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Animal Genetics Glossary Only letters to which there are corresponding words within this Glossary are clickable. select a letter A Word/Phrase Definition Adaptation traits Complex of traits related to reproduction and survival of the individual in a particular production environment. Adaptation traits contribute to individual fitness and to the evolution of animal genetic resources. By definition, these traits are also important to the ability of the animal genetic resource to be sustained in the production environment. Agrobiodiversity OR agricultural biological diversity That component of biodiversity that contributes to food and agriculture production. The term agrobiodiversity encompasses within-species, species and ecosystem diversity. Alleles The variant forms of each gene. Animal genetic resources databank:  A databank that contains inventories of farm animal genetic resources and their immediate wild relatives, including any information that helps to characterize these resources. Animal genome (gene) bank A planned and managed repository containing animal genetic resources. Repositories include the environment in which the genetic resource has developed, or is now normally found (in situ) or facilities elsewhere (ex situ – in vivo or in vitro). For in vitro, ex situ genome bank facilities, germplasm is stored in the form of one or more of the following: semen, ova, embryos and tissue samples. Animal model This is a system for genetic evaluations that estimates breeding values of bulls and cows at the same time. The system uses production data on all known relatives in calculating a genetic evaluation B Word/Phrase Definition Back crossing A form of crossbreeding in which an offspring is mated to either of its parents. The mating of a hybrid to a purebred of a parent breed or line. The mating of an individual (purebred or hybrid) to any other individual (purebred or hybrid) with which it has one or more ancestral breeds or lines in common Best linear unbiased prediction A method of genetic prediction that is particularly appropriate when performance data come from genetically diverse contemporary groups Biodiversity OR biological diversity The variety of life in all its forms, levels and combinations, encompassing genetic diversity, species diversity and ecosystem diversity. Breed  Either a sub specific group of domestic livestock with definable and identifiable external characteristics that enable it to be separated by visual appraisal from other similarly defined groups within the same species or a group for which geographical and/or cultural separation from phenotypic ally similar groups has led to acceptance of its separate identity. Breed at risk  Any breed that may become extinct if the factors causing its decline in numbers are not eliminated or mitigated. Breeds may be in danger of becoming extinct for a variety of reasons. Risk of extinction may result from, inter alia, low population size; direct and indirect impacts of policy at the farm, country or international levels; lack of proper breed organization; or lack of adaptation to market demands. Breeds are categorized as to their risk status on the basis of, inter alia, the actual numbers of male and/or female breeding individuals and the percentage of pure-bred females. FAO has established categories of risk status; critical, endangered, critical-maintained, endangered-maintained, and not at risk. Breed complementarity An improvement in the overall performance of crossbred offsprings resulting from crossing breeds of different but complementary biological types. Breed not at risk  A breed where the total number of breeding females and males is greater than 1 000 and 20 respectively; or the population size approaches 1 000 and the percentage of pure-bred females is close to 100 percent, and the overall population size is increasing. Breeding objective A weighted combination of traits defining aggregate breeding value for use in an economic selection index. A general goal for a breeding program - a notion of what constitutes the best animal Breeding value The value of an individual as a (genetic) parent. The part of an individual's genotypic value that is due to independent and therefore transmittable gene effects. C Word/Phrase Definition Characterization of animal genetic resources:  All activities associated with the description of AnGR aimed at better knowledge of these resources and their state. Characterization by a country of its AnGR will incorporate development of necessary descriptors for use, identification of the country’s sovereign AnGR; baseline and advanced surveying of these populations including their enumeration and visual description, their comparative genetic description in one or more production environments, their valuation, and ongoing monitoring of those AnGR at risk. Cloner A genetic replica of another organism obtained through a non-sexual (no fertilization) reproduction process. Cloning by nucleus transfer involves the transfer of a donor nucleus from (cultured) cells of embryonic, fetal or adult origin into the recipient cytoplasm of an enucleated oocyte or zygote, and the subsequent development of embryos and animals. These clones usually have different mitochondria: genomes. Composite (synthetic) breed A hybrid with at least two and typically more breeds in its background. Composites are expected to be bred to their own kind, retaining a level of hybrid vigour normally associated with traditional crossbreeding systems Conservation of farm animal genetic