Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

Autor: Saranga Wijeratne, Gregor Durstewitz, Martin W. Ganal, C. Robin Buell, Mathilde Causse, Ralf Wieseke, David M. Francis, Allen Van Deynze, Jörg Plieske, John P. Hamilton, Sung Chur Sim
Přispěvatelé: Ohio State University [Columbus] (OSU), GmbH, University of California [Davis] (UC Davis), University of California, Michigan State University [East Lansing], Michigan State University System, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Ohio State University, Partenaires INRAE, United States Department of Agriculture/National Institute of Food and Agriculture (USDA/NIFA) [2008-55300-04757, 2009-85606-05673], German Federal Ministry of Education and Research (BMBF) [0315639A], Agropolis Fondation, French foundation for Agricultural Sciences and Sustainable Development
Jazyk: angličtina
Rok vydání: 2012
Předmět:
0106 biological sciences
IN-SITU HYBRIDIZATION
CULTIVATED TOMATO
LYCOPERSICON-PENNELLII
DISEASE RESISTANCE
GENOME SEQUENCE
LINKAGE MAPS
DISCOVERY
MARKERS
FRUIT
LOCI
Genetic Linkage
[SDV]Life Sciences [q-bio]
Population genetics
Plant Science
Plant Genetics
01 natural sciences
Genome
Solanum lycopersicum
Vegetables
Plant Genomics
2. Zero hunger
Genetics
0303 health sciences
Multidisciplinary
Chromosome Mapping
Agriculture
Genomics
SNP genotyping
Medicine
Genome
Plant
Research Article
DNA
Plant
Genotype
Science
Crops
Single-nucleotide polymorphism
Biology
Polymorphism
Single Nucleotide
03 medical and health sciences
Gene mapping
Genome Analysis Tools
Genetic linkage
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
030304 developmental biology
Crop Genetics
Whole genome sequencing
Computational Biology
Genetic Maps
légume
Genetic marker
Genetic Polymorphism
Population Genetics
010606 plant biology & botany
Zdroj: PLoS ONE
PLoS ONE, Public Library of Science, 2012, 7 (7), ⟨10.1371/journal.pone.0040563⟩
PLoS ONE, Vol 7, Iss 7, p e40563 (2012)
Plos One 7 (7), . (2012)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0040563⟩
Popis: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F-2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
Databáze: OpenAIRE
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