Advances in genome technology and its application to Brassica improvement. (2003)

The application of genomic technologies to molecular breeding is now starting to impact on the methods applied to crop improvement. The discovery and application of molecular markers for valuable traits reduces the requirement for complex phenotypic analysis and the time required for the development of new commercial varieties. Molecular markers have themselves evolved from laborious, slow and expensive tools to rapid and inexpensive high throughput technologies. In examining the direction of developments in genome technology, we may predict the future benefits to crop improvement programs. The sequencing of complete plant genomes provides the ultimate tool for understanding the genetic variation underlying inherited traits and the sequencing of a complete Brassica genome would revolutionise Brassica improvement in Australia. Molecular plant breeding Crop plants have evolved over the last ten thousand years in close association with humans. This is exemplified by the great differences in form and habit between wild progenitors of cultivated species and the crops we grow and eat. In more recent times, agriculturists have applied scientific methods to variety improvement, both selecting for desirable traits and engineering specific crosses to produce germplasm with enhanced characteristics. Much progress in crop improvement has come about through the design of breeding and selection procedures. One factor limiting progress, using this traditional breeding method, is the ability to identify robust selection methods for desirable traits. The effective design of field experiments goes some way towards efficient selection, however, the local environment can frequently foil such experimental designs. For example, selection for disease resistance traits requires disease pressure which may vary from year to year. Likewise, many other desirable traits such as response to water availability or temperature are directly influenced by the variable environmental conditions. Even for traits where there may be no obvious link to environmental variation, there are often environmental influences which may confuse or confound phenotypic assessment. Plant stresses, which result in loss of yield, may also be interactive. For example, losses due to poor soil conditions may be amplified when the crop is also under water or disease stress. As a result of these difficulties, crop breeders are looking for the ability to move away from the phenotypic assessment of plants in the field to concentrate on the underlying causes of inherited phenotypic variation. This has been made possible with the assistance of the great advances and rapid growth in genomic technologies in the past few years. This unleashed potential of genomics, along with the application of transgenic technologies, is likely to change way crop improvement is applied across a range of crops. One of the first genomic technologies to be applied to crop improvement and plant breeding is the use of molecular markers, such as RAPDs (Randomly Amplified Polymorphic DNA), RFLPs (Randomly Amplified Polymorphic DNA), AFLPs (Amplified Fragment Length Polymorphisms), SSRs (Simple Sequence Repeats) and SNPs (Single Nucleotide Polymorphisms) (Mohan et al. 1997). The molecular marker systems employed in genomic research have continued to evolve with the technology, however, all types of modern molecular marker share one common feature: they all permit the distinction between individuals at the DNA level. Since it is the underlying DNA sequence, the genetic content, which is responsible for inherited variation, the direct assessment of this genotypic information may overcome the requirement for continuous and difficult phenotypic selection in breeding experiments. Early molecular marker technologies, such as RAPDs and RFLPs, were indirect and anonymous, in that the differences detected between individuals did not relate to specific, known changes in DNA sequence. They also generally required moderate to large amounts of plant tissue, were laborious, expensive and occasionally used toxic or radioactive laboratory procedures. As a result of these features, molecular markers were rarely applied to crop breeding programs. With advances in high