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. 2013;8(3):e59562.
doi: 10.1371/journal.pone.0059562. Epub 2013 Mar 28.

Genome-wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus Mume Sieb. Et Zucc.)

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Free PMC article

Genome-wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus Mume Sieb. Et Zucc.)

Lidan Sun et al. PLoS One. .
Free PMC article

Abstract

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.

Conflict of interest statement

Competing Interests: CC is an employee of Beijing Microread Genetics Co., Ltd. The authors acknowledge Ye Tao of Majorbio, Shanghai for technical support in bioinformatics. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

Figures

Figure 1
Figure 1. Framework genetic map of P. mume ‘Fenban’×P. mume ‘Kouzi Yudie’.
Numbers to the left of each LG are marker positions identified in cM. Markers that show distorted segregation distributions are starred (*; P<0.05). Ovals indicated gaps are greater than 20 cM. SDRs are shown by boxes.
Figure 2
Figure 2. Anchoring the mei genome to the framework genetic map.
Scaffolds representing 66 Mb of assembled sequences are mapped to the genetic map with 144 SSRs. Markers and genetic distances in cM are showed on the left. Scaffold names and lengths in Kb are showed on the right. Purple scaffolds are oriented in forward direction, yellow in reverse direction, and blue not oriented.
Figure 3
Figure 3. Comparative analysis between genomes of mei and Prunus.
Comparison between mei genome (PM1 to PM8) and Prunus T×E reference map (PG1 to PG8) . Different colors represent different pseudochromosomes between the genomes of mei and Prunus. Orthologous sequences are linked by solid lines. For visibility, the syntenic relationships are revealed by four circles, each showing the syntenies of two pairs of pseudochromosomes.

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References

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Grant support

The work was supported by the State Forestry Administration of China (201004012), and Ministry of Science and Technology (2011AA100207). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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