Associative transcriptomics of traits in the polyploid crop species Brassica napus

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Abstract

Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. But most crops are polyploid, making it difficult to identify the required markers and to assemble a genome sequence to order those markers. To circumvent this difficulty, we developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers representing variation in both gene sequences and gene expression, and correlate this with trait variation. Applying the method in the recently formed tetraploid crop Brassica napus, we identified genomic deletions that underlie two quantitative trait loci for glucosinolate content of seeds. The deleted regions contained orthologs of the transcription factor HAG1 (At5g61420), which controls aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. This approach facilitates the application of association genetics in a broad range of crops, even those with complex genomes.

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Figure 1: Collinearity of chromosome C2 with the genome of A. thaliana.
Figure 2: Distribution of mapped markers associating with the erucic acid trait.
Figure 3: The identification of sequence variation–based (SNP) and expression variation–based (GEM) markers providing the transcription factor HAG1 gene family as a candidate in the quantitative control of glucosinolate content of rapeseed.

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References

  1. 1

    Garrigan, D. & Hammer, M.F. Reconstructing human origins in the genomic era. Nat. Rev. Genet. 7, 669–680 (2006).

  2. 2

    Li, J.Z., Absher, D.M., Tang, H., Southwick, A.M. & Casto, A.M. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100–1104 (2008).

  3. 3

    Tian, F. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159–162 (2011).

  4. 4

    Zhao, K. et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2, 467 (2011).

  5. 5

    Atwell, S. et al. Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines. Nature 465, 627–631 (2010).

  6. 6

    Cockram, J. et al. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc. Natl. Acad. Sci. USA 107, 21611–21616 (2010).

  7. 7

    Trick, M., Long, Y., Meng, J. & Bancroft, I. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol. J. 7, 334–346 (2009).

  8. 8

    Bancroft, I. et al. Genome dissection in the polyploid crop oilseed rape by transcriptome sequencing. Nat. Biotechnol. 29, 762–766 (2011).

  9. 9

    Ng, S.B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009).

  10. 10

    Adams, K.L., Cronn, R., Percifield, R. & Wendel, J.F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100, 4649–4654 (2003).

  11. 11

    Pires, C.J. et al. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol. J. Linn. Soc. 82, 675–688 (2004).

  12. 12

    Arabidopsis Genome Initiative. Analysis of the genome of the flowering plant Arabidopsis thaliana. Nature 408, 796 (2000).

  13. 13

    Schmidt, R. & Bancroft, I. (eds.). Genetics and Genomics of the Brassicaceae. Plant Genetics and Genomics: Crops and Models, Vol. 9 (Springer, 2011).

  14. 14

    O'Neill, C.M. & Bancroft, I. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23, 233 (2000).

  15. 15

    Yang, T.J. et al. Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18, 1339 (2006).

  16. 16

    Town, C.D. et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18, 1348–1359 (2006).

  17. 17

    Cheung, F. et al. Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell 21, 1912 (2009).

  18. 18

    The Brassica rapa Genome Sequencing Project Consortium. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 1035–1039 (2011).

  19. 19

    Higgins, J., Magusin, A., Trick, M., Fraser, F. & Bancroft, I. Use of mRNA-Seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics 13, 247 (2012).

  20. 20

    Parkin, I.A.P., Sharpe, A.G. & Lydiate, D.J. Patterns of duplication within the Brassica napus genome. Genome 46, 291–303 (2003).

  21. 21

    Howell, P.M., Sharpe, A.G. & Lydiate, D.J. Homeologous loci control the accumulation of seed glucosinolates in oilseed rape (Brassica napus). Genome 46, 454–460 (2003).

  22. 22

    Hasan, M. et al. Analysis of genetic diversity in the Brassica napus L. gene pool using SSR markers. Genet. Resour. Crop Evol. 53, 793–802 (2006).

  23. 23

    Fourmann, M. et al. The two genes homologous to Arabidopsis FAE1 co-segregate with the two loci governing erucic acid content in Brassica napus. Theor. Appl. Genet. 96, 852–858 (1998).

  24. 24

    James, D.W.J. et al. Directed tagging of the Arabidopsis fatty acid elongase-1 (FAE1) gene with the maize transposon activator. Plant Cell 7, 309–319 (1995).

  25. 25

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

  26. 26

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

  27. 27

    Stokes, D. et al. An association transcriptomics approach to the prediction of hybrid performance. Mol. Breed. 26, 91–106 (2010).

  28. 28

    Hirai, M.Y. et al. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. USA 104, 6478–6483 (2007).

  29. 29

    Grabherr, M. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).

  30. 30

    Trick, M. et al. A newly developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. BMC Plant Biol. 9, 50 (2009).

  31. 31

    Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

  32. 32

    Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).

  33. 33

    Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

  34. 34

    Zhang, B. & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, 17 (2005).

  35. 35

    Langfelder, P. & Horvath, S. WGCNA: an R package for weighted gene co-expression network analysis. BMC Bioinformatics 9, 559 (2008).

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Acknowledgements

We thank The Genome Analysis Centre for generating Illumina sequence data. This work was supported by UK Biotechnology and Biological Sciences Research Council (BBSRC BB/H004351/1 (IBTI Club), BB/E017363/1, ERAPG08.008) and UK Department for Environment, Food and Rural Affairs (Defra IF0144). We would like to thank R. Snowdon, J. Barker and G. Teakle for providing germplasm. We would like to thank D. Manning and M. Turner of KWS-UK and P. Tillmann of Verband Deutscher Landwirtschaftlicher Untersuchungs und Forschungsanstalten (VDLUFA) Qualitatssicherung NIRS/NIT, Kassel, Germany, for their assistance with NIRS measurements.

Author information

I.B. and A.L.H. conceived and planned the project. A.L.H., F.F., R.W., L.C. and C.H. carried out the experiments. I.B., A.L.H., M.T., J.H. and F.F. performed data analysis. P.W. provided materials and field data. I.B. and A.L.H. wrote the manuscript and all authors reviewed it.

Correspondence to Ian Bancroft.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 11057 kb)

Supplementary Table 1

B. rapa and B. oleracea genome scaffolds forming the B. napus pseudomolecules (XLSX 93 kb)

Supplementary Table 2

Coordinates for splitting of Brassica rapa and Brassica oleracea genome assembly scaffolds (XLSX 14 kb)

Supplementary Table 3

Unigene-based map of the Brassica napus genome (XLSX 9050 kb)

Supplementary Table 4

Brassica napus accessions (XLSX 11 kb)

Supplementary Table 5

mRNAseq coverage data (XLSX 16 kb)

Supplementary Table 6

GWAS data matrix for 84 Brassica napus accessions (XLSX 22226 kb)

Supplementary Table 7

NIRS data for 53 accessions (XLSX 13 kb)

Supplementary Table 8

Structure Q matrix for K=2 populations (XLSX 12 kb)

Supplementary Table 9

WGCNA analysis (XLSX 39 kb)

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Harper, A., Trick, M., Higgins, J. et al. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30, 798–802 (2012) doi:10.1038/nbt.2302

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