria. 
Conformation The physical extranal apperance of an animal A team of professional people specialising in the assessment of both dairy and beef cattle conformation traits according to a series of carefully defined, internationally agreed criteria. 
CPI Cow Production Index A forerunner of genetic indexes, developed in the 1970's, now outmoded and largely replaced by the subsequent development of more useful genetic indexes. See PI definition (2) Production Index.
Daughter Proven Daughter Proven Bull A bull with daughter information used in calculating his genetic merit.  Originally applied to bulls who had only daughter information used in their evaluation. This later grew to include ancestors and siblings and can now include a bull who has both his own direct genomic test results included, supplemented by daughter results.
dCE Direct Calving Ease The ease with which the calf is born. Derived from recorded calving experince (itself measured on a scale from 1-5). Usually attributed to the calf's sire, since many of the key factors affecting the difficulty of calving (e.g. size, shape) are determined by the calf's sire. Values range from -4.0 to +4.0, with results above 0 indicating easier calving sires compared to those with negative scores (tending to more difficult).
DGV Direct Genomic Value Daughter proof converted back to a 'phenotype' for use in estimating SNP effects. Also known as de-regressed EBV.  
DNA Deoxyribo Nucleic Acid - a protein based complex molecule found in the nucleus of living cells carrying the organism's genetic instructions. A molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms. Constructed from four proteins,  cytosine (C), guanine (G), adenine (A), or thymine (T), plus a monosaccharide sugar called deoxyribose and a phosphate group.
Dominant Dominant Gene Effects phenotype (i.e. causes a change in form or function of animal) when one or two copies are present.
EBV Estimated Breeding Value A statistical estimate of an animal's own genetic merit for a particular trait (2 x its PTA).
Environment The surroundings and management of a farmed animal, as opposed to its genetic code. Conditions within which the animal exists; i.e. Feeding regime and nutritional level, weather (temperature, humidity), disease challenges, behaviour of herd mates, the management regime an animal is kept under, etc...
ET Embryo Transfer A process by which viable embryos can taken from one animal, the "donor" (usually of high or exceptional genetic merit) and implanted in the womb of another animal, the "recipient" to be developed as a pregnancy and progressed through to birth. The ET process may or may not involve fertilisation of the embryo outside the animal (known as "in vitro" fertilisation). ET is most often carried out under veterinary supervision by non-surgical procedures which do not harm either the donor or recipient in any way. But enables the genetics of a high merit animal (usually a female) to be transferred to a greater number of offspring than would be possible by more traditional reproduction, by not requiring the donor to carry each embryo to a full term pregnancy. Removal of the embryo(s) early in the reproductive cycle enable the donor animal to produce further ova and offspring more frequently. Donor females are often also given hormonal treatments to create multiple ova (eggs) to be generated simultaneously, so further increasing the number of recipient pregnancies that can be achieved from the embryos produced by the donor. The suffix "ET" applied to an animal's name is used to denote the animal was born by embryo transfer.
ETN Enucleated Transfer Cloned Animal.
Fertility Haplotypes Groups of similar genes affecting Fertiltiy. Groups of genes inherited together which appear to have a recessive inheritance. I.E. Two copies and the embryo dies is not viable.
FI Fertiltiy Index Selection index for fertility traits.
Flushing The process by which ova/eggs or fertilised embryos are removed from a donor female. See "ET"
Full Pedigree An animal which has been accepted into and registered in the main section of a breed society herdbook. The third (and usually final*) stage or generation of progress from a non-registered / non-pedigree animal towards becoming fully accepted into a herdbook, or "pedigree".  The offspring of a BSR or existing "Full Pedigree" animal may be accepted into the main section of the herdbook if at least 87.5% pure in the relevant breed. See ASR and BSR.
Functional Trait   Traits impacting commercial dairy production such as mammary and feet and legs. As opposed to traits such as angularity or style.
Gene A section of genetic material or DNA of a living creature or organism which affects a particular aspect or characteristic of the organism's phenotypic traits, its morphology or metabolism. A chunk of DNA on a Chromosome which codes (i.e. Is the 'instructions') for an Amino Acid (the building blocks of Proteins). Often used when referring to parts of a gene rather than the gene itself, genes often have several variants (Alleles),  each with a slightly different DNA sequence.
