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. 2019 Apr 12;9(1):5985.
doi: 10.1038/s41598-019-42428-y.

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Shubin Li  1 , Guoqian Yang  2   3   4 , Shuhua Yang  5 , Jeremy Just  6 , Huijun Yan  1 , Ningning Zhou  1 , Hongying Jian  1 , Qigang Wang  1 , Min Chen  1 , Xianqin Qiu  1 , Hao Zhang  1 , Xue Dong  2 , Xiaodong Jiang  2   3 , Yibo Sun  2   3 , Micai Zhong  2   3 , Mohammed Bendahmane  6 , Guogui Ning  7 , Hong Ge  8 , Jin-Yong Hu  9 , Kaixue Tang  10
Affiliations

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Shubin Li et al. Sci Rep. .

Abstract

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Linkage group length and marker distribution on the Version 1.0 genetic map (a) and Version 2.0 genetic map (b) of rose. Genetic map details are provided in Supplementary Table S2.
Figure 2
Figure 2
Distribution of distorted markers on the Version 1.0 rose genetic map.
Figure 3
Figure 3
Heat maps reflecting the recombination relationship between markers in each linkage group. Each cell represents the recombination rate of two markers. Yellow color indicates a lower recombination rate while red color indicates higher recombination rate.
Figure 4
Figure 4
High conservation level of synteny between the constructed genetic map and the OB reference chromosomes. (a,c) Comparison of the syntenic relationship between the seven LGs (LG1-7) constructed in this research (in black) with the seven published OB reference Chromosomes (Chr1-7, in brown). 1–6 marks the unassigned and unordered contigs in OB reference genome. (b,d) Comparison of the syntenic relationship between seven LGs published by Yan et al. (in black) with the reference OB genomes (in brown). Chromosome 0–7 marks the published OB assembly.
Figure 5
Figure 5
Comparison of the newly constructed linkage map and Fragaria vesca genome. (a,c) Comparison of the syntenic relationship between the LGs constructed in this study (LG1-7) with the seven F. vesca chromosomes (v1.1; Chr1-7). (b,d) Detailed comparison of the syntenic relationship between LG1 and LG5 with F. vesca Chr1 and Chr6 showing chromosomal rearrangements.
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References

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    1. Zhang, L. Genetic linkage mapping in tetraploid and diploid rose Ph.D thesis, Clemson University (2003).
    1. Smulders, M. J. M. et al. In Wild Crop Relatives: Genomic and Breeding Resources: Plantation and Ornamental Crops (ed. Chittaranjan Kole) 243–275 (Springer Berlin Heidelberg, 2011).

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