Development of novel polymorphic microsatellite markers in the invasive plant shortawn foxtail (Alopecurus aequalis Sobol.)

Abstract Shortawn foxtail ( Alopecurus aequalis Sobol.) is an invasive and highly troublesome weed species originating from North America that has become widespread across China. Since its proliferation seriously threatens crop production worldwide, understanding its genetic diversity is critical for developing a forecasting system for integrated pest management plans. To accelerate the application of molecular markers in A . aequalis , this study aimed to develop a set of expressed sequence tag-simple sequence repeat (SSR) markers using previous high-throughput sequencing data. In this study, a total of 1411 SSR loci were identified from 95,479 unigenes. Tri-nucleotide repeat motifs were the most abundant type with a frequency of 66.27%, followed by di- (24.95%) and tetra-nucleotide (8.78%). Among the loci, 584 primer pairs were successfully designed for marker development. Subsequently, a subset of 36 primer pairs was randomly selected and synthesized, of which 12 (33.33%) pairs successfully revealed abundant allelic polymorphism. Additionally, to investigate their utility, the genotypes of 160 individuals from 20 natural populations representing diverse wild genotypes of A. aequalis were analysed by using these 12 polymorphic markers. These novel SSR markers developed here are reliable and useful for genetic analysis on this invasive plant and will greatly enrich its genetic resource.