Genome divergence in Brassica rapa subspecies revealed by whole genome analysis on a doubled-haploid line of turnip

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.