Abstract
High-density genetic maps play a vital role in dissecting genetic components of biologically or agronomically important traits and molecular marker-assisted selection breeding, especially for a species with limited genomic information. Tree Peony (Paeonia suffruticosa Andr. Moutan DC.) is a traditional flowering plant in China, with important ornamental value, which have been spread around the world. However, less genetic and genomic information is available for the tree peony molecular studies. Here, we performed restriction site-associated DNA sequencing (RADseq) of an F1 population, derived from a traditional variety “Qing Long Wo Mo Chi (QL)” and a variety “Mo Zi Lian (MZL)”. High-density genetic maps were developed using RADseq markers for female (1471 markers) and male (793 markers) parents. They covered 965.69 and 870.21 cM, with the average marker intervals of 0.66 and 1.10 cM along the seven and five linkage groups (LGs), respectively. Furthermore, the identified markers were assigned to 1671 bins, representing the unique genetic positions in LGs, and inter-marker distances smaller than 5 cM covered 97.93% of genetic maps. This study suggests that rapid de novo construction of genetic maps in peony could be conducted through RADseq approach, which provides an important tool for further linkage mapping and genomic structure analysis, and enable development of molecular markers for molecular breeding in tree peony.
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Abbreviations
- RADseq:
-
restriction site-associated DNA sequencing
- MZL:
-
Mo Zi Lian
- QL:
-
Qing Long Wo Mo Chi
- SSR:
-
simple sequence repeat
- AFLP:
-
amplified fragment length polymorphism
- RAPD:
-
random amplified polymorphic DNA
- EST:
-
expressed sequence tag
- SNP:
-
single nucleotide polymorphism
- NGS:
-
next-generation sequencing
- GBS:
-
genotyping-by-sequencing
- ddRADseq:
-
double digest RADseq
- SLAFseq:
-
specific locus amplified fragment sequencing
- Gb:
-
gigabases
- LG:
-
linkage group
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Acknowledgments
We are grateful to all participants of the Agriculture Department at BGI.
Data archiving statement
The sequencing data of 122 samples, including 120 F1 progenies and two parental lines, from this study is currently being submitted to NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) under the BioProject accession PRJNA529307 with Run accession numbers from SRR8936609 to SRR8936730.
Funding
The work was supported by Science, Technology and Innovation Commission of Shenzhen Municipality under grant no. JCYJ20160331150844452 and no. JCYJ20150831201123287 and Luoyang Municipal Government of China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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JH and GZ conceived and designed the project. SZL, ZW, EW, and JH collected the plant materials and performed the experiments. SML, KY, YL, XN, XJ, GH, JW, and SC analyzed the data. SML, KY, SZL, JH, and GZ wrote the paper. All authors read and consented to the final version of the manuscript.
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Li, S., Lv, S., Yu, K. et al. Construction of a high-density genetic map of tree peony (Paeonia suffruticosa Andr. Moutan) using restriction site associated DNA sequencing (RADseq) approach. Tree Genetics & Genomes 15, 63 (2019). https://doi.org/10.1007/s11295-019-1367-0
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DOI: https://doi.org/10.1007/s11295-019-1367-0