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Sci Rep. 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.

Author information

1
National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
2
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
3
Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China.
4
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
5
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
6
Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France.
7
Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
8
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. gehong@caas.cn.
9
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. hujinyong@mail.kib.ac.cn.
10
National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China. kxtang@hotmail.com.

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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