Microsatellite DNA markers in Shorea platyclados (Dipterocarpaceae): genetic diversity, size homoplasy and mother trees

Abstract

ABSTRACT:Cross-specific amplification of microsatellite loci greatly enhances the effectiveness of this marker system. This shortcut would greatly enhance our examination of the gene flow and population structure of trees in diverse tropical rainforests. To explore the effectiveness and limitations of this approach, we examined allelic diversity at six microsatellite loci, originally developed in a congeneric species, in three populations of Shorea platyclados from Peninsular Malaysia. Fragment sizing was performed by an efficient and sensitive (1 bp resolution) technique using capillary electrophoresis, ethidium bromide detection, and minimal clean-up. Fragment size ranges were conserved between species and null allele frequencies were low. Higher overall levels of genetic diversity were detected in our study. Variation among populations was directly related to geographic distance. Fragment size class distributions suggest that each locus should be studied using different evolutionary models. Direct sequencing of SSR fragments revealed that size differences were due to changes in both the flanking regions and repeat motifs. Several clear examples of size homoplasy were observed, along with the disruption of perfect repeats, suggesting that cross-specific amplification of microsatellite loci requires an additional level of confirmation at the DNA sequence level before the influence of size homoplasy and changes in repeat structure can be assessed. Simulation studies demonstrate that the increasing intensity of timber harvest leads to higher variability in levels of potential heterozygosity and decreasing total number of alleles in the remnant "mother trees" The careful selection of "mother" trees can greatly enhance the future genetic diversity of populations.

Microsatellite allele length variations in inter-specific hybrids of Eucalyptus

“…Variations in fl anking regions and repeat numbers refl ect the occurrence of mutational processes in both the repeat and fl anking regions. Similar observations were made in Vitis (Masi et al 2004) and Shorea (Javed et al 2014) and insisting the requirement of information on underlying DNA sequence. However, with the availability of genome sequence of E. grandis, the primer sequence similarity search can be applied to fi nd the primer binding regions.…”

“…Recently, it was emphasized that the sequence verifi cation of SSR alleles is critical for interpretation of the SSR polymorphism for genetic analysis (Barthe et al 2012). Further, size homoplasy is commonly reported among the SSR alleles (Curtu et al 2004, Javed et al 2014, hence, information on DNA sequence is essential before the utilization of SSR loci variations. Thus, in the present study, attempts were made to sequence the SSR-PCR amplicons generated in the inter-specifi c hybrid populations, E. tereticornis × E. camaldulensis and E. tereticornis × E. grandis.…”

Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing

“…Microsatellites [(SSRs) or short tandem repeats (STR)] are a commonly used marker system in plant genetics and breeding 42 . Chloroplastic microsatellites were widely used in population genetics of Dipterocarpaceae to assess genetic variation and population spatial structure at lower spatial and temporal scale 47–49 , and the genetic diversity and gene flow with closely related species 50 . Our analyses of repeated regions, microsatellites, and the comparative plastomes analyses showed that a higher portion of the number and characteristics variations were found between species than between genera.…”

Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers

“…S2), homoplasy may be a serious problem when only fragment length analysis is performed, leading to underestimation of genetic variability and consequently to errors in population genetic inferences. Although the chance of homoplasy is proportional to the genetic distance between two individuals (Selkoe and Toonen, 2006), the few existing sequence-based studies revealed a high degree of fragment length homoplasy not only among different species but also within one species or a population (Estoup et al, 2002;Curtu et al, 2004;Anmarkrud et al, 2008;Javed et al, 2014;Germain-Aubrey et al, 2016). Our sequence analysis provide clear evidence of homoplasy at loci containing (1) SNPs or indels in FRs (5K23, Rub238h, Rub123a, 1G16, 1B06, 72H02 and Rub26a); ( 2) multiple repeat motifs (compound SSR; Rub47a, Rub238h, 1G16, Rub26a and Rub35a); and (3) interrupted (imperfect) repeats (mainly 5K23).…”