Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Napier Grass (Pennisetum purpureum Schum)

Abstract

Napier grass (Pennisetum purpureum Schum.) is an economically important species used as a fodder crop, reflecting its high biomass, perennial nature and pest resistance. In order to understand the genomic information and development of this species based on SSR markers, the transcriptome for Napier grass was obtained using next-generation sequencing. A total of 117,076 sequence contigs were obtained, with lengths of 201–10,652 bp. Among these contigs, 44,313 (37.85%) sequences were annotated against public protein databases (E-value <10−5). In addition, the contigs generated from the transcript sequencing were also analysed for the presence of simple sequence repeats (SSRs). A total of 12,744 SSR motifs were identified with in these contigs and corresponding primer pairs were designed. Empirical validation of a cohort of 200 SSRs was performed, with 34% being polymorphic for 20 Napier grass accessions. The polymorphic index content values for each primer ranged from 0.105 to 0.749, with an average of 0.409. The development of genetic, genomic resources and EST-SSRs for Napier grass will contribute to novel gene discovery and the marker-assisted selective breeding of this species.