基于SNP分子标记的澳洲坚果种质遗传多样性分析

Genetic Diversity Analysis of Macadamia Varieties Based on Single-Nucleotide Polymorphism

为了明确澳洲坚果品种的遗传多样性,本研究利用基因组随机扩增序列SNP多态性及甲基化多态性技术对45份澳洲坚果种质的单核苷酸多态性(SNPs)位点进行了基因分型,分析其亲缘关系与遗传多样性。结果表明,种质测序中SNPs数量有427 736个,插入或缺失(indels)数量有26 055个,SNPs中发生转换概率与发生颠换概率的比值ts/tv为0.77,1 st ALT为0.79;单一序列中SNPs占3.5%,ts/tv为0.71,indels占3.5%。群体结构分析将45份澳洲坚果种质分为4类群,类群分别用红色、荧光绿色、蓝色和紫色表示。4个类群间基因交流密切,可根据条带颜色的比例判断类群。第1类群有2份种质,第2类群有1份种质,第3类群有4份种质,第4类群有38份种质,利用UPGMA法得到的聚类结果,同样表明45份种质分为4个类群。澳洲坚果种质资源存在很多品系,本研究结果为澳洲坚果分子标记辅助育种提供科学依据。

In order to identify the genetic diversity of macadamia(Macadamia spp.) cultivars, in this study, random amplified sequence SNP polymorphism and methylation polymorphism were used to genotype the single nucleotide polymorphism(SNPs) loci of 45 macadamia germplasms, and analyzed their relationship and genetic diversity. The results showed that there were 427 736 SNPs and 26 055 indels in germplasm sequencing, the ratio of the conversion probability to the probability of inversion in SNPs was 0.77 for ts/TV and 0.79 for 1 st ALT,single sequence SNPs accounted for 3.5%, ts/tv for 0.71, and indels for 3.5%. The analysis of population structure divided 45 macadamia cultivars into four sub-groups, which genes exchange were close. The four sub-groups coloured red, fluorescent green, blue and purple respectively. Each species was replaced by a line with four colors,and the sub-group to which the species belongs to can be inferred according to the color ratio. The first subgroups had 2 materials, the second subgroups had 1 material, and the third subgroups had 4 materials, and the fourth subgroups had 38 materials. Examination of multivariate relationships among accessions using a cluster analysis resulted in the identification of four clusters. There were many varieties of macadamia nut germplasm resources.The results of this study provide ascientific basis for molecular marker assisted breeding.