resources Refers to all human activities including strategies, plans, policies and actions undertaken to ensure that the diversity of farm animal genetic resources is being maintained to contribute to food and agricultural production and productivity, now and in the future. Correlation coefficient A measure of the interdependence of two random variables that ranges in value from −1 to +1, indicating perfect negative correlation at −1, absence of correlation at zero, and perfect positive correlation at +1. It determines the degree to which two variable's movements are associated. Covariance functions A function that gives covariance between records taken at times ti and tj as a function of the times. They are infinite dimensional equivalent to covariance matrices. Critical breed A breed where the total number of breeding females is less than 100 or the total number of breeding males is less than or equal to five; or the overall population size is close to, but slightly above 100 and decreasing, and the percentage of pure-bred females is below 80 percent. Critical-maintained breed and endangered-maintained breed Categories where critical or endangered breeds are being maintained by an active public conservation programme or within a commercial or research facility. Crossbreeding Mating of sires of one breed or breed combination to dams of another breed or breed combination Cryo-preservation A process where cells or whole tissues are preserved by cooling to low sub-zero temperatures, such as (typically) -80°C or -196°C (the boiling point of liquid nitrogen). At these low temperatures, any biological activity, including the biochemical reactions that would lead to cell death is effectively stopped. Maintenance of the viability of excised tissues or organs by freezing at extremely low temperatures D Word/Phrase Definition Diagnostic alleles These are unique alleles to certain breeds, e.g. allele unique to indicine breeds or taurine breeds. They are used to determine the purity of breeds, the introgression by one breed type into a population and to determine the genetic composition of breeds Direct use value (DUV) The financial value of resources used domestically DNA (deoxyribonucleic acid) The long chain of molecules in most cells that carries the genetic message and controls al cellular functions in most forms of life. DNA bank Storage of DNA, which may or man not be the complete genome, but should always be accompanied by inventory information. (Note: at the present time, animals cannot be reestablished from DNA alone). Domestic animal diversity (DAD) The spectrum of genetic differences within each breed, and across all breeds within each domestic animal species, together with the species differences; all of which are available for the sustainable intensification of food and agriculture production. E Word/Phrase Definition Embryo transfer A reproductive technology in which embryos from donor females are collected and transferred in fresh or frozen form to recipient females. Endangered breed A breed where the total number of breeding females is between 100 and 1 000 or the total number of breeding males is less than or equal to 20 and greater than five; or the overall population size is close to, but slightly above 100 and increasing and the percentage of pure-bred females is above 80 percent; or the overall population size is close to, but slightly above 1 000 and decreasing and the percentage of pure-bred females is below 80 percent. Environmental variance The variance due to environmental variation (see also genetic variation) Estimated breeding value A prediction of a breeding value. See breeding value. Evaluation Measurement of the characteristics that are important for production and adaptation, either of individual animals or of populations, most commonly in the context of comparative evaluation of the traits of animals or of populations. Ex situ conservation This is literally “Off-site conservation”. It is the process of protecting an endangered species of plant or animal by removing it from an unsafe or threatened habitat and placing it or part of it under the care of humans e.g. zoos, arboretums and gene banks. Ex situ conservation of farm animal genetic diversity All conservation of farm animal genetic material in vivo, but out of the environment in which it developed, and in vitro including, inter alia, the cryoconservation of semen, oocytes, embryos, cells or tissues. Note that ex situ conservation and ex situ preservation are considered here to be synonymous. Extinct breed A breed where it is no longer possible to recreate the breed population. Extinction is absolute when there are no breeding males (semen), breeding females (oocytes), nor embryos remaining. F Word/Phrase Definition Farm animal genetic resources (AnGR) Those animal species that are used, or may be used, for the production of food and agriculture, and the populations within each of them. These populations within each species can be classified as wild and feral populations, landraces and primary populations, standardized breeds, selected lines, and any conserved genetic material. G Word/Phrase Definition Gene The unit of heredity transmitted from generation to generation during sexual or asexual reproduction. More generally, the term "gene" may be used in relation to the transmission and inheritance of particular identifiable traits. Genetic A measure of the genetic similarity between any pair of populations. Such distance may be based on phenotypic traits, allele frequencies or DNA sequences. For example, genetic distance between two