• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. May 2004; 167(1): 471–483.
PMCID: PMC1470838

Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor.

Abstract

Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.

Full Text

The Full Text of this article is available as a PDF (134K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Baudry E, Kerdelhué C, Innan H, Stephan W. Species and recombination effects on DNA variability in the tomato genus. Genetics. 2001 Aug;158(4):1725–1735. [PMC free article] [PubMed]
  • Bergelson J, Kreitman M, Stahl EA, Tian D. Evolutionary dynamics of plant R-genes. Science. 2001 Jun 22;292(5525):2281–2285. [PubMed]
  • Bishop JG, Dean AM, Mitchell-Olds T. Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci U S A. 2000 May 9;97(10):5322–5327. [PMC free article] [PubMed]
  • Bowers John E, Abbey Colette, Anderson Sharon, Chang Charlene, Draye Xavier, Hoppe Alison H, Jessup Russell, Lemke Cornelia, Lennington Jennifer, Li Zhikang, et al. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics. 2003 Sep;165(1):367–386. [PMC free article] [PubMed]
  • Bustamante Carlos D, Nielsen Rasmus, Sawyer Stanley A, Olsen Kenneth M, Purugganan Michael D, Hartl Daniel L. The cost of inbreeding in Arabidopsis. Nature. 2002 Apr 4;416(6880):531–534. [PubMed]
  • Charlesworth B. Measures of divergence between populations and the effect of forces that reduce variability. Mol Biol Evol. 1998 May;15(5):538–543. [PubMed]
  • Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993 Aug;134(4):1289–1303. [PMC free article] [PubMed]
  • Boughaleb D, Mansourati J, Genet L, Barra J, Mondine P, Blanc JJ. Stimulation cardiaque définitive après remplacement valvulaire aortique: incidence, facteurs prédictifs et pronostic à long terme. Arch Mal Coeur Vaiss. 1994 Jul;87(7):925–930. [PubMed]
  • Clegg MT, Cummings MP, Durbin ML. The evolution of plant nuclear genes. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7791–7798. [PMC free article] [PubMed]
  • Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS. Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4441–4446. [PMC free article] [PubMed]
  • Fay JC, Wyckoff GJ, Wu CI. Positive and negative selection on the human genome. Genetics. 2001 Jul;158(3):1227–1234. [PMC free article] [PubMed]
  • Gale MD, Devos KM. Plant comparative genetics after 10 years. Science. 1998 Oct 23;282(5389):656–659. [PubMed]
  • Gaut BS, Doebley JF. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809–6814. [PMC free article] [PubMed]
  • Hill WG. Estimation of linkage disequilibrium in randomly mating populations. Heredity (Edinb) 1974 Oct;33(2):229–239. [PubMed]
  • Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May;116(1):153–159. [PMC free article] [PubMed]
  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES., 4th Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11479–11484. [PMC free article] [PubMed]
  • Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992 Oct;132(2):583–589. [PMC free article] [PubMed]
  • Rozas J, Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics. 1999 Feb;15(2):174–175. [PubMed]
  • Savolainen O, Langley CH, Lazzaro BP, Fr H. Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Mol Biol Evol. 2000 Apr;17(4):645–655. [PubMed]
  • Kondrashov Fyodor A, Rogozin Igor B, Wolf Yuri I, Koonin Eugene V. Selection in the evolution of gene duplications. Genome Biol. 2002;3(2):RESEARCH0008–RESEARCH0008. [PMC free article] [PubMed]
  • Schloss J, Mitchell E, White M, Kukatla R, Bowers E, Paterson H, Kresovich S. Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet. 2002 Nov;105(6-7):912–920. [PubMed]
  • Liu F, Charlesworth D, Kreitman M. The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics. 1999 Jan;151(1):343–357. [PMC free article] [PubMed]
  • Shepard Kristen A, Purugganan Michael D. Molecular population genetics of the Arabidopsis CLAVATA2 region. The genomic scale of variation and selection in a selfing species. Genetics. 2003 Mar;163(3):1083–1095. [PMC free article] [PubMed]
  • Long AD, Langley CH. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 1999 Aug;9(8):720–731. [PMC free article] [PubMed]
  • Sunyaev SR, Lathe WC, 3rd, Ramensky VE, Bork P. SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends Genet. 2000 Aug;16(8):335–337. [PubMed]
  • McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991 Jun 20;351(6328):652–654. [PubMed]
  • Morrell Peter L, Lundy Karen E, Clegg Michael T. Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):10812–10817. [PMC free article] [PubMed]
  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161–9166. [PMC free article] [PubMed]
  • Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9650–9655. [PMC free article] [PubMed]
  • Nordborg M, Donnelly P. The coalescent process with selfing. Genetics. 1997 Jul;146(3):1185–1195. [PMC free article] [PubMed]
  • Wakeley J. The variance of pairwise nucleotide differences in two populations with migration. Theor Popul Biol. 1996 Feb;49(1):39–57. [PubMed]
  • Wakeley J, Aliacar N. Gene genealogies in a metapopulation. Genetics. 2001 Oct;159(2):893–905. [PMC free article] [PubMed]
  • Wang RL, Stec A, Hey J, Lukens L, Doebley J. The limits of selection during maize domestication. Nature. 1999 Mar 18;398(6724):236–239. [PubMed]
  • Nordborg Magnus, Borevitz Justin O, Bergelson Joy, Berry Charles C, Chory Joanne, Hagenblad Jenny, Kreitman Martin, Maloof Julin N, Noyes Tina, Oefner Peter J, et al. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2002 Feb;30(2):190–193. [PubMed]
  • Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975 Apr;7(2):256–276. [PubMed]
  • Ohta T. Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics. 1993 Aug;134(4):1271–1276. [PMC free article] [PubMed]
  • White SE, Doebley JF. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics. 1999 Nov;153(3):1455–1462. [PMC free article] [PubMed]
  • Ohta Tomoko. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16134–16137. [PMC free article] [PubMed]
  • Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE. Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci. Science. 1995 Sep 22;269(5231):1714–1718. [PubMed]
  • Wright Stephen I, Lauga Beatrice, Charlesworth Deborah. Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol Ecol. 2003 May;12(5):1247–1263. [PubMed]
  • Pollak E. On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics. 1987 Oct;117(2):353–360. [PMC free article] [PubMed]
  • Rafalski Antoni. Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol. 2002 Apr;5(2):94–100. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • GSS
    GSS
    Published GSS sequences
  • MedGen
    MedGen
    Related information in MedGen
  • Nucleotide
    Nucleotide
    Published Nucleotide sequences
  • PopSet
    PopSet
    Published population set
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...