Skip to main content
SpringerLink
Log in

Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

The assessment of genetic diversity and structuration of germplasm is essential for the efficient organization of breeding material. The objectives of the study were to (i) examine the population structure of elite sugar beet germplasm, (ii) investigate genetic diversity within and among subgroups of elite sugar beet germplasm, and (iii) assess the extent of linkage disequilibrium (LD) within elite sugar beet germplasm. A total of 111 and 178 inbred lines from the seed and pollen parent (SP and PP) heterotic gene pools, respectively, which had been genotyped with 23 SSR markers, were used in this study. Two distinct subgroups were detected within the entire germplasm set by STRUCTURE and principal coordinate analysis (PCoA). This observation was not expected because the SP heterotic pool of sugar beet was developed out of the PP heterotic pool in the late 1970s. Our observation of high LD in elite sugar beet germplasm suggests that association mapping will be possible in the examined germplasm set using a relatively low numbers of markers. However, to reduce the problem of false-positive marker-phenotype association, it might be necessary to examine the subgroups separately or apply association mapping methods which take into account this structure.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Andersen NS, Siegismund HR, Meyer V, Jorgensen RB (2005) Low level of gene flow from cultivated beets (Beta vulgaris L. ssp vulgaris) into Danish populations of sea beet (Beta vulgaris L. ssp. maritima (L.) Arcangeli). Mol Ecol 14:1391–1405

    Article  CAS  PubMed  Google Scholar 

  • Arnaud JF, Viard F, Delescluse M, Cuguen J (2003) Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages. Proc R Soc Lond 1524:1565–1571

    Article  Google Scholar 

  • Arnaud JF, Fénart S, Gode C, Deledicque S, Touzet P, Cuguen J (2009) Fine-scale geographical structure of genetic diversity in inland wild beet populations. Mol Ecol 18:3201–3215

    Article  PubMed  Google Scholar 

  • Bartsch D, Lehnen M, Clegg J, Pohl-Orf M, Schuphan I, Ellstrand NC (1999) Impact of gene flow from cultivated beet on genetic diversity of wild sea beet populations. Mol Ecol 8:1733–1741

    Article  PubMed  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Cao WG, Hucl P, Scoles G, Chibbar RN (1998) Genetic diversity within spelta and macha wheats based on RAPD analysis. Euphytica 104:181–189

    Article  Google Scholar 

  • Desplanque B, Viard F, Bernard J, Forcioli D, Saumitou-Laprade P, Cuguen J, Dijk HV (2000) The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies. Mol Ecol 9:141–154

    Article  CAS  PubMed  Google Scholar 

  • Draycott AP (2006) Sugar beet, 1st edn. Blackwell, Oxford

    Google Scholar 

  • Duvick DN, Smith JSC, Cooper M (2004) Long-term selection in a commercial hybrid maize breeding program. Plant Breed Rev 24:109–151

    Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Fénart S, Arnaud J, Cauwer ID, Cuguen J (2008) Nuclear and cytoplasmic genetic diversity in weed beet and sugar beet accessions compared to wild relatives: new insights into the genetic relationships within the Beta vulgaris complex species. Theor Appl Genet 116:1063–1077

    Article  PubMed  Google Scholar 

  • Fernie AR, Tadmor Y, Zamir D (2006) Natural genetic variation for improving crop quality. Curr Opin Plant Biol 9:196–202

    Article  PubMed  Google Scholar 

  • Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–338

    Google Scholar 

  • Kraft T, Hansen M, Nilsson NO (2000) Linkage disequilibrium and fingerprinting in sugar beet. Theor Appl Genet 101:323–326

    Article  Google Scholar 

  • Laurent V, Devaus P, Thiel T, Viard F, Mielordt S, Touzet P, Quillet MC (2007) Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome. Theor Appl Genet 115:793–805

