Abstract: Rapid advances in genomics are providing the tools to determine the genetic basis of quality (both nutritional and functional) in cereals. This promises to allow increased rates of genetic gain in breeding by reducing the need for extensive end-product testing of new varieties. Many quality traits are the result of relatively recent human selection and are thus likely to be controlled by only a few major genes. This makes identification of these genes for use in breeding selection an attractive target for breeders. Examples of the discovery of genes that are major contributors to key grain quality attributes include, fragrance and cooking temperature in rice (identified by re-sequencing) and loaf volume and milling yield in wheat (identified by transcriptome analysis). Extension of genomic tools to an analysis of the wider gene pool including wild relatives will enable the identification of alleles that may contribute to improved or novel grain quality in the future and may be critical to ensuring quality is retained in a changed climate. Completely new cereal species might be produced.

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei's distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years.