# Evaluation of Fire Blight Resistance of Eleven Apple Rootstocks Grown in Kazakhstan Fields
## 3 Results
### Genetic Determinants Influencing Resistance to Erwinia amylovora in Apple Rootstocks  
Eleven types of apple rootstocks, developed by crossing genetically dissimilar parents, were analyzed to reveal the carriers of resistant alleles to _E. amylovora_, which causes fire blight in apple trees. The SNP markers AH0 JFXM, AH21B92, AH4 AAAGA, AH5I8 MI, and AH6R6 SQ--for confirming fire blight-resistant loci situated on LG3--and the SCAR markers AE10-375 and GE-8019--to verify the presence of the pathogen-resistant locus FB_F7--were analyzed in the present study. We identified the resistant allele of SCAR marker AE10-375 in rootstocks 'MM106', '62-396', and 'Geneva 16' (Tables 5 and S1, Figures 3 and 4). The resistant form of GE-8019 was not found to be present in the analyzed samples. The presence of dominant alleles of the markers AE10-375 and GE-8019, 375 and 397 bp in length, respectively, are indicative of resistant genotypes, as previously shown in the progeny of two crosses between the cultivar 'Fiesta' and either the 'Discovery' or 'Prima' cultivars [6; 10]. Those genotypes with high resistance to the pathogen have previously been shown to harbor resistance alleles for both markers, in contrast to less-resistant genotypes bearing a resistance allele for only one of the two markers [10]. In the present study, no specimens were found to bear resistance alleles for both markers. Figure 2: Weather conditions for two-year monitoring of apple rootstocks in the Almaty and Zhambyl regions. The researched SNP markers were identified in the 'Geneva 41', 'Geneva 16', and '62-396' rootstocks (Figure 4, Tables 5 and S1). G.41 harbors resistant alleles for all markers because the apple rootstock is a progenitor of Malus \(\times\) robusta 'Robusta 5', which is the origin of LG3 resistance [19]. The resistant form of the four markers (except AH6R6 SQ) were identified in the '62-396' rootstock, which is used only rarely for grafting of commercial cultivars in Kazakhstan compared with 'MM106' and 'M9'. There was no evidence that the 'MM106' and 'M9' rootstocks carry any of the resistant forms of SNP markers, and only MM106 was positive for the allele of SCAR marker AE10-375. G.16 was found to harbor the resistant allele for marker AH4 AAGA. None of the resistant forms of the researched markers were identified in the 'Arm18', 'B9', Zh.5, 'M9', 'B.7-35', _M. siversii_, and 'B16-20' rootstocks. _M. siversii_, randomly collected from the field, was represented by 10 different genotypes. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline \multirow{2}{*}{**Rootstock Name**} & \multicolumn{2}{c}{**SCAR Markers**} & \multicolumn{3}{c}{**SNP Markers**} \\ \cline{2-7}  & **AE10-375** & **GE-8019** & **AH0 JFKM** & **AH21B92** & **AH4 AAGA** & **AH5I8 MI** & **AH6R6 SQ** \\ \hline
62-396 & 375 bp & - & **G/T** & **A/G** & **A/C** & **C/A** & A/A \\ \hline M9 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline Apm 18 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline G.41 & - & - & **G/T** & **A/G** & **A/C** & **C/A** & **A/T** \\ \hline G.16 & 375 bp & - & T/T & G/G & **A/C** & C/C & A/A \\ \hline B.9 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline Zh.5 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline B.7-35 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline B.16-20 & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline _M. siversii_ & - & - & T/T & G/G & C/C & C/C & A/A \\ \hline MM106 & 375 bp & - & T/T & G/G & C/C & C/C & A/A \\ \hline \hline \end{tabular}
\end{table} 
Table 5: Results of SCAR amplification and SNP genotyping. Figure 3: SNP-genotyping by five markers associated with resistant loci to fire blight. The local rootstocks Zh.5 and especially _M. siversii_ are starting to become more popular in Kazakhstan because they are much better adapted to local environmental conditions. However, the genetic background of local apple rootstocks has still not been fully characterized; indeed, it has been barely researched to date. Consequently, the local breeding of pome fruit crops is based mainly on phenotypic data.