基于草莓全基因组SSR标记的开发和应用

基于基因组序列信息,研究了二倍体森林草莓和八倍体栽培草莓染色体上SSR位点的分布特点。利用AutoSSR软件在森林草莓和栽培草莓中分别发掘到153826个和329801个SSR位点,发生频率分别为1.43 kb/SSR和2.44 kb/SSR。SSR重复基序为单核苷酸的数量最多,分别占总数的40.92%和38.94%,其次为二核苷酸类型,分别占22.79%和20.04%。在二倍体草莓和八倍体草莓中分别鉴定到454和479种SSR重复类型,其中A/T重复类型的SSR出现的频率最高,分别占总SSR位点的39.45%和37.08%。二核苷酸重复类型中,二倍体草莓的AT/AT占比最高,为11.61%,其次为AG/CT(8.74%);八倍体草莓中AG/CT重复类型占比最高(9.94%),其次为AT/AT(7.35%)。用Beacon Designer软件设计SSR引物,随机挑选了59对SSR引物在77份草莓材料中进行验证分析。研究结果显示,59对SSR引物共扩增出254个多态性位点,平均扩增4.31个位点,位点的平均多态信息量(PIC)为0.26,介于0.07~0.97之间,其中35个SSR位点PIC≥0.50,为高多态性位点,聚类分析显示品种间的相似系数范围为0.47~0.99。该研究为草莓种质资源的遗传多样性评价、变异分析、分子标记辅助育种等工作提供了技术支持。

Development of Genome-wide SSR Marker and Application in Strawberry

The distribution of simple sequence repeat(SSR)was studied in diploid woodland strawberry(Fragaria vesca,2n=2x=14)and octoploid cultivated strawberry(Fragaria×ananassa,2n=8x=56).153826 SSR sites were retrieved in diploid woodland strawberry with a frequency of 1.43 kb/SSR by AutoSSR software,and 329801 SSR sites in octoploid cultivated strawberry with a frequency of 2.44 kb/SSR.The most common SSR repeat type is mononucleotide,accounting for 40.92%and 38.94%of the total SSR sites in diploid woodland strawberry and octoploid cultivated strawberry,respectively.Dinucleotide SSR loci was 22.79%and 20.04%in diploid woodland strawberry and octoploid cultivated strawberry.454 and 479 repeat motives were identified in the two strawberries.The content of A/T repeat SSR was the highest,accounting for 39.45%and 37.08%.The results indicated that AT/AT(11.61%)and AG/CT(8.74%)repeat types were the most common of dinucleotide repeat SSRs in diploid woodland strawberry.The most common dinucleotide repeat SSRs were AG/CT(9.94%)and AT/AT(7.35%)in octoploid cultivated strawberry.The SSR primers were designed by Beacon Designer software,and 59 pairs of SSR primers were randomly selected for validation analysis in 77 strawberry samples.The results showed that 254 polymorphic alleles were revealed by these 59 primer pairs,with a mean of 4.31 alleles.The average polymorphism information content(PIC)was 0.26,with a range from 0.07 to 0.97.35 SSR were highly polymorphic markers with PIC≥0.50.The SSR-based genetic distances varied from 0.47 to 0.99.The results in present study can provide technological support for the genetic diversity evaluation,variation analysis and molecular marker assisted breeding in strawberries.