Complete chloroplast genome sequencing of vetiver grass (Chrysopogon zizanioides) identifies markers that distinguish the non-fertile 'Sunshine' cultivar from other accessions

Non-fertile accessions of vetiver grass (Chrysopogon zizanioides (L.) Roberty) have been utilized in many parts of the world for environmental remediation and erosion control, but fertile plants can become noxious weeds. Due to the global interest in the environmental benefits of sterile vetiver, unique polymorphisms are needed to distinguish non-fertile from fertile plants. In this research, the chloroplast (cp) genomes of three non-fertile and two fertile vetivers were sequenced. The size, structure, and content of the vetiver cp genomes were typical of other grasses within the Andropogoneae. However, the total cp polymorphism rate of 0.02% was 5- to 7-fold lower, suggesting a recent divergence or slower rate of evolution in non-fertile and fertile vetivers relative to other grasses. In total, 28 polymorphisms--including 14 single nucleotide polymorphisms (SNPs), 11 microsatellites, two small indels, and one microinversion--were identified that distinguished the sterile Sunshine from fertile accessions. In a broader survey of Poaceae cp genomes, one of the SNPs was used to develop a cleaved amplified polymorphic sequence (CAPS) assay to uniquely identify Sunshine genomes. In a panel of 26 fertile and sterile vetivers, the four Sunshine and six additional non-fertile vetivers were distinguished from all other accessions. Two other sterile accessions were not detected by the assay, suggesting that sterility has originated more than once in vetiver. These variations in cp genome sequence can be used to assess sterility in other accessions through sequencing or by the newly developed CAPS assay.