Genomics Glossary

Genomics Glossary - Beef CRC - Beef Genetic Technologies

There are some very long and complicated words used in genomics research. This glossary will unravel some of them for you.

Abbreviation Definition ABRI Agricultural Business Research Institute - based at UNE, ABRI provides a wide range of agribusiness information services, including delivery of BREEDPLAN ACIAR Australian Centre for International Agricultural Research. An Australian research funding agency that uses Australian research capacity to solve agricultural research problems in developing countries. adipocytes The cells that make up fat or adipose tissues adipogenesis The cellular developmental process that leads to fat AGBU Animal Genetics and Breeding Unit - based at UNE, AGBU is a joint venture of UNE and NSW Department of Primary Industries ALFA Australian Lot Feeders' Association represents feedlots in Australia at every level, as the industry's national peak body allele One variant of a gene ARC Australian Research Council AUS-MEAT AUS-MEAT Limited is responsible for establishing and maintaining National Industry Standards for Meat Production and Processing Beef-N-omics A decision support system developed by NSW DPI for southern beef production systems which combines herd dynamics, pasture availability and gross margin budgets bioinformatics The computational and mathematical backgrounds to modern biology and genomics; bioinformaticians can be database specialists, statisticians and/or computer programmers biopsy Removal and examination of tissue, cells or fluids from the living body Bos indicus Breeds of cattle originating from the Indian sub-continent; sometimes called Zebu breeds and includes Brahman and Sahiwal Bos taurus Temperate British and European breeds of cattle e.g. Hereford, Angus, Charolais BREEDOBJECT A computer software package used to derive beef breeding objectives by weighting traits in the selection program for their relative economic values BREEDPLAN Australia's beef genetic evaluation system that estimates the genetic merit of animals for economically important traits calpain Calcium activated proteases believed to be important in the initial stages of breakdown of structural proteins in muscle. candidate gene Gene that is thought to be directly involved in a particular cell’s, tissue’s or animal’s characteristics CCA Cattle Council of Australia, the peak producer organisation representing Australia's beef cattle producers cDNA 'Complementary DNA', a DNA molecule derived from RNA by the use of the enzyme reverse transcriptase; in this form, the molecule can be cloned and sequenced cDNA library A collection of cloned cDNAs cDNA microarray An ordered array of thousands of cDNA inserts, printed as probes on a glass microscope slide cloning In context of tissue culture, establishment of a cell line from a single cell cohort see Management group collagen An insoluble fibrous protein that occurs in vertebrates as the chief constituent of the fibrils of connective tissue and of the organic substance of bones composite A breed resulting from the matings of two or more existing breeds and animals are selected from within the progeny to continue the breed (e.g. Belmont Red, Santa Gertrudis) confirmation Confirming the significance and existence of an association between a DNA marker and an economically important trait in a totally independent cattle population. Beef CRC will confirm in at least 1,000 animals that are measured for the trait of interest and that are totally unrelated to the animals in the discovery population. confounding To correctly evaluate the performance of animals, all factors influencing performance must be able to be measured. Confounding occurs when some of the factors are not independent of others. For example, if all progeny of a sire are reared in the same paddock without representative progeny of other sires, then confounding of sire and paddock occurs and neither the effect of the sire nor the effect of the paddock can be determined. Confounding can be total (as in the above example) or it can be partial, where for example, only progeny of some sires may receive favourable treatment such as supplementary feeding because they are performing poorly relative to