Species-diagnostic markers in Larix spp. based on RAM and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications
Species-diagnostic markers in Larix spp. based on RAM and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications
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DOI：
10.1007/s11295-005-0007-z
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发表时间：
2005-10-01
影响因子：
2.4
通讯作者：
Isabel, Nathalie
中科院分区：
文献类型：
--
作者：
Gros-Louis, Marie-Claude;Bousquet, Jean;Isabel, Nathalie
开发了来自细胞核、叶绿体和线粒体基因组的遗传标记，以明确地区分北美东部集约林业中使用的四种落叶松物种 [Larix laricina (Du Roi) K. Koch、Larix decidua (Mill.)、Larix kaempferi (Lamb.) Sarg. 和 Larix sibirica (Ledeb.)]。 9 个随机扩增多态性 DNA (RAPD) 片段具有良好的诊断价值，12 个核基因中有 3 个被发现具有固定的种间多态性，涉及总共 17 个单核苷酸多态性 (SNP) 和 2 个插入缺失。对 5 个 mtDNA 内含子（cox1-intron1、matR-intron1、nad1-intron b/c、nad3-intron1 和 nad5-intron 1）和 4 个 cpDNA 区域（matK、trnL-intron、trn T-trnL 和 trnL-trnF 基因间间隔区）进行测序，鉴定出 4 个物种之间具有固定种间差异的 14 个位点。包括10个落叶松属物种在内，核基因每47个核苷酸位点检测到1个多态性位点，cpDNA每283个位点检测到1个多态性位点，mtDNA每374个位点检测到1个多态性位点。该属的系统发育可以根据在两个 cpDNA 基因间区域和四个 mtDNA 内含子中检测到的 10 个物种之间的变异来估计。 cpDNA 和 mtDNA 系统发育与三大类群之间存在一致性：北美、北欧亚和南亚类群。西伯利亚 L. sibirica 的位置在细胞器基因组之间有所不同。它在 cpDNA 树上与南亚物种重新组合，但在 mtDNA 树上与北欧亚物种重新组合。为了简化四个主要落叶松物种之间诊断性 DNA 序列多态性的检测，根据不同基因组中鉴定的多态性开发了切割扩增多态性序列 (CAPS) 测定。测试了 17 种引物-酶组合，并选择了 6 种，因为它们的信息量很高。这些新的物种特异性诊断标记应可用于北半球集约化林业中使用的落叶松育种材料和杂交种群的认证。
Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among four larch species [Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had good diagnostic value, and 3 out of 12 nuclear genes were found to harbor fixed interspecific polymorphisms implicating a total of 17 single nucleotide polymorphisms (SNPs) and 2 indels. The sequencing of five mtDNA introns (cox1-intron1, matR-intron1, nad1-intron b/c, nad3-intron1, and nad5-intron 1) and four cpDNA regions (matK, trnL-intron, trn T-trnL and trnL-trnF intergenic spacers) resulted in the identification of 14 sites with fixed interspecific differences among the four species. Including the ten Larix species, one polymorphic site per 47 nucleotide sites sampled was observed for nuclear genes, one per 283 sites for cpDNA, and one per 374 sites for mtDNA. The phylogeny of the genus could be estimated from variation among the ten species detected in two cpDNA intergenic regions and four mtDNA introns. There was congruence between cpDNA and mtDNA phylogenies with three large groups delineated: the North American, North Eurasian, and South Asian taxa. The position of L. sibirica differed between organelle genomes. It was regrouped with South Asian species on the cpDNA tree, but with its North Eurasian congencrics on the mtDNA tree. To simplify the detection of diagnostic DNA sequence polymorphisms among the four main Larix species, cleaved amplified polymorphic sequence (CAPS) assays were developed from the polymorphisms identified in the various genomes. Seventeen primer-enzyme combinations were tested, and six were selected for their high level of informativeness. These new species-specific diagnostic markers should be useful for the certification of larch breeding materials and hybrid stocks used in intensive forestry in the northern hemisphere.