Genetic Literally "of the genes" Generic term for the eddect/influence of DNA.
Genetic Base Genetic Base Year See base.
Genetic Evaluation The process of assessing an animal's breeding merit. The statistical process which uses pedigree, milk recording, classification and genomic information to calculate genetic merit values for animals.
Genetic Merit   A statistical measure of of the breeding worth of an animal.
Genetic Trait Genetic traits other than Type and Production. Used to refer to non-complex traits e.g. recessives, polled, haplotypes, colour.
Genomic Literally "of the genome" (i.e. All Chromosomal DNA). An animal with genotype information included in its genetic evaluation.
Genotype DNA Information Identity of nucleotide base code (A, T, G or C) in DNA. E.g. 50K Genomic test will identify the code at 50,000 DNA sites (SNP's) in the Genome.
Genotype File   Computer file with genotype information for an animal.
GMACE Genomic MACE Genomic evaluation  using genomic information and MACE data for young international sires.
GPLI Genomic PLI PLI for an animal that has been genotyped.
Grade up Process of converting from a non pedigree to a pedigree herd or animal. Process by which a herd comprising commercial, non-pedigree animals can progress to being fully accepted into the pedigree herd book.
GTPI Genomic TPI TPI for an animal that has been genotyped.
Haplotype DNA Haplotype. Group of genes next to each other on a chromosome and which are generally inherited together.
HBN Herd Book Number 12 alpha-numeric characters (excluding the UK Breed Code) comprising the reference identifier of an animal in a breed society herdbook. 
HCD Haplotype Cholesterol Deficiency  A group of recessive haplotypes which affect calf survival when animals with the "bad" version of the haplotype produce little or no cholesterol in the bloodstream, which in turn severely reduces the newborn calf's ability to digest food (milk). First identified in the Holstein population during 2015.
HD High Density (genotype)
Genomic test which typically genotypes over 50k SNP's
Health Trait   Trait indicating animal health such as SCC.
Heritability How much of a particular trait can be expected to be passed from one generation to the next, on average. A statistical estimate (for the average animal in a population) of the proportion of an animals phenotype which is due to its genetic makeup. Applies to a population rather than an individual animal.
ICAR International Committee for Animal Recording. The international voluntary body that sets standards and guidelines for a range of activities including milk recording, animal identification, data transfers, conformation ("Type") assessment and genetic evaluation for a range of farmed animal species. With the objective that results gathered and used in those countries should remain comparable internationally. Over 32 countries involved worldwide. see http://www.icar.org/
IGM International Genomic MACE UK labelling of Interbull GMACE evaluation results for Type (used from December 2014).
ITEM Index of Total Economic Merit A defunct genetic index that superseded PIN but was itself replaced by PLI in October 1998. ITEM was the first index in the UK to include both production and type traits (Foot Angle, udder Depth and Teat Length) in a single overall index. 
Imputation Genotype Imputation A process used in in genomic evaluations by which animals with LD genotype results may be assigned extra SNP information from the parent genotypes and from intermediate locations between those actually measured by the LD analysis to give results equivalent to HD analyses.
Inbreeding Inbreeding Coefficient Likelihood of an animal inheriting two copies of an allele from the same ancestor (which appears more than once in its pedigree), expressed as a % probability.
Inovulation The process by which a viable embryo "flushed" from a donor female can be implanted into a recipient female. See "ET"
Insemination The process of transferring sperm/semen from a male into the reproductive tract of a female. Can be "Natural" as during the mating of a male and female. Or "Artificial", whereby semen produced by a male is diluted and packed into small plastic straws, enabling easy transportation and storage* before being inserted into the female by a human operator using  specialised equipment. Straws can be frozen in liquid nitrogen which enables their contents to remain viable over extremely long periods and easily transported worldwide. The techniques for AI were first developed in the UK during the 1950's by veterinary scientists working for the Milk Marketing Board in collaboration with other private organisations involved in the cattle breeding industry.
ITB Interbull. The International genetic evaluations centre for bovines. International body overseeing and calculating genomic evaluations using data from up to 30+ countries worldwide (actual number of countries whose data is used varies from trait to trait. Interbull is a wholly owned sub-organisation of ICAR.
