Developing Genetic and Genomic Resources for Intermediate Wheatgrass (Thinopyrum intermedium): a 'Breeding-Assisted Genomics' Approach

The cultivation of perennial species improved through domestication and selection has been proposed as an approach to facilitate the sustainable intensification of agriculture, conserving natural resources while producing food.  Intermediate wheatgrass (IWG), a perennial relative of wheat, was selected for domestication as a dual grain and biofuel crop because of its relatively large seeds and high grain and biomass yield.  After only three cycles of selection, a plant with larger, free-threshing seeds, was achieved.  However, with the increased genetic complexity due to the vast allelic diversity and heterozygosity in this outcrossing polyploid, it has been difficult to stack and fix traits in the population with traditional breeding.  We have utilized several IWG breeding populations during the past two breeding cycles to develop genetic markers, construct a consensus genetic map, investigate colinearity with barley, and identify major quantitative trait loci (QTL) underlying important domestication-related traits, including free-threshing and non-shattering.  Additionally, the primary wheat domestication gene, Q, has been partially cloned in intermediate wheatgrass and the population genotyped at five tiQ alleles.  Three tiQ alleles associate with free-threshing seed, with one of the three and two additional alleles contributing to non-shattering.  QTL analyses have revealed several additional loci that contribute to free-threshing and shattering, as well as several QTL influencing important plant architecture and seed characteristics.  These findings, in combination with future phenotyping and genotyping, will allow for the implementation of marker-assisted and genomic selection to rapidly fix beneficial alleles in the breeding population.