Genetic diversity and population structure analysis of Amaryllis ( <i>Hippeastrum hybridum</i> ) revealed by SSR markers

Abstract Hippeastrum hybridum is a showy ornamental plant. The genetic diversity and population structure of 48 Hippeastrum hybridum germplasms were investigated using eight SSR markers. The average values of observed heterozygosity, expected heterozygosity, polymorphism information content and genetic differentiation were 0.622, 0.545, 0.536 and 0.024, respectively. Population structure analysis and principal coordinate analysis revealed that the 48 H. hybridum genotypes were divided into two moderate subgroups. Analysis of molecular variance results indicated that 10% of the genetic variation was attributed to differences among subgroups, while 90% of the genetic variation was found within subgroups. These findings provide a comprehensive description of the population structure and genetic relationships among the 48 H. hybridum genotypes, thereby offering a genetic foundation for parental selection and the utilization of heterosis in breeding programmes. Significance of the study What is already known on this subject? Hippeastrum hybridum is an ornamental plant with rich genetic resources. Previous studies using molecular markers, such as random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR), have confirmed its high genetic diversity. However, limitations remain in understanding its population structure, constraining practical breeding applications. What are the new findings? Using eight SSR markers, this study analysed 48 accessions and confirmed high genetic diversity (average observed heterozygosity = 0.622, expected heterozygosity = 0.545 and polymorphism information content = 0.536). Population structure and principal coordinate analysis divided the genotypes into two distinct subgroups. Analysis of molecular variance revealed that 90% of genetic variation resides within subgroups, while 10% exists among them. What are the expected impacts on horticulture? The findings provide a genetic basis for parental selection and heterosis utilization, which can guide breeding programmes and improve efficiency. This work supports the development of new cultivars with desirable traits and promotes the advancement of the H. hybridum horticultural industry.