others under dry seasonal conditions connective tissue The sinuous material that runs between muscle cells and binds them together; in the concentrated and cooked form, it is the gristle in meat CRC Cooperative Research Centre crossbreeding Mating system in which two or more straight breeds are combined CSIRO Commonwealth Scientific and Industrial Research Organisation discovery The discovery phase of DNA markers occurs when an association between a DNA marker and an economically important trait is first identified in a population of cattle that has been accurately measured for the trait of interest. Beef CRC will undertake its discovery phase in at least 1,000 animals DNA Deoxyribonucleic acid - contains the genetic information that is passed from one generation of animals to the next. It is a long double-stranded molecule made up of nucleotides A,T, G and C DNA fingerprinting A method of determining the parentage of animals using DNA extracted from samples such as blood or tissue obtained from the animals. Each animal has a unique genetic makeup (DNA fingerprint). By comparing the DNA fingerprint of progeny with potential parents, it is possible to determine actual parentage DNA marker DNA markers - stretches of DNA closely linked to the genes that underlie an economically important trait. They are used to detect different forms of genes. Tests based on DNA markers are used to predict the breeding performance (genotype) or the lifetime performance (phenotype) of animals for the particular traits. They use a wide range of tissue samples such as blood, skin, hair or muscle collected at any age after conception DPI Department of Primary Industries dressing percentage Ratio of carcase weight to pre-slaughter live weight EBV Estimated Breeding Value – an estimate of an animal’s genetic value for measurable traits such as growth rate, meat tenderness etc. EBVs are calculated from the measured performance of animals and their close relatives compared to other animals measured in an identical way EBVm see MA-EBV EMA Eye muscle area EST ‘Expressed sequence tag’, a short (several hundred bases) nucleotide sequence derived from one end of a cDNA close; usually serves to determine the likely identity of the cDNA clone expression profiling The use of microarrays to study the gene expression profile of a particular tissue or cell flight time A measure of temperament in animals, it is the electronically recorded time taken (in tenths of a second) for an animal to cover a fixed distance (1.7 – 2.2 metres) after leaving a weighing crush GxE Genotype x environment interaction - GxE interactions occur when a breed or DNA marker (genotype) ranks differently in different environments e.g. British breed cattle grow well but Bos indicus breeds grow relatively poorly in temperate environments. In tropical environments, where levels of environmental stress are high, better adapted Bos indicus breeds grow much faster than British breeds. This same scenario could occur when DNA markers rank differently in different environments gene The basic unit of heredity. Each gene has two or more forms which can be the same or different gene expression The process by which a gene code is transcribed into messenger RNA and exported to the nucleus for translation into proteins. Beef CRC uses this term to describe research aimed at understanding the function of the genes associated with expression of economically important genes and identifying non-genetic approaches (for example, changed management practices, modified diets, water medications, vaccines etc) that can be used to ‘switch on’ favourable genes or ‘switch off’ unfavourable genes in cattle where the form of the gene has been identified, so the cattle can be individually managed to better comply with market specifications gene marker See DNA marker genetic correlation Extent to which two attributes are determined by the same genes. Genetic correlations range from -1.0 to +1.0. A high negative relationship means an increase in one trait leads to a decrease in the other; a high positive relationship indicates an increase in one trait leads to an increase in the other trait. A low or zero correlation indicates there is little genetic relationship between the two traits

