However, due to decreased costs the genomes of many crops like rice, maize, potato, and bread wheat have now been sequenced and techniques for genomic selection in plant breeding are being developed. The procedure, in principal, is the same as in livestock, but the genomic complexity in terms of polyploidy and the modes of reproduction differ greatly among plant species. Trees are a great example of plants where breeding would benefit from genomic selection because their reproductive period and time until harvest are very long. The ability to predict future wood or fruit quantity and quality at an early stage of development would, therefore, be highly beneficial. Samples could be collected at an early stage and their genotypic data could be compared to older trees with known phenotypic measures. The application of this technique will not be as easy in crop species where reproduction and breeding schemes differ among species, and the approaches must be adjusted to different breeding populations. Genomic selection is still a promising method in plant breeding, but it might be that it will only be fully employed in the breeding of trees. PROTEOMICS AND METABOLOMICS Proteomics is the study of the protein makeup of an organism. Genomics can be compared to a cookbook filled with recipes, and proteomics can be compared to the wide variety of dishes that can be created by following the recipes in the book. While genomics to some extent can predict the phenotype of an organism, largescale measurements of proteins and metabolites – proteomics and metabolomics, respectively – provide a more accurate view of the true phenotype and are easier to interpret. Proteins make up the machinery of the cells, and they mediate signalling and chemical events by catalysing a vast array of chemical reactions. Measuring the levels of specific proteins can be used to predict the features that will occur in different crosses in breeding programmes and
can be used as an alternative or complement to the use of genomic markers. One way to study the different proteins in a sample is to first digest them with a specific enzyme to obtain peptides (small proteins). The peptides in the mixture are then separated based on their polarity, and the levels of specific peptides are measured. Highly reproducible measurements can be achieved with a technique called Selected Reaction Monitoring that allows hundreds of peptides to be measured in a large sample cohorts. Metabolites are small molecules such as various types of carbohydrates and amino acids in the cells. Those are usually separated in the same manner as the proteins but the metabolites are identified using, for example, mass spectral fingerprint libraries. There are still many technical challenges to be overcome before complete proteomic and metabolomic measurements can be made, but the use of these techniques in breeding is promising. GENETIC ENGINEERING This section describes modifications of plant genes using molecular approaches. This includes breeding methods in which the expression of a target gene is altered or a foreign gene is introduced into the genome of a target crop for developing a desirable trait. Depending on which technology is used, the product obtained may or may not be defined as a genetically modified organism (GMO). The technologies that are in use in plant breeding today are explained along with some of the new methods that are expected to have broad applications in crop development in the future. For definition of GMO, see page 67. GENETIC TRANSFORMATION Even though one might change a trait or introduce a new one using the classical techniques described previously, the desired results can be difficult, and in some cases impossible, to obtain. These are cases where genetic transformation can prove useful. This technique is particularly 39