Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae

• DOI: 10.1186/s12863-015-0178-z
• Publication Date: 2015-02-17T10:56:49Z
• Authors: Yi Wang; Chao Yang; Qiaojun Jin; Dongjie Zhou; Shuangshuang Wang; Yuanjie Yu; Long Yang
• Keywords: 0301 basic medicine; 2. Zero hunger; Base Composition; DNA, Plant; 15. Life on land; Poaceae; 03 medical and health sciences; Databases, Genetic; Genetics; Genetics(clinical); Genome, Plant; Research Article; Microsatellite Repeats

The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are main sources for food and animal feed. With rapid growth genomic data from members, comparative genomics becomes a convinent method study genetics diffierent species. SSRs (Simple Sequence Repeats) widely used markers in studies their high abundance stability. In this study, using sequences 9 species, we detected 11,993,943 SSR loci developed 6,799,910 primer pairs. results show that distributed on all elements grass. Hexamer most frequent motif AT/TA dimer. has positive linear relationship with recombination rate. coding regions involve higher GC content than other 70-80 bp length showed highest AT/GC base ratio among these loci. result shows polymorphism rate belongs ranged 30 40 bp. Using primers Japonica, nineteen universal were selected located genome grass family. information loci, tools mining analyzing provided PSSRD (Poaceae Database, http://biodb.sdau.edu.cn/pssrd/ ). Our database provide foundation will accelerate application, gene mapping molecular breeding.