Linkage and Association Mapping of Intermediate Wheatgrass (Thinopyrum intermedium) Height and Seed Size

Thinopyrum intermedium, commonly known as intermediate wheatgrass, is genetically related to wheat, belonging to the Triticeae tribe. Intermediate wheatgrass, however, is a perennial crop that produces large biomass that can be used for forage and biofuel. It also shows great potential to be developed as a grain crop, and provides sustainable environmental services. The environmental benefits of perennial crops relative to annual grain crops are widely recognized, including reduced soil and water erosion, reduced soil nitrate leaching, increased carbon sequestration, and reduced inputs of energy and pesticide. Intermediate wheatgrass has historically been used as a forage crop with only recent efforts to improve agronomic traits such as grain yield. With the advancements of new genotyping by sequencing approaches, it is feasible to utilize all genetic information for a new crop species such as intermediate wheatgrass. The goal of this study is to identify major quantitative trait loci (QTL) for plant height and seed size using association mapping in a breeding population containing 1,126 representative genets from 58 half-sib families, and linkage mapping in a bi-parental population with 178 genets. We generated more than 3,000 ordered markers using genotyping by sequencing to perform association mapping using a model that accounts for population structure and genetic relatedness. Linkage mapping was conducted using composite interval mapping to identify genetic regions responsible for height and seed size.