Marker-assisted Selection

Using one of the above approaches to identify molecular markers, in combination with an appropriate mapping population of plants plus or minus the trait of interest, many markers have been identified which are closely linked to genes for agronomic traits of interest. These include markers for genes for:
(i) pest and disease resistance (against viruses, fungi, bacteria, nematodes, insects);

(ii) quality traits (e.g. malting quality barley, bread or noodle wheats, alkaloid levels, etc.);
(iii) abiotic stresses (e.g. tolerance to salinity or toxic elements such as boron or aluminium);
(iv) developmental traits (e.g. flowering time, vegetative period).
If the molecular marker is in the target gene itself, it has been called a ‘perfect’ marker. Clearly, the closer the molecular marker is linked to the target gene, the better. The overall process of developing a marker thus involves setting up appropriate mapping populations, looking for polymorphic DNA sequences closely linked to the trait of interest, conversion of the polymorphism to a routine marker (usually PCR based), validation and implementation.
Quantitative trait loci (QTLs) are the genes which control quantitative traits such as yield for which the final character is controlled by several genes. To identify and map QTLs, a defined mapping population is required which is screened for polymorphisms by RFLPs, AFLPs and SSRs which can be mapped. Statistical approaches are then used to identify associations between the traits of interest and specific markers.
Although the location of QTLs is usually not known exactly, the association of a genotype at a marker/locus and a contribution to the trait indicates that there is a QTL near that marker. The promise of molecular marker-assisted selection for crop improvement is in the following: increased speed and accuracy of selection; stacking genes, including minor genes; following genes in backcross populations; and reduced costs of field-based selection. Thus, rather than growing breeding lines in the field and challenging or testing for important traits over the growing season, it is possible to extract DNA from 50mg of a seedling leaflet and test for the presence or absence of a range of traits in that DNA sample in one day. Plants lacking the required traits can then be removed early in the breeding programme. With the availability of more validated molecular markers, marker-assisted selection therefore becomes a highly cost-effective and efficient process.
 Examples of Marker-assisted Selection
There are now many examples of the use of molecular markers for selection in plant breeding.3 Examples include (i) the microsatellite locus HSP176 of soybean , which is closely linked to a
gene (Rsv) conferring resistance to soybean mosaic virus, (ii) a perfect marker for noodle quality starch in wheat and (iii) a marker for early flowering in lupins.

Western Australia exports specialty wheat to the Asian market to make white alkaline salted noodles. This segment of the export trade is worth $250 million per annum. White noodles require specific swelling properties of starch. Noodle quality wheats all have two rather than three copies of granule bound starch synthase (GBSS), the enzyme which synthesizes amylose, the linear polymer of starch. This reduces the ratio of amylose to amylopectin by 1.5–2%, increasing the flour swelling volume. A ‘perfect’ PCR molecular marker was developed which identified presence or absence of the GBSS gene on chromosome A, i.e. ‘bad’ or ‘good’ noodle starch. This molecular marker test is now used as a primary screen for all noodle wheat breeding lines in Western Australia and has resulted in the accelerated production of a series of new noodle quality wheat varieties.
Narrow-leafed lupin is the major grain legume grown in Australia. Early flowering is required for the crop to complete its life-cycle before the rain limits growth in areas of Mediterranean climate where it is grown. Using fluorescent AFLPs, a marker linked to early flowering of lupins was identified (using a DNA sequencer). The AFLP was then run as a radioactive version, the polymorphic band isolated, cloned and sequenced and a co-dominant PCR-based marker developed for routine implementation.