Usage of microsatellite markers for characterization of polyploids: a case study in reference to hexaploid bamboo species

Abstract

Microsatellite markers are most valuable tools for characterization of plant genetic resources or population genetic analysis. Since they are codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, microsatellite markers are usually analyzed by treating them as dominant marker. In the current study, it has been showed that despite of losing the advantage of co-dominance, microsatellite markers are still powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of nineteen sub populations of Dendrocalamus hamiltonii (hexaploid bamboo species) with seventeen polymorphic SSR primer pairs. Among these, ten primers gave typical banding pattern of microsatellite marker as expected in diploid species but rest seven gave unusual pattern i.e. more than two bands per locus per genotype. In such case genotyping data are generally analyzed by considering as dominant markers. Given these facts, data were analyzed in both ways as dominant and codominant. All the seventeen primer were first scored as non-allelic data and analyzed; later ten primer pairs giving standard banding pattern were analyzed as allelic data and the results were compared. The UPGMA clustering and genetic structure showed that results obtained with both the data sets were very similar, and therefore the SSR marker could be utilized to characterize polyploid species by considering them as dominant marker. The study is highly useful to widen the scope of SSR markers applications and beneficial to the researchers dealing with polyploid species.

Genetic diversity and structure analysis of Croatian garlic collection assessed by SSR markers

“…To eliminate the possibility of error, all samples in which the appearance of multiple peaks was detected were analysed several times. Multiple peaks can be addressed by picking two 'main' peaks to allow further analysis of co-dominant markers (Ma et al, 2009) or by treating SSRs as dominant markers and recording the presence or absence of all specific alleles (Pan, 2006;Arroyo et al, 2010;Trapnell et al, 2011;Wang et al, 2014;Meena et al, 2020) to avoid bias in the elimination of specific and reproducible peaks. We used the latter approach in genetic structure analysis.…”

An Improved Method for Assessing Simple Sequence Repeat (SSR) Variation in Echinochloa crus-galli (L.) P. Beauv (Barnyardgrass)

“…Microsatellites, or Simple Sequence Repeats (SSRs), appear to be the most appropriate markers to study genetic variability as they are highly informative and powerful tools for plant genetic analysis, being codominant, multiallelic, highly mutable, and polymorphic [29][30][31]. Since SSR alleles differ in length by many base pairs, SSR markers are well resolved on agarose gel [25,26].…”