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A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map.

Jacobs MM, Vosman B, Vleeshouwers VG, Visser RG, Henken B, van den Berg RG - Theor. Appl. Genet. (2009)

Bottom Line: Putative map positions arising from this analysis were validated using markers mapped in the segregating population.The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance.Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

View Article: PubMed Central - PubMed

Affiliation: Biosystematics Group, Wageningen University and Research Centre, Generaal Foulkesweg 37, Wageningen, The Netherlands. m.jacobs@senternovem.nl

ABSTRACT
Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

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Marker CD67 shows co-segregation with P. infestans resistance in populations ver03-392 and ver03-394 after digestion with HpyCH4IV and digestion with SsiI
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Fig2: Marker CD67 shows co-segregation with P. infestans resistance in populations ver03-392 and ver03-394 after digestion with HpyCH4IV and digestion with SsiI

Mentions: To verify the deduced map positions, we used markers that were expected to be (closely) linked based on their position on the potato maps (http://www.gabipd.org/database/maps.html and http://www.sgn.cornell.edu/). For each population, flanking markers were tested on the parents and all offspring that could be scored as clearly resistant or susceptible. The results are presented in Table 4. For populations ver03-392 and ver03-394 sequence similarity suggested that the resistance gene was positioned on chromosome 11. Several CAPS markers for chromosome 11 were tested, but none of those displayed any polymorphisms. The marker sequence was compared to a sequence database containing NBS profiling marker sequences that were mapped in the SHxRH potato mapping population (van der Linden et al., unpublished results), and was found to be nearly identical to a marker mapped on chromosome 6. This mapping position was confirmed by marker CD67 digested with enzyme HpyCH4IV and with enzyme SsiI that both produced a polymorphic band that co-segregated with the resistance (see Fig. 2). An extra band is visible in the resistant parent and the resistant offspring in both S. verrucosum populations.Table 4


A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map.

Jacobs MM, Vosman B, Vleeshouwers VG, Visser RG, Henken B, van den Berg RG - Theor. Appl. Genet. (2009)

Marker CD67 shows co-segregation with P. infestans resistance in populations ver03-392 and ver03-394 after digestion with HpyCH4IV and digestion with SsiI
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2812419&req=5

Fig2: Marker CD67 shows co-segregation with P. infestans resistance in populations ver03-392 and ver03-394 after digestion with HpyCH4IV and digestion with SsiI
Mentions: To verify the deduced map positions, we used markers that were expected to be (closely) linked based on their position on the potato maps (http://www.gabipd.org/database/maps.html and http://www.sgn.cornell.edu/). For each population, flanking markers were tested on the parents and all offspring that could be scored as clearly resistant or susceptible. The results are presented in Table 4. For populations ver03-392 and ver03-394 sequence similarity suggested that the resistance gene was positioned on chromosome 11. Several CAPS markers for chromosome 11 were tested, but none of those displayed any polymorphisms. The marker sequence was compared to a sequence database containing NBS profiling marker sequences that were mapped in the SHxRH potato mapping population (van der Linden et al., unpublished results), and was found to be nearly identical to a marker mapped on chromosome 6. This mapping position was confirmed by marker CD67 digested with enzyme HpyCH4IV and with enzyme SsiI that both produced a polymorphic band that co-segregated with the resistance (see Fig. 2). An extra band is visible in the resistant parent and the resistant offspring in both S. verrucosum populations.Table 4

Bottom Line: Putative map positions arising from this analysis were validated using markers mapped in the segregating population.The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance.Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

View Article: PubMed Central - PubMed

Affiliation: Biosystematics Group, Wageningen University and Research Centre, Generaal Foulkesweg 37, Wageningen, The Netherlands. m.jacobs@senternovem.nl

ABSTRACT
Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

Show MeSH