Genome divergence in Brassica rapa subspecies revealed by whole genome analysis on a doubled-haploid line of turnip
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Subspecies of Brassica rapa are morphologically and genetically diverse, and include a variety of fresh vegetables grown worldwide. Among them, turnip (B. rapa subsp. rapa) produces a large bulbous taproot, and thus is primarily consumed as a root vegetable in Europe and Asia. In comparison to Chinese cabbage (B. rapa subsp. pekinensis), however, genetic analysis and breeding of turnip is hampered in practice due in part to scarcity of useful genetic resources. In this study, we produced a doubled haploid (DH) line of Ganghwa turnip, an heirloom specialty crop in Korea that is usually propagated by open pollination. Microspores were isolated from young flower buds of Ganghwa turnip, and shoots and roots were sequentially regenerated in vitro. Chromosome doubling was induced with the colchicine treatment, and verified by flow cytometry analysis. The G14 DH line displayed uniformity in overall morphology compared to heterogeneous commercial Ganghwa turnips. The whole genome of G14 was sequenced on an Illumina HiSeq 4000 platform, and the reads mapped onto the B. rapa reference genome identified 1,163,399 SNPs and 779,700 indels. Despite high similarity in overall genome sequence, turnips and Chinese cabbage have different compositions of transposable elements (TEs). In particular, long terminal repeat (LTR) retrotransposons are more enriched in turnips than in Chinese cabbage genomes, in which the gypsy elements are classified as major LTR sequences in the turnip genome. These findings suggest that subspecies-specific TE divergence is in part responsible for huge phenotypic variations observed within the same species.
KeywordsBrassica rapa Turnip Doubled haploid Whole genome sequencing Molecular marker
This work was supported by the Agri-Bio Industry Technology Development Program (117045-3) from Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry, and Fisheries (IPET), Ministry of Agriculture, Food and Rural Affairs (MAFRA), and by the Next-Generation BioGreen 21 Program (PJ01120301) and the National Agricultural Genome Program (PJ013440) by Rural Development Administration (RDA).
- Belandres HR, Waminal NE, Hwang YJ, Park BS, Lee SS, Huh JH, Kim HH (2015) FISH karyotype and GISH meiotic pairing analyses of a stable intergeneric hybrid xBrassicoraphanus line BB#5. Kor J Hortic Sci Technol 33:83–92Google Scholar
- Goubert C, Modolo L, Vieira C, ValienteMoro C, Mavingui P, Boulesteix M (2015) De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol 7(4):1192–1205PubMedPubMedCentralCrossRefGoogle Scholar
- Hong SY, Lee SS (1995) Microspore culture of xBrassicoraphanus. J Kor Soc Hort Sci 36:453–459Google Scholar
- Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997Google Scholar
- Yuan S, Su Y, Liu Y, Li Z, Fang Z, Yang L, Zhuang M, Zhang Y, Lv H, Sun P (2015) Chromosome doubling of microspore-derived plants from cabbage (Brassica oleracea var. capitate L.) and broccoli (Brassica oleracea var. italic L.). Front Plant Sci 6:1118Google Scholar
- Zhang QJ, Gao LZ (2017) Rapid and recent evolution of LTR retrotransposons drives rice genome evolution during the speciation of AA-genome Oryza species. G3 7(6):1875–1885.Google Scholar
- Zhang N, Zhao J, Lens F, de Visser J, Menamo T, Fang W, Xiao D, Bucher J, Basnet RK, Lin K, Cheng F, Wang X, Bonnema G (2014) Morphology, carbohydrate composition and vernalization response in a genetically diverse collection of Asian and European turnips (Brassica rapa. subsp. rapa). PLoS One 9:e114241. https://doi.org/10.1371/journal.pone.0114241 CrossRefPubMedPubMedCentralGoogle Scholar