L&F Legs and Feet A composite type trait derived from the key individual linear assessment conformation traits describing the morphology of the animal's feet and legs, combined into a single score.
LD Genotype Low Density Genotype Basic genomic test which typically genotypes (reads) a lower number of SNP than HD tests (typical 30k or less).
LIFT Linear Inspection for Type Scheme to progeny test UK bulls for type merit conducted by HUK, Genus and Cogent.
Linear Linear Type Trait Linear display of type traits, as assessed during classification or genetic evaluation and displayed on an animal's Factsheet.
LP Lactation Period The portion of an individual lactation from Calving up to and including the 305th day. See "Natural Lactation".
LPI Lifetime Production Index The primary overall selection index used in Canada. Comparable to the UK's PLI but using some different traits and weightings of common traits to derive an overall index.
LS Lifespan Index Lifespan of the cow expressed in lactations.
MACE Multiple Across Country Evaluation Comparison method that enables translation of a foreign genetic evaluation into a set of UK results.  Most commonly used in respect of Type evaluations.
MAM Mammary composite index A composite type trait derived from the key individual linear assessment conformation traits describing the morphology of the animal's udder, combined into a single score.
mCE Maternal Calving Ease The ease with which an animal can calve itself as a mature animal. Values range from -2.0 to +2.0. Positive values indicate easier than negative. Derived from the cow's own recorded calving experience and the traits associated with the cow herself (e.g. Pelvic size, Pelvic shape).
Natural Natural Lactation Technically the portion of an animal's lactation beyond the 305th day (See "LP") up to the cessation of milk production, due to events such as beinge declared Dry, its death or other end of lactation event (as defined under Milk Recording rules). 
NRR Non Return Rate % of daughters returning into season within 56 days. 1 point equals half a day. 
Pedigree An animal's ancestry The documented ancestry of an animal. Usually applied to that ancestry recorded in a breed society's herdbook.
Pedigree Index A breeding Index substitute, derived by reference to an animal's ancestors rather than measured more directly. A substitute for a genetic evaluation, usually applied to newborn and younger animals.  Calculated from the relatives of the animal only. Used until the animal can gain a more reliable evaluation its own right. (No daughter or genomic information is included). Pedigree Index values are normally only calculated for the main overall composite traits. Individual Type Traits being omitted.
Persistency Persistency of lactation Milk yield at day 280 of lactation as a percentage of yield at day 60.
Phenotype A physical characteristic, observable or measurable in the "real world". E.g. Milk yield or conformation; Genotype + Environment = Phenotype.
PI(1) Pedigree Index An estimate of a young animal's genetic potential before it has any production or genomic information of its own. The Pedigree Index is based on the average of the parents' genetic merit, but in the absence of parent information, indexes from further back in the pedigree are used. Pedigree Indexes can be calculated for almost any trait or other derived index ranging from the basic PTA to the more complex economic indexes or even type indexes. The effective use of a pedigree index enables breeding decisions to be made at an early age and can therefore reduce heifer rearing costs. A Pedigree Index is less reliable than either a genomic test result of the animal's own genetic code or a full evaluation of its own production or progeny information, such as the "proof" it would normally obtain later in life. The PI should therefore be used with the appropriate caution. The reliability of Pedigree Indexes generally ranges from about 20 to 40%.
PI(2) Production Index A measure of a cow's individual, single lactation production of milk solids  compared to the production of herdmates and contemporaries at a particular point in time.  Calculated at the end of each Lactation Period and assesed against the herd average weight of Fat & protein over the previous 12-months (called the "Herd Base"). An animal would therefore normally expect to get a different Production Index for each lactation during its lifetime.  Each Production Index takes the animal's own production, adjusted for age, month of calving and lactation number to bring its procuction closer to a heifer equivalent, then expressed as a percentage of the Herd base at that time. Hence the Production Index  can vary widely from lactation to lactation, as also can the Herd Base. A Production Index should not be confused with any genetic index as there is no genetic element in its calculation. 
PI(3) Pure Import A suffix applied to an animal's name, denoting it was a pure-bred imported animal. Used extensively by the former British Holstein Cattle Society. 
