苹果属植物种质多样性的SLAF-seq分析

利用简化基因组测序技术—特异性位点扩增片段测序技术(Specific-locus amplified fragment sequencing,SLAF-seq)对509份苹果属植物种质进行测序,获得586 454个SLAF标签,其中多态性SLAF标签463 612个;经过序列比对,根据完整度> 0.94、次要等位基因频率(MAF)> 0.05,过滤筛选得到46460个多态性单核苷酸(SNP)位点;基于这些SNP位点构建苹果属植物不同种的系统发生树并分析主成分。结果表明,通过SLAF-seq技术能够在全基因组范围内快速开发高通量的SNP标记,并直接用于苹果属植物种质资源遗传多样性研究中。34种509份苹果属植物的多样性水平较高(H_e=0.318,I=0.488,A_e=1.520),在多于1份试材的种群中,变叶海棠的遗传多样性水平最高,中国苹果的遗传多样性水平最低。综合聚类分析和主成分分析结果表明,供试苹果属植物分为5个基本的类群,Ⅰ山荆子类群,Ⅱ苹果属植物野生种类群,Ⅲ苹果栽培品种类群,Ⅳ以中国苹果、八棱海棠、花红、楸子和海棠花为主...

Analysis of Genetic Diversity of Apple Germplasms of Malus Using SLAF-seq Technology

In this study，the specific-locus amplified fragment sequencing（SLAF-seq）was used to sequence 509 accessions of Malus Mill.，and 586 454 SLAF tags were obtained，including 463 612 polymorphic SLAF tags. After sequence alignment analysis，46 460 polymorphic single nucleotide（SNP）loci were screened out according to the filter with integrity > 0.94 and minor allele frequency（MAF）> 0.05. Based on these SNP loci，phylogenetic trees among different species of Malus Mill. were constructed and principal component analysis was done. The results showed that high-throughput SNP markers could be rapidly developed in the whole genome by SLAF-seq technology，and could be directly used in the genetic diversity research of apple germplasm resources. Thirty-four species of 509 apple accessions of Malus Mill. had high levels of diversity. Among groups with more than one accession，M. toringoides had the highest level of genetic diversity，and M. × domestica subsp. chinensis had the lowest level of genetic diversity. The results of cluster analysis and principal component analysis showed that the tested accessions of Malus Mill. were divided into 5 basic groups，the groupⅠwas M. baccata，the groupⅡwas wild species of Malus Mill.，the group Ⅲ was a cluster of apple cultivars，the group Ⅳ mainly contained M. × domestica subsp. chinensis，M. robusta，M. asiatica，M. prunifolia and M. spectabilis，and the groupⅤwas M. sieversii. M. rockii，M. komarovii，M. kansuensis，M. toringoides，M. transitoria，M. yunnanensis and M. ombrophila were clustered together. The relationships among cultivated species of Malus Mill. were relatively closer. Cultivars got together with M. orientalis，M. sylveseris and some other wild species. And the relationship between M. sieversii and the cultivated species of Malus Mill. in China needed further study. The results provided a reference for further study on the classification，origin and evolution of apple germplasm resources，and provided a basis for further collection and protection.