Function-Finding Platforms that Integrate Genome and Phenome in Wheat

Wheat is one of the most important staple crops globally and the improvement of its yield and grain quality is a major priority in many countries. Applications of genomics in wheat improvement have been hampered by the complexity of its polyploid genome and there is still not a robust reference genome available for this crop. Nonetheless, wheat molecular geneticists have used short-read genome and transcriptome sequencing combined with very well defined genetic stocks to develop workable interim methods for genomic analysis. At CSIRO in Australia, a range of platforms have been developed to identify genomic regions associated with important disease resistance, grain quality, abiotic stress tolerance and yield traits. Platforms have been developed that can take quantitative trait loci to a genomic region and gene with subsequent functional confirmation via mutant identification and transgenesis. A powerful starting point for this is the ‘multiparent advanced generation intercross’ or MAGIC population, and near-isogenic lines derived from it using the heterogeneous inbred family (HIF) method that provide a means to study multiple traits at the genomic level. New sophisticated phenomics imaging tools are being added to the arsenal available to dissect wheat traits with aerial, mobile and fixed centres providing real-time measurements of plant performance. From a practical point of view it is important to focus on the most impactful traits and comparative field analysis of trait value is now guiding the focus for the trait development for breeding and gene discovery research. Finally, rapid test platforms have emerged that provide precise functional information, down to the role of individual amino acid residues in enzymes critical for wheat quality. Taken together these approaches are being used at CSIRO to generate and integrated molecular improvement program for wheat that can tackle critical challenges of grain quality, disease resistance and yield.