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.

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.

High temperature is a major determinant of wheat development and growth and causes yield loss in many regions of the world. This study was conducted to assess heat stress effects on yield and yield related traits of wheat. The 144 recombinant inbred lines derived from the cross of Kauz (heat tolerant) and MTRWA116 (susceptible) together with some commercial cultivars were evaluated during 2006–2007, 2007–2008 under normal and heat stress (late sowing) conditions. Grain yield, head length, kernels per spike, spiklets per spike, plant height, grain filling duration, peduncle length and 1000 kernels weight were measured. The results showed a significant difference among RILs for all traits in stress and control conditions. High temperature significantly decreased all traits specially grain yield (46.63%), 1000-kernel weight (20.61%) and grain filling duration (20.42%). Grain yield was most affected and spikelets per spike was least affected (11.77%). Grain yield under heat stress was directly correlated (r = 0.49) with yield in normal condition. Head length and grain yield had the highest (93.18%) and the lowest (62.97%) heritability, respectively. Peduncle length and grain filling duration showed the highest correlation with yield under both normal and heat stress conditions suggesting that these two traits could be used as reliable screening tools for development of heat-tolerant genotypes