The formation and maintenance of the cytotype mixture in plant natural populations has been found related to genetic and epigenetic variations of genomes. We investigated the patterns of genetic variation, genetic structure and methylation levels, as well as epigenetic differentiation, of a cytotype mixture population of the Actinidia chinensis complex by amplified fragment-length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). The mixture population had high genetic and epigenetic diversity. The relationship between population genetic diversity and altitude but not epigenetic diversity and altitude was significant (P<0.05). As well, patterns of genetic and epigenetic variation were not positively correlated. Analysis of molecular variance revealed that most genetic and epigenetic variations occurred within ploidy races (97.65% vs 99.84%, P<0.05). Neighbor-joining tree analysis based on AFLP analysis revealed that the same ploidy individuals clustered preferentially, with no obvious cluster based on ploidy levels in the MSAP tree. The total methylation level in the cytotype mixture population was 24.86%. Moreover, tetraploids and hexa-ploids showed more variation than diploids in genomic methylation, including increase and loss of methylation loci. We provide a theoretical basis to understand the formation and maintenance mechanism in the cytotype mixture population of A. chinensis.%植物倍性混合居群的形成和维系常伴随着明显的基因组遗传及表观遗传变异.利用AFLP和MSAP两种分子标记探讨了中华猕猴桃复合体(Actinidia chinensis)倍性混合居群的遗传变异和结构及其基因组甲基化变异方式.结果表明,该倍性混合居群具有较高的遗传和表观遗传多样性,但两者之间没有明显的相关性.种群的遗传多样性与海拔呈显著的负相关(P＜0.05),但表观遗传多样性与海拔不具显著相关性.AMOVA分析显示,主要的遗传和表观遗传分化出现在倍性小种内部(97.65％ vs 99.84％,P＜0.05)；同时,AFLP邻接聚类分析显示二者存在一定程度的倍性相关性,MSAP分析则未显示有明显的倍性相关性.进一步研究发现,中华猕猴桃居群的总甲基化程度为24.86％,且多倍体具有更多的甲基化位点变异.该研究结果为深入探讨猕猴桃倍性混合居群的形成和维系机制奠定了基础.
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