Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

Abstract

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

“…Short tandem repeats (STRs), or microsatellite loci, are useful markers for numerous applications and widely implemented in the field of conservation genetics to evaluate genetic diversity and population structure (e.g., Bilska and Szczecińska 2016;Arbogast et al 2017). Capillary electrophoresis (CE), a fragment size genotyping technique, was previously standard practice for microsatellite genotyping, but the advent of high-throughput sequencing (HTS) introduced new possibilities (Curto et al 2019;Tibihika et al 2019).…”

The complete plastid genome and nuclear genome markers provide molecularevidence for the hybrid origin of Pulsatilla × hackelii Pohl.

“…Reliable identification of hybrids requires an analysis of the nuclear genome, which should contain copies of both parent genomes. Previously identified nuclear material of the Pulsatilla species was limited to SSR markers (Szczecińska et al 2013Bilska and Szczecińska, 2016), ISJ markers (Bilska and Szczecińska, 2016), and rRNA clusters (Szczecińska and Sawicki, 2015).…”

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

“…Penerapan teknik molekuler SSR pada analisis sidik jari DNA banyak digunakan pada tanaman jagung (Enoki et al, 2002) dan kelapa sawit (Billote et al, 2005;Abdullah et al, 2011). Keunggulan marka SSR antara lain memiliki polimorfisme yang tinggi, kodominan, dan efektif untuk membedakan populasi yang tidak dipengaruhi interaksi genotipe dengan lingkungan (Bilska dan Szczeciñska, 2016 (Billote et al, 2005).…”