鸭茅基因组Genomic-SSR标记开发

Development and Verification of Orchardgrass Genomic-SSR

鸭茅是重要的冷季型禾本科牧草,而优质分子标记的缺乏制约了鸭茅分子育种的进程。本研究从鸭茅基因组序列中鉴定出78 984个SSR位点,其中单核苷酸、二核苷酸和三核苷酸的SSR类型共占98.1%。共鉴定出212种重复基元,A/T、AG/CT、CCG/CGG、AGAT/ATCT、AAAAG/CTTTT和AGAGAT/ATCTCT分别为各重复类型中最丰富的重复基元。通过鉴定出的SSR位点开发出67 216对Genomic-SSR引物,选取50对进行验证试验,其扩增成功率达94%,多态性比例44%。通过开发的Genomic-SSR引物和EST-SSR引物在20个鸭茅品种(系)中进行试验,得到其引物多态性信息含量(PIC)平均值为0.370,分子标记指数(MI)为2.86。以上数据均高于通过鸭茅转录组开发的EST-SSR标记。证明本试验所开发的大量genomic-SSR标记是扩增成功率高、多态性强且高效率的分子标记,有望在鸭茅分子育种中发挥重要作用。

Orchardgrass is an important cool-season forage grass, however, the lack of high-quality molecular markers is one of the main obstacles of orchardgrass breeding. In this study, 78 984 SSR motifs were identified including mono-nucleotides, di-nucleotides, tri-nucleotides, which accounted for 98.1% of SSRs. A total of 212 kinds of repeat motifs were found with A/T, AG/CT, CCG/CGG, AGAT/ATCT, AAAAG/CTTTT, and AGAGAT/ATCTCT being the most abundant in different repeat motifs respectively. We have developed 67 216 pairs of genomic-SSR primers from detected SSR sequences. Fifty pairs of genomic-SSR primers were Randomly chose to test the success rates of amplification accounting for 94% and polymorphism accounted for 44%. The newly developed genomic-SSR primers were also applied on 20 orchardgrass accessions with the marker index（MI）2.86. Those data from genomic-SSR primers are higher than EST-SSR primers which means genomic-SSR markers developed from orchardgrass genome are high-quality and efficient. Those results indicate the potential of genomic-SSR markers which could play an important in molecular breeding of orchardgrass genome.