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Characterisation of the late blight resistance in potato differential MaR9 reveals a qualitative resistance gene, R9a, residing in a cluster of Tm-2 (2) homologs on chromosome IX.

Jo KR, Visser RG, Jacobsen E, Vossen JH - Theor. Appl. Genet. (2015)

Bottom Line: CDP(Tm2)2 flanked R9a on the proximal side (2.9 cM).CDP(Tm2)6 and CDP(Tm2)7 fully co-segregated with resistance and had high homology to Tm-2 (2) , showing that R9a resides in a cluster of NBS-LRR genes with homology to Tm-2 (2) .Besides R9a, additional resistance of quantitative nature is found in MaR9, which remains to be genetically characterized.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.

ABSTRACT

Key message: The durable late blight resistance in potato plant Ma R9 is genetically characterized. A novel R -gene is mapped. The monogenic nature and map positions of R9 are negated and rectified. Late blight of potato (Solanum tuberosum), caused by Phytophthora infestans, can effectively be managed by genetic resistance. The MaR9 differential plant provides durable resistance to a broad spectrum of late blight strains. This resistance is brought about by at least seven genes derived from S. demissum including R1, Rpi-abpt1, R3a, R3b, R4, R8 and, so far uncharacterized resistance gene(s). Here we set out to genetically characterize this additional resistance in MaR9. Three BC1 populations derived from MaR9 were identified that segregated for IPO-C resistance but that lacked R8. One BC1 population showed a continuous scale of resistance phenotypes, suggesting that multiple quantitative resistance genes were segregating. In two other BC1 populations resistance and susceptibility were segregating in a 1:1 ratio, suggesting a single qualitative resistance gene (R9a). A chromosome IX PCR marker, 184-81, fully co-segregated with R9a. The map position of R9a on the distal end of the lower arm of chromosome IX was confirmed using PCR markers GP101 and Stm1021. Successively, cluster-directed profiling (CDP) was carried out, revealing six closely linked markers. CDP(Sw)58, CDP(Sw)59 and CDP(Sw5)10 flanked the R9a gene at the distal end (5.8 cM) and, as expected, were highly homologous to Sw-5. CDP(Tm2)2 flanked R9a on the proximal side (2.9 cM). CDP(Tm2)6 and CDP(Tm2)7 fully co-segregated with resistance and had high homology to Tm-2 (2) , showing that R9a resides in a cluster of NBS-LRR genes with homology to Tm-2 (2) . Besides R9a, additional resistance of quantitative nature is found in MaR9, which remains to be genetically characterized.

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Comparison of R9a map with R8 map and potato DM genome in the distal end of potato chromosome IX. Blue dotted arrows indicate similar or identical markers/sequences in different maps. Genetic distances in centimorgan are indicated by black arrows. The R9a gene maps proximal to the R8 locus (color figure online)
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Fig2: Comparison of R9a map with R8 map and potato DM genome in the distal end of potato chromosome IX. Blue dotted arrows indicate similar or identical markers/sequences in different maps. Genetic distances in centimorgan are indicated by black arrows. The R9a gene maps proximal to the R8 locus (color figure online)

