Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences
Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences
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DOI：
10.1007/s11032-014-0144-x
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发表时间：
2014-12-01
影响因子：
3.1
通讯作者：
Zhou, Hua
中科院分区：
文献类型：
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作者：
Wu, Jing;Cai, Changfu;Zhou, Hua
牡丹是中国著名的观赏和药用植物，也是最近被证明具有巨大食用油生产潜力的新作物。然而，目前仅有有限的分子标记可用于该物种，这阻碍了其遗传和育种研究。本研究的目的是基于牡丹转录组序列构建表达序列标签(EST)-简单序列重复（SSR）标记。从3787个单基因序列中共鉴定出4373个EST-SSRs，平均每9.24 kb有1个SSR。二核苷酸重复序列最多（46.26%），其次是三、六、四和五核苷酸重复序列。共合成了788对引物，其中373对（47.3%）引物扩增成功，149对（39.9%）引物在一个定位群体的双亲中均多态。随机选取30个具有多态性的EST-SSR标记，对36份牡丹材料进行多态性评价，多态性信息含量在0.36 ~ 0.85之间，平均值为0.69，具有较高的信息性。可转移性研究表明，95.3%的EST-SSR标记可转移到其他9个芍药品种，从而扩大了其应用范围。此外，为了证明该方法的实用性，对56份材料进行了亲缘关系研究。聚类分析表明，主要的聚类与已知的系谱树相对应。因此，这些新发现的标记对牡丹及其近缘品种的标记辅助选择育种具有重要意义。
Tree peony is a well-known ornamental and medicinal plant in China, as well as a new crop that has been recently demonstrated to exhibit a great potential for edible oil production. However, only limited molecular markers are currently available in this species, which hinders its genetic and breeding studies. The objective of this study was to develop expressed sequence tag (EST)-simple sequence repeat (SSR) markers based on transcriptome sequences in tree peony. A total of 4,373 EST-SSRs were identified from 3,787 unigene sequences with an average of one SSR per 9.24 kb. Di-nucleotide repeats (46.26 %) were the most abundant type followed by tri-, hexa-, tetra-, and penta-nucleotide repeats. Moreover, 788 primer pairs were synthesised, out of which 373 primer pairs (47.3 %) produced successful amplifications, and 149 primer pairs (39.9 %) were polymorphic in both parents of one mapping population. The 30 polymorphic EST-SSR markers were randomly selected to assess polymorphism further in 36 tree peony accessions, in which the polymorphism information content values ranged from 0.36 to 0.85 with a mean of 0.69, thereby indicating a high level of informativeness. Transferability studies indicated that 95.3 % EST-SSR markers were transferable to nine other Paeonia species, thereby expanding their utility. In addition, as a demonstration of utility, a genetic relationship study was performed in 56 accessions. Cluster analysis using the neighbour-joining tree method demonstrated that major clusters corresponded to known pedigree trees. Thus, these newly developed markers will be valuable in facilitating marker-assisted selection breeding in tree peony and its related species.