Marek L F, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow J A, Retzel E, Young N D, Shoemaker R C
US Department of Agriculture, Corn Insect and Crop Genetics Research Unit, Iowa State University, Ames 50011, USA.
Genome. 2001 Aug;44(4):572-81.
We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC- end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.
我们正在构建一个跨越大豆基因组的框架物理基础设施，通过使用SSR（简单序列重复）和RFLP（限制性片段长度多态性）标记，从两个大豆BAC文库中鉴定BAC（细菌人工染色体）。这些文库由两种基因型制备，每种基因型用不同的限制性内切酶消化。每个标记鉴定出的BAC被分组形成重叠群。我们已经从每个重叠群中的BAC获得了BAC末端序列。明尼苏达大学计算基因组学和生物信息学中心使用BLAST算法对这些序列进行分析，以搜索核苷酸和蛋白质数据库。与RFLP鉴定的BAC相比，SSR鉴定的BAC有更高比例的显著BLAST匹配。这种差异是由于SSR鉴定的BAC对重复型序列的匹配比例更高，不过，部分被RFLP鉴定的与实验定义基因和大豆EST（表达序列标签）相似的显著匹配的更大比例所抵消。这些基因代表了广泛的代谢功能。在这些分析中，只有来自SSR鉴定的重叠群的重复序列似乎是成簇的。BAC末端序列还使我们能够鉴定大豆与模式植物拟南芥和蒺藜苜蓿之间的微同线性。这种基于图谱的基因组采样方法提供了一种分析大豆基因组结构和组织的手段。
