SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping
<p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP d...
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| Format: | Article |
| Language: | English |
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BMC
2012-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/13 |
| _version_ | 1818346561476755456 |
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| author | Ollitrault Patrick Terol Javier Garcia-Lor Andres Bérard Aurélie Chauveau Aurélie Froelicher Yann Belzile Caroline Morillon Raphaël Navarro Luis Brunel Dominique Talon Manuel |
| author_facet | Ollitrault Patrick Terol Javier Garcia-Lor Andres Bérard Aurélie Chauveau Aurélie Froelicher Yann Belzile Caroline Morillon Raphaël Navarro Luis Brunel Dominique Talon Manuel |
| author_sort | Ollitrault Patrick |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus <it>Citrus </it>of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated <it>Citrus </it>species.</p> <p>Results</p> <p>Fifty-four accessions covering the main <it>Citrus </it>species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within <it>C. maxima, C. medica, C. reticulata </it>and <it>C. micrantha</it>. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in <it>C. medica, C. maxima </it>and wild <it>Citrus </it>species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the <it>C. reticulata </it>diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.</p> <p>Conclusions</p> <p>A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole <it>Citrus </it>gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around <it>C. maxima, C. medica </it>and <it>C. reticulata </it>as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in <it>Citrus </it>and genetic association in <it>C. reticulata</it>.</p> |
| first_indexed | 2024-12-13T17:20:13Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
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| spelling | doaj.art-8071f85b0b4c45f0b68934ee1da2554c2022-12-21T23:37:19ZengBMCBMC Genomics1471-21642012-01-011311310.1186/1471-2164-13-13SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mappingOllitrault PatrickTerol JavierGarcia-Lor AndresBérard AurélieChauveau AurélieFroelicher YannBelzile CarolineMorillon RaphaëlNavarro LuisBrunel DominiqueTalon Manuel<p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus <it>Citrus </it>of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated <it>Citrus </it>species.</p> <p>Results</p> <p>Fifty-four accessions covering the main <it>Citrus </it>species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within <it>C. maxima, C. medica, C. reticulata </it>and <it>C. micrantha</it>. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in <it>C. medica, C. maxima </it>and wild <it>Citrus </it>species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the <it>C. reticulata </it>diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.</p> <p>Conclusions</p> <p>A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole <it>Citrus </it>gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around <it>C. maxima, C. medica </it>and <it>C. reticulata </it>as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in <it>Citrus </it>and genetic association in <it>C. reticulata</it>.</p>http://www.biomedcentral.com/1471-2164/13/13 |
| spellingShingle | Ollitrault Patrick Terol Javier Garcia-Lor Andres Bérard Aurélie Chauveau Aurélie Froelicher Yann Belzile Caroline Morillon Raphaël Navarro Luis Brunel Dominique Talon Manuel SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping BMC Genomics |
| title | SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping |
| title_full | SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping |
| title_fullStr | SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping |
| title_full_unstemmed | SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping |
| title_short | SNP mining in <it>C. clementina </it>BAC end sequences; transferability in the <it>Citrus </it>genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping |
| title_sort | snp mining in it c clementina it bac end sequences transferability in the it citrus it genus rutaceae phylogenetic inferences and perspectives for genetic mapping |
| url | http://www.biomedcentral.com/1471-2164/13/13 |
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