Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines

Abstract

Microsatellite transfer across coniferous species is a valued methodology because de novo development for each species is costly and there are many species with only a limited commodity value. Cross-species amplification of orthologous microsatellite regions provides valuable information on mutational and evolutionary processes affecting these loci. We tested 19 nuclear microsatellite markers from Pinus taeda L. (subsection Australes) and three from P. sylvestris L. (subsection Pinus) on seven Eurasian hard pine species ( P. uncinata Ram., P. sylvestris L., P. nigra Arn., P. pinaster Ait., P. halepensis Mill., P. pinea L. and P. canariensis Sm.). Transfer rates to species in subsection Pinus (36-59%) were slightly higher than those to subsections Pineae and Pinaster (32-45%). Half of the trans-specific microsatellites were found to be polymorphic over evolutionary times of approximately 100 million years (ten million generations). Sequencing of three trans-specific microsatellites showed conserved repeat and flanking regions. Both a decrease in the number of perfect repeats in the non-focal species and a polarity for mutation, the latter defined as a higher substitution rate in the flanking sequence regions close to the repeat motifs, were observed in the trans-specific microsatellites. The transfer of microsatellites among hard pine species proved to be useful for obtaining highly polymorphic markers in a wide range of species, thereby providing new tools for population and quantitative genetic studies.

Insertions–Deletions in a Microsatellite Flanking Region May Be Resolved by Variation in Stuttering Patterns

“…However, the degree of flanking sequence variation shows positional effects, with above-average mutation rates in the nucleotide stretches directly adjacent to repeat regions (5-10 bp; Brohede and Ellegren 1999;González-Martínez et al 2004). These findings agree with our result of the AA indel (or mutation) downstream of the microsatellite region (positions 114/115; Fig.…”

Transferability of Simple Sequence Repeat (SSR) Markers Developed in Litchi chinensis to Blighia sapida (Sapindaceae)

“…An SSR marker was deemed transferable if the amplification of a PCR band of the expected size was observed (González-Martinez et al 2004). The program Micro-Checker (van Oosterhout et al 2004) was used to check for scoring errors, allele dropouts, and null alleles.…”

Genetic variation and divergence in Scots pine (Pinus sylvestris L.) within its natural range in Italy

“…Twelve simple sequence repeat markers (SSR) were selected from the published literature and tested on our plant material (Table 2). While the SPAC and SPAG series consisted of primers specific for P. sylvestris (Soranzo et al 1998), the PtTX series included primers originally designed for Pinus taeda, but they also proved to be as useful as the markers selected for P. sylvestris (Elsik et al 2000;Auckland et al 2002;González-Martinez et al 2004).…”