High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species
<p>Abstract</p> <p>Background</p> <p>High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing inter...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-04-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/11/65 |
| _version_ | 1828741512005943296 |
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| author | de Lima Bruno Kirst Matias Silva-Junior Orzenil B Grattapaglia Dario Faria Danielle A Pappas Georgios J |
| author_facet | de Lima Bruno Kirst Matias Silva-Junior Orzenil B Grattapaglia Dario Faria Danielle A Pappas Georgios J |
| author_sort | de Lima Bruno |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera.</p> <p>Results</p> <p>We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of <it>Eucalyptus </it>from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for <it>E. grandis</it>. A systematic assessment of <it>in silico </it>SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous <it>in silico </it>constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.</p> <p>SNP reliability was high across nine <it>Eucalyptus </it>species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased.</p> <p>Conclusions</p> <p>This study indicates that the GGGT performs well both within and across species of <it>Eucalyptus </it>notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple <it>Eucalyptus </it>species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in <it>Eucalyptus</it>.</p> |
| first_indexed | 2024-04-13T01:01:22Z |
| format | Article |
| id | doaj.art-b1f577f7c85b4cf8bba05affb366c8cb |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-13T01:01:22Z |
| publishDate | 2011-04-01 |
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| series | BMC Plant Biology |
| spelling | doaj.art-b1f577f7c85b4cf8bba05affb366c8cb2022-12-22T03:09:28ZengBMCBMC Plant Biology1471-22292011-04-011116510.1186/1471-2229-11-65High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across speciesde Lima BrunoKirst MatiasSilva-Junior Orzenil BGrattapaglia DarioFaria Danielle APappas Georgios J<p>Abstract</p> <p>Background</p> <p>High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera.</p> <p>Results</p> <p>We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of <it>Eucalyptus </it>from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for <it>E. grandis</it>. A systematic assessment of <it>in silico </it>SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous <it>in silico </it>constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.</p> <p>SNP reliability was high across nine <it>Eucalyptus </it>species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased.</p> <p>Conclusions</p> <p>This study indicates that the GGGT performs well both within and across species of <it>Eucalyptus </it>notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple <it>Eucalyptus </it>species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in <it>Eucalyptus</it>.</p>http://www.biomedcentral.com/1471-2229/11/65 |
| spellingShingle | de Lima Bruno Kirst Matias Silva-Junior Orzenil B Grattapaglia Dario Faria Danielle A Pappas Georgios J High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species BMC Plant Biology |
| title | High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species |
| title_full | High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species |
| title_fullStr | High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species |
| title_full_unstemmed | High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species |
| title_short | High-throughput SNP genotyping in the highly heterozygous genome of <it>Eucalyptus</it>: assay success, polymorphism and transferability across species |
| title_sort | high throughput snp genotyping in the highly heterozygous genome of it eucalyptus it assay success polymorphism and transferability across species |
| url | http://www.biomedcentral.com/1471-2229/11/65 |
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