The Use of DNA Markers in Rice Breeding

The development of molecular maps and the complete sequencing of the rice genome have created many opportunities for the application of DNA markers in breeding and genetics. Markerassisted selection (MAS) has become a practical tool in cultivar improvement. MAS is time-saving, very efficient, can promote bio-safety (no need for pathogen or insect pest inoculations during screening trials), reliable, and consistent in dealing with traits whose phenotype is affected by the environment [1]. DNA markers are powerful tools in the indirect selection of important traits at the early growth stages before advancing selected lines to the next generation, thereby speeding up conventional breeding. Selection can be made before flowering, thus allowing breeders to manage crossing and generation advance properly and improve the quality of the breeding materials. DNA markers can facilitate the improvement of traits that are difficult to improve or very expensive to evaluate using conventional breeding methods. For instance, restorer genes in hybrid rice breeding are difficult to evaluate, requiring the testing of spikelet sterility in test cross progenies. MAS can also increase flexibility and efficiency in breeding programs. MAS can reach 95 to 96% accuracy in finding homozygous plants, thus reducing the duration of cultivar release by 2 to 3 years [2]. The varieties ‘Cadet’ and ‘Jacinto’ were released in the U.S. in less than 10 years of breeding work, a rarity in traditional rice breeding. DNA markers are very useful in gene transfer and pyramiding to improve germplasm, as it can accelerate the backcrossing of a gene, group of genes, or minor genes called quantitative trait loci (QTL) into an elite breeding line or cultivar. DNA markers are important tools in selecting plants having the gene or combination of genes of interest and those plants that are genetically similar to the recurrent parents in a large-scale backcrossing program. Markers are also very useful in the transfer and tracking of useful genes found in wild rice into cultivated rice. These DNA markers can also provide a safety net to the environment. Screening for pest resistant plants without having to maintain inoculations of pathogen or insect culture, both in the field and in the greenhouse, is a major advantage. Since the plants with the pest resistance gene can be identified without the presence of the insect or pathogen pest, the introduction and proliferation of new races or biotypes that are resistant pathogens and insects can be avoided or minimized. DNA markers for important traits in U.S. rice have been developed and several other studies on the development of markers are ongoing. Molecular markers are now available for the granule bound starch synthase (waxy) gene that controls grain amylose content and the soluble starch synthase IIa (Alk) gene that controls alkali spreading value (ASV) [3; 4]. Costly laboratory tests for these traits can be deferred or eliminated by using DNA markers during selection