Mentions: As described, R8 (CDPHero3 marker and AVR8 response) was absent from the 3154 population. Interestingly, when the 184-81 marker that flanked the R8 gene at 1 cM distance was tested in the 3154 population we found that this marker fully co-segregated with the resistance. This suggests that, like R8, R9a locates on chromosome IX. To verify this finding, we set out to develop additional commonly used markers (GP101, S2g3, TG591A, GP41, CT220, T0521, S1d11, S1d5-a, T1065, TG328, TG424, St_At3g23400) from the SGN and GABI databases on the long arm of chromosome IX. A cleaved amplified polymorphism (CAPS) in GP101 was found and located 2.9 cM proximal (two recombinants) relative to R9a in population 3154 (Fig. 1). A polymorphism in SSR marker Stm1021, which is present in RH9 BIN65 of the SH x RH map (Van Os et al. 2006), mapped at 20.3 cM (14 recombinants) proximal to R9a. In this interval of chromosome IX, two R gene clusters (C42 and C43) are known (Jupe et al. 2012). These clusters were targeted for R gene cluster-directed profiling (CDP; Vossen et al. 2013). Using eight Tm-22 primers, population 3154 was screened for linked markers. Three markers, CDPTm22 (120 bp), CDPTm26 (375 bp) and CDPTm27 (430 bp) were identified (Fig. 2) that mapped in close proximity to R9a. CDPTm22 marker is at 1.5 cM distance (one recombinant), proximal from R9a and the other two markers fully co-segregated with the resistance in population 3154 (Figs. 1, 2). Using Sw-5-CDP, three linked markers were found; CDPSw58, CDPSw59 and CDPSw510 (Fig. 2). All CDPSw5 markers were located at 5.8 cM (4 recombinants) to the opposite side (distal) of the CDPTm2 markers from the R9a gene (Fig. 1). The CDP markers were excised from the gel and subjected to sequence analysis. The sequence of CDPTm22 was identical to CDPTm22 found in mapping R8 gene (Jo et al. 2011; Genbank accession number JF317285.1). All three CDPTm2 markers identified showed similarity to Tm-22 and showed 90–92 % identity with PGSC0003DMG402020585. This is an NB-LRR gene which locates in the Tm-22-like cluster C42 (Jupe et al. 2012). CDPSw58, CDPSw59 and CDPSw510 were confirmed to be similar to Sw-5, an S. lycopersicon tospovirus resistance gene (Brommonschenkel and Tanksley 1997). When the CDPSw5 markers from the R9a and R8 maps were compared with the physical map of unique DMGs encoding NB–LRR-type proteins (Jupe et al. 2012), they were found in cluster C43. Marker CDPSw510 in the R9a map and CDPSw54 in R8 map had 70 and 85 % of identity to DMG400016601, respectively. There is a good agreement between the relative positions of the Tm-22 and Sw-5 homologous markers identified in the MaR9-derived BC1 population and the R8 map (Jo et al. 2011) and DMG maps (Fig. 1). In conclusion, R9a resides on the telomeric end of the southern arm of chromosome IX and locates in or near a Tm-22 cluster.Fig. 1


Characterisation of the late blight resistance in potato differential MaR9 reveals a qualitative resistance gene, R9a, residing in a cluster of Tm-2 (2) homologs on chromosome IX.

Jo KR, Visser RG, Jacobsen E, Vossen JH - Theor. Appl. Genet. (2015)

Comparison of R9a map with R8 map and potato DM genome in the distal end of potato chromosome IX. Blue dotted arrows indicate similar or identical markers/sequences in different maps. Genetic distances in centimorgan are indicated by black arrows. The R9a gene maps proximal to the R8 locus (color figure online)
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Related In: Results  -  Collection

