Establishment and Optimization of Genomic Selection to Accelerate the Domestication and Improvement of Intermediate Wheatgrass (Thinopyrum intermedium) Using Recurrent Selection.

Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D.R. Dewey; IWG] is a perennial species and has edible and nutritious grain and desirable agronomic traits, including large seed size, high grain yield and biomass. IWG also has the potential to provide ecosystem services and an economic return to farmers. However, because of its allo-hexaploidy and self-incompatibility, developing molecular markers for genetic analysis and molecular breeding has been challenging. In the present study, using genotyping-by-sequencing technology, 3,436 genome-wide markers discovered in a bi-parental population with 178 genets, were mapped to 21 linkage groups corresponding to 21 chromosomes of IWG. Genomic prediction models were developed using 3,883 markers discovered in a breeding population containing 1,126 representative genets from 58 half-sib families. High predictive ability was observed for seven agronomic traits using cross-validation, ranging from 0.46 for biomass to 0.67 for seed weight. Optimization results indicated that 8-10 genets from each half-sib family can form a good training population to predict the breeding value of their siblings, and 1,600 genome-wide markers are adequate to capture the genetic variation in the current breeding population for genomic selection. Thus, with the advances in sequencing based marker technologies, it was practical to perform molecular genetic analysis and molecular breeding on a new and challenging species like IWG, and genomic selection could increase the efficiency of recurrent selection and accelerate the domestication and improvement of IWG.