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.
Highlights
Introgression breeding has been an important method for improving barley since domestication, and it remains a key tool for expanding genetic diversity to meet current and future challenges to crop production
Selection for novel phenotypes would increase their frequency in these land races, and the naturally occurring outcrossing (∼2%) that occurs in barley (Abdel-Ghani et al, 2004) and/or the environmentally induced outcrossing the can occur in selfing species would increase the frequency of favorable alleles introgressed into locally adapted genomes
The use of Next-generation sequencing (NGS) methods to rapidly discover thousands of genetic variants in coding or non-coding regions is becoming a standard tool for plant breeders to characterize existing germplasm, analyze genes/Quantitative trait loci (QTL) underlying traits of interest, estimate breeding values based on genotypic information, conduct marker assisted selection (MAS) and genomic selection (GS), and target specific alleles in the population (Muñoz-Amatriaín et al, 2014b; Varshney et al, 2014)
Summary
Introgression breeding has been an important method for improving barley since domestication, and it remains a key tool for expanding genetic diversity to meet current and future challenges to crop production. This drawback can be overcome, to some extent, by relying on the linkage disequilibrium (LD) of SNPs that are in LD with causal genes that are underlying the targeted phenotypic differences (Flint-Garcia et al, 2003; Myles et al, 2009; Lipka et al, 2015) Besides this potential downside, the use of NGS methods to rapidly discover thousands of genetic variants in coding or non-coding regions is becoming a standard tool for plant breeders to characterize existing germplasm, analyze genes/QTLs underlying traits of interest, estimate breeding values based on genotypic information, conduct marker assisted selection (MAS) and genomic selection (GS), and target specific alleles in the population (Muñoz-Amatriaín et al, 2014b; Varshney et al, 2014). A validation process of assessing novel qualitative, or quantitative, trait alleles is warranted (Bilgic et al, 2005; Richardson et al, 2006; Sharma et al, 2018; Hernandez et al, 2019)
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