Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny
Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single...
| Autores principales: | , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2017
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| Acceso en línea: | http://hdl.handle.net/20.500.11939/5073 |
| _version_ | 1855032221357834240 |
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| author | Cuenca, José Aleza, Pablo Navarro, Luis Ollitrault, Patrick |
| author_browse | Aleza, Pablo Cuenca, José Navarro, Luis Ollitrault, Patrick |
| author_facet | Cuenca, José Aleza, Pablo Navarro, Luis Ollitrault, Patrick |
| author_sort | Cuenca, José |
| collection | ReDivia |
| description | Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average 09796; s.d. 00094) between the allele ratio and two parameters [THETA angle tan(1) (y/x) and y y/(x y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 9971 correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis. |
| format | article |
| id | ReDivia5073 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia50732025-04-25T14:45:18Z Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny Cuenca, José Aleza, Pablo Navarro, Luis Ollitrault, Patrick Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average 09796; s.d. 00094) between the allele ratio and two parameters [THETA angle tan(1) (y/x) and y y/(x y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 9971 correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis. 2017-06-01T10:11:39Z 2017-06-01T10:11:39Z 2013 APR article Cuenca, J., Aleza, P., Navarro, L., & Ollitrault, P. (2013). Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny. Annals of botany, 111(4), 731-742. 0305-7364 http://hdl.handle.net/20.500.11939/5073 10.1093/aob/mct032 en openAccess Impreso |
| spellingShingle | Cuenca, José Aleza, Pablo Navarro, Luis Ollitrault, Patrick Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title | Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title_full | Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title_fullStr | Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title_full_unstemmed | Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title_short | Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny |
| title_sort | assignment of snp allelic configuration in polyploids using competitive allele specific pcr application to citrus triploid progeny |
| url | http://hdl.handle.net/20.500.11939/5073 |
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