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.

Pre-harvest sprouting (PHS) constrains wheat production worldwide by reducing both wheat grain yield and end-use quality. TaPHS1 on wheat chromosome 3AS and TaMKK3-A on chromosome 4AL are two cloned genes with major effects on PHS resistance and they are independent from grain color (GC). In this study, we used marker-assisted backcrossing (MAB) to introgress TaPHS1 and TaMKK3-A from two PHS resistant sources—‘Tutoumai A’ and ‘AUS1408′—into a sprouting-susceptible white wheat line, NW97S186. Progeny were tested in four environments to investigate individual and combined effects of those two genes. TaPHS1 significantly reduced PHS and its effect on PHS varied with environments and gene sources. In contrast, the TaMKK3-A gene also significantly reduced PHS but its effectiveness was influenced by environments. The two genes had additive effects on PHS resistance, indicating pyramiding those two quantitative trait lici (QTLs) could increase PHS resistance. The additive effects were greater in a mild environment, such as a greenhouse, than in a dry and hot environment during maturation.

The wheat curl mite, Aceria tosichella Keifer, (WCM) is a global pest of bread wheat that reduces yields significantly. In addition, WCM carries Wheat streak mosaic virus (WSMV, family Potyviridae, genus Tritimovirus), the most significant wheat virus in North America; High Plains wheat mosaic virus (HPWMoV, genus Emaravirus, formerly High plains virus); and Triticum mosaic virus (TriMV, family Potyviridae, genus Poacevirus). Viruses carried by WCM have reduced wheat yields throughout the U.S. Great Plains for >50 yr, with average yield losses of 2-3% and occasional yield losses of 7-10%. Acaricides are ineffective against WCM, and delayed planting of winter wheat is not feasible. Five wheat breeding lines containing Cmc4, a WCM resistance gene from Aegilops tauschii, and Wsm2, a WSMV resistance gene from wheat germplasm CO960293-2 were selected from the breeding process and assessed for phenotypic reaction to WCM feeding, population increase, and the degree of WSMV, HPWMoV, and TriMV infection. Experiments determined that all five lines are resistant to WCM biotype 1 feeding and population increase, and that two breeding lines contain resistance to WSMV, HPWMoV, and TriMV infection as well. These WCM-, WSMV-, HPWMoV-, and TriMV-resistant genotypes can be used improve management of wheat yield losses from WCM–virus complexes.