Genomic profiling of plastid DNA variation in the Mediterranean olive tree.
Genomic profiling of plastid DNA variation in the Mediterranean olive tree.
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DOI：
10.1186/1471-2229-11-80
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发表时间：
2011-05-10
影响因子：
5.3
通讯作者：
Savolainen V
中科院分区：
文献类型：
--
作者：
Besnard G;Hernández P;Khadari B;Dorado G;Savolainen V
质体基因组（或 cpDNA）多态性的表征通常用于植物的系统发育地理学、群体遗传和法医分析，但检测 cpDNA 变异有时具有挑战性，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 谱系的树木的完整质体基因组进行测序，筛选了橄榄树 (Olea europaea L.) 的 cpDNA 多态性。我们的目标是开发新的标记，用于地中海橄榄树 cpDNA 单倍型的快速基因组分析（通过多重 PCR）。对 Olea 的 8 个完整 cpDNA 基因组进行了从头测序。橄榄cpDNA谱系之间的核苷酸差异较低，不超过0.07%。基于这些序列，开发了用于研究两个单核苷酸取代和 62 个区域的长度多态性（具有可变微卫星基序或其他插入缺失）的标记。然后，它们被用于对栽培和野生地中海橄榄树（315 株）的 cpDNA 变异进行基因分型。在该样本上检测到 40 个多态性位点，从而可以区分属于三个地中海 cpDNA 谱系（E1、E2 和 E3）的 22 个单倍型。对于具有一种主要单倍型的栽培橄榄树，cpDNA 变异的区分能力特别低，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稀有单倍型。相比之下，野生种群中的高 cpDNA 变异表明我们的标记可能对欧洲野生稻的系统发育地理学和种群遗传学研究有用。
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.
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影响因子：
4
作者：
BENDICH, AJ
通讯作者：
BENDICH, AJ
影响因子：
5.4
作者：
Besnard, G;Khadari, B;Bervillé, A
通讯作者：
Bervillé, A
影响因子：
4.9
作者：
Arroyo-Garcia, R.;Ruiz-Garcia, L.;Martinez-Zapater, J. M.
通讯作者：
Martinez-Zapater, J. M.
影响因子：
5.4
作者：
Besnard, G;Khadari, B;Bervillé, A
通讯作者：
Bervillé, A
DOI：
10.1080/14620316.2008.11512346
发表时间：
2008-01-01
影响因子：
1.9
作者：
Besnard, Guillaume
通讯作者：
Besnard, Guillaume