Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

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Abstract

Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation1 and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the efficiency of predictive breeding even in the absence of a complete genome sequence.

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Figure 1: Schematic representation of sequence polymorphism types in homozygous lines.
Figure 2: Transcript abundance and comparative analysis of linkage group A1.
Figure 3: Origins of alleles of loci mapped to linkage group A1.

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Sequence Read Archive

References

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Acknowledgements

We thank The Genome Analysis Centre for generating Illumina sequence data and the Warwick HRI Genetic Resources Unit for seeds of cultivar Regent. This work was supported by UK Biotechnology and Biological Sciences Research Council (BBSRC BB/E017363/1, ERAPG08.008), UK Department for Environment, Food and Rural Affairs (Defra IF0144) and by China National Basic Research and Development Program (2006CB101600 and 2011CB109300).

Author information

I.B. and M.T. conceived and planned the project. F.F., L.C. and D.B. carried out the experiments. I.B., C.M., J.H., R.W. and M.T. performed data analysis. Y.L. and J.M. provided materials and scoring data for conventional markers on the population. X.W. and S.L. provided access to unpublished genome sequence scaffolds. I.B. and M.T. 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 Tables 1, 2 and Supplementary Figures 1–6 (PDF 1058 kb)

Supplementary Data Set 1

Marker details for the cognate linkage map (XLS 17059 kb)

Supplementary Data Set 2

Marker details for the non-cognate linkage map (XLS 1280 kb)

Supplementary Data Set 3

Base counts at IHP positions in Tapidor and Ningyou 7 (XLS 9928 kb)

Supplementary Data Set 4

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

Supplementary Data Set 5

B. rapa and B. oleracea genome scaffolds anchored to the B. napus (XLS 781 kb)

Supplementary Data Set 6

Marker alleles scored in ancestors of Tapidor and Ningyou 7 (XLS 4352 kb)

Supplementary Data Set 7

Perl script combiner.pl (TXT 20 kb)

Supplementary Data Set 8

Perl script cure_cycle.pl (TXT 2 kb)

Supplementary Data Set 9

Perl script cure_refseqs.pl (TXT 3 kb)

Supplementary Data Set 10

Perl script ihp.pl (TXT 11 kb)

Supplementary Data Set 11

Perl script tag_counter.pl (TXT 2 kb)

Supplementary Data Set 12

Perl script AC_count.pl (TXT 7 kb)

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