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Example 4
In total, 23,400 lines were screened from crosses segregating for Sm1 with ten SNP markers distributed across the Sm1 locus in order to search for extra recombinants within this region. In total, 576 putative recombinants were identified and these, plus their parental lines, were also genotyped with two Real-Time PCR markers developed from RGA 1 and RGA 2 (Table 1B) and 46 markers that included 24 SNPs from within the interval and 22 markers tightly flanking the region. The results showed that no recombination events were found between the two RGA genes and no recombinant plants were found within the small 0.067 cM region identified in the Xi19 x Robigus bi-parental mapping population. The lack of recombination within the region is due to the absence of any sequence homology between resistant and susceptible lines. Moreover, all the lines that carried the two Robigus RGA genes shared the Robigus haplotype based on the 24 markers within the target interval suggesting a single origin and a common ancestor for the Sm1 resistance locus.
Amongst the 576 lines, a sub-panel of 113 diverse lines was selected for phenotypic analysis. This sub-panel contained many recombinant plants arising from different genetic origins in order to validate any potential diagnostic SNP markers. All the recombinant plants and their parental lines were sown and genotyped in summer 2014. The presence of the two RGA genes was always shown to be 100% diagnostic for the presence of Sm1. From these 24 markers within the interval, five were found to be correlated with the presence and absence of the two RGAs (Table 1A), which makes them ideal for marker-assisted selection of the Sm1 gene.
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