Characterization of nuclear microsatellite markers for Rumex bucephalophorus (Polygonaceae) using 454 sequencing

Abstract

Premise of the study:Nuclear microsatellite markers were developed in Rumex bucephalophorus subsp. canariensis (Polygonaceae) to investigate its genetic diversity and structure.Methods and Results:Sixteen polymorphic microsatellite markers were obtained using 454 next-generation sequencing with di-, tri-, and tetranucleotide repeats. The average number of alleles was 5.688 and 3.813 for R. bucephalophorus subsp. canariensis var. canariensis and var. fruticescens, respectively. Slightly higher levels of mean genetic diversity were found in var. canariensis (expected heterozygosity = 0.600) than in var. fruticescens (expected heterozygosity = 0.514). Cross-amplifications in related taxa within R. bucephalophorus showed good amplification and polymorphic patterns.Conclusions:These 16 novel nuclear microsatellite markers are the first in the genus Rumex and may serve as valuable tools to carry out studies on genetic diversity and structure as well as progeny studies.

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

“…Primers were designed with MSATCOMMANDER 0.8.2.0 (Faircloth, ); duplicated reads and those containing more than one SSR array were removed. Primers fulfilling the following criteria were selected (Viruel et al., ): optimal size 20–25 bp, not directly flanking the SSR motif, lacking ambiguous bases, low self‐ and pair product complementary parameters, amplicon expected size <390 bp, and melting temperature ( T m ) difference <1.5°C.…”

“…These markers will likely continue to be widely used because budgets are affordable once a set of SSRs is characterized for a taxon (Jennings et al., ). Although several studies in the past decade have focused on SSR isolation and characterization strategies (Zane et al., ; Viruel et al., , ; Meglécz et al., ; Merritt et al., ), few improvements on the genotyping procedures of microsatellite markers can be found in the literature (e.g., Suez et al., ).…”

Origin and genetic variability of populations of the invasive plant Rumex alpinus L. in the Giant (Krkonoše) Mountains

“…Indeed, the physiology and ecology of R. alpinus have been studied (Hujerová et al, 2013 ; Jungová et al, 2022 ; Řičařová, 2011 ) much more than genetic variability, with the only published genetic work being on Rumex bucephalophorus subsp. canariensis (Viruel et al, 2015 ). Unfortunately, Rumex bucephalophorus is an annual Mediterranean plant.…”