Liewlaksaneeyanawin Cherdsak, Ritland Carol E, El-Kassaby Yousry A, Ritland Kermit
Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
Theor Appl Genet. 2004 Jul;109(2):361-9. doi: 10.1007/s00122-004-1635-7. Epub 2004 Mar 26.
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.
微卫星，即简单序列重复（SSRs），通常被视为群体遗传学研究中的“首选标记”，因为它们具有高度变异性。这些标记的开发成本通常很高。此外，为一个物种开发的微卫星引物通常不能在相关物种中进行跨扩增，每个物种都需要单独开发。然而，在表达序列标签（ESTs）中发现的微卫星可能更易于跨扩增，因为它们位于保守的编码DNA中或附近。在本研究中，我们从公共EST数据库中鉴定出14个火炬松（Pinus taeda）EST-SSRs，并测试了它们对扭叶松（P. contorta ssp. latifolia）、西黄松（P. ponderosa）和欧洲赤松（P. sylvestris）的跨物种转移性。作为我们开发扭叶松微卫星组的一部分，我们还将它们的转移性与在火炬松中开发并在扭叶松亚种上测试的99个传统微卫星标记的转移性进行了比较。与传统微卫星相比，EST-SSRs在松树物种间具有更高的转移率；然而，来自ESTs的微卫星的多态性水平较低。序列分析表明，EST-SSRs中插入/缺失和碱基替换的频率低于其他类型的微卫星，这证实了EST-SSRs比传统SSRs更保守。我们的结果还为扭叶松提供了一组23个多态性、稳健性良好的微卫星引物对。
