Genome Sequences from Diploids and Wild Relatives of Wheat for Comparative Genomics and Alien Introgressions

Abstract Bread wheat is an important food source worldwide, contributing ~20% of the caloric intake per person worldwide. Due to a domestication bottleneck and highly selective breeding for key traits, modern wheat cultivars have a narrow genetic base. Wheat production faces several challenges due to both abiotic and biotic stresses as well as changing climatic conditions and genetic improvement of wheat is generally considered to be the most sustainable approach to develop climate resilient cultivars with improved yield and end-use traits. Since wheat cultivars and landraces have been explored extensively to identify novel genes and alleles, one way to overcome these pitfalls is by looking into the proverbial treasure trove of genomic diversity that is present in wheat’s wild relatives. These wild relatives hold reservoirs of genes that can confer broad-spectrum resistance to pathogens, increase yield, provide additional nutrition, and improve dough quality. Genetic approaches and techniques have existed to introgress wild chromatin to bread wheat, as well as trace introgressions present in the germplasm for over 7 decades. However with the availability of NGS technologies, it is now easier to detect and efficiently integrate the genetic diversity that lies within wheat’s gene pools into breeding programs and research. This chapter provides a concise explanation of current technologies that have allowed for the progression of genomic research into wheat’s primary, secondary, and tertiary gene pools, as well as past technologies that are still in use today. Furthermore, we explore resources that are publicly available that allow for insight into genes and genomes of wheat and its wild relatives, and the application and execution of these genes in research and breeding. This chapter will give an up-to-date summary of information related with genomic resources and reference assemblies available for wheat’s wild relatives and their applications in wheat breeding and genetics.