genomic selection Simultaneous selection for hundreds or thousands of DNA markers covering the entire bovine genome with the markers alone accounting for a significant proportion of the targeted genetic variation (i.e. selection will be based only on knowledge of the markers in the absence of pedigree and phenotypic selection as required to calculate MA-EBVs) genotype Genetic makeup of an animal, but is also sometimes used to indicate the breed composition of an animal heritability Proportion of variation for a measurable trait attributable to variation in genetic factors and is therefore passed on to offspring. Heritabilities (h2) range from 0.0 to 1.0. A h2 = 0 means the trait is not controlled by genetic factors and h2 = 1.0 means the trait is under total genetic control. In general, traits that have h2 > 0.4 are considered to be highly heritable HGP Hormonal Growth Promotant homeostasis The processes that keep a mammalian body metabolically stable in terms of temperature, energy supply, waste removal etc IGF-1 Insulin-like growth factor 1, a factor that can be measured in blood and is associated with feed efficiency and fatness traits IMF% Intra-muscular fat percentage or fat within the muscle (marbling is a visually-assessed score of intramuscular fat) inbreeding A mating system in which mates are more closely related than average individuals of the population to which they belong in vitro Literally “in glass” and it refers to experiments that mimic life in a test tube or by tissue culture Examining the reactions of life by experimentation with the living animal link sire To validly compare the performance of animals across herds, it is necessary for those herds to be genetically linked. The usual method for linking these herds is to use a common (or link) sire in all herds where performance of animals is to be compared management group A management group comprises a group of animals receiving identical treatment for the duration of the evaluation. For BREEDPLAN evaluations, this means that animals are born in the same paddock over the same time period and are exposed to the same management routines (supplementary feeding, weaning times etc.) throughout the period of the evaluation metabolism Processes of synthesis, degradation and transformation that occur within living organisms, and are responsible for all functions of that organism microarray An ordered array of thousands of gene probes, printed onto glass slides microsatellite A genetic marker that is highly polymorphic, that is it has many alleles MA-EBV Marker-assisted EBV – an estimated breeding value calculated using pedigrees and phenotypes for direct and indirect selection traits) and also DNA marker information MLA Meat and Livestock Australia a beef-industry owned company with responsibility for red meat industry R&D and for promotion and marketing of red meat within Australia and internationally molecular techniques Laboratory procedures that allow a researcher to investigate a scientific problem at the level of individual molecules. The term normally refers to nucleic acid techniques but is equally valid for protein techniques MSA Meat Standards Australia, Australia’s meat grading scheme based on guaranteed beef eating quality NFI Net Feed Intake - a measure of feed efficiency that refers to variation in feed intake between animals after differences due to weight and growth rate have been accounted for. Low (more negative) NFI is desirable NPG Northern Pastoral Group of Companies, a loose alliance of major pastoral companies operating in northern Australia ossification score A visual scoring system to describe the development of bone in the bovine, and utilising the progression of calcification in the vertebrae. It is used to estimate maturity of the carcass P8 fat thickness Fat thickness in mm recorded at the P8 rump site PCR Polymerase chain reaction, a technique to amplify DNA strands and used as a diagnostic tool to detect the presence of particular genetic sequences e.g. to identify a particular bacteria or a virulence factor in a bacteria pH pH value of meat sample calculated as the mean of 4 measurements using a probe-type combined electrode (normal values 5.5 to 5.7) phenotype The appearance, structure or biochemical characteristics of an organism, contrasted against genotype, which refers to sequences within the DNA. In the context of discovery of DNA markers, it means the accurately measured record of an animal for a particular trait of interest polymorphic Having many forms. In this context, the term refers to multiple forms of a gene that lead to slight but measurable variation in phenotype. Also relates to the various forms in which fat crystallizes polymorphism The situation where more than one allele or variant of a gene is found in a population quantitative real time PCR (qRT-PCR) A technique that allows quantification of extremely low amounts of nucleic acid: both RNA and DNA QTL Quantitative Trait Loci – stretches of DNA that are closely linked to the genes that underlie an economically important trait (see DNA marker) RBY% Retail beef yield percentage – is generally referred to when carcasses are boned out to commercial standards and trim. RBY% - saleable meat divided by cold carcass weight multiplied by 100 RNA Ribonucleic acid, the string of nucleotides (usually single-stranded) that is “transcribed” from DNA Sanga Adapted Bos taurus breeds that evolved in Southern Africa independent of the European Bos taurus. They retain the productive attributes of the European Bos taurus but have resistance closer to that of the Bos indicus sequencing DNA, RNA, protein or oligosaccharide structure determination shear force An objective measure of meat toughness, measured as the force required to sever the muscle fibres of a meat sample (measured in kgs, with the higher the value, the tougher the meat) SNP Single nucleotide polymorphism. A polymorphism at a specific base or nucleotide in the DNA sequence. For instance, at a point in the DNA sequence where one allele contains an ’A’, another allele contains a ‘T’ supply chain Enterprises acting in concert to improve the economies of specific activities. The relationship may include alliances to vertically or horizontally integrated individuals in (a) sector(s) of the beef industry trait Attribute or characteristic of animals that can be improved genetically (for example, growth rate, fertility, carcase or meat quality etc) UNE University of New England USDA United States Department of Agriculture validation Validation of DNA markers occurs after the discovery and confirmation phases, when prediction equations from those phases are tested independently in another set of cattle that have been measured for the trait. Where possible, Beef CRC plans to use at least 5,000 animals to validate the prediction equations to provide an unbiased estimate of the correlation between prediction and breeding value or phenotype

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