The Principle: Identification and Application of Molecular Markers

Abstract

Plant breeding is based around the identification and utilisation of genetic variation. The breeder makes decisions at several key points in the process. First in deciding on the most appropriate parents to use for the initial cross or crosses and then in the selection strategy used in identifying the most desirable individuals amongst the progeny of the cross. The efficiency of the breeding and selection process can be assessed in many different ways including the ultimate success of the varieties released and the frequency with which new varieties are produced. A major cost and logistical issue in plant breeding are the actual number of lines that need to be carried through the evaluation and selection phases of a program. Large breeding programs for annual crops may carry hundreds of thousands of lines to produce a new variety only once every few years. Field trials can be expensive and evaluation of some traits, such as quality and yield stability can be expensive to assess. Molecular markers have proved to be a powerful tool in replacing bioassays and there are now many examples available to show the efficacy of such markers. The use of molecular markers to track loci and genome regions in crop plants is now routinely applied in many breeding programs. The location of major loci is now known for many disease resistance genes, tolerances to abiotic stresses and quality traits. Improvements in marker screening techniques have also been important in facilitating the tracking of genes. For markers to be effective, they must be closely linked to the target locus and be able to detect polymorphisms in material likely to be used in a breeding program. The prime applications of markers in most breeding programs have been in backcross breeding where loci are tracked to eliminate specific genetic defects in elite germplasm, for the introgression of recessive traits and in the selection of lines with a genome make-up close to the recurrent parent. In progeny breeding, markers have proved valuable in building crucial parents and in enriching F1s from complex crosses. Markers have also improved the strategies for gene deployment and enhanced the understanding of the genetic control of complex traits such as components of quality and broad adaptation.