High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping
<p>Abstract</p> <p>Background</p> <p><it>Cucurbita pepo </it>is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini an...
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| Format: | Article |
| Language: | English |
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BMC
2012-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/80 |
| _version_ | 1828271817765158912 |
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| author | Esteras Cristina Gómez Pedro Monforte Antonio J Blanca José Vicente-Dólera Nelly Roig Cristina Nuez Fernando Picó Belén |
| author_facet | Esteras Cristina Gómez Pedro Monforte Antonio J Blanca José Vicente-Dólera Nelly Roig Cristina Nuez Fernando Picó Belén |
| author_sort | Esteras Cristina |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Cucurbita pepo </it>is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.</p> <p>The first <it>Cucurbita </it>transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of <it>Cucurbita </it>and map quantitative trait <it>loci </it>(QTL).</p> <p>Results</p> <p>We herein present the construction of the first SNP-based genetic map of <it>Cucurbita pepo </it>using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. <it>pepo</it>) × Scallop (subsp. <it>ovifera</it>). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified <it>in silico </it>after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between <it>C. pepo </it>and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.</p> <p>Conclusion</p> <p>Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in <it>Cucurbita</it>. This is the first SNP-based genetic map in the <it>Cucurbita </it>genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.</p> |
| first_indexed | 2024-04-13T05:58:11Z |
| format | Article |
| id | doaj.art-e9cacc1e58f6413290bb6fae29e0e8ac |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T05:58:11Z |
| publishDate | 2012-02-01 |
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| spelling | doaj.art-e9cacc1e58f6413290bb6fae29e0e8ac2022-12-22T02:59:34ZengBMCBMC Genomics1471-21642012-02-011318010.1186/1471-2164-13-80High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mappingEsteras CristinaGómez PedroMonforte Antonio JBlanca JoséVicente-Dólera NellyRoig CristinaNuez FernandoPicó Belén<p>Abstract</p> <p>Background</p> <p><it>Cucurbita pepo </it>is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.</p> <p>The first <it>Cucurbita </it>transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of <it>Cucurbita </it>and map quantitative trait <it>loci </it>(QTL).</p> <p>Results</p> <p>We herein present the construction of the first SNP-based genetic map of <it>Cucurbita pepo </it>using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. <it>pepo</it>) × Scallop (subsp. <it>ovifera</it>). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified <it>in silico </it>after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between <it>C. pepo </it>and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.</p> <p>Conclusion</p> <p>Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in <it>Cucurbita</it>. This is the first SNP-based genetic map in the <it>Cucurbita </it>genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.</p>http://www.biomedcentral.com/1471-2164/13/80 |
| spellingShingle | Esteras Cristina Gómez Pedro Monforte Antonio J Blanca José Vicente-Dólera Nelly Roig Cristina Nuez Fernando Picó Belén High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping BMC Genomics |
| title | High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping |
| title_full | High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping |
| title_fullStr | High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping |
| title_full_unstemmed | High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping |
| title_short | High-throughput SNP genotyping in <it>Cucurbita pepo </it>for map construction and quantitative trait <it>loci </it>mapping |
| title_sort | high throughput snp genotyping in it cucurbita pepo it for map construction and quantitative trait it loci it mapping |
| url | http://www.biomedcentral.com/1471-2164/13/80 |
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