番茄基因组中插入缺失多态性的电子鉴定与实验验证

In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome.

作者信息

Yang Jingjing, Wang Yuanyuan, Shen Huolin, Yang Wencai

机构信息

Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China.

出版信息

DNA Res. 2014 Aug;21(4):429-38. doi: 10.1093/dnares/dsu008. Epub 2014 Mar 11.

Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion-deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.

使用MUGSY软件对番茄品种Heinz 1706和醋栗番茄种质LA 1589的基因组序列进行比较分析，鉴定出145695个插入缺失（InDel）多态性。对整个番茄基因组中一组选定的3029个候选InDel（≥2 bp）进行PCR验证，其中82.4%可得到验证。在LA 1589和Heinz 1706之间的2272个多态性InDel中，分别有61.6%、45.2%和31.6%在8份醋栗番茄、4份樱桃番茄变种和10个普通番茄品种中表现出多态性。醋栗番茄的遗传距离为0.216，樱桃番茄变种的遗传距离为0.202，普通番茄的遗传距离为0.108。数据表明从醋栗番茄到樱桃番茄变种和普通番茄，遗传变异减少。聚类分析表明，8份醋栗番茄种质聚为一组，而4份樱桃番茄变种和10个普通番茄品种聚为同一组。