title: Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae.
abstract: BACKGROUND
  The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability.
  
  
  RESULTS
  In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/).
  
  
  CONCLUSIONS
  Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.
authors.affiliation: Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. wangyi19881107@163.com.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. ileman@sdau.edu.cn.
authors.forename: Chao
authors.initials: C
authors.lastname: Yang
authors.affiliation: College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, 712100, China. jqiaojun@yahoo.com.
authors.forename: Qiaojun
authors.initials: Q
authors.lastname: Jin
authors.affiliation: Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China. zhoudongjie1633@163.com.
authors.forename: Dongjie
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China. wangss900909@126.com.
authors.forename: Shuangshuang
authors.initials: S
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. yuanjy@sdau.edu.cn.
authors.forename: Yuanjie
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. lyang@sdau.edu.cn.|Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China. lyang@sdau.edu.cn.
authors.forename: Long
authors.initials: L
authors.lastname: Yang
mesh_terms: D001482:Base Composition; D018744:DNA, Plant / Q000737:chemistry; D030541:Databases, Genetic; D018745:Genome, Plant; D018895:Microsatellite Repeats; D006109:Poaceae / Q000145:classification* / Q000235:genetics*
chemical_list: D018744:DNA, Plant