Phenotyping

Abstract

The ultimate goal of plant breeding is to develop cultivars that have consistently good performance for the primary traits of interest. Primary traits are usually agronomically and economically important traits and will vary among crop species. These traits are quantitative, rather than qualitative, in nature. Quantitative traits vary continuously (e.g. yield, quality and stress tolerance), whereas qualitative ones are usually (not always) binary (yes vs. no; e.g. resistance to a fungus and colour of flower). Quantitative traits are typically governed by a number of genes, while qualitative ones are often simply inherited (decided by one or two genes; hence called as simpler or major traits). Although progress had been made in cultivar development in most crop species since the rediscovery of Mendelism, further genetic progress required more information on the inheritance of the primary traits and associations with other traits that are needed in improved cultivars. Quantitative geneticists believed that they could enhance breeding methods if the inheritance of quantitative traits was better understood. However, some of the assumptions (random mating populations, linkage equilibrium, two alleles per locus, no epistasis, etc.) used by the quantitative geneticists in developing the theory and methods of estimation did not seem realistic to practicing plant breeders. Initially, greater efforts were given to studies related to types of gene action. Identifying the genes for primary traits will help in answering several genetic questions: How many genes influence the given traits, and what are their relative effect sizes? Do these genes show evidence of non-neutral evolution at the sequence level? What environmental and evolutionary forces lead to the maintenance of variation at these loci? Do ecologically similar environments favour the same genes or is it possible to achieve a similar phenotype with different genetic mechanisms?