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OALib Journal期刊
ISSN: 2333-9721
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杉木est-ssr与基因组ssr引物开发
DOI: 10.3969/j.issn.1000-2006.2014.01.002, PP. 9-14
Keywords: 杉木,基因组ssr,est-ssr
Abstract:
利用已经公布的杉木444条est序列和未公布的杉木基因组文库中1142条基因序列,进行引物开发效率的比较。去冗余后,利用misa搜索ssr位点,分别得到109个和39个含有ssr的位点。杉木est序列中ssr分布密度为964.58个/mbp,基因组中平均每mbp出现1037.24个ssr。在两个独立来源的数据库序列中,六核苷酸重复均为最多的重复类型,且at-rich的重复类型占较大比例。agc/ctg是杉木est序列和基因组库中最多的三碱基重复,通过primer3.0分别设计出ssr引物95对和37对。为考察设计引物在杉木不同种源(群体)中的有效性,取12个种源(个体)的优良个体,利用随机抽取的10个est-ssr和8个gssr(基因组ssr)进行引物筛选,结果表明:est-ssr和gssr各有4对引物在12个种源(个体)中表现出明显的多态性,多态率分别为40%和50%。8对多态性的ssr引物共扩增出25个多态性等位位点,平均每个引物产生3.125个多态性等位位点,平均有效的等位位点为2.3995,pic平均值为0.5191;hot平均为0.3074。其中gssr标记在检测群体间存在较大的分化,4个gssr比4个est-ssr扩增出更多的等位位点数、平均等位位点数,以及更大的pic值。
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