populations having the same allele frequencies at a particular locus, and based solely on that locus, is zero. The distance for one locus is maximum when the two populations are fixed for different alleles. When allele frequencies are estimated for many loci, the genetic distance is obtained by averaging over these loci. Genetic distances This is a measure of gene differences between populations (and hence genetic relationships among them) measured by some numerical quantity and usually refer to the gene differences as measured by a function of gene frequencies Genetic distancing The collection of the data on phenotypic traits, marker allele frequencies or DNA sequences for two or more populations, and estimation of the genetic distances between each pair of populations. From these distances, the best representation of the relationships among all the populations may be obtained. Genetic gain Genetic gain is the amount of increase in performance that is achieved through genetic selection after one generation of selection Genetic improvement programme A systematic plan to enhance the genetic of animal performance Genetic markers A gene or DNA sequence having a known location on a chromosome and associated with a particular gene or trait. A gene phenotypically associated with a particular, easily identified trait and used to identify an individual or cell carrying that gene. Genetic markers associated with certain diseases can be detected in the blood and used to determine whether an individual is at risk for developing a disease. Genetic variance Phenotypic variance resulting from the presence of different genotypes in the population. Within a population, the measure of how much of the variance of a particular phenotype is due to genotype variation Genetic variation In the context of the key equation for genetic change, variability of breeding values within a population for a trait under selection Genome The complete set of genes and non-coding sequences present in each cell of an organism, or the genes in a complete haploid set of chromosomes of a particular organism. Genotype by Environment interaction A dependent relationship between genotypes and environments in which the difference in performance between two or more genotypes changes from one environment to another H Word/Phrase Definition Heterosis An increase in the performance of crossbreds over that of purebreds, most noticeably in traits like fertility and survival ability High-input production environment A production environment where all rate-limiting inputs to animal production can be managed to ensure high levels of survival, reproduction and output. Output and production risks are constrained primarily by managerial decisions. I Word/Phrase Definition Ideal model A model that is close to a true model based on an understanding of the problem (See true model). In situ conservation On-site conservation. It is the process of protecting an species in its natural habitat, either by protecting or cleaning up the habitat itself, or by defending the species from predator In situ conservation of farm animal genetic diversity All measures to maintain live animal breeding populations, including those involved in active breeding programmes in the agro-ecosystem where they either developed or are now normally found, together with husbandry activities that are undertaken to ensure the continued contribution of these resources to sustainable food and agricultural production, now and in the future. Indirect use values (IUV) These are values of functions of livestock which do not have monetary quantification for consideration in a commercial market. Individual heterosis The advantage of the crossbred individual relative to the average of the purebred individuals. Introgression A breeding strategy for transferring specific favourable alleles from a donor population to a recipient population. This would, for example, be of great interest for genes responsible for disease resistance genes, which could be introgressed into a susceptible but otherwise economically superior breed. L Word/Phrase Definition Linear functions function which satisfies and for all and in the domain, and all scalars . Livestock revolution is a convenient expression that summarizes a complex series of interrelated processes and outcomes in production, consumption, and economic growth arising comes from the participation of developing countries in large-scale transformations that had previously occurred mostly in the temperate zones of developed countries longitudinal data Data resulting from the observation of a population on a number of variables over time. Whenever observations are made more than once, the data is considered to be longitudinal Low-input production environment A production environment where one or more rate-limiting inputs impose continuous or variable severe pressure on livestock, resulting in low survival, reproductive rate or output. Output and production risks are exposed to major influences which may go beyond human management capacity M Word/Phrase Definition Management of farm animal genetic resources The sum total of technical, policy, and logistical operations involved in understanding (characterization), using and developing (utilization), maintaining (conservation), accessing, and sharing the benefits of animal genetic resources. Marker–assisted selection (MAS) Selection for specific alleles using genetic markers Market-oriented dairy technology Dairy technologies geared towards markets e.g. fermentation, pasteurization e.t.c. Mass selection A form of artificial