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
[目的]基于文冠果全基因组信息开发文冠果SSR标记,为文冠果种质资源鉴定和遗传图谱的构建奠定基础。[方法]以文冠果基因组为分析材料,分别利用Krait、Primer软件查找SSR位点和设计SSR引物,并利用 1%琼脂糖凝胶和聚乙丙烯凝胶进行初步筛选和多态性筛选。[结果]结果可知,文冠果全基因组全长 477 586 502 bp,共存在 253 336个SSR位点,平均每 1 870 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。[结论]文冠果基因组SSR位点具有较高的出现频率和分布密度,基元类型和重复次数相对较高,具有高多态性的潜能,可以进行有目的的引物设计和开发。
[Objective]To develop SSR markers based on the whole genome information of Xanthoceras sorbifolium a nd to lay the foundation for the identification of germplasm resources and the construction of a genetic map of X.sorbifo lium.[Methods]Using the genome of X.sorbifolium as analysis material,SSR loci were searched and SSR primers were designed using Krait and Primer software,and 1%agarose gel and polyethylene-propylene gel were used for preliminary s creening and polymorphism screening.[Results]The results showed that the whole genome of X.sorbifolium was 477 586 502 bp in length,and there were 253 336 SSR loci,with an average of one SSR per 1 870 bp.The GC content was 3 4.96%.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 the 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 from 4 to 13 times,and the frequency of SSR loci decreased with the increase in 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,trinucleoti de,tetranucleotide,pentanucleotide,and hexanucleotide repeating units,A/T,AT/AT,AAG/TTC,AAAT/TTTA,AAAAT/TTT TA,AAAACG/TTTTCG,which appeared the most times,exhibiting obvious A/T preference.The sequence lengths of diffe rent SSR repeat units were different,whereas they all showed a trend that the number of SSR sites decreased with the in crease in 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.[Conclusion]The S SR loci of the genome of X.sorbifolium have a high frequency of occurrence and distribution density,relatively high mot if type and the number of repeats,and have the potential for high polymorphism,which can be designed and developed with purposeful primers.
乐琳琳;曹福亮;杨晓明;郁万文;蔡金峰;汪贵斌;李守科;赵祥树;
南京林业大学南方现代林业协同创新中心, 南京, 210037;南京林业大学南方现代林业协同创新中心, 南京, 210037;南京林业大学南方现代林业协同创新中心, 南京, 210037;南京林业大学南方现代林业协同创新中心, 南京, 210037;南京林业大学南方现代林业协同创新中心, 南京, 210037;南京林业大学南方现代林业协同创新中心, 南京, 210037;山东沃奇农业开发有限公司, 潍坊, 262100;山东沃奇农业开发有限公司, 潍坊, 262100;
文冠果(Xanthoceras sorbifolium Bunge.) 基因组 SSR 标记开发
Xanthoceras sorbifolium Bunge Genome SSR Mark development
2061-2071 / 11
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