A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera
A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera
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一套用于分析柑橘及相关属叶绿体 DNA 多样性的引物
DOI：
10.1093/treephys/25.6.661
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发表时间：
2005-06-01
期刊：
影响因子：
4
通讯作者：
Deng, XX
中科院分区：
文献类型：
--
作者：
Cheng, YJ;De Vicente, MC;Deng, XX
建立了柑橘叶绿体简单序列重复（cpSSR）标记，用于柑橘及其近缘属叶绿体多样性分析。利用烟草（Nicotiana tabacum L.）和拟南芥（Arabidopsis）叶绿体基因组中的14对cpSSR引物对柑橘叶绿体基因组（cpDNA）进行了分析，并以SPCC （SSR Primers for Citrus chloroplast）为前缀进行了重新编码。14对引物中有11对在柑橘、黄柳、黄柳及其部分杂种的34个基因型中存在一定程度的多态性，多态性信息含量（PIC）值在0.057 ~ 0.732之间，共鉴定出18个单倍型。利用NTSYS-pc软件对cpSSR数据进行分析，UPGMA树形图的非加权对群法（unweighted pair group method based on arithmetic means， UPGMA）得到的亲缘关系与以往的分类调查结果一致，结果表明，所有样本均可归为7个主要聚类：Citrus medica L.、Poncirus、Fortunella、C. ichangensis Blanco、C. reticulata Swingle、C. aurantifolia （Christm.）。Swingle和C. grandis （L.）等。结果表明：(1)Calamondin （C. madurensis Swingle）是金桔（Fortunella）与柑桔（C. reticulata）杂交的结果，其中金桔为母本；(2)宜昌木瓜（C. ichangensis）具有独特的分类地位；(3)本底广柑柑与萨摩柑柑果实形状和叶片形态相似，但母本不同。本底广柑的细胞质与甜橙相同，而蜜橘的细胞质与网状甜橙相同。对SPCC1的17个PCR产物和SPCC11的21个PCR产物进行了克隆和测序。结果表明，单核苷酸重复以及DNA小片段的插入和缺失与SPCC1多态性相关，而SPCC11产生的多态性主要是由于单核苷酸重复长度的变化。
Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and used to analyze chloroplast diversity of Citrus and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco (Nicotiana tabacum L.) and Arabidopsis were found useful for analyzing the Citrus chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for Citrus Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of Citrus, Fortunella, Poncirus and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e., Citrus medica L., Poncirus, Fortunella, C. ichangensis Blanco, C. reticulata Swingle, C. aurantifolia (Christm.) Swingle and C. grandis (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin (C. madurensis Swingle) is the result of hybridization between kumquat (Fortunella) and mandarin (C. reticulata), where kumquat acted as the female parent; (2) Ichang papeda (C. ichangensis) has a unique taxonomic status; and (3) although Bendiguangju mandarin (C. reticulata) and Satsuma mandarin (C. reticulata) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange (C. sinensis), whereas Satsuma mandarin has the cytoplasm of C. reticulata. Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism generated by SPCC11 was essentially due to the variation in length of the mononucleotide repeats.