BackgroundSingle nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.ResultsMost of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM).ConclusionsGenome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schwein.)], also known as scab, is a destructive disease of wheat (Triticum aestivum L; T. turgidum L. var durum) and barley (Hordeum vulgare L.). Host resistance has long been considered the most practical and effective means of control, but breeding has been hindered by a lack of effective resistance genes and by the complexity of the resistance in identified sources. This paper will provide an overview of progress in developing host plant resistance for FHB, primarily in the USA, by review of the sources of resistance in wheat and barley, and their utilization in breeding programs. Although there are no reported sources of immunity, considerable genetic variability exists for resistance in both wheat and barley. Sources of resistance in durum, however, are limited. The strategy of breeding programs is to recombine different types and sources of resistance steadily through traditional breeding strategies. To facilitate selection, artificial inoculation techniques are used in both the field and greenhouse. This enables breeders to select simultaneously for resistance and desirable agronomic characteristics. Incremental increases in resistance are being reported in hexaploid wheat and to a lesser extent in barley and durum wheat. It is anticipated that the development of molecular markers will improve the efficiency of developing FHB wheat and barley cultivars.

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

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The rye (Secale cereale L.) chromosome arm 1RS is one of the most successfully used alien resources in wheat (Triticum aestivum L.) improvement, and it is still being widely utilized by many breeding programmes. With increasing application of marker-assisted selection in wheat breeding, development of an efficient molecular marker system to monitor and track 1AL.1RS and 1BL.1RS wheat-rye translocations is of practical value. In this study, we systematically evaluated the utility of eight rye-specific molecular markers in detecting 1RS chromatins with different origins in diverse wheat genetic backgrounds. Two such markers, PAWS5/S6 and SCM9 were identified that were able to differentiate multiple sources of wheat-rye translocations involving 1RS. A duplex polymerase chain reaction (PCR) procedure was developed with two rye-specific markers PAWS5/S6 and RIS and tested in a set of representative wheat lines. The two rye-specific markers and the duplex PCR procedure established in this study provided a useful tool in marker-assisted selection of materials containing desirable 1RS chromatin in wheat breeding.

Wheat streak mosaic (WSM), caused by Wheat streak mosaic virus (WSMV), is a devastating disease in wheat (Triticum aestivum L.) in the Great Plains of North America. Use of resistance is an effective and environmentally sound method to control the disease. In this study, six wheat genotypes were compared for their responses to WSMV infection under growth chamber conditions. The three resistant genotypes, KS96HW10‐3 (Wsm1), Mace (Wsm1), and CO960293‐2, had disease scores significantly lower than the remaining three genotypes without major resistance. Disease in TAM 111 and TAM 112 was consistently less severe than Karl 92. A population consisting of 188 F2:3 families derived from the cross CO960293‐2 × TAM 111 was used for determining inheritance of the WSMV resistance and for molecular mapping of the resistance in CO960293‐2. Data on segregation of resistance indicated that the resistance in CO960293‐2 is conditioned by a single dominant gene, which was named Wsm2 Transgressive segregation toward susceptibility occurred in the population suggesting a minor gene in the moderately susceptible parent TAM 111, which was not allelic to Wsm2. Wsm2 was mapped to the short arm of chromosome 3B with two flanking simple sequence repeat markers. The single dominant gene inheritance for WSMV resistance in CO960293‐2 has been consistent with the observations that the resistance can be readily transferred to adapted cultivars.

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Biotic stresses including diseases (leaf, stem and stripe rusts), arthropods (greenbug [GB], Hessian fly [Hf], Russian wheat aphid [RWA], and wheat curl mite [WCM]) and their transmitted viral diseases significantly affect grain yield and end‐use quality of hard winter wheat (Triticum aestivum L.) in the U.S. Great Plains. Many genes or quantitative trait loci (QTL) have been identified for seedling or adult‐plant resistance to these stresses. Molecular markers for these genes or QTL have been identified using mapping or cloning. This study summarizes the markers associated with various effective genes, including genes or QTL conferring resistances to arthropods, such as GB (7), RWA (4), Hf (9), and WCM (4) and diseases including leaf, stem and stripe rusts (26) and Wheat streak mosaic virus (WSMV; 2); genes or QTL for end‐use quality traits such as high (3) and low (13) molecular weight glutenin subunits, gliadin (3), polyphenol oxidase (2), granule‐bound starch synthase (3), puroindoline (2), and preharvesting sprouting (1); genes on wheat–rye (Secale cereale L.) chromosomal translocations of 1AL.1RS and 1BL.1RS; and genes controlling plant height (12), photoperiod sensitivity (1), and vernalization (2). A subset of the markers was validated using a set of diverse wheat lines developed by breeding programs in the Great Plains. These analyses showed that most markers are diagnostic in only limited genetic backgrounds. However, some markers developed from the gene sequences or alien fragments are highly diagnostic across various backgrounds, such as those markers linked to Rht‐B1, Rht‐D1, Ppd‐D1, Glu‐D1, Glu‐A1, and 1AL.1RS. Knowledge of both genotype and phenotype of advanced breeding lines could help breeders to select the optimal parents to integrate various genes into new cultivars and increase the efficiency of wheat breeding.