Discovery of Genes for Crop Improvement from Wild Ancestor Plants

Only a small fraction of the naturally occurring genetic diversity available in rice germplasm repositories around the world has been explored to date. This is beginning to change with the advent of affordable, high throughput genotyping approaches coupled with robust statistical analysis methods that make it possible to examine genome-wide patterns of natural variation and to link sequence polymorphism with complex trait variation. Genome-wide association (GWA) mapping offers one way of identifying genes and quantitative trait loci (QTL) underlying complex variation in both plants and animals based on the analysis of diverse collections of wild and domesticated strains. However, in rice and many other species, GWA mapping is complicated by the presence of deep population structure that is significantly correlated with phenotypic variation. While the subpopulation structure limits the power to identify genotype-phenotype associations for many traits, it has a silver lining in the context of plant breeding; it helps to predict and explain the generation of transgressive variation. Positive transgressive variation is commonly observed in crosses between divergent parents where some of the offspring out perform the better parent. Because this occurs at relatively high frequency in populations derived from inter-specific or inter-subpopulation crosses, there is growing interest in using wild and exotic donors to drive improvements in crop performance. We take advantage of high resolution genotyping to evaluate population structure at the sub-genomic level and use insights gained from association analysis to design and construct inter-mated populations and libraries of chromosome segment substitution lines that manifest transgressive variation for traits of interest. These genetic materials allow us to simultaneously dissect the complex genetics of transgressive variation and to efficiently synthesize new crop varieties designed to outperform existing elite materials under both favorable and unfavorable conditions.