As pointed out in Section 3, the phenotype is a result of both genotype and the environment. The animal phenotypes of interest can be divided into three main categories: 1) physical description or measurements; 2) performance characteristics; and 3) adaptation to the environment. Characterisation of animal genetic resources requires that data be collected on all these characteristics (see Section 2, this module).
Physical characteristics include such characteristics as presence or absence of horns, coat colour, body length, withers height, heart girth, tail length, tail type, presence or absence of hump, fur type (wool versus hair) etc. Some of these (e.g. presence or absence of horns) have simple Mendelian inheritance and have been studied extensively, at least in temperate livestock. Others such as withers height, heart girth and body length are obviously quantitative in nature. Physical characteristics are arguably the most commonly used criteria for breed or strain definitions. For this reason, attempts have been made to use these traits in classifying hitherto uncharacterised populations. One such example is the classification of Ethiopian and Eritrean goat populations based on multivariate analyses of physical characteristics (see Section 2, this module).
Performance characteristics are the traits most familiar to animal breeders. In mainstream, 'western-type' animal production, they tend to be limited to such traits as milk yield and quality, meat characteristics (measures of growth and carcass quality), egg production and wool production (fleece yield and quality). They also include reproductive traits (age at first parturition, calving interval, prolificacy etc.). In traditional livestock production in the tropics, various species are also used for draft power and/or as pack animals [Yak]. Indeed, in these systems there is really no distinction between performance and adaptive traits. Thus, animals are expected to walk long distances in search of feed and water and to produce milk, pull a plough, produce offspring etc. Analyses at this level of complexity have generally been ignored in teaching of animal breeding in the tropics. Indeed, not much thought has gone into this area and sometimes the animals are unfairly condemned for under-performing, when indeed the whole picture has not been taken into account. As a result, breeding strategies for tropical low- and medium-input systems, which are generally livelihood-oriented, do not exist. Greater care should be taken to better design breeding strategies that best utilise breeds that would otherwise be unfairly condemned or ignored (see Module 1, Sections 5 and 7).
It is not good enough to only consider what may be important today, but rather a futuristic angle in which the potentials or importance of such genes in the predictable future are equally if not more important. Efforts should therefore be made to predict what genes would be important should the environment change in a given way or direction. Given that environment changes are predictable, with increasing degree of accuracy over time, livestock genotypes that thrive or perform best under environments that are similar to the future predictions however remotely would provide sources of candidate genes for conservation. In this regard, adaptive traits should be targeted. Traits such as trypanotolerance, helminth tolerance and the quantitative trait loci (QTL) associated with each of these are important in this respect
Adaptive characteristics include such traits as disease resistance [CS 1.19 by Yapi-Gnaore]; [CS 1.24 by Dempfle and Jaitner], cold tolerance [CS 1.37 by Kharel et al]; heat tolerance, salt tolerance goat of India ability to utilise low quality feeds, selective grazing [CS 1.1 by Mpofu and Rege] etc. Indigenous tropical livestock have, through millennia of exposure to the rigours of the tropical environment, evolved coping mechanisms. As has been alluded to above, the adaptive traits are probably the least studied in tropical livestock. Ironically, it is precisely because indigenous tropical breeds possess these characteristics that they need to be studied and conserved and genetically improved (selected or utilised in well structured crossbreeding programmes) [CS 1.36 by Sartika and Noor]; [CS 1.35 by Shreeram and Prakash]. Admittedly, studying these complex traits is an expensive enterprise. Yet, without adequate characterisation of individual traits, including estimation of relevant genetic parameters, it is impossible to incorporate them into meaningful breeding programmes.