基于文冠果(Xanthoceras sorbifolium Bunge.)基因组SSR标记的开发及初步验证

Development and Preliminary Verification of SSR Markers Based on the Genome of Xanthoceras sorbifolium Bunge.

本研究基于文冠果全基因组信息,开展SSR分子标记鉴定与分析研究。结果表明,文冠果全基因组全长477586502 bp,共存在253336个SSR位点,平均每1870 bp出现一个SSR位点,GC含量为34.96%;不同染色体上的SSR位点数量不同,其中,SSR位点数量最多的是1号染色体,SSR位点数量最少的是15号染色体。SSR位点的平均长度为18.92 bp,且重复单元中单核苷酸到六核苷酸的数量呈下降趋势。SSR位点的重复次数主要集中在4~13次重复范围内,且同一重复类型,重复次数越多,SSR位点出现的频率越低。文冠果基因组中共存在268种SSR重复类别,重复基元种类随重复次数增加而增加。单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸、六核苷酸的重复单元中,出现最多的分别是A/T、AT/AT、AAG/TTC、AAAT/TTTA、AAAAT/TTTTA和AAAACG/TTTTCG,显示出明显的A/T偏好性。虽然不同的SSR重复单元的序列长度有所不同,但其均显示出SSR重复单元的序列长度的增加,而SSR位点数减少的趋势。进一步利用6份不同种源的文冠果对待测引物进行多样性分析,得到30对条带清晰、多态性好的SSR引物。本研究将为今后文冠果种质资源鉴定和遗传图谱的构建奠定重要基础。

In this study,the identification and analysis of SSR molecular markers were carried out based on the whole genome information of Xanthoceras sorbifolium.The results showed that the whole genome of X.sorbifolium was 477586502 bp in length,and there were 253336 SSR loci,with an average of one SSR per 1870 bp.The GC content was 34.96%.The number of SSR loci on different chromosomes was different.The number of SSR loci on chromosome 1 was the most,and the number of SSR loci on chromosome 15 was the least.The average length of SSR locus was 18.92 bp,and the number of single nucleotide to hexanucleotide in the repeating unit showed a decreasing trend.The number of repetitions of SSR loci mainly ranged of 4 to 13 times,and the frequency of SSR loci decreased with the increase of the number of repetitions in the same repeat type.A total of 268 SSR repeat categories were found in the X.sorbifolium genome,and the types of repeat motifs increased with the number of repeats.In single nucleotide,dinucleotide,trinucleotide,tetranucleotide,pentanucleotide,and hexanucleotide repeating units,A/T,AT/AT,AAG/TTC,AAAT/TTTA,AAAAT/TTTTA,AAAACG/TTTTCG,which appeared the most times,exhibiting obvious A/T preference.The sequence lengths of different SSR repeat units were different,whereas they all showed a trend that the number of SSR sites decreased with the increase of length.The diversity analysis of the primers to be tested was further conducted with 6 different provenances of X.sorbifolium,and 30 pairs of SSR primers with clear bands and good polymorphism were obtained.This research will lay an important foundation for the identification of germplasm resources and the construction of genetic maps of X.sorbifolium.