Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

Abstract

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC 2 F 4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r 2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for highresolution gene mapping and discovery of novel allelic variation using wild barley germplasm.KEYWORDS wild barley; advanced backcross; nested association mapping population; association mapping; plant genetic resources; Multiparent Advanced Generation Inter-Cross (MAGIC); multiparental populations; MPP D IVERSE germplasm collections are valuable resources for crop improvement. However, breeders often neglect these resources due to the time and effort required to identify and deploy beneficial exotic alleles. Breeding for complex traits requires balancing the introduction of genetic diversity with maintaining the selective progress obtained over many cycles of breeding (Bernardo 2002). Due to the malting quality requirements imposed by North American malting and brewing industries, barley (Hordeum vulgare subsp. vulgare) breeding has been restricted to a narrow germplasm base and focused on elite-by-elite crosses (Rasmusson and Phillips 1997). Over many cycles of breeding, extensive genome-wide linkage disequilibrium (LD) can develop in closed breeding populations (Fang et al. 2013), and the genetic diversity of these populations becomes reduced (Condón et al. 2008;Fu and Somers 2009;Muñoz-Amatriaín et al. 2010;Poets et al. 2015). The need to expand the genetic diversity of the breeding pool has become evident as breeders face disease and environmental pressures which are threatening crop production. Today, genomics technologies are advancing our ability to understand the genetic basis of ...

Past and Future Use of Wild Relatives in Crop Breeding

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Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

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A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

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