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For all other phenotypes, the most significant interval did not change between the noUFE and stringent filtering.
Under these filtering criteria, the most significant interval for avrRpt2 was found in a region nearby two R-genes.
In the case of leaf rolling at 10 ° C (Leaf roll 10), the most significant interval covered a cluster of receptor-like proteins.
For lesioning, the most significant interval encoded a chloroquine resistance transporter, which was previously shown to be important for resistance to Phytophthora brassicae (Maughan et al., 2010).
For the lesioning or yellowing phenotype (LY), there was a cluster of RING domain/U-box proteins in the most significant interval.
As a post-processing step, only the most significant interval in the cluster, i.e. the one with the smallest P-value, is kept.
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The most significant intervals for two of the phenotypes that indicated reduced chloroplast function (YEL and Chlorosis 22) contained a gene that encoded a protein that was predicted to be localized to the chloroplast.
Under the noUFE filtering, the most significant intervals for avrPhpB and avrRpt2 were found in close proximity (<10 kb) to the corresponding R-genes [ RESISTANCE TO PSEUDOMONAS SYRINGAE 5 (RPS5) and RESISTANCE TO PSEUDOMONAS SYRINGAE 2 (respectivelyctively].
This interval was also identified in association with the response to another bacterial pathogenesis factor, avrRpm1 where it was the second-most significant interval.
LOD scores were computed for the marker intervals on the chromosome containing the most significant marker interval for the significant probes to reduce the computational burden.
The most significant was interval from the end of previous treatment to entry into a phase II study.
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