Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China.
BMC Plant Biol. 2020 Nov 16;20(1):522. doi: 10.1186/s12870-020-02727-3.
The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.
In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.
This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.
石蒜属包括许多具有观赏和药用价值的重要物种。多倍体化和杂交被认为是该属物种形成的模式，这意味着其具有巨大的遗传多样性。然而，缺乏有效的分子标记限制了该属的遗传分析。
本研究利用忽地笑转录组序列进行 EST-SSR 标记的挖掘，成功设计了 839 对非冗余 EST-SSR 引物。随机选择了 60 对进行验证，其中 44 对可以扩增出预期大小的产物。在红花石蒜、忽地笑、中国石蒜和安徽石蒜中评估了这 60 对引物在石蒜属物种间的跨物种转移能力，其中 38%至 77%的引物能够在这些石蒜属物种中扩增出产物。此外，在忽地笑和红花石蒜中分别选择了 20 个和 10 个扩增产物进行测序验证。所有产物均被验证为预期的 SSR。此外，选择了 15 个 SSR，包括 10 个序列验证和 5 个未验证的 SSR，用于评估 7 个红花石蒜品系的遗传多样性。其中包括 3 个不育系、3 个可育系和 1 个代表 1 个可育系后代的系。非加权配对组平均法（UPGMA）分析表明，外类群忽地笑与红花石蒜品系分离，7 个红花石蒜品系聚为 2 组，与它们的育性一致。有趣的是，即使是一个包含 34 个个体的红花石蒜系的系统发育树也几乎与育性一致。
本研究为石蒜属的遗传分析提供了 839 对非冗余 SSR 标记，这些标记具有高扩增率、可转移性和效率，将有助于石蒜属的遗传分析和育种计划。
