背景:猕猴桃(Actinidiaceae家族)是中国和新西兰经济上重要的果树。这是一种典型的雌雄异株植物,经过频繁的自然杂交,以及猕猴桃属的染色体倍性多样性,导致种间和种内性状之间更高的遗传差异和园艺多样性。这种多样性为育种提供了丰富的遗传基础。中国不仅是猕猴桃属物种的原始中心,也是其分布中心,居住最驯化的物种:A.chinensisvar。中国,A.中国变种。deliciosa,A.阿古塔,和一夫多妻制。然而,关于猕猴桃植物DNA标记的应用和遗传基础的研究相对较少。通过结合来自叶绿体特异性SNP和核SCoT(nSCoT)标记的信息,我们可以发现遗传变异的互补方面,人口结构,和进化关系。在这项研究中,从9个cpDNA候选对中选择一个叶绿体DNA(cpDNA)标记对。选择了20个nSCoT标记,并用于评估55种猕猴桃植物(猕猴桃)的种群结构和叶绿体特异性DNA单倍型多样性,包括20个中国A.中国,22个A.chinensisvar样品。deliciosa,11个阿古塔的样本,和两个多边形的样本,根据从中国收集的形态学观察。
结果:对于叶绿体特异性SNP标记,55个样品之间的平均遗传距离为0.26,对于nSCoT标记为0.57。Mantel检验显示出非常小的相关性(r=0.21)。使用贝叶斯分析将55个样本分为不同的亚群,带算术平均值的未加权对组方法(UPGMA),和主成分分析(PCA)方法,分别。基于对205个可变位点的分析,共观察到15种叶绿体特异性DNA单倍型,有助于更高水平的多态性,Hd为0.78。大多数叶绿体特异性DNA单倍型多样性分布在种群中,但在种群内也观察到显著的多样性。H1由24个样本共享,其中包括12个中国的变种。中国和12个中国的变种。deliciosa,表明H1是55个叶绿体特异性序列中的一种古老的显性单倍型。H2可能没有进一步演化。其余的单倍型是罕见和独特的,其中一些似乎是特定品种的专属,并且经常在单个个体中检测到。例如,H15单倍型仅在多利马A中发现。
结论:叶绿体特异性SNP标记解释的群体遗传变异比nSCoTs解释的具有更大的功效,叶绿体特异性DNA单倍型是最有效的。A.chinensisvar之间的基因流似乎更为明显。中国和A.chinensisvar。deliciosa,因为它们共享叶绿体特异性DNA单倍型,相比之下,A.arguta和A.polygama拥有自己的特征单倍型,源自A.chinensisvar的单倍型。中国。与A.chinensis相比,A.arguta和A.polygama显示出更好的分组。筛选出来似乎也至关重要,对于每种类型的分子标记,尤其是单倍型,猕猴桃属的核心标记。
BACKGROUND: Kiwifruit (Actinidiaceae family) is an economically important fruit tree in China and New Zealand. It is a typical dioecious plant that has undergone frequent natural hybridization, along with chromosomal ploidy diversity within the genus Actinidia, resulting in higher genetic differences and horticultural diversity between interspecific and intraspecific traits. This diversity provides a rich genetic base for breeding. China is not only the original center of speciation for the Actinidia genus but also its distribution center, housing the most domesticated species: A. chinensis var. chinensis, A. chinensis var. deliciosa, A. arguta, and A. polygama. However, there have been relatively few studies on the application of DNA markers and the genetic basis of kiwifruit plants. By combining information from chloroplast-specific SNPs and nuclear SCoT (nSCoT) markers, we can uncover complementary aspects of genetic variation, population structure, and evolutionary relationships. In this study, one chloroplast DNA (cpDNA) marker pair was selected out of nine cpDNA candidate pairs. Twenty nSCoT markers were selected and used to assess the population structure and chloroplast-specific DNA haplotype diversity in 55 kiwifruit plants (Actinidia), including 20 samples of A. chinensis var. chinensis, 22 samples of A. chinensis var. deliciosa, 11 samples of A. arguta, and two samples of A. polygama, based on morphological observations collected from China.
RESULTS: The average genetic distance among the 55 samples was 0.26 with chloroplast-specific SNP markers and 0.57 with nSCoT markers. The Mantel test revealed a very small correlation (r = 0.21). The 55 samples were categorized into different sub-populations using Bayesian analysis, the Unweighted Pair Group Method with the Arithmetic Mean (UPGMA), and the Principal Component Analysis (PCA) method, respectively. Based on the analysis of 205 variable sites, a total of 15 chloroplast-specific DNA haplotypes were observed, contributing to a higher level of polymorphism with an Hd of 0.78. Most of the chloroplast-specific DNA haplotype diversity was distributed among populations, but significant diversity was also observed within populations. H1 was shared by 24 samples, including 12 of A. chinensis var. chinensis and 12 of A. chinensis var. deliciosa, indicating that H1 is an ancient and dominant haplotype among the 55 chloroplast-specific sequences. H2 may not have evolved further.The remaining haplotypes were rare and unique, with some appearing to be exclusive to a particular variety and often detected in single individuals. For example, the H15 haplotype was found exclusively in A. polygama.
CONCLUSIONS: The population genetic variation explained by chloroplast-specific SNP markers has greater power than that explained by nSCoTs, with chloroplast-specific DNA haplotypes being the most efficient. Gene flow appears to be more evident between A. chinensis var. chinensis and A. chinensis var. deliciosa, as they share chloroplast-specific DNA haplotypes, In contrast, A.arguta and A. polygama possess their own characteristic haplotypes, derived from the haplotype of A. chinensis var. chinensis. Compared with A. chinensis, the A.arguta and A. polygama showed better grouping. It also seems crucial to screen out, for each type of molecular marker, especially haplotypes, the core markers of the Actinidia genus.