Genomic Prediction Accuracy of Stripe Rust in Six Spring Wheat Populations by Modeling Genotype by Environment Interaction

Some previous studies have assessed the predictive ability of genome-wide selection on stripe (yellow) rust resistance in wheat, but the effect of genotype by environment interaction (GEI) in prediction accuracies has not been well studied in diverse genetic backgrounds. Here, we compared the predictive ability of a model based on phenotypic data only (M1), the main effect of phenotype and molecular markers (M2), and a model that incorporated GEI (M3) using three cross-validations (CV1, CV2, and CV0) scenarios of interest to breeders in six spring wheat populations. Each population was evaluated at three to eight field nurseries and genotyped with either the DArTseq technology or the wheat 90K single nucleotide polymorphism arrays, of which a subset of 1,058- 23,795 polymorphic markers were used for the analyses. In the CV1 scenario, the mean prediction accuracies of the M1, M2, and M3 models across the six populations varied from 0.11 to 0.07, from 0.22 to 0.49, and from 0.19 to 0.48, respectively. Mean accuracies obtained using the M3 model in the CV1 scenario were significantly greater than the M2 model in two populations, the same in three populations, and smaller in one population. In both the CV2 and CV0 scenarios, the mean prediction accuracies of the three models varied from 0.53 to 0.84 and were not significantly different in all populations, except the Attila/CDC Go in the CV2, where the M3 model gave greater accuracy than both the M1 and M2 models. Overall, the M3 model increased prediction accuracies in some populations by up to 12.4% and decreased accuracy in others by up to 17.4%, demonstrating inconsistent results among genetic backgrounds that require considering each population separately. This is the first comprehensive genome-wide prediction study that investigated details of the effect of GEI on stripe rust resistance across diverse spring wheat populations

Genetic and molecular studies of loose smut resistance in Durum Wheat

The most economic and effective way to control loose smut disease of wheat is by the development of resistant cultivars. This study was conducted to screen tetraploid species of wheat resistant to Ustilago tritici races, to investigate the genetic similarities among different races of U. tritici, to determine the genetic control of resistance to race T33 in three crosses and to identify molecular markers linked to loose smut resistance. About 160 selected lines of tetraploid species of Triticum carthlicum, T. dicoccoides, T. dicoccum, T. polonicum, T. turanicum, and T. turgidum were screened for resistance to three races (T33, T32, and T26). The highest percentage of resistant lines was observed in three species, T. carthlicum, T. dicoccoides, and T. dicoccum to the three races of U. tritici. T. polonicum, T. turanicum, and T. turgidum had a lower percentage of resistant lines. Twenty races of U. tritici collected from durum and bread wheat were analysed to assess the degree of similarity based on molecular genetic data. Cluster analysis indicated that races collected from durum and bread wheat did not have any consistent grouping according to the wheat species they were collected from. Three crosses (Stewart 63 x Biodur, DT662 x D93213, and D93221 x DT658)were evaluated to determine the inheritance of resistance to race T33 of U. tritici. In Stewart 63 x Biodur, resistance appeared to be dominant and under the control of more than one gene, probably one major gene along with minor gene(s). Resistance in DT662 x D93213 was dominant and controlled by a single gene whereas in D93221 x DT658, resistance was recessive and conditioned by three genes. Although, allelic studies were not conclusive, the presence of smutted progenies from crosses among the resistant parents as well as the results of molecular studies indicate that the resistance genes studied may not be allelic. To identify molecular markers linked to loose smut resistance, bulked segregant analysis was used to screen two recombinant inbred populations from the crosses Stewart 63 x Biodur and DT662 x D93213. In the Stewart 63 x Biodur population, five Amplified Fragment Length Polymorphism (AFLP) markers were identified. Two markers were on one side of a smut resistance locus at a distance of 19.3 cM whereas three markers were on the other side at a distance of 15.5 cM. Marker E32/M55R accounted for up to 41% of the disease reaction variability. Since these markers were flanking the smut resistance locus, they can be effectively used for marker-assisted selection despite being loosely linked. In DT662 x D93213, five markers including two AFLP, two wheat microsatellites (WMS) and one Sequence Characterized Amplified Region (SCAR) were identified. The SCAR marker was on the one side of a smut resistance locus at a distance of 3.2 cM and accounted for up to 64% of the disease reaction variability whereas the other markers were on the other side of the smut resistance locus at distances ranging from 5.9 cM to 35.9 cM

Phylogenetic comparison of ARGONAUTE4_9.

<p>Comparison of ARGONAUTE4_9 class of genes using a Phylogenetic tree from wheat, barley, rice, maize, sorghum and Arabidopsis.</p

Mapping of Major Fusarium Head Blight Resistance from Canadian Wheat cv. AAC Tenacious

Fusarium head blight (FHB) is one of the most devastating wheat disease due to its direct detrimental effects on grain-yield, quality and marketability. Resistant cultivars offer the most effective approach to manage FHB; however, the lack of different resistance resources is still a major bottleneck for wheat breeding programs. To identify and dissect FHB resistance, a doubled haploid wheat population produced from the Canadian spring wheat cvs AAC Innova and AAC Tenacious was phenotyped for FHB response variables incidence and severity, visual rating index (VRI), deoxynivalenol (DON) content, and agronomic traits days to anthesis (DTA) and plant height (PHT), followed by single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker genotyping. A high-density map was constructed consisting of 10,328 markers, mapped on all 21 chromosomes with a map density of 0.35 cM/marker. Together, two major quantitative trait loci for FHB resistance were identified on chromosome 2D from AAC Tenacious; one of these loci on 2DS also colocated with loci for DTA and PHT. Another major locus for PHT, which cosegregates with locus for low DON, was also identified along with many minor and epistatic loci. QTL identified from AAC Tenacious may be useful to pyramid FHB resistance

Analysis of a retro-transposon insertion in the <i>AGO802B</i> transcripts.

<p>Polymorphism as observed on agarose gel in different wheat varieties with varying reaction to pre-harvest sprouting, due to insertion of a retro-transposon insertion in the <i>AGO802B</i> transcripts.</p

Comparing wheat homoeologs.

<p>DNA sequence comparison of wheat homoeologs of <i>AGO802</i> and <i>AGO804</i>. The three wheat <i>AGO802</i> homoeologs are almost 100% identical for the sequence and <i>AGO804</i> has sequence homology of about 98% among its three homoeologs.</p