Skip to main content

Advertisement

SpringerLink
Log in

Patterns of molecular variation in a species-wide germplasm set of Brassica napus

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r 2 > Q 95 unlinked loci pairs) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers.

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

  • Basunanda P, Spiller TH, Hasan M, Gehringer A, Schondelmaier J, Lühs W, Friedt W, Snowdon RJ (2007) Marker-assisted increase of genetic diversity in a double-low seed quality winter oilseed rape genetic background. Plant Breed 126:581–587

    Article  Google Scholar 

  • Becker HC, Engqvist GM, Karlsson B (1995) Comparison of rapeseed cultivars and resynthesized lines based on allozyme and RFLP markers. Theor Appl Genet 91:62–67

    Article  CAS  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 

  • Chen BY, Heneen WK (1989) Resynthesized Brassica napus L.: a review of its potential in breeding and genetic analysis. Hereditas 111:255–263

    Article  Google Scholar 

  • Chen S, Nelson MN, Ghamkhar K, Fu T, Cowling WA (2008) Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia. Genome 51:1–10

    Article  PubMed  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Cruz VMV, Luhman R, Marek LF, Rife CL, Shoemaker RC, Brummer EC, Gardner CAC (2007) Characterization of flowering time and SSR marker analysis of spring and winter type Brassica napus L. germplasm. Euphytica 153:43–57

    Article  CAS  Google Scholar 

  • Diers BW, Osborn TC (1994) Genetic diversity of oilseed Brassica napus germ plasm based on restriction fragment length polymorphisms. Theor Appl Genet 88:662–668

    Article  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 

  • Ecke W, Clemens R, Honsdorf N, Becker HC (2010) Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.). Theor Appl Genet 120:921–931

    Article  PubMed  CAS  Google Scholar 

  • Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequilibrium and association mapping in crop plants. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement, vol 1: genomics approaches and platforms. Springer, Dordrecht, pp 97–119

    Chapter  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  PubMed  CAS  Google Scholar 

  • Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Longman Group Ltd, London

    Google Scholar 

  • Friedt W, Snowdon RJ (2009) Oilseed rape. In: Vollmann J, Rajcan, I (eds) Handbook of plant breeding, vol 4: oil crops breeding. Springer, New York, pp 91–126

    Google Scholar 

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

    Google Scholar 

  • Hasan M, Friedt W, Pons-Kühnemann J, Freitag NM, Link K, Snowdon RJ (2008) Association of gene-linked SSR markers to seed glucosinolate content in oilseed rape (Brassica napus ssp. napus). Theor Appl Genet 116:1035–1049

    Article  PubMed  CAS  Google Scholar 

  • Hasan M, Seyis F, Badani AG, Pons-Kühnemann J, Friedt W, Lühs W, Snowdon RJ (2006) Analysis of genetic diversity in the Brassica napus L. gene pool using SSR markers. Genet Resour Crop Evol 53:793–802

    Article  CAS  Google Scholar 

  • Haussmann BIG, Parzies HK, Presterl T, Sušić Z, Miedaner T (2004) Plant genetic resources in crop improvement. Plant Genet Resour 2:3–21

    Article  Google Scholar 

  • Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174:2095–2105

    Article  PubMed  CAS  Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

    Article  Google Scholar 

  • Iñiguez Luy FL, Federico ML (2011) The genetics of Brassica napus L. In: Bancroft I and Schmidt R (eds) Genetics and genomics of the Brassicaceae. Springer, New York Dordrecht Heidelberg London, pp 291–322

    Chapter  Google Scholar 

  • Kebede B, Thiagarajah M, Zimmerli C, Rahman MH (2010) Improvement of open-pollinated spring rapeseed (Brassica napus L.) through introgression of genetic diversity from winter rapeseed. Crop Sci 50:1236–1243

    Article  Google Scholar 

  • Kimber D, McGregor DI (1995) Brassica oilseeds: production and utilization. CAB International, Wallingford

    Google Scholar 

  • Li JQ, Schulz B, Stich B (2010) Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers. Euphytica 175:35–42