PIN Profit Index A defunct economic index based on an animals genetic ability for milk production. Based purely on milk and solids production weighted for expected milk prices and the amount of feed energy required to produce each component of the milk. Expressed as additional profit expected per lactation over a zero PIN animal.  Was developed during  early 1990s to replace the Cow Genetic Index. Was superseded by ITEM and later PLI (which includes many more diverse traits) and eventually ceased publication in 2014.
PLI Profitable Lifetime Index UK selection index combining key genetic traits and represented as a £ value. From August 2014 this is a total lifetime value. The £PLI value represents the additional profit a high £PLI animal is expected to return over its lifetime compared to an average bull of £0 animal.  In the case of a bull, this is additional profit from each of the bull's milking daughters.
Polled   Polled = no horns, single gene. Polled gene is dominant.
Proof The collected range of genetic evaliation reuslts for an animal across all traits. Refers to a bull's genetic merit being based on his daughter information, stemming from the era when the only method to measure a bull's genetic merit was to "prove" his genetic characteristics by the production and conformation of his daughters. This is a misnomer however as at best any genetic index it is only a 'good' statistical estimate, not actual definite 'proof' of genetic merit.
PTA Predicted Transmitting Ability A statistical estimate of the genetic merit an animal will, on average, pass on to its progeny (defined as half of the animals own EBV).
PTAT Predicted Transmitting Ability for Type An overall composite index of key type traits weighted according to importance in breeding a functional animal. In the UK we use the Type Merit figure as the overall PTAT.
Recessive Recessive Allele The effects of such a gene are only observed if two copies are present in the animal (one inherited from each parent).
REL Reliability The % of the animal's genetic merit which is estimatable from available information (relatives and/or progeny and/or genomic), giving a gauge to how reliably an accompanying Genetic Index might be reflected in the performance of the animal's offspring.
RZG   German selection index for Holsteins. Broadly similar in usage if not calculation, to the UK's PLI.
SCC Somatic Cell Count The most commonly used measure of white blood cells in milk. An indirect method of assessing the volume of bacteria in the udder by measuring the animal's defence against those bacteria. Measured in '000 cells per ml. High values (>100,000) indicate udder infection (mastitis). The SCC PTA is expressed as a %. Also refers to SCC index.
SCI Spring Calving Index Selection index aimed at spring calving herds.
SD Standard Deviation. A statistical measure of the variability amoung a set of data. Type trait PTA's are expressed as standard deviations (from the mean of the population). I.E. A bull with 2 points of type has a PTA 2 SD better than breed average and is in the top 2.5% of the population (3 points = top 0.15%)...see also STA.
Selection Index E.g. PLI, TPI, LPI. Overall breeding index for an animal which weights the genetic merit of key traits according to their economic value in commercial dairy production.
SNP Single Nucleotide Polymorhism Genetic marker which is genotyped in current genomic tests, informs as to genotype of DNA in the physical vicinity on a Chromosome. Often referred to in conjunction with Haplotypes. As such a Haplotype will typically have one SNP within it. 
SRUC Scotland's Rural Agricultural College Genetic evaluation service provider (Calculate genetic merit for production and management traits). 
TM Type Merit PTA for Type. Derived from a weighted combination of several of the animals and/or offspring's conformation or "Type" traits. Does not include Production, Health or Fitness traits.
TPI Total Performance Index Main selection index for Holsteins in the USA. Broadly similar in usage if not calculation, to the UK's PLI.
Trait Physical Trait Physical characteristic, also know as phenotype.
Type Type trait(s) Literally what 'type' or external form of animal is this. Describes the animal's physical form as measured over 20-25 distinct individual points of its conformation. (N.B. can also refer to either phenotypic classification scores or genetic PTA values).
WebMate The Breeding Toolbox cow mating selection and reccomendation tool. A free to use Breeding Toolbox application that optimises the possible bulls available to recommend matings  for each of a herd's eligible cows. The only such application covering the "whole of market" in the UK. This has been succinctly described as "Computer dating for cows"!
Young Genomic Bull A male who's genetic evaluation results consist solely of genomic derived information. Usually younger bulls.  A bull whose genetic evaluation results are based solely on his genomic sample results, with no daughter information included in the evaluation. Usually applied to younger males who do not yet have daughters whose results can be measured.