Implementation of molecular markers for quantitative traits in breeding programs - challenges and opportunities

Molecular marker assisted selection (MAS) has been touted as a means to improve the efficiency and speed of plant selection programs. The most widespread use of MAS to date is to assist backcrossing of major genes into already proven, elite cultivars. Markers can aid selection for target alleles that are not easily assayed in individual plants, minimize linkage drag around the target gene, and reduce the number of generations required to recover a very high percentage of the recurrent parent genetic background. The use of MAS in forward-selection programs is less common and is mainly restricted to marker loci linked to major-effect genes with consistent linkage phase across numerous populations. MAS has not been widely used for the improvement of polygenic traits because quantitative trait loci (QTL) mapping techniques remain insufficiently precise and because QTL information cannot be easily extrapolated from mapping populations to other breeding populations. The accuracy of QTL mapping can be improved by increasing population sizes and the number of testing environments, but these same techniques also improve conventional phenotypic selection. Therefore, MAS for polygenic traits is mainly restricted to situations where phenotypic selection cannot be easily implemented (such as for traits that are difficult to phenotype on individual plants or in offseason nurseries). MAS will remain a specialized breeding tool until QTL mapping can be extended to estimation of breeding values across many diverse breeding crosses and subpopulations such as those that compose typical plant breeding programs. Media summary DNA fingerprinting techniques can be applied to plant breeding, mainly to rapidly transfer single genes between varieties, but conventional selection programs are still necessary.