Dissecting Sub-Genomes of the Promising Perennial Crop Thinopyrum intermedium Using Functional Genes and Genome-Wide Molecular Markers

Intermediate wheatgrass (Thinopyrum intermedium, 2n = 6x = 42) is a perennial crop that possesses desirable agronomic traits and provides environmental services and is currently being domesticated as a perennial grain crop. Genetic analyses in this outcrossing allohexaploid have been limited and its sub-genome donors have not been conclusively identified. The identification of sub-genome donors would help facilitate the genetic analysis and improvement of intermediate wheatgrass. Here we report the sub-genome analysis of intermediate wheatgrass using high-molecular-weight glutenin subunits (HMW-GS) genes and genome-wide markers. Five HMW-GS genes and their allelic variants were isolated from three individual intermediate wheatgrass plants. Sequence alignments showed that TiHGS1 and TiHGS2 genes shared high identities (> 96%) with the Glu-1Dx and Glu-1Dy genes, respectively, in Aegilops species. TiHGS3 showed much higher identities with HMW-GS genes from Dasypyrum or Pseudoroegneria than those from the other species; and TiHGS4 and TiHGS5 had the highest similarity with HMW-GS genes from Thinopyrum elongatum among several hundreds of HMW-GS sequences in GenBank. This work provides substantial new evidence about the genome components of intermediate wheatgrass. Now, we are collecting the candidate species of sub-genome donors for intermediate wheatgrass. These species will be investigated using Genotyping-By-Sequencing to discover genome-wide SNPs. These SNP markers will help to perform phylogenetic inference, detect ancestral hybridization, and then identify the sub-genome donor species of intermediate wheatgrass.