Original Article
You have free access to this content
Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

Article first published online: 3 DEC 2012
DOI: 10.1111/mec.12139
© 2012 Blackwell Publishing Ltd
Additional Information
How to Cite
Dussert, Y., Remigereau, M.-S., Fontaine, M. C., Snirc, A., Lakis, G., Stoeckel, S., Langin, T., Sarr, A. and Robert, T. (2013), Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet. Molecular Ecology, 22: 327–340. doi: 10.1111/mec.12139
Publication History
- Issue published online: 3 JAN 2013
- Article first published online: 3 DEC 2012
- Manuscript Accepted: 17 OCT 2012
- Manuscript Revised: 12 OCT 2012
- Manuscript Received: 3 AUG 2012
Corrected by:
Corrigendum: Corrigendum
Vol. 22, Issue 8, 2358, Article first published online: 3 APR 2013
References
- , , , , et al. (2008) Role of seed flow on the pattern and dynamics of pearl millet (Pennisetum glaucum [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger. Genetica, 133, 167–178.
- , , , , (2001) Construction of a BAC library of pearl millet, Pennisetum glaucum. Theoretical and Applied Genetics, 102, 1200–1205.
- , (1993) Evidence of partial reproductive barrier between wild and cultivated pearl millets (Pennisetum glaucum). Euphytica, 67, 19–26.
- (1987) Autocorrelation of gene frequencies under isolation by distance. Genetics, 117, 777–782.
- , (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London Series B, Biological Sciences, 263, 1619–1626.
- , , , , (2004) GENETIX 4.05, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier, France.
- , , (1977) The morphology and domestication of pearl millet. Economic Botany, 31, 163–174.
- , (1994) Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell, 6, 907–916.
- , , , (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Molecular Ecology Notes, 7, 747–756.
- , , , (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics, 38, 594–597.
- , , , , et al. (2012) Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication. Molecular Biology and Evolution, 29, 1199–1212.
- (2010) SMOGD: Software for the Measurement of Genetic Diversity. Molecular Ecology Resources, 10, 556–557.
- , , , (1999) The TCP domain: a motif found in proteins regulating plant growth and development. The Plant Journal, 18, 215–222.
- , (1991) Genetic analysis of the morphological differences between maize and teosinte. Genetics, 129, 285–295.
- , , (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics, 141, 333–346.
- , , (1997) The evolution of apical dominance in maize. Nature, 386, 485–488.
- , , (2006) The molecular genetics of crop domestication. Cell, 127, 1309–1321.
- , , , (2009) Spatial inference of admixture proportions and secondary contact zones. Molecular Biology and Evolution, 26, 1963–1973.
- , , , , , et al. (2012) Data from: polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet. Dryad Digital Repository, doi:10.5061/dryad.vk67d.
- , (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and Applied Genetics, 92, 832–839.
- , , (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.
- , , (2005) Arlequin ver. 3.0: An Integrated Software Package for Population Genetics Data Analysis. Evolutionary Bioinformatics Online, 1, 47–50.
- , , (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481–501.
- , , (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567–1587.
- , , (2002) Plant transposable elements: where genetics meets genomics. Nature Reviews: Genetics, 3, 329–341.
- , (2010) Spatially explicit Bayesian clustering models in population genetics. Molecular Ecology Resources, 10, 773–784.
- , , (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics, 174, 805–816.
- , , , , , et al. (2000) fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size. Science, 289, 85–88.
- (2004) Crop domestication as a long-term selection experiment. Plant Breeding Reviews, 24, 1–44.
- (2001) FSTAT, A Program to Estimate and Test Gene Diversities and Fixation Indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html. Updated from Goudet (1995).
- (1999) BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
- (1971) Agricultural origins: centers and non centers. Science, 174, 468–474.
- (2005) A standardized genetic differentiation measure. Evolution, 59, 1633–1638.
- , , , (2002) Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte. Genetics, 162, 1927–1935.
- , (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147–164.
- , (2007) CLUMPP: A Cluster Matching and Permutation Program for Dealing with Label Switching and Multimodality in Analysis of Population Structure. Bioinformatics, 23, 1801–1806.
- , , et al. (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proceedings of the National Academy of Sciences of the United States of America, 104, 1424–1429.
- , , , , (2006) A SNP caused loss of seed shattering during rice domestication. Science, 312, 1392–1396.
- , , et al. (2012a) Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication. PLoS ONE, 7(5), e36642. doi:10.1371/journal.pone.0036642.
