Summary: High‐density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene‐associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome‐wide distributed SNPs that are represented in populations of diverse geographical origin. We used density‐based spatial clustering algorithms to enable high‐throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model‐free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low‐intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Theoretical considerations suggest that wheat yield potential could be increased by up to 50% through the genetic improvement of radiation use efficiency (RUE). However, to achieve agronomic impacts, structural and reproductive aspects of the crop must be improved in parallel. A Wheat Yield Consortium (WYC) has been convened that fosters linkage between ongoing research platforms in order to develop a cohesive portfolio of activities that will maximize the probability of impact in farmers’ fields. Attempts to increase RUE will focus on improving the performance and regulation of Rubisco, introduction of C₄-like traits such as CO₂-concentrating mechanisms, improvement of light interception, and improvement of photosynthesis at the spike and whole canopy levels. For extra photo-assimilates to translate into increased grain yield, reproductive aspects of growth must be tailored to a range of agro-ecosystems to ensure that stable expression of a high harvest index (HI) is achieved. Adequate partitioning among plant organs will be critical to achieve favourable expression of HI, and to ensure that plants with heavier grain have strong enough stems and roots to avoid lodging. Trait-based hybridization strategies will aim to achieve their simultaneous expression in elite agronomic backgrounds, and wide crossing will be employed to augment genetic diversity where needed; for example, to introduce traits for improving RUE from wild species or C₄ crops. Genomic selection approaches will be employed, especially for difficult-to-phenotype traits. Genome-wide selection will be evaluated and is likely to complement crossing of complex but complementary traits by identifying favourable allele combinations among progeny. Products will be delivered to national wheat programmes worldwide via well-established international nursery systems and are expected to make a significant contribution to global food security.

Cellulose synthase-like CslF genes have been implicated in the biosynthesis of (1,3;1,4)-beta-d-glucans, which are major cell wall constituents in grasses and cereals. Seven CslF genes from barley (Hordeum vulgare) can be divided into two classes on the basis of intron-exon arrangements. Four of the HvCslF genes have been mapped to a single locus on barley chromosome 2H, in a region corresponding to a major quantitative trait locus for grain (1,3;1,4)-beta-d-glucan content. The other HvCslF genes map to chromosomes 1H, 5H, and 7H, and in two cases the genes are close to other quantitative trait loci for grain (1,3;1,4)-beta-d-glucan content. Spatial and temporal patterns of transcription of the seven genes have been defined through quantitative polymerase chain reaction. In developing barley coleoptiles HvCslF6 mRNA is most abundant. Transcript levels are maximal in 4- to 5-d coleoptiles, at a time when (1,3;1,4)-beta-d-glucan content of coleoptile cell walls also reaches maximal levels. In the starchy endosperm of developing grain, HvCslF6 and HvCslF9 transcripts predominate. Two peaks of transcription are apparent. One occurs just after endosperm cellularization, 4 to 8 d after pollination, while the second occurs much later in grain development, more than 20 d after pollination. Marked varietal differences in transcription of the HvCslF genes are observed during endosperm development. Given the commercial importance of cereal (1,3;1,4)-beta-d-glucans in human nutrition, in stock feed, and in malting and brewing, the observation that only two genes, HvCslF6 and HvCslF9, are transcribed at high levels in developing grain is of potential relevance for the future manipulation of grain (1,3;1,4)-beta-d-glucan levels.