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Organization of the genome sequence of the polyploid crop species Brassica juncea

Nature Genetics volume 50, pages 1496–1497 (2018)Cite this article

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To the Editor — A draft genome sequence of Brassica juncea, a member of the Brassicaceae and therefore a species benefiting from the functional genomics advances in the ‘model’ species Arabidopsis thaliana, was reported recently by Yang et al.1. B. juncea is a recently formed allotetraploid, whose diploid progenitors were mesohexaploids: Brassica rapa (which contributed the A genome) and Brassica nigra (which contributed the B genome). In addition to underpinning future trait-oriented work in this important crop species, which includes both vegetable and oil types, the sequences were analyzed for characteristics of genome evolution under crop selection. For both purposes, the genome sequences must represent with high fidelity (though not perfectly in ‘draft’ form) both the gene complement and gene order of the species. As a model for addressing the challenges of achieving an adequate representation of the latter for allopolyploid crops, the construction methodology employed short shotgun sequence reads, single-molecule long reads, BioNano sequencing and high-resolution genetic mapping.

A particular problem in genetic mapping in polyploids is the confounding effects of single nucleotide polymorphisms (SNPs) resulting from interhomeolog polymorphisms (IHPs), which are much more abundant than the allelic SNPs needed for genetic (linkage) mapping. In species such as B. juncea and B. napus (which also contains the A genome contributed by a B. rapa progenitor, but in this species in combination with the C genome contributed by a Brassica oleracea progenitor), further complications arise from the mesohexaploid nature of the genomes of the diploid progenitors, resulting in interparalog polymorphisms (IPPs). However, as long as sufficient sequencing redundancy has been obtained to overcome stochastic sampling effects and differentiate allelic SNPs (which will segregate across a linkage mapping population) from IHPs and IPPs (which should be invariant), the confounding effects can be overcome. Even using transcriptome sequence data, robust methodologies have been developed in B. napus to score allelic SNPs for high-resolution linkage map construction and to underpin association genetics2,3,4.

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Fig. 1: Quality control assessment of genome sequence organization of B. juncea using genome-ordered graphical genotypes, chromosomes A1 and J1 as an example.

Data availability

The B. juncea mRNA-seq data used for production of the graphical genotypes have been deposited in the SRA data library under project ID PRJNA471033.

References

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Acknowledgements

This work was supported by the UK Biotechnology and Biological Sciences Research Council (BB/L002124/1, BB/L011751/1), including work carried out within the ERA-CAPS Research Program (BB/L027844/1). We would like to thank I. Parkin and A. Harper for their valuable comments on a draft of this manuscript.

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  1. Department of Biology, University of York, Heslington, York, UK

    Zhesi He & Ian Bancroft

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  1. Zhesi He
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  2. Ian Bancroft
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Z.H. and I.B. designed the study and analyzed the data. I.B. wrote the manuscript and Z.H. read and approved the manuscript for publication.

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Correspondence to Ian Bancroft.

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He, Z., Bancroft, I. Organization of the genome sequence of the polyploid crop species Brassica juncea. Nat Genet 50, 1496–1497 (2018). https://doi.org/10.1038/s41588-018-0239-0

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