Analysis of genetic diversity and population structure in Asparagus species using SSR markers

Abstract

Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

“…Molecular markers can be used for genome mapping, identification of genetic relationships, and systematic classification of species (Kapoor et al, 2020). Among different types of DNA molecular markers, SSRs are highly polymorphic, codominant, and widely distributed across genomes and therefore are useful for studies of genetic diversity and relationships among plant populations (Saha et al, 2019;Li et al, 2020).…”

Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution

“…These special SSRs can be used for the identification and classification of species within the Amaryllidaceae. Many SSRs have been detected and used for species identity and delimitation (e.g., Lycoris , Psidium , and Asparagus ) [ 85 – 87 ]. Therefore, we believe that the repeat sequences detected in this study will provide useful information for studies of Amaryllidaceae in the future.…”

Research Progress and Future Development Trends in Medicinal Plant Transcriptomics

“…Owing to the high polymorphism, simple operation, codominance, easy detection, and wide coverage, SSRs have been widely used in genetic map construction, genetic diversity analysis, gene mapping, and identification of parental relationships. Kapoor et al (2020) used SSR markers to study the genetic diversity of Asparagus varieties from different areas of production in northwest India. A total of 122 alleles were amplified, ranging from three to eight, with an average of five alleles for each marker, and the size of the amplified alleles ranged from 90 to 680 bp.…”