- , , et al. (2012b) Evolutionary dynamics of cycle length in pearl millet: the role of farmer's practices and gene flow. Genetica, 139, 1367–1380.
- , (2003) Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics, 164, 1205–1219.
- , (1973) Distribution of gene frequencies as a test of the theory of selective neutrality of polymorphisms. Genetics, 74, 175–195.
- , (2009) DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data. Bioinformatics, 25, 1451–1452.
- , (2011) Transposable element origins of epigenetic gene regulation. Current Opinion in Plant Biology, 14, 156–161.
- (1994) Wild pearl millet population (Pennisetum glaucum, Poaceae) integrity in agricultural Sahelian areas. An example from Keita (Niger). Plant Systematics and Evolution, 189, 233–245.
- , , et al. (2006a) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theoretical and Applied Genetics, 114, 49–58.
- , , et al. (2006b) Genetic diversity and gene flow among pearl millet crop/weed complex: a case study. Theoretical and Applied Genetics, 113, 1003–1014.
- (1975) Conditions for the existence of clines. Genetics, 80, 595–615.
- (1978) Estimation of average heterozygosity and genetic distance for small number of individuals. Genetics, 89, 583–590.
- (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
- , , , (2008) Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci. Theoretical and Applied Genetics, 117, 489–497.
- , (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA, 14, 814–821.
- , , , , , (2000) Genetic control of domestication traits in pearl millet (Pennisetum glaucum L, Poaceae). Theoretical and Applied Genetics, 100, 147–159.
- , , (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
- , (2009) The nature of selection during plant domestication. Nature, 457, 843–848.
- , , , , , (2001) Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning. BioTechniques, 31, 355–362.
- , , et al. (2004) An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum. Theoretical and Applied Genetics, 109, 1485–1493.
- R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, Available from http://www.R-project.org/.
- , (1995) GENEPOP (version 1.2): Population Genetics Software for Exact Tests and Ecumenicism. Journal of Heredity, 86, 248–249.
- , , , , , (2006) Tuareg, a novel miniature-inverted repeat family of pearl millet (Pennisetum glaucum) related to the PIF superfamily of maize. Genetica, 128, 205–216.
- , , et al. (2011) Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PLoS ONE, 6, e22404. doi:10.1371/journal.pone.0022404.
- , , , (1991) Gametophytic competition as influencing gene flow between wild and cultivated forms of pearl millet (Pennisetum typhoïdes). Genome, 34, 195–200.
- , , et al. (2011) Pennisetum. In: Wild crop relatives: genomic and breeding resources. (ed. Kole C), pp. 217–255. Springer, Berlin Heidelberg.
- (2004) Distruct: A Program for the Graphical Display of Population Structure. Molecular Ecology Notes, 4, 137–138.
- , , (2007) Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proceedings of the National Academy of Sciences of the United States of America, 104(Suppl. 1), 8641–8648.
- (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219–1228.
- (2008) Genepop'007: A Complete Reimplementation of the Genepop Software for Windows and Linux. Molecular Ecology Resources, 8, 103–106.
- (2009) Genes and mutations underlying domestication transitions in grasses. Plant Physiology, 149, 63–70.
- , , et al. (2008) Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biology, 8, 119.
- , , et al. (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics, 40, 1023–1028.
- , , et al. (2006) Molecular characterization of the major wheat domestication gene Q. Genetics, 172, 547–555.
- , (1983) A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics, 105, 219–237.
- , , et al. (2010) Patterns of molecular and phenotypic diversity in pearl millet [Pennisetum glaucum (L.) R. Br.] from West and Central Africa and their relation to geographical and environmental parameters. BMC Plant Biology, 10, Article ID 216.
- , , , (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics, 43, 1160–1163.
- (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.
- , , (1994) ClustalW—Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22, 4673–4680.
- (1992) Enzyme diversity in pearl millet (Pennisetum glaucum). 3. Wild millet. Theoretical and Applied Genetics, 83, 736–742.
- , (1989) Enzyme diversity in pearl millet (Pennisetum glaucum). 2. Africa and India. Theoretical and Applied Genetics, 77, 634–640.
- , , , , (1999) The limits of selection during maize domestication. Nature, 398, 236–239.
- , (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370.
- , , (1995) LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Current Opinion in Genetics & Development, 5, 814–821.
- , , , , , (2005) A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter. Plant Cell, 17, 1559–1568.
- , , et al. (2009) Selection on grain shattering genes and rates of rice domestication. New Phytologist, 184, 708–720.

1365-294X/asset/MEC_centre.gif?v=1&s=a3addb330bee9658564df3325c89548d75a4238d)
