Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of , 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as , , or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the genus.