Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.
Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.
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DOI：
10.1371/journal.pone.0166969
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Nakamura Y
中科院分区：
文献类型：
--
作者：
Shimizu T;Kitajima A;Nonaka K;Yoshioka T;Ohta S;Goto S;Toyoda A;Fujiyama A;Mochizuki T;Nagasaki H;Kaminuma E;Nakamura Y
大多数本土柑橘品种被认为是天然杂交品种，但由于其广泛的遗传多样性和DNA标记的低可转移性，迄今为止仅在少数情况下确定了它们的亲本。本文利用从柑桔基因组序列资源中开发的简单序列重复和indel标记对柑桔本土品种的亲本进行了推测。使用选定的DNA标记对122个已知杂交品种进行亲子鉴定，证明它们在这些杂交品种之间具有可转移性。鉴定证实，大多数变异菌株是选择突变体，但我们发现四种库南波（柑橘nobilis）和三种立花（柑橘tachibana），我们认为它们的起源不同。利用Hardy-Weinberg平衡的DNA标记进行结构分析，推断出三个基本类群，与目前对柑橘祖先的认识一致。对101个地方柑桔品种进行基因分型分析，利用123个选择的DNA标记，通过等位基因共享和亲本鉴定，推断出萨摩、坦普尔、伊育等22个地方柑桔品种的亲本，以及昆嫩波、昌柑、昌柠檬等45个地方柑桔品种的单亲亲本。利用11个DNA标记对叶绿体和线粒体基因组进行基因分型分析，将其细胞质基因型分为18类，并推断出种子和花粉亲本的组合。似然比分析以显著分数验证了推断的父母关系。重建的家谱鉴定出Kishu、kunenbo、yuzu、koji、酸橙、舞蹈、kobeni mikan、甜橙、立花、克利奥帕特拉、柳叶柑和柚子等12种品种，这些品种在这些地方品种的发生中发挥了关键作用。根据最近的研究，推断出的本地品种的亲缘关系证实了它们的杂交起源。
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.
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