Use of molecular markers in plant breeding

Molecular markers provide plant breeding with an important and valuable new source of information. Linkage between molecular markers can be translated to genetic linkage maps, which have become an important tool in plant and animal genetics. Linkage between (quantitative) trait-data and occurrences of marker alleles allow identification of important genetic factors, underlying observable traits. Knowledge that results from such analyses, i.e. the location on the genome of important genetic factors (quantitative trait loci or QTLs), can and should be applied when making selection and breeding decisions.Selection of parents is an important issue in plant breeding. Basing selection on QTL information, i.e. applying marker-assisted selection, can result in an increased selection efficiency. This is especially true for quantitative traits with a low heritability. For efficient application of marker-assisted selection reliable and fairly complete QTL-mapping results are required. When QTLs were mapped for several traits a multiple trait-selection can be devised, through the use of a suitable index. In this case an ideal target genotype, containing favourable alleles for QTLs that affect the traits of interest, can be constructed and crosses can be made between selected parents in such a way that the probability of obtaining the target genotype is maximised. Although this approach looks promising, and simulation results show an improved selection performance, several problems remain which are limiting application in practise. A more reliable and complete mapping of QTLs, including mapping of interaction between QTLs, mapping of QTLs with a higher reliability, for instance resulting from a combined mapping of several traits, and mapping of QTLs in more diverse non-mapping types of populations could greatly contribute to an increased application of marker-assisted selection, and hence a more efficient selection in plant breeding.Although it is common practise to resort to unadapted material when searching for new genetic variation, the undesired characteristics that accompany the genes coding for the target trait of interest, limit the applicability of introducing 'foreign' genes. With the help of marker and QTL-analysis the genome region that harbours genes which are responsible for the desired characteristics can be identified more precisely and thus the size of the fragment that needs to be introgressed can remain restricted. Marker-assisted backcrossing allows a much more controlled method of gene introgression, limiting the amount of 'linkage-drag' and requiring less generations of backcrossing than conventional backcrossing for yielding suitable genotypes.Developments that favour application of marker-assisted selection are still progressing at a high rate. New technical enhancements in the field of molecular biology, new protocols and methods for identification of genetic factors, new versatile software for data analysis and visualisation all contribute to new ways of selection and breeding that take advantage of this newly acquired knowledge and information. These novel methods should be used to continue to create genetic improvement, in a faster or more efficient way than before, and to introduce quality enhancing genetic factors into cultivated crops