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 ...

Crop improvement relies on the ability to utilize novel genetic variation. Six‐rowed malting barley (Hordeum vulgare L. subsp. vulgare) developed in the US Midwest has an especially narrow genetic base. Therefore, developing strategies to widen the genetic base in barley is important for continued crop improvement. A wild barley [Hordeum vulgare L. subsp. spontaneum (K. Koch) Thell.] advanced backcross–nested association mapping (AB‐NAM) population was developed to assess wild‐barley‐derived alleles in an elite spring six‐rowed malting barley background. The 796 BC2F4:6 lines in the AB‐NAM were derived from 25 wild barley accessions backcrossed to the cultivar Rasmusson. Because the AB‐NAM design minimizes the deleterious and unadapted traits of the wild barley parents, the population was screened in five field environments for the agronomic traits: days to heading, height, productive tiller number (PTN), test weight, and yield. The number of loci identified ranged from two (PTN, the trait with the lowest heritability) to 19 (height). Domestication‐related genes were identified for each trait, particularly the photoperiod gene Ppd‐H1 for days to heading, height, and PTN and the nonbrittle Btr1/Btr2 loci for test weight and yield. Only a single variant showed beneficial variation for yield from a wild barley allele, but positive effects were identified for the other traits examined, including positive variants for test weight on chromosomes 1H and 3H. The AB‐NAM population is a novel resource to map agronomically important traits associated with wild barley alleles.

BackgroundSoybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance.ResultsA total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN.ConclusionsIn this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCNresistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWASderived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.

No abstract

No abstract

No abstract

No abstract