Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs.
Microsatellites, or simple sequence repeats (SSRs), are usually regarded as the "markers of choice" in population genetics research because they exhibit high variability. The development cost of these markers is usually high. In addition, microsatellite primers developed for one species often do not cross-amplify in related species, requiring separate development for each species. However, microsatellites found in expressed sequence tags (ESTs) might better cross-amplify as they reside in or near conserved coding DNA. In this study, we identified 14 Pinus taeda (loblolly pine) EST-SSRs from public EST databases and tested for their cross-species transferability to P. contorta ssp. latifolia, P. ponderosa, and P. sylvestris. As part of our development of a P. contorta microsatellite set, we also compared their transferability to that of 99 traditional microsatellite markers developed in P. taeda and tested on P. contorta ssp. latifolia. Compared to traditional microsatellites, EST-SSRs had higher transfer rates across pine species; however, the level of polymorphism of microsatellites derived from ESTs was lower. Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST-SSRs are more conserved than traditional SSRs. Our results also provide a battery of 23 polymorphic, robust microsatellite primer pairs for lodgepole pine.
Liewlaksaneeyanawin
Cherdsak
C
Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada. cliewlak@interchange.ubc.ca
Ritland
Carol E
CE
El-Kassaby
Yousry A
YA
Ritland
Kermit
K
D000483:Alleles; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D017931:DNA Primers; D020224:Expressed Sequence Tags; D016468:Forestry / Q000379:methods; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D028223:Pinus / Q000235:genetics*; D041603:Pinus taeda / Q000235:genetics*; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D017931:DNA Primers