Introgression Breeding in Barley: Perspectives and Case Studies

Abstract

Changing production scenarios resulting from unstable climatic conditions are challenging crop improvement efforts. A deeper and more practical understanding of plant genetic resources is necessary if these assets are to be used effectively in developing improved varieties. In general, current varieties and potential varieties have a narrow genetic base, making them prone to suffer the consequences of new and different abiotic and biotic stresses that can reduce crop yield and quality. The deployment of genomic technologies and sophisticated statistical analysis procedures has generated a dramatic change in the way we characterize and access genetic diversity in crop plants, including barley. Various mapping strategies can be used to identify the genetic variants that lead to target phenotypes and these variants can be assigned coordinates in reference genomes. In this way, new genes and/or new alleles at known loci present in wild ancestors, germplasm accessions, land races, and un-adapted introductions can be located and targeted for introgression. In principle, the introgression process can now be streamlined and linkage drag reduced. In this review, we present an overview of (1) past and current efforts to identify diversity that can be tapped to improve barley yield and quality, and (2) case studies of our efforts to introgress resistance to stripe and stem rust from un-adapted germplasm. We conclude with a description of a modified Nested Association Mapping (NAM) population strategy that we are implementing for the development of multi-use naked barley for organic systems and share perspectives on the use of genome editing in introgression breeding.

Keywords: genetic diversity; genetic mapping; genetic resources; haplotype; high throughput genotyping; multi-rust resistance.

FIGURE 1a

Haplotypes and linkage disequilibrium heat maps based on high density SNP genotyping of Cycle I and Cycle II introgression lines that are resistant to barley stripe rust compared to resistant and susceptible checks. Details on the resistance QTLs are provided in the narrative. The size of each QTL interval (in Mb) is inferred from the barley consensus sequence. Most significant SNPs are in bold. Closer SNP from most significant marker in italic.

FIGURE 1b

Haplotypes and linkage disequilibrium heat maps based on high density SNP genotyping of Cycle I and Cycle II introgression lines resistant to barley stem rust compared to resistant and susceptible checks. Details on the resistance QTLs and rpg4/Rpg5 are provided in the narrative. The size of each QTL interval (in Mb) is inferred from the barley consensus sequence. Most significant SNPs are in bold. Closer SNP from most significant marker in italic.

FIGURE 1c

Haplotypes and linkage disequilibrium heat maps based on high density SNP genotyping of selected Cycle I and Cycle II introgression lines at loci determining inflorescence type (VRS1 and INT-C) and hull adherence (NUD). Details on the genes determining these morphological traits are provided in the narrative. The size of each introgression interval (in Mb) is inferred from the barley consensus sequence. Most significant SNPs are in bold. Closer SNP from most significant marker in italic.

FIGURE 2

Flow chart showing the introgression process involved in development of the Cycle I and Cycle II barley populations.

FIGURE 3

An introgression breeding scheme for modified NAM population development using naked, multi-use barley for organic systems as a model.