Challenges of Phenotyping.

One bottleneck in applying new genetic technologies to crop research is precision phenotyping. In the case of gene discovery within mapping populations some high throughput phenotyping techniques -such as thermal imaging for canopy temperature and spectral reflectance for ground cover and stem carbohydrates- permit large numbers of genotypes to be screened with high efficiency. However, confounding factors still need to be resolved in studies where genes of major effect are not controlled in experimental populations. This leads to the phenomenon of multiple interactions between agronomic type and environment because genes for height and flowering date not only affect the crops morphology but also its micro-environment or the timing with which key growth stages experience the environment. These factors may cause QTLs to be falsely identified as well as further complicating the already complex challenge of dissecting genotype x environment interaction effects. New generations of mapping populations are being developed that contrast in drought adaptive traits but not in flowering time or height to permit QTL identification in random progeny of bi-parental crosses. However, such populations still may encompass the problem that transgressive segregation of parental alleles may result in significant numbers of agronomically inferior genotypes and as a result QTLs identified may be dominated by traits long since optimized in plant breeding. Association genetics provides an alternative where genetically diverse but elite cultivars can be used for gene discovery and populations controlled for potentially confounding factors. The push towards gene discovery accelerated development of precision phenotyping techniques and at the same time demonstrated the complex nature of QTL x environment interaction. One outcome is the affirmation that some complex physiological traits may serve as proxy genetic markers since it is axiomatic that, in a given environment, their favorable expression indicates the presence of the desired QTLs.