    Article  CAS  PubMed  Google Scholar 

  • Lewis PO, Zaykin D (2001) Genetic Data Analysis: computer program for the analysis of allelic data. Version 1.0 (d16c). http://lewis.ccb.uconn.edu/lewishome/software.html

  • Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128

    CAS  PubMed  Google Scholar 

  • Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Ndjeunga J, Bezançon G, Pham J-L, Vigouroux Y (2006) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58

    Article  CAS  PubMed  Google Scholar 

  • McGrath JM, Derrico CA, Yu Y (1999) Genetic diversity in selected, historical US sugar beet germplasm and Beta vulgaris ssp. maritima. Theor Appl Genet 98:968–976

    Article  Google Scholar 

  • McGrath JM, Trebbi D, Fenwich A, Panella L, Schulz B, Laurent V, Barnes S, Murray SC (2007) An open-source first-generation molecular genetic map from a sugar beet × table beet cross and its extension to physical mapping. Crop Sci 47(S1):S27–S44

    Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Ober ES, Luterbacher MC (2002) Genotypic variation for drought tolerance in Beta vulgaris. Ann Bot 89:917–924

    Article  PubMed  Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    Google Scholar 

  • Pritchard JK, Wen W (2004) Documentation for STRUCTURE software. The University of Chicago Press, Chicago

    Google Scholar 

  • Pritchard JK, Stephens M, Donelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  • Richards CM, Brownson M, Mitchell SE, Kresovich S, Panella LE (2004) Polymorphic microsatellite markers for inferring diversity in wild and domesticated sugar beet (Beta vulgaris). Mol Ecol Notes 4:243–245

    Article  CAS  Google Scholar 

  • Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

    Article  Google Scholar 

  • Smith JSC, Smith OS (1992) Fingerprinting crop varieties. Rev Agric Acad Press, USA

    Google Scholar 

  • Soleimani VD, Baum BR, Johnson DA (2002) AFLP and pedigree based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. Theor Appl Genet 104:350–357

    Article  CAS  PubMed  Google Scholar 

  • Stich B, Melchinger AE, Frich M, Maurer HP, Heckenberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730

    Article  PubMed  Google Scholar 

  • Stich B, Piepho HP, Schulz B, Melchinger AE (2008) Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor Appl Genet 117:947–954

    Article  PubMed  Google Scholar 

  • Tani N, Yoshimaru H, Kawahara T, Hoshi Y, Nobushima F, Yasui T (2006) Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan. BMC Ecol 6:14

    Article  PubMed  Google Scholar 

  • Viard F, Bernard J, Desplanque B (2002) Crop-weed interactions in the Beta vulgaris complex at a local scale: allelic diversity and gene flow within sugar beet fields. Theor Appl Genet 104:688–697

    Article  CAS  PubMed  Google Scholar 

  • Viard F, Arnaud JF, Delescluse M, Cuguen J (2004) Tracing back seed and pollen flow within the crop-wild Beta vulgaris complex: genetic distinctiveness vs. hot spots of hybridization over a regional scale. Mol Ecol 13:1357–1364

    Article  CAS  PubMed  Google Scholar 

  • Wilson LM, Whitt SR, Ibáňez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733

    Article  CAS  PubMed  Google Scholar 

  • Wright S (1978) Evolution and genetics of populations, vol IV. The University of Chicago Press, Chicago, p 91

    Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen D, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank the editors and the anonymous reviewers for their valuable suggestions. This study was funded by the Max Planck Society.

Author information

Authors and Affiliations

  1. Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany

    Jinquan Li & Benjamin Stich

  2. KWS SAAT AG, Grimsehlstr. 31, 37555, Einbeck, Germany

    Britta Schulz

Authors
  1. Jinquan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Britta Schulz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Benjamin Stich
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Benjamin Stich.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(DOC 548 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, J., Schulz, B. & Stich, B. Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers. Euphytica 175, 35–42 (2010). https://doi.org/10.1007/s10681-010-0161-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-010-0161-8

Keywords

Search

Navigation