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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.

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Number of SFPs per gene is not correlated with UniGene contig length. Box plots of UniGene contig length for each SFP/gene category. The length of the original contig from which the probes were designed. Descriptive statistics of UniGene length for each SFP/gene category were calculated. Medians of UniGene lengths are represented by horizontal thick lines in the boxes and box borders represent the 25th and 75th percentiles. Medians are approximately the same for all categories.
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Figure 4: Number of SFPs per gene is not correlated with UniGene contig length. Box plots of UniGene contig length for each SFP/gene category. The length of the original contig from which the probes were designed. Descriptive statistics of UniGene length for each SFP/gene category were calculated. Medians of UniGene lengths are represented by horizontal thick lines in the boxes and box borders represent the 25th and 75th percentiles. Medians are approximately the same for all categories.

Mentions: Based on the distribution of SFPs per gene (Figure 3), most of the genes (~90%) accumulating SFPs possessed one or two SFPs per gene. One might postulate that this is because most of the UniGenes, from which the probes present on the array were designed, are short or partial, and therefore the real number of SFPs per gene cannot be determined. However, the length of the UniGenes is variable and cannot explain the SFP/UniGene variation. For each SFP density category (one SFP per UniGene to 18 SFPs per UniGene), the mean UniGene length was approximately constant at 800 ± 300 bp (Figure 4). In other words, length medians do not increase linearly with SFP per gene category as it would be expected if number of SFPs that were found were due to UniGene length. Therefore, it is reasonable to assume that the SFP/gene distribution was the actual distribution, and it was consistent with the SFP density that has been previously reported for Arabidopsis [7].


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)

Number of SFPs per gene is not correlated with UniGene contig length. Box plots of UniGene contig length for each SFP/gene category. The length of the original contig from which the probes were designed. Descriptive statistics of UniGene length for each SFP/gene category were calculated. Medians of UniGene lengths are represented by horizontal thick lines in the boxes and box borders represent the 25th and 75th percentiles. Medians are approximately the same for all categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Number of SFPs per gene is not correlated with UniGene contig length. Box plots of UniGene contig length for each SFP/gene category. The length of the original contig from which the probes were designed. Descriptive statistics of UniGene length for each SFP/gene category were calculated. Medians of UniGene lengths are represented by horizontal thick lines in the boxes and box borders represent the 25th and 75th percentiles. Medians are approximately the same for all categories.
Mentions: Based on the distribution of SFPs per gene (Figure 3), most of the genes (~90%) accumulating SFPs possessed one or two SFPs per gene. One might postulate that this is because most of the UniGenes, from which the probes present on the array were designed, are short or partial, and therefore the real number of SFPs per gene cannot be determined. However, the length of the UniGenes is variable and cannot explain the SFP/UniGene variation. For each SFP density category (one SFP per UniGene to 18 SFPs per UniGene), the mean UniGene length was approximately constant at 800 ± 300 bp (Figure 4). In other words, length medians do not increase linearly with SFP per gene category as it would be expected if number of SFPs that were found were due to UniGene length. Therefore, it is reasonable to assume that the SFP/gene distribution was the actual distribution, and it was consistent with the SFP density that has been previously reported for Arabidopsis [7].

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