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Fig2: Comparison of R9a map with R8 map and potato DM genome in the distal end of potato chromosome IX. Blue dotted arrows indicate similar or identical markers/sequences in different maps. Genetic distances in centimorgan are indicated by black arrows. The R9a gene maps proximal to the R8 locus (color figure online)
Mentions: As described, R8 (CDPHero3 marker and AVR8 response) was absent from the 3154 population. Interestingly, when the 184-81 marker that flanked the R8 gene at 1 cM distance was tested in the 3154 population we found that this marker fully co-segregated with the resistance. This suggests that, like R8, R9a locates on chromosome IX. To verify this finding, we set out to develop additional commonly used markers (GP101, S2g3, TG591A, GP41, CT220, T0521, S1d11, S1d5-a, T1065, TG328, TG424, St_At3g23400) from the SGN and GABI databases on the long arm of chromosome IX. A cleaved amplified polymorphism (CAPS) in GP101 was found and located 2.9 cM proximal (two recombinants) relative to R9a in population 3154 (Fig. 1). A polymorphism in SSR marker Stm1021, which is present in RH9 BIN65 of the SH x RH map (Van Os et al. 2006), mapped at 20.3 cM (14 recombinants) proximal to R9a. In this interval of chromosome IX, two R gene clusters (C42 and C43) are known (Jupe et al. 2012). These clusters were targeted for R gene cluster-directed profiling (CDP; Vossen et al. 2013). Using eight Tm-22 primers, population 3154 was screened for linked markers. Three markers, CDPTm22 (120 bp), CDPTm26 (375 bp) and CDPTm27 (430 bp) were identified (Fig. 2) that mapped in close proximity to R9a. CDPTm22 marker is at 1.5 cM distance (one recombinant), proximal from R9a and the other two markers fully co-segregated with the resistance in population 3154 (Figs. 1, 2). Using Sw-5-CDP, three linked markers were found; CDPSw58, CDPSw59 and CDPSw510 (Fig. 2). All CDPSw5 markers were located at 5.8 cM (4 recombinants) to the opposite side (distal) of the CDPTm2 markers from the R9a gene (Fig. 1). The CDP markers were excised from the gel and subjected to sequence analysis. The sequence of CDPTm22 was identical to CDPTm22 found in mapping R8 gene (Jo et al. 2011; Genbank accession number JF317285.1). All three CDPTm2 markers identified showed similarity to Tm-22 and showed 90–92 % identity with PGSC0003DMG402020585. This is an NB-LRR gene which locates in the Tm-22-like cluster C42 (Jupe et al. 2012). CDPSw58, CDPSw59 and CDPSw510 were confirmed to be similar to Sw-5, an S. lycopersicon tospovirus resistance gene (Brommonschenkel and Tanksley 1997). When the CDPSw5 markers from the R9a and R8 maps were compared with the physical map of unique DMGs encoding NB–LRR-type proteins (Jupe et al. 2012), they were found in cluster C43. Marker CDPSw510 in the R9a map and CDPSw54 in R8 map had 70 and 85 % of identity to DMG400016601, respectively. There is a good agreement between the relative positions of the Tm-22 and Sw-5 homologous markers identified in the MaR9-derived BC1 population and the R8 map (Jo et al. 2011) and DMG maps (Fig. 1). In conclusion, R9a resides on the telomeric end of the southern arm of chromosome IX and locates in or near a Tm-22 cluster.Fig. 1

Bottom Line: CDP(Tm2)2 flanked R9a on the proximal side (2.9 cM).CDP(Tm2)6 and CDP(Tm2)7 fully co-segregated with resistance and had high homology to Tm-2 (2) , showing that R9a resides in a cluster of NBS-LRR genes with homology to Tm-2 (2) .Besides R9a, additional resistance of quantitative nature is found in MaR9, which remains to be genetically characterized.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.

ABSTRACT

Key message: The durable late blight resistance in potato plant Ma R9 is genetically characterized. A novel R -gene is mapped. The monogenic nature and map positions of R9 are negated and rectified. Late blight of potato (Solanum tuberosum), caused by Phytophthora infestans, can effectively be managed by genetic resistance. The MaR9 differential plant provides durable resistance to a broad spectrum of late blight strains. This resistance is brought about by at least seven genes derived from S. demissum including R1, Rpi-abpt1, R3a, R3b, R4, R8 and, so far uncharacterized resistance gene(s). Here we set out to genetically characterize this additional resistance in MaR9. Three BC1 populations derived from MaR9 were identified that segregated for IPO-C resistance but that lacked R8. One BC1 population showed a continuous scale of resistance phenotypes, suggesting that multiple quantitative resistance genes were segregating. In two other BC1 populations resistance and susceptibility were segregating in a 1:1 ratio, suggesting a single qualitative resistance gene (R9a). A chromosome IX PCR marker, 184-81, fully co-segregated with R9a. The map position of R9a on the distal end of the lower arm of chromosome IX was confirmed using PCR markers GP101 and Stm1021. Successively, cluster-directed profiling (CDP) was carried out, revealing six closely linked markers. CDP(Sw)58, CDP(Sw)59 and CDP(Sw5)10 flanked the R9a gene at the distal end (5.8 cM) and, as expected, were highly homologous to Sw-5. CDP(Tm2)2 flanked R9a on the proximal side (2.9 cM). CDP(Tm2)6 and CDP(Tm2)7 fully co-segregated with resistance and had high homology to Tm-2 (2) , showing that R9a resides in a cluster of NBS-LRR genes with homology to Tm-2 (2) . Besides R9a, additional resistance of quantitative nature is found in MaR9, which remains to be genetically characterized.

Show MeSH
Related in: MedlinePlus