Background: Genetic diversity is an essential resource for breeders to improve new cultivars with desirable characteristics. Recently, genotyping-by-sequencing (GBS), a next-generation sequencing (NGS) technology that can simplify complex genomes, has now be used as a high-throughput and cost-effective molecular tool for routine breeding and screening in many crop species, including the species with a large genome.Results: We genotyped a diversity panel of 369 Iranian hexaploid wheat accessions including 270 landraces collected between 1931 and 1968 in different climate zones and 99 cultivars released between 1942 to 2014 using 16,506 GBS-based single nucleotide polymorphism (GBS-SNP) markers. The B genome had the highest number of mapped SNPs while the D genome had the lowest on both the Chinese Spring and W7984 references. Structure and cluster analyses divided the panel into three groups with two landrace groups and one cultivar group, suggesting a high differentiation between landraces and cultivars and between landraces. The cultivar group can be further divided into four subgroups with one subgroup was mostly derived from Iranian ancestor(s). Similarly, landrace groups can be further divided based on years of collection and climate zones where the accessions were collected. Molecular analysis of variance indicated that the genetic variation was larger between groups than within group.Conclusion: Obvious genetic diversity in Iranian wheat was revealed by analysis of GBS-SNPs and thus breeders can select genetically distant parents for crossing in breeding. The diverse Iranian landraces provide rich genetic sources of tolerance to biotic and abiotic stresses, and they can be useful resources for the improvement of wheat production in Iran and other countries.

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The Rht-B1b and Rht-D1b alleles, which occur at homoeologous loci on chromosomes 4B and 4D, respec-Reduced height alleles at the Rht-B1 and Rht-D1 loci have been tively, reduce sensitivity to gibberellic acid (GA), which widely incorporated into wheat (Triticum aestivum L.) cultivars with the intent of improving partitioning of assimilates to grain. Although is necessary for stem elongation (Flintham et al., 1997). generally effective at increasing yield in high yield environments, In favorable environments, the reduced demand for astheir effects under heat and drought stress have been variable. We similates by a shorter stem results in improved assimilate undertook this study to evaluate the effects of the Rht-B1b and Rhtpartitioning to the developing head, leading to higher D1b dwarfing alleles in a recombinant inbred line (RIL) spring wheat spikelet fertility and more but smaller grain per head. population under a range of soil moisture conditions. Rht-B1 and Semidwarf wheats have smaller leaves, but compensate Rht-D1 genotypes of 140 RILs derived from a cross between 'Kauz' with increased photosynthetic rates resulting in a bioand MTRWA116 were determined by polymerase chain reactions mass similar to that of tall lines (LeCain et al., 1989;(PCR). The population was evaluated for yield and agronomic traits Morgan et al., 1990;Flintham et al., 1997). in four Colorado environments under fully irrigated, partially irri-The relative yield advantage of dwarf and semidwarf gated, and rainfed conditions in 2001 and 2002. Lines with both dwarfing alleles were significantly (P Ͻ 0.01) shorter, lower yielding, and cultivars varies with spring or winter habit, genetic backlater heading in all environments compared with lines with one or no ground, and environmental conditions. The benefits of dwarfing allele. Lines with both tall alleles performed equal to or the dwarfing alleles are more pronounced in high yieldbetter (P Ͻ 0.05) than all other classes for grain yield, test weight, ing winter wheat environments (Flintham et al., 1997) and kernel weight in all environments. Among lines with a single and in high yielding spring wheat locations at latitudes dwarfing allele, those with Rht-B1b on average outyielded those with less than 40Њ (Fischer and Quail, 1990). However, under Rht-D1b in the fully irrigated environment (5432 versus 4993 kg heat and drought stress, there may be no benefit of the ha Ϫ1 , P Ͻ 0.05), but elsewhere their yields did not differ (P Ͼ 0.05).dwarfing alleles in spring wheat (Flintham et al., 1997; Desirable values for most traits occurred across a relatively wide range Nizam Uddin and Marshall, 1989; Richards, 1992a,b). of plant heights, with the best performing lines either shorter lines inRichards (1992a) concluded that grain yield does not the tall class or taller lines in the semidwarf classes. edu).Published in Crop Sci. 45:939-947 (2005).

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Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular technology for genetic and breeding applications in bread wheat (Triticum aestivum L.) and many other plant species. Although GBS can discover millions of SNPs, a high rate of missing data is a major concern for many applications. Accurate imputation of those missing data can significantly improve the utility of GBS data. This study compared imputation accuracies among four genome references including three wheat references (Chinese Spring survey sequence, W7984, and IWGSC RefSeq v1.0) and one barley reference genome by comparing imputed data derived from low-depth sequencing to actual data from high-depth sequencing. After imputation, the average number of imputed data points was the highest in the B genome (~48.99%). The D genome had the lowest imputed data points (~15.02%) but the highest imputation accuracy. Among the four reference genomes, IWGSC RefSeq v1.0 reference provided the most imputed data points, but the lowest imputation accuracy for the SNPs with < 10% minor allele frequency (MAF). The W7984 reference, however, provided the highest imputation accuracy for the SNPs with < 10% MAF.