To characterize breeds and learn about their potential utilities in the respective environments, measures of body size and conformation, yields and qualities of products and their social behavior need to be recorded. A comprehensive and detailed description of phenotypes, linked with new molecular technologies, allows unprecedented insights into the genetics of traits and the reaction of particular breeds to changing environments.
Traits that have been recorded traditionally to characterize breeds and ecotypes are body size and conformation. Weights, distances (e.g. height at withers) and circumferences (e.g. of the chest) are measured routinely. Information on age at measurement is often available, allowing inference about growth curves. Quantities and qualities of products are often recorded as part of the genetic management of livestock breeds. Typical products in such systems are milk, meat and fibre. Information is available for commercial, transboundary breeds but not always for local and endangered breeds. In industrial breeds data are also recorded on fertility and somatic cell count as measure of mastitis.
The efficiency of production, e.g. the total energy consumed in feed relative to the energy stored in the product, is economically important, but information is frequently missing. Information on the length of productive life is mostly available but often ignored.
Rapid development of technologies allows recording of traits related to the metabolic condition of animals, at least for limited numbers of samples. Relevant traits may include methane production, nitrogen and phosphor excretions as components of the environmental footprints. Blood parameters provide information on, inter alia, energy balance and health status of animals. Near or mid infrared spectra of animal products are about to become available and may give information about traits related to product quality (e.g. fatty acid composition of milk). Remote sensing techniques allow us to learn about the social behavior of animals, particularly interesting for species foraging on pasture.
Information on disease diagnoses of animals of particular economic interest. EU regulations request veterinarians to leave information on each diagnosis, including the animal ID, on farm. This information is already being collected routinely in Nordic countries but has been deemed impossible everywhere else. This attitude is changing. Disease diagnosis information is collected in Austria since 2006 and may be available soon in other countries.
Classical tools of phenotyping are weighting scales, measuring sticks (see Fig. 3), measuring tapes and sliding callipers. The qualities of products are measured with specialized equipment like milk and fibre analyzers. Instruments originally developed for human medicine, like ultrasound machine, X-ray and CT-scanner, are used to compile information about body composition and skeletal proporties. Blood testing is applied to learn about metabolic characters. Near or mid infrared spectrography of milk, blood, urine or meat is yet to be implemented as a comparatively accurate and inexpensive tool of learning about properties of products as well as disease related traits.
Measurement or recording is mostly not a one time exercise, but occurs repeatedly over time (e.g. across duration of growth, lactation or lifetime). Strategies need to be devised depending on the nature of the characterisation exercise. For example, for analysis of growth curves, cross-sectional approaches, i.e. measuring a large number of animals with known ages may be as informative as longitudinal approaches of repeatedly measuring the same batch of animals.