Wang Dan, Zhou Qi, Le Linlin, Fu Fangfang, Wang Guibin, Cao Fuliang, Yang Xiaoming
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Plants (Basel). 2023 Jul 6;12(13):2567. doi: 10.3390/plants12132567.
As a "living fossil", ginkgo ( L.) has significant ornamental, medicinal, and timber value. However, the breeding improvement of ginkgo was limited by the lack of enough excellent germplasms and suitable molecular markers. Here, we characterized numerous polymorphic insertion/deletion (InDel) markers using RAD-seq in 12 different ginkgo cultivars. The total of 279,534 InDels identified were unequally distributed across 12 chromosomes in the ginkgo genome. Of these, 52.56% (146,919) and 47.44% (132,615) were attributed to insertions and deletions, respectively. After random selection and validation, 26 pairs of polymorphic primers were used for molecular diversity analysis in 87 ginkgo cultivars and clones. The average values of observed heterozygosity and polymorphism information were 0.625 and 0.517, respectively. The results of population structure analyses were similar to those of neighbor-joining and principal component analyses, which divided all germplasms into two distinct groups. Moreover, 11 ginkgo core collections accounted for approximately 12.64% of the total ginkgo germplasms obtained, representing well the allelic diversity of all original germplasms. Therefore, these InDels can be used for germplasm management and genetic diversity analyses in ginkgo and the core collections will be used effectively for ginkgo genetic improvement.
作为一种“活化石”，银杏（Ginkgo biloba L.）具有显著的观赏、药用和木材价值。然而，银杏的育种改良受到优良种质缺乏和合适分子标记的限制。在此，我们利用RAD-seq技术在12个不同的银杏品种中鉴定了大量多态性插入/缺失（InDel）标记。在银杏基因组中，共鉴定出279,534个InDel，它们在12条染色体上分布不均。其中，52.56%（146,919个）和47.44%（132,615个）分别归因于插入和缺失。经过随机选择和验证，26对多态性引物用于87个银杏品种和无性系的分子多样性分析。观察杂合度和多态性信息的平均值分别为0.625和0.517。群体结构分析结果与邻接法和主成分分析结果相似，将所有种质分为两个不同的组。此外，11个银杏核心种质约占所获银杏种质总数的12.64%，很好地代表了所有原始种质的等位基因多样性。因此，这些InDel可用于银杏种质管理和遗传多样性分析，核心种质将有效地用于银杏遗传改良。
