Genome-Wide Development and Characterization of 169 gSSR Markers in the Invasive Plant Xanthium strumarium L

Xanthium strumarium L. is a plant species native to North America; however, it has become a serious invasive threat in northern China due to its great environmental adaptability in the colonized regions. Therefore, elucidating its genetic traits is crucial to understanding its adaptive success. Simple sequence repeats (SSRs) comprise 1-6 nucleotides within plant genomes, which are available for evaluating the level of plant genetic diversity. However, the comprehensive analysis of high-coverage SSR markers in Xanthium is limited. This study identified 450,847 SSR loci in the X. strumarium genome. The number of SSR loci decreased with increasing SSR length within the range of 10-100 bp. Dinucleotide repeats constituted the majority (49.81%), totaling 221,154, with AT/TA motifs being the most frequent (66.62%). We developed 169 gSSR markers covering all X. strumarium chromosomes, with 5-15 markers per chromosome. Moreover, the number of different alleles (Na), number of effective alleles (Ne), Shannon's information index (I), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were varied from 1.2 to 3.3, 1.077 to 2.385, 0.087 to 0.903, 0 to 1, 0.056 to 0.558, and 0.161 to 0.853, respectively. This marks the first systematic development of high-coverage SSR markers in the genus Xanthium, which increases the number of available SSR markers and reveals the molecular foundation of adaptation to invasion.