selection in which only individuals with phenotypic values greater or less than some threshold level are used for breeding. Maternal heterosis The advantage of the crossbred mother over the average of purebred mothers. Microsatellites Short, noncoding DNA sequence (a tandemly repetitive DNA sequence) that is repeated many times within the genome of an organism. Many repeats tend to be concentrated at the same locus Repetitive stretches of short sequences of DNA used as genetic markers to track inheritance in families. Molecular genetics The branch of genetics that deals with hereditary transmission and variation on the molecular level. It deals with the expression of genes by studying the DNA sequences of chromosomes. N Word/Phrase Definition Nucleus herds These are herds at the top of the tier in the breeding scheme and are the source of superior genetic material to the cooperating herds. O Word/Phrase Definition Observed heterozygosity The percentage of loci heterozygous per individual or the number of individuals heterozygous per locus. Open nucleus schemes A nucleus breeding scheme in which the flow of germ plasm is bidirectional- from the nucleus to cooperating herds or flocks and from cooperating herds or flocks to the nucleus Operational model a generic of an ideal model usually simplified due to missing information or computational problems. The model allows a certain level of accuracy in predictions and is based on some underlying principles and assumptions about an ideal model. Option values (OV) These are values derived from the value given to safeguard an asset for the option of using it in future. It is a kind of insurance value against the occurrence of, for example, a new animals disease or drought changes. P Word/Phrase Definition Pleiotropy The control by a single gene of several distinct and seemingly unrelated phenotypic effects. Production environment All input-output relationships, over time, at a particular location. The relationships will include biological, climatic, economic, social, cultural and political factors, which combine to determine the productive potential of a particular livestock enterprise. Production traits Characteristics of animals, such as the quantity or quality of the milk, meat, fibre, eggs, draught, etc. they (or their progeny) produce, which contribute directly to the value of the animals for the farmer; and that are identifiable or measurable at the individual level. Production traits of farm animals are generally quantitatively inherited, i.e. they are influenced by many genes whose expression in a particular animal also reflects environmental influences. Progeny testing A test used to help predict an individual's breeding values involving multiple matings of that individual and evaluation of its offspring. Pure breeding Also straightbreeding. The mating of purebreds of the same breed. Q Word/Phrase Definition Quantitative trait loci (QTL) A loci that affect a quantitative trait(s) R Word/Phrase Definition Regression coefficient The slope of a line obtained using linear least square fitting. S Word/Phrase Definition Selection criteria Phenotypic values or other pieces of information that form the basis for selection decisions Selection index A linear combination of phenotypic information and weighting factors used for genetic prediction when performance data comes from generally similar contemporary groups. Selection intensity A measure of how particular breeders are in deciding which individuals are selected. The difference between the mean selection criterion of those individuals selected to be parents and the average selection criterion of all potential parents, expressed in standard deviation units Smallholder This is a producer who typically keep 1-3 animals Super-ovulation The administration of a hormone causing a female to develop and release more eggs than normal Sustainable intensification of national production systems The manipulation of inputs to, and outputs from, livestock production systems aimed at increasing production and/or productivity and/or changing product quality, while maintaining the long- term integrity of the systems and their surrounding environment, so as to meet the needs of both present and future human generations. Sustainable agricultural intensification respects the needs and aspirations of local and indigenous people, takes into account the roles and values of their locally adapted genetic resources, and consider the need to achieve long-term environmental sustainability within and beyond the agro-ecosystem. T Word/Phrase Definition Total economic value Total economic value = direct use value + indirect use value + optional value + non-use value True model A model that describes the pattern of the data perfectly. This is usually unknown U Word/Phrase Definition Utilisation of farm animal genetic resources The use and development of animal genetic resources for the production of food and agriculture. The use in production systems of AnGRs that already possess high levels of adaptive fitness to the environments concerned, and the deployment of sound genetic principles, will facilitate sustainable development of the AnGRs and the sustainable intensification of the production systems themselves. The wise use of AnGRs includes a broad mix of ongoing activities that must be well planned and executed for success, and compounded over time, hence with high value. It requires careful definition of breeding objectives, and the planning, establishment and maintenance of effective and efficient animal recording and breeding strategies.