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Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula
Article first published online: 27 SEP 2012
DOI: 10.1111/1755-0998.12021
© 2012 Blackwell Publishing Ltd
Additional Information
How to Cite
Loridon, K., Burgarella, C., Chantret, N., Martins, F., Gouzy, J., Prospéri, J.-M. and Ronfort, J. (2013), Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Molecular Ecology Resources, 13: 84–95. doi: 10.1111/1755-0998.12021
Publication History
- Issue published online: 11 DEC 2012
- Article first published online: 27 SEP 2012
- Manuscript Accepted: 20 AUG 2012
- Manuscript Revised: 16 AUG 2012
- Manuscript Received: 11 MAY 2012
Funded by
- INRA (French National Institute of Agronomical Research)
- Department of Genetics and Plant Breeding
- ARCAD
- Agropolis Foundation
References
- , , (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theoretical Applied Genetics, 119, 507–517.
- , , et al. (2004) Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science, 303, 1364–1367.
- , , , (1998) Molecular phylogenetic approach for studying life-history evolution: the ambiguous example of the genus Medicago L. Proceedings. Biological scienc, 265, 1141–1151.
- , , , (2001) Spatial effects and rare outcrossing events in Medicago truncatula (Fabaceae). Molecular Ecology, 10, 1371–1383.
- , , et al. (2011) Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences of the United States of America, 108, E864–E870.
- , , , (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249–256.
- , , , (2009) FLYSNPdb: a high-density SNP database of Drosophila melanogaster. Nucleic Acids Research, 37, D567–D570.
- , , et al. (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theoretical Applied Genetics, 123, 869–879.
- , , et al. (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Research, 15, 1496–1502.
- , , et al. (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10, 582.
- , , et al. (2008) SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis. BMC Medical Genetics, 9, 18.
- , (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Molecular Breeding, 25, 553–570.
- , , et al. (2010) Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC Genomics, 11, 468.
- (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87–112.
- , , et al. (2003) Highly parallel SNP genotyping. Cold Spring Harbor Laboratory of Quantitative Biology, 68, 69–78.
- , , et al. (2006) Illumina universal bead arrays. Methods in Enzymology, 410, 57–73.
- , , , et al. (2011) A map of local adaptation in Arabidopsis thaliana. Science, 334, 86–89.
- , , , (2011) Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations. Molecular Ecology, 20, 3540–3554.
- , , et al. (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biology, 11, 65.
- , , (2008) Array-based high-throughput DNA markers for crop improvement. Heredity, 101, 5–18.
- , , (2011) Adaptation to climate across the Arabidopsis thaliana genome. Science, 334, 83–86.
- , , , , (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11(Suppl. 1), 150–161.
- , , et al. (2005) Conservation of Arabidopsis flowering genes in model legumes. Plant Physiology, 137, 1420–1434.
- , , et al. (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theoretical Applied Genetics, 116, 945–952.
- International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNP. Nature, 449, 851–861.
- , , (2009) Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.). Molecular Breeding, 24, 165–176.
- , , (2009) FastPCR software for PCR primer and probe design and repeat search. Genes, Genomes and Genomics, 3, 1–14. [http://primerdigital.com/fastpcr.html].
- , (2007) SNP genotyping: technologies and biomedical applications. Annual Review of Biomedical Engineering, 9, 289–320.
- , , et al. (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genetics, 39, 1151–1155.
- , , , (2000) Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics, 156, 439–447.
- , , , (2009) Medium-to high-throughput SNP genotyping using VeraCode microbeads. Methods in Molecular Biology, 496, 129–142.
- , , et al. (2010) Development of genome-wide SNP assays for rice. Breeding Science, 60, 524–535.
- , (2012) EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genetics, 13, 27.
- , , , , , (2007) Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in Nod factor signaling in Medicago truncatula. Genetics, 177, 2123–2133.
- , , , , (2011) Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula. BMC Evolutionary Biology, 11, 229.
- , , , the SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208–216.
- (1987) Molecular Evolutionary Genetics. Columbia University Press, New York, New York.
- (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154, 931–942.
- , , , (2009) Quantifying adaptive evolution in the Drosophila immune system. Plos Genetics, 5, e1000698.
- , , et al. (2009) AER1, a major gene conferring resistance to Aphanomyces euteiches in Medicago truncatula. Phytopathology, 99, 203–208.
- R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
- (2002) Novel genetic mapping tools in plant: SNPs and LD-based approaches. Plant Science, 162, 329–333.
- , , , , , (2006) Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biology, 6, 28.
- , , et al. (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. , 103, 18656–18661.
- , (2000) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Krawetz S & Misener S), pp. 365–386. Humana Press, Totowa, NJ. Software available at http://fokker.wi.mit.edu/primer3/input.htm.
- , , , , (2007) Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula. Evolutionary Biology, 20, 2349–2360.
- , , , (2008) How multilocus genotypic pattern helps to understand the history of selfing populations: a case study in Medicago truncatula. Heredity, 100, 517–525.
- , , (2010) The population genomics of plant adaptation. New Phytologist, 188, 313–332.
- (1996) The Staden sequence analysis package. Molecular Biotechnology, 5, 233–241.
- (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.
- , , et al. (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding, 29, 875–886.
- (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256–276.
- , , et al. (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics, 26, 2952–2960.
- , , et al. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480, 520–524.
- , (2009) Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics, 182, 943–954.

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