Molecular genetic diversity and population structure of a selected core set in garlic and its relatives using novel SSR markers

Abstract

Garlic is widely consumed for its culinary and medical benefits. Six hundred and thirteen accessions of garlic and its relatives with diverse origin were evaluated for genetic diversity at eight recently novel simple sequence repeat loci in this study. A total of 113 alleles were detected, the average allelic richness was 14.1 alleles per locus. Using a heuristic approach, a core set of 95 accessions was successfully developed, which showed 100% coverage of alleles with minimum redundancy. The model-based structure analysis here revealed the presence of four subpopulations in the selected core set, which was basically consistent with clustering based on the genetic distance. The analysis of molecular variance based on this core set showed that between-population component of genetic variance is <15.6% in contrast to 84.4% for the within population component. Overall F ST value was 0.1560, indicating a moderate differentiation among the four groups. These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs.

Genetic Assessment of <i>Amaranthus</i> Linn. Genotypes in Treatment Combinations of <i>Glomus clarum</i> and <i>Leucaena leucocephala</i> Lam. Using Simple Sequence Repeat (SSR) Marker

“…The performance of GM implies that it can be harnessed for agricultural productivity in order to reduce the effect of chemical fertilizers as reported by Sobulo (2000). Notable amongst the molecular marker used for genetic diversity studies, linkage map construction, and marker-assisted selection (MAS) is Microsatellites (Chung et al, 2009;Zhao et al, 2011). All primers used were polymorphic across all the Amaranthus genotype with amplified microsatellites loci.…”

Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

“…Strong genetic diversity provides diverse morphological traits and potentially valuable genetic information, and therefore lays a good foundation for breeding (Upadhyay et al, 2012). Microsatellites have become one of the most widely used molecular markers for genetic diversity studies, linkage map construction, and marker-assisted selection (MAS) (Chung et al, 2009;Zhao et al, 2011).…”

“…DNA molecular markers based on PCR have proved to be a useful and informative tool for estimating the genetic diversity and genetic relationships in crop germplasm (Gwag et al, 2010;Li and Park, 2012;Zhao et al, 2010;Zhao et al, 2011). Several molecular approaches have been employed to assess genetic diversity in Amaranthus.…”

Diversity evaluation based on morphological, physiological and isozyme variation in genetic resources of garlic (<i>Allium sativum</i> L.) collected worldwide

“…This situation complicates the characterization of garlic clones (Mario et al, 2008). Many researchers have studied morphological traits and molecular markers such as isozymes and DNA to evaluate the diversity of garlic (Pooler and Simon, 1993;Maass and Klaas, 1995;Etoh et al, 2001;Zhao et al, 2011;Jo et al, 2012). Isozyme analysis has long been used to evaluate genetic diversity in animals, fungi and higher plants (Micales and Bonde, 1995).…”