Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

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BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.

A simple, rapid method for determining total anthocyanins was developed for use in developing wheat cultivars with dark‐blue grains. The method was evaluated as a screening test and for quantification of total anthocyanins in blue and purple wheats and related cereals. Wheat anthocyanins were significantly more extractable in ethanol or methanol than in water at different pH levels. A sample‐to‐solvent ratio of 1:8 at pH 1 and 25°C was used. Anthocyanin extracts of pigmented wheat and barley grains exhibited absorbance spectra similar to cyanidin 3‐glucoside. The absorbance of anthocyanin extracts of 160 blue wheat experimental lines were significantly correlated with whole‐grain Hunterlab color values. Total anthocyanins averaged 157 mg/kg in blue wheat whole meal and 104 mg/kg in purple wheat whole meal, whereas blue wheat bran contained 458 mg/kg as compared with 251 mg/kg in purple wheat bran.

Mature wheat (Triticum aestivum L.) endosperm contains two types of starch granules: large A‐type and small B‐type. Two methods, microsieving or centrifugal sedimentation through aqueous solutions of sucrose, maltose, or Percoll were used to separate A‐ and B‐type starch granules. Microsieving could not completely separate the two types of starch granules, while centrifuging through maltose and sucrose solutions gave a homogenous population for B‐type starch granules only. Centrifuging through two Percoll solutions (70 and 100%, v/v) produced purified populations of both the A‐ and B‐type starch granules. Analysis of starch granule size distribution in the purified A‐ and B‐type granule populations and in the whole‐starch granule population obtained directly from wheat endosperm confirmed that the purified A‐ and B‐type starch granule populations represented their counterparts in mature wheat endosperm. Centrifugations through two Percoll solutions were used to purify A‐ and B‐type starch granule populations from six wheat cultivars. The amylose concentrations and gelatinization properties of these populations were analyzed. All of the A‐type starch granules contained higher amylose concentrations and had higher gelatinization enthalpies than did B‐type starch granules. Although A‐ and B‐type starch granules started to gelatinize at a similar temperature, B‐type starch granules had higher gelatinization peak and completion temperatures than did A‐type starch granules