Identification, validation, and pyramiding of quantitative trait loci for resistance to crown rot in wheat

[Abstract]: Crown rot (causal organism: Fusarium pseudograminearum) is a significant disease affecting wheat in Australia. Although first reported over 60 years ago, the disease has become more prevalent in recent years due to the adoption of minimum tillage and stubble retention practices. Breeding for resistance to crown rot is difficult - phenotypic selection, which is usually done at harvest, is time-consuming, expensive, and subject to between year variability due to sensitivity to environmental conditions. For these reasons, the coupling of molecular techniques with conventional plant breeding (marker-assisted selection) has the potential to more rapidly and reliably identify genomic regions that contribute to resistance. The objective of this study was to identify, validate, and pyramid quantitative trait loci (QTL) for resistance to crown rot present in a W21MMT70 x Mendos doubled haploid wheat population. Replicated seedling trials were conducted in 2001, 2003, and 2005. In each seedling trial, W21MMT70 displayed partial resistance to crown rot whereas Mendos seedlings were susceptible. A bulked segregant analysis (BSA), using 390 simple sequence repeat (SSR) markers chosen for their coverage of the wheat genome, was initially conducted based upon the 2001 seedling trial data in an attempt to rapidly identify genomic regions associated to resistance. The BSA did not reveal any markers associated with resistance to crown rot. As a result, a full mapping study was conducted. One hundred and twenty eight (128) SSR markers were mapped across the population to produce a framework map. Previously screened AFLP markers were added to the map. Composite interval mapping revealed eight QTL associated with resistance. Of these, three (located on chromosomes 2B, 2D, and 5D) were consistently detected in each of the three seedling trials. Two QTL (on chromosomes 1A and 3B) were detected in two of the three trials. The 2D, 3B, and 5D QTL were inherited from W21MMT70, whereas the 1A and 2B QTL were inherited from Mendos. Two software programs were used to identify epistatic interactions between QTL. While the results of the two programs differed markedly, both programs detected a highly significant interaction between the W21MMT70 inherited 5D QTL and a locus on chromosome 2D inherited from Mendos. The overall effect of the epistatic interactions was not as great as the additive effects of nonepistatic QTL. Nonetheless, the presence of epistasis may indicate that, particularly in the case of 5D, the effect of this QTL may be dependent on the background into which it is introgressed. Validation of three W21MMT70-inherited QTL (on chromosomes 2D, 3B, and 5D) was conducted on three F2 populations with W21MMT70 as one of the parents. While the 5D QTL was validated in two of the three crosses, neither the 2D nor the 3B QTL were detected in any of the F2 validation populations. It is likely that the size of the F2 populations (the largest composed of 94 individuals), in conjunction with the variability that is inherent when screening for resistance to crown rot, precluded validation of these regions. Validation of the 2B Mendos-inherited QTL was conducted on a Sunco x Batavia doubled haploid population because Sunco possesses the same Triticum timopheevi 2B introgression that is present in Mendos. This validated QTL (designated Q.CR.usq-2B2) explained 11 % of the phenotypic variance in the Sunco x Batavia population. To assess the effectiveness of pyramiding QTL for resistance to crown rot, a 2-49 x W21MMT70 population was examined. A number of lines of this population performed significantly better than each of the parents in the replicated seedling trial that was conducted. Four QTL, located on chromosomes 1A, 1D, 2D, and 3B, were detected. The 1A and 1D QTL were inherited from 2-49 whereas the 2D and 3B QTL were inherited from W21MMT70. The 1A QTL from 2-49 has not been previously validated, and this QTL has been designated QCr.usq-1A1. The 3B QTL (designated QCr.usq-3B1) had the highest effect (LRS 42.1; explaining 21.0 % of the phenotypic variance) in the 2-49 x W21MMT70 population. The 2D QTL (QCr.usq-2D1) was shown to have a minor effect. The 5D QTL that was inherited from W21MMT70 in the W21MMT70 x Mendos population was not detected in the 2-49 x W21MMT70 population. A number of possible explanations for the inability to detect this QTL in the 2-49 x W21MMT70 population are discussed.