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High-throughput marker discovery in melon using a self-designed oligo microarray.

Ophir R, Eshed R, Harel-Beja R, Tzuri G, Portnoy V, Burger Y, Uliel S, Katzir N, Sherman A - BMC Genomics (2010)

Bottom Line: Testing the SFPs on another mapping population of melon confirmed that many of them are conserved.A portion of these SFPs are conserved and can be used in different breeding populations.Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Sciences Institute, Volcani Center, Agricultural Research Organization, Bet Dagan, Israel.

ABSTRACT

Background: Genetic maps constitute the basis of breeding programs for many agricultural organisms. The creation of these maps is dependent on marker discovery. Melon, among other crops, is still lagging in genomic resources, limiting the ability to discover new markers in a high-throughput fashion. One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different accessions can reveal differences between them--single-feature polymorphisms (SFPs). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation, using Affymetrix arrays that exist for only a few organisms. We applied this approach with some modifications for marker discovery in melon.

Results: Using a custom-designed oligonucleotide microarray based on a partial EST collection of melon, we discovered 6184 putative SFPs between the parents of our mapping population. Validation by sequencing of 245 SFPs from the two parents showed a sensitivity of around 79%. Most SFPs (81%) contained single-nucleotide polymorphisms. Testing the SFPs on another mapping population of melon confirmed that many of them are conserved.

Conclusion: Thousands of new SFPs that can be used for genetic mapping and molecular-assisted breeding in melon were discovered using a custom-designed oligo microarray. A portion of these SFPs are conserved and can be used in different breeding populations. Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources.

Show MeSH
Conservation of genetic markers between two mapping populations. Shared SFPs between two mapping populations, PI161375 (PIS)/'Piel de Sapo' (PS) and PI414723 (PI)/'Dulce'. If the same probe was found statistically significant in both comparisons, the SFP was flagged as common. The subset of intersecting SFPs is presented in a Venn diagram. The number of genes including these SFPs is presented in brackets.
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Figure 5: Conservation of genetic markers between two mapping populations. Shared SFPs between two mapping populations, PI161375 (PIS)/'Piel de Sapo' (PS) and PI414723 (PI)/'Dulce'. If the same probe was found statistically significant in both comparisons, the SFP was flagged as common. The subset of intersecting SFPs is presented in a Venn diagram. The number of genes including these SFPs is presented in brackets.

Mentions: The ability of SFPs to function as markers in different genetic backgrounds is crucial for their use in MAS, association studies and genetic mapping. As plants host large genetic diversity, we decided to test the use of a set of SFPs across different melon cultivars. We tested this question using parents of another melon mapping population, 'Piel de Sapo' and PI161375 [18]. We performed hybridizations of two biological replicates (pool of 10 plants) from each genotype on two arrays. The SFPs, i.e., statistically significant signal ratios, that were independently found in both comparisons--'Piel De Sapo' vs. PI161375 and 'Dulce' vs. PI414723 were designated as shared SFPs. In comparisons between the Spanish mapping population's parents, PI161375 and 'Piel de Sapo', and the corresponding genotypes PI414723 and 'Dulce', the number of SFPs was 6598 and 6184 in 3820 and 3849 genes, respectively (Figure 5). Using this set of genetic markers between the two cultivars ('Piel de Sapo' and 'Dulce') and the wild accessions PI414723 and PI161375, we defined the shared SFP set of mapping markers, i.e. the intersection between the 6598 SFPs that differentiate 'Piel de Sapo' from PI161375 and the 6184 SFPs that differentiate 'Dulce' from PI414723. This subset included 2213 SFPs in 1548 UniGenes. An example of five genes from this intersecting subset is illustrated in Figure 6. From the data presented in Figures 5 and 6, we concluded that SFPs can be used across different genetic backgrounds in melon.


High-throughput marker discovery in melon using a self-designed oligo microarray.

Ophir R, Eshed R, Harel-Beja R, Tzuri G, Portnoy V, Burger Y, Uliel S, Katzir N, Sherman A - BMC Genomics (2010)

Conservation of genetic markers between two mapping populations. Shared SFPs between two mapping populations, PI161375 (PIS)/'Piel de Sapo' (PS) and PI414723 (PI)/'Dulce'. If the same probe was found statistically significant in both comparisons, the SFP was flagged as common. The subset of intersecting SFPs is presented in a Venn diagram. The number of genes including these SFPs is presented in brackets.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874814&req=5

Figure 5: Conservation of genetic markers between two mapping populations. Shared SFPs between two mapping populations, PI161375 (PIS)/'Piel de Sapo' (PS) and PI414723 (PI)/'Dulce'. If the same probe was found statistically significant in both comparisons, the SFP was flagged as common. The subset of intersecting SFPs is presented in a Venn diagram. The number of genes including these SFPs is presented in brackets.
Mentions: The ability of SFPs to function as markers in different genetic backgrounds is crucial for their use in MAS, association studies and genetic mapping. As plants host large genetic diversity, we decided to test the use of a set of SFPs across different melon cultivars. We tested this question using parents of another melon mapping population, 'Piel de Sapo' and PI161375 [18]. We performed hybridizations of two biological replicates (pool of 10 plants) from each genotype on two arrays. The SFPs, i.e., statistically significant signal ratios, that were independently found in both comparisons--'Piel De Sapo' vs. PI161375 and 'Dulce' vs. PI414723 were designated as shared SFPs. In comparisons between the Spanish mapping population's parents, PI161375 and 'Piel de Sapo', and the corresponding genotypes PI414723 and 'Dulce', the number of SFPs was 6598 and 6184 in 3820 and 3849 genes, respectively (Figure 5). Using this set of genetic markers between the two cultivars ('Piel de Sapo' and 'Dulce') and the wild accessions PI414723 and PI161375, we defined the shared SFP set of mapping markers, i.e. the intersection between the 6598 SFPs that differentiate 'Piel de Sapo' from PI161375 and the 6184 SFPs that differentiate 'Dulce' from PI414723. This subset included 2213 SFPs in 1548 UniGenes. An example of five genes from this intersecting subset is illustrated in Figure 6. From the data presented in Figures 5 and 6, we concluded that SFPs can be used across different genetic backgrounds in melon.

Bottom Line: Testing the SFPs on another mapping population of melon confirmed that many of them are conserved.A portion of these SFPs are conserved and can be used in different breeding populations.Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Sciences Institute, Volcani Center, Agricultural Research Organization, Bet Dagan, Israel.

ABSTRACT

Background: Genetic maps constitute the basis of breeding programs for many agricultural organisms. The creation of these maps is dependent on marker discovery. Melon, among other crops, is still lagging in genomic resources, limiting the ability to discover new markers in a high-throughput fashion. One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different accessions can reveal differences between them--single-feature polymorphisms (SFPs). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation, using Affymetrix arrays that exist for only a few organisms. We applied this approach with some modifications for marker discovery in melon.

Results: Using a custom-designed oligonucleotide microarray based on a partial EST collection of melon, we discovered 6184 putative SFPs between the parents of our mapping population. Validation by sequencing of 245 SFPs from the two parents showed a sensitivity of around 79%. Most SFPs (81%) contained single-nucleotide polymorphisms. Testing the SFPs on another mapping population of melon confirmed that many of them are conserved.

Conclusion: Thousands of new SFPs that can be used for genetic mapping and molecular-assisted breeding in melon were discovered using a custom-designed oligo microarray. A portion of these SFPs are conserved and can be used in different breeding populations. Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources.

Show MeSH