    Article  CAS  Google Scholar 

  • Lombard V, Baril CP, Dubreuil P, Blouet F, Zhang D (2000) Genetic relationships and fingerprinting of rapeseed cultivars by AFLP: consequences for varietal registration. Crop Sci 40:1417–1425

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Wen W (2004) Documentation for structure software: Version 2. http://pritch.bsd.uchicago.edu/software/readme_2_1/readme.html

  • Qian W, Meng J, Li M, Frauen M, Sass O, Noack J, Jung C (2006) Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed. Theor Appl Genet 113:49–54

    Article  PubMed  CAS  Google Scholar 

  • R Development Core Team (2011) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  • Rahman MH, Bennett RA, Yang RC, Kebede B, Thiagarajah MR (2011) Exploitation of the late flowering species Brassica oleracea L. for the improvement of earliness in B. napus L.: an untraditional approach. Euphytica 177:365–374

    Article  Google Scholar 

  • Ramanatha Rao V, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult 68:1–19

    Article  Google Scholar 

  • Ramsay LD, Bradshaw JE, Griffiths DW, Kearsey MJ (2001) The inheritance of quantitative traits in Brassica napus ssp. rapifera (swedes): augmented triple test cross analyses of production characters. Euphytica 121:65–72

    Article  Google Scholar 

  • Rudh A, Rogell B, Höglund J (2007) Non-gradual variation in colour morphs of the strawberry poison frog Dendrobates pumilio: genetic and geographical isolation suggest a role for selection in maintaining polymorphism. Mol Ecol 16:4284–4294

    Article  PubMed  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Snowdon RJ, Lühs W, Friedt W (2007) Oilseed rape. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 2: oilseeds. Springer, Berlin Heidelberg, pp 55–114

    Google Scholar 

  • Stich B, Melchinger AE, Frisch 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, Möhring J, Piepho HP, Heckenberger M, Buckler ES, Melchinger AE (2008) Comparison of mixed-model approaches for association mapping. Genetics 178:1745–1754

    Article  PubMed  Google Scholar 

  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  PubMed  CAS  Google Scholar 

  • Van Inghelandt D, Melchinger AE, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet 120:1289–1299

    Article  PubMed  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–30

    Article  PubMed  CAS  Google Scholar 

  • Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland

    Google Scholar 

  • Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159

    PubMed  CAS  Google Scholar 

  • Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395–420

    Article  Google Scholar 

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

  • Zapata C, Carollo C, Rodriguez S (2001) Sampling variance and distribution of the D’ measure of overall gametic disequilibrium between multiallelic loci. Ann Hum Genet 65:395–406

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Wolfgang Ecke (University of Göttingen, Germany), the Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany), Nordic Gene Bank, Alnarp (Sweden), The Centre for Genetic Resources (Netherlands), and Warwick Horticulture Research International Genetic Resources Unit (UK) for providing the seeds of the examined germplasm. Agriculture and Agri-Food Canada kindly shared the proprietary Brassica SSR markers and their map positions. We are grateful to Sarah Nele Kaul and Bent Müller for the technical assistance, as well as to the Max Planck Genome Centre Cologne for providing the genotyping facilities. The funding of this work is kindly provided by the Deutsche Forschungsgemeinschaft (DFG) and the Max Planck Society. This work was performed in the framework of the ERA-NET PG project “ASSYST”. Finally, we thank the associate editor C. Quiros and three anonymous reviewers for their valuable suggestions.

Author information

Authors and Affiliations

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

    Anja Bus, Niklas Körber & Benjamin Stich

  2. Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Rod J. Snowdon

Authors
  1. Anja Bus
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Niklas Körber
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rod J. Snowdon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Benjamin Stich
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Benjamin Stich.

Additional information

Communicated by C. Quiros.

Electronic supplementary material

Below is the link to the electronic supplementary material.

XLS (63 KB)

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bus, A., Körber, N., Snowdon, R.J. et al. Patterns of molecular variation in a species-wide germplasm set of Brassica napus . Theor Appl Genet 123, 1413–1423 (2011). https://doi.org/10.1007/s00122-011-1676-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-011-1676-7

Keywords

Search

Navigation