1. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea
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Judith Burstin, Cécile Donnadieu, Grégoire Aubert, Chrystel Deulvot, Amandine Marty, Isabelle Lejeune-Hénaut, Hélène Charrel, Françoise Jacquin, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Euralis Semences, Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, and Aubert, Gregoire
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0106 biological sciences ,[SDV]Life Sciences [q-bio] ,Molecular Inversion Probe ,luzerne ,01 natural sciences ,Databases, Genetic ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,Inbreeding ,Association mapping ,pisum sativum ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,education.field_of_study ,Chromosome Mapping ,food and beverages ,Tag SNP ,single-nucleotide polymorphism ,SNP genotyping ,Seeds ,[SDE]Environmental Sciences ,Research Article ,sélection assistée par marqueurs ,Biotechnology ,Genetic Markers ,microsatellite ,Genotype ,lcsh:QH426-470 ,lcsh:Biotechnology ,Population ,medicago sativa ,Biology ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Gene mapping ,lcsh:TP248.13-248.65 ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,education ,Genotyping ,Alleles ,Crosses, Genetic ,030304 developmental biology ,crop improvement ,linkage map ,retrotransposon ,molecular marker ,Genetic diversity ,génome ,Peas ,Genetic Variation ,légume ,lcsh:Genetics ,pois ,Software ,010606 plant biology & botany - Abstract
Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.
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