Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

Abstract

Abstract. Vanijajiva O, Pornpongrungrueng P. 2020. Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand. Biodiversitas 21: 3919-3928. Cissampelopsis is a small climbing tropical Asian genus of Asteraceae-Senecioneae. In Thailand, the genus is represented by two species, C. corifolia and C. Volubilis, distributed through the mountain evergreen forest. Study on the genetic diversity and structure of populations of both Cissampelopsis species provide better understanding of the biology and pattern of species diversification in the genus. To identify the genetic diversity, we used the inter-primer binding site (iPBS) retrotransposon system, in 96 accessions of Cissampelopsis species collected from different regions in Thailand. A total of 120 iPBS bands were scored as presence⁄ absence characters. Results from UPGMA and PCoA analyses indicated that C. corifolia and C. volubilis are different species. Genetic diversity and genetic differentiation among and within populations of C. volubilis is higher than C. corifolia. Molecular Variance (AMOVA) analysis of both species indicated that the genetic variance value within populations is higher than among populations of each species. Bayesian model-based STRUCTURE analysis detected two gene pools for both Cissampelopsis and showed admixture within individuals. Differences among the two Cissampelopsis species, in total diversities and levels of population differentiation, indicated that the genetic structure of Cissampelopsis populations are congruent with long-lived perennial habit with regional distribution, even for congeneric species, may vary considerably. This study suggests the effectiveness of the iPBS marker system to estimate the population genetic diversity and structure of Cissampelopsis genotypes.

Molecular evaluation of genetic diversity and relationships of Musa cultivars in Thailand using Start Codon Targeted (SCoT) markers

“…Using this method, Markov chain Monte Carlo (MCMC) posterior probabilities were approximated. The MCMC chains were run with a 10,000-iteration burn-in period, followed by 100,000 iterations using a model allowing admixture and correlated allele frequencies (Vanijajiva and Pornpongrungrueng 2020). The most anticipated value for K was predicted with Evanno's ΔK method (Evanno et al 2005) using STRUCTURE HARVESTER (Earl and van Holdt 2012).…”

The effect of plant growth regulators on micropropagation of Melientha suavis Pierre. and assessment of genetic fidelity of regenerants based on iPBS and SRAP markers

“…For the iPBS analysis, PCR amplifications were conducted using a Thermohybaid Px2 (Roche Molecular Systems, Inc., USA), following the method of Vanijajiva and Pornpongrungrueng (2020). Each 20 μL reaction mixture comprised PCR buffer (Promega; 20 mM Tris-HCl (pH 8.4), 50 mM KCl), 2 mM MgCl2, 0.24 mM of each deoxyribonucleotide triphosphate, 0.5 units of Taq polymerase (Promega), and 0.8 μm of primer.…”

“…Initially, 27 iPBS primers were tested, and all 27 primers produced unambiguous and clear amplification patterns (Vanijajiva and Pornpongrungrueng 2020). These 27 iPBS primers yielded a total of 262 scorable bands, with an average of 9.70±2.26 bands per primer (Figure 2).…”

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

“…Thus, the use of PCR methods based on highly conserved sequences of interspersed mobile genetic elements allows efficient and versatile detection of polymorphisms for nearly all eukaryotic species [ 38 ]. Such markers were used to assess the genetic polymorphism in rare and poorly studied plant species [ 14 , 39 , 40 , 41 ]. However, insufficient data are available on the use of such markers for studying the biological diversity of endemic onion species living in stressful conditions, although retrotransposons are involved in plant adaptation to stressful environmental conditions.…”