National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
Sci Rep. 2019 Apr 12;9(1):5985. doi: 10.1038/s41598-019-42428-y.
Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis 'Old Blush' (OB) and R. wichuraiana 'Basyes' Thornless' (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
玫瑰是一类重要的木本植物，具有一系列重要的特性，这些特性在传统的模式植物中无法研究。在这里，我们使用限制性位点相关 DNA 测序 (RAD-seq) 技术，为中国玫瑰‘老玫瑰’（OB）和无刺‘巴塞斯’（BT）回交后代（BC1F1）构建了高密度的连锁图谱。我们获得了 6.4363 亿对末端 reads，并鉴定出 139,834 个均匀分布在玫瑰基因组中的多态性标签。2,213 个可靠的标记被分配到 7 个连锁群（LG）中。遗传图谱的总长度为 1,027.425cM，每个标记位点的平均距离为 0.96cM。这个新的连锁图谱将额外的 1.21/23.14Mb（12.18/44.52%）的未组装 OB 支架锚定到 7 个参考假染色体上，从而显著提高了 OB 参考基因组的组装质量。我们证明，尽管这个新的连锁图谱与草莓基因组具有高度的共线性水平，但它还具有两个染色体重排，这表明它作为理解蔷薇科基因组进化情况的资源具有一定的用处。结合新发布的 OB 基因组序列，这个连锁图谱将有助于鉴定支持关键农业和生物学特性的遗传成分，因此将极大地推动玫瑰的研究和育种工作。
