Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases.

Common wheat (Triticum aestivum) is a hexaploid crop comprising three diploid sub-genomes labeled A, B, and D. The objective of this study is to investigate whether there is a discernible influence pattern from the D sub-genome with epistasis in genomic models for wheat diseases. Four genomic statistical models were employed; two models considered the linear genomic relationship of the lines. The first model (G) utilized all molecular markers, while the second model (ABD) utilized three matrices representing the A, B, and D sub-genomes. The remaining two models incorporated epistasis, one (GI) using all markers and the other (ABDI) considering markers in sub-genomes A, B, and D, including inter- and intra-sub-genome interactions. The data utilized pertained to three diseases: tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB), for synthetic hexaploid wheat (SHW) lines. The results (variance components) indicate that epistasis makes a substantial contribution to explaining genomic variation, accounting for approximately 50% in SNB and SB and only 29% for TS. In this contribution of epistasis, the influence of intra- and inter-sub-genome interactions of the D sub-genome is crucial, being close to 50% in TS and higher in SNB (60%) and SB (60%). This increase in explaining genomic variation is reflected in an enhancement of predictive ability from the G model (additive) to the ABDI model (additive and epistasis) by 9%, 5%, and 1% for SNB, SB, and TS, respectively. These results, in line with other studies, underscore the significance of the D sub-genome in disease traits and suggest a potential application to be explored in the future regarding the selection of parental crosses based on sub-genomes.

Genomic Prediction of Resistance to Tan Spot, Spot Blotch and Septoria Nodorum Blotch in Synthetic Hexaploid Wheat.

Genomic prediction combines molecular and phenotypic data in a training population to predict the breeding values of individuals that have only been genotyped. The use of genomic information in breeding programs helps to increase the frequency of favorable alleles in the populations of interest. This study evaluated the performance of BLUP (Best Linear Unbiased Prediction) in predicting resistance to tan spot, spot blotch and Septoria nodorum blotch in synthetic hexaploid wheat. BLUP was implemented in single-trait and multi-trait models with three variations: (1) the pedigree relationship matrix (A-BLUP), (2) the genomic relationship matrix (G-BLUP), and (3) a combination of the two matrices (A+G BLUP). In all three diseases, the A-BLUP model had a lower performance, and the G-BLUP and A+G BLUP were statistically similar (p ≥ 0.05). The prediction accuracy with the single trait was statistically similar (p ≥ 0.05) to the multi-trait accuracy, possibly due to the low correlation of severity between the diseases.

Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat.

Spot blotch (SB) caused by Bipolaris sorokiniana (Sacc.) Shoem is a destructive fungal disease affecting wheat and many other crops. Synthetic hexaploid wheat (SHW) offers opportunities to explore new resistance genes for SB for introgression into elite bread wheat. The objectives of our study were to evaluate a collection of 441 SHWs for resistance to SB and to identify potential new genomic regions associated with the disease. The panel exhibited high SB resistance, with 250 accessions showing resistance and 161 showing moderate resistance reactions. A genome-wide association study (GWAS) revealed a total of 41 significant marker-trait associations for resistance to SB, being located on chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5D, 6D, 7A, and 7D; yet none of them exhibited a major phenotypic effect. In addition, a partial least squares regression was conducted to validate the marker-trait associations, and 15 markers were found to be most important for SB resistance in the panel. To our knowledge, this is the first GWAS to investigate SB resistance in SHW that identified markers and resistant SHW lines to be utilized in wheat breeding.

Genome-Wide Association Study for Resistance to Tan Spot in Synthetic Hexaploid Wheat.

Synthetic hexaploid wheat (SHW) has shown effective resistance to a diversity of diseases and insects, including tan spot, which is caused by Pyrenophora tritici-repentis, being an important foliar disease that can attack all types of wheat and several grasses. In this study, 443 SHW plants were evaluated for their resistance to tan spot under controlled environmental conditions. Additionally, a genome-wide association study was conducted by genotyping all entries with the DArTSeq technology to identify marker-trait associations for tan spot resistance. Of the 443 SHW plants, 233 showed resistant and 183 moderately resistant reactions, and only 27 were moderately susceptible or susceptible to tan spot. Durum wheat (DW) parents of the SHW showed moderately susceptible to susceptible reactions. A total of 30 significant marker-trait associations were found on chromosomes 1B (4 markers), 1D (1 marker), 2A (1 marker), 2D (2 markers), 3A (4 markers), 3D (3 markers), 4B (1 marker), 5A (4 markers), 6A (6 markers), 6B (1 marker) and 7D (3 markers). Increased resistance in the SHW in comparison to the DW parents, along with the significant association of resistance with the A and B genome, supported the concept of activating epistasis interaction across the three wheat genomes. Candidate genes coding for F-box and cytochrome P450 proteins that play significant roles in biotic stress resistance were identified for the significant markers. The identified resistant SHW lines can be deployed in wheat breeding for tan spot resistance.