Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK.
BMC Plant Biol. 2011 May 10;11:80. doi: 10.1186/1471-2229-11-80.
Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.
Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations.
We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.
质体基因组（或 cpDNA）多态性的特征通常用于植物的系统地理学、群体遗传学和法医学分析，但有时检测 cpDNA 变异具有挑战性，限制了这种方法的应用。在本研究中，我们通过对具有独特 cpDNA谱系的树木进行完整质体基因组测序来筛选橄榄树（Olea europaea L.）中的 cpDNA 多态性。我们的目的是开发新的标记物，用于快速基因组分析（通过多重 PCR）地中海橄榄树的 cpDNA 单倍型。
我们从头测序了 8 个橄榄质体基因组。橄榄质体谱系之间的核苷酸差异较小，不超过 0.07%。基于这些序列，开发了用于研究两个单核苷酸替换和 62 个区域（具有可变微卫星基序或其他插入缺失）长度多态性的标记物。然后，它们被用于对栽培和野生地中海橄榄树（315 个个体）的 cpDNA 变异进行基因分型。在该样本中检测到 40 个多态性位点，可区分属于已知的三个地中海 cpDNA 谱系 E1、E2 和 E3 的 22 个单倍型。栽培橄榄树的 cpDNA 变异区分能力特别低，主要为一个单倍型，但在野生种群中检测到更多的多样性。
我们提出了一种快速鉴定地中海橄榄种质资源的方法。栽培橄榄树的低变异表明，cpDNA 变异在法医分析中的应用仅限于罕见的单倍型。相比之下，野生种群中 cpDNA 的高度变异表明，我们的标记物可能对 O. europaea 的系统地理学和群体遗传学研究有用。
