Abstract
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.
Similar content being viewed by others
References
Barro F, Marti A (1999) Response of different genotypes of Brassica carinata to microspore culture. Plant Breed 118:79–81
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 33:83–92
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL (2012) Domain enhanced lookup time accelerated BLAST. Biol Direct 7:1–12
Cheng F, Sun R, Hou X et al (2016) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nature Genet 48:1218–1224
Chun C, Park H, Na H (2011) Microspore-derived embryo formation in Radish (Raphanus sativus L.) according to nutritional and environmental conditions. Hortic Environ Biotechnol 52:530–535
Ferrie A (2003) Microspore culture of Brassica species. In: Maluszynski M (ed) Doubled haploid production in crop plants, 1st edn. Kluwer Academic Publishers, Dordrecht, pp 205–215
Ferrie AMR, Caswell KL (2011) Isolated microspore culture techniques and recent progress for haploid and doubled haploid plant production. Plant Cell Tissue Org Cult 104:301–309
Ferrie AMR, Epp DJ, Keller WA (1995) Evaluation of Brassica rapa L. genotypes for microspore culture response and identification of a highly embryogenic line. Plant Cell Rep 14:580–584
Feulner PGD, De-Kayne R (2017) Genome evolution, structural rearrangements and speciation. J Evol Biol 30:1488–1490
Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158
Gil-Humanes J, Barro F (2009) Production of Doubled Haploids in Brassica. In: Touraev A (ed) Advances in haploid production in higher plants. Springer, London, pp 65–73
Gómez-Campo C, Prakash S (1999) Origin and domestication. In: Gómez- Campo C (ed) Biology of Brassica Coenospecies. Elsevier, Amsterdam, pp 33–58
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):1192–1205
Hochholdinger F, Baldau JA (2018) Heterosis in plants. Curr Biol 28:R1075–1095
Hong SY, Lee SS (1995) Microspore culture of xBrassicoraphanus. J Kor Soc Hort Sci 36:453–459
Jeong YM, Kim N, Ahn BO et al (2016) Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes. Theor Appl Genet 129(7):1357–1372
Kim S, Park J, Yeom SI et al (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18:210
Klopsch R, Witzel K, Börner A, Schreiner M, Hanschen FS (2017) Metabolic profiling of glucosinolates and their hydrolysis products in a germplasm collection of Brassica rapa turnips. Food Res Int 100:392–403
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549
Kwon JK, Kim BD (2009) Localization of 5S and 25S rRNA genes on somatic and meiotic chromosomes in Capsicum species of chili pepper. Mol Cells 27:205–209
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:3
Lee SS, Lee SA, Yang JM, Kim JK (2011) Developing stable progenies of xBrassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture. Theor Appl Genet 122:885–891
Lee JG, Bonnema G, Zhang N, Kwak JH, de Vos RCH, Beekwilder J (2013) Evaluation of glucosinolate variation in a collection of turnip (Brassica rapa) germplasm by the analysis of intact and desulfo glucosinolates. J Agric Food Chem 61:3984–3993
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997
Lichter R (1982) Induction of haploid plants from isolated pollen of Brassica napus. Z Pflanzenphysiol 105:427–434
Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RGF, Wang X, de Ridder D, Bonnema G (2014) Beyond genomic variation—comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genom 15:250
Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14:49–61
Liu S, Liu Y, Yang X et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–479
Na H, Kwak J, Chun C (2011) The effect of plant growth regulators, activated charcoal, and AgNO3 on microspore derived embryo formation in broccoli (Brassica oleracea L. var. italica). Hortic Environ Biotechnol 52:524–529
Pang W, Li X, Chio SR et al (2015) Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis. Mol Breeding 35:54
Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH (2017) Structural variants caused by Alu insertions are associated with risks for many human diseases. Proc Natl Acad Sci 114(20):E3984–E3992
Pfosser M, Amon A, Lelley T, Heberle-Bors E (1995) Evaluation of sensitivity of flow cytometry in detecting aneuploidy in wheat using disomic and ditelosomic wheat-rye addition lines. Cytometry 21:387–393
Seo M, Sohn S, Park B, Ko H, Jin M (2014) Efficiency of microspore embryogenesis in Brassica rapa using different genotypes and culture conditions. J Plant Biotechnol 41:116–122
Smykalova I, Vetrovcova M, Klima M, Machackova I, Griga M (2006) Efficiency of microspore culture for doubled haploid production in the breeding project “Czech winter rape”. Czech J Genet Plant Breed 42:58–71
Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucl Acids Res 40(15):e115
Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039
Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB (2009) Mobile elements create structural variation: analysis of a complete human genome. Genome Res 19(9):1516–1526
Yuan SX, Liu YM, Fang ZY, Yang LM, Zhuang M, Zhang YY, Sun PT (2011) Effect of combined cold pretreatment and heat shock on microspore cultures in broccoli. Plant Breed 130:80–85
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 6:1118
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.
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
Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F, Liang J, Cai C, Liu Z, Liu B (2018) Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic Res 5:50
Acknowledgements
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).
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Park, H.R., Kang, T., Yi, G. et al. Genome divergence in Brassica rapa subspecies revealed by whole genome analysis on a doubled-haploid line of turnip. Plant Biotechnol Rep 13, 677–687 (2019). https://doi.org/10.1007/s11816-019-00565-w
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11816-019-00565-w