Primary synthetic wheat has been confirmed as a reservoir of genes for tolerances to various biotic and abiotic stresses in wheat. It has been intensively used in spring wheat breeding, especially for drought and heat tolerances. In this project, we genotyped more than 500 lines using genotyping-by-sequencing. We compared the new alleles of primary synthetic wheat with adapted hard red winter wheat in the US Great Plains. We linked the alleles to their resistances to greenbug, Hessian fly, and wheat curl mite. New sources of resistance genes will be identified by comparing the linked single nucleotide polymorphisms from genotyping-by-sequencing and known genes based on their physical chromosome locations. The utilization of these synthetic lines to develop adapted or elite winter wheat lines for high yield potential is discussed. In addition, we employed DNA microarray and RNA sequencing to identify differentially expressed genes associated with drought tolerance and greenbug resistance. We also have developed kompetitive allele specific PCR markers for greenbug resistance genes Gb3 and Gb7, Hessian fly resistance gene H32, wheat curl mite resistance gene CmcTAM112, a major stripe rust resistance QTL and kernel weight QTL in cultivar TAM 111. Genomic prediction and its assisted breeding for hard red winter wheat will be discussed.