Exploiting the Transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to Develop and Characterize New EST-SSR Markers and Construct an EST-SSR Database

被引：34

作者：

Du, Fang K. ^{[1
]}

Xu, Fang ^{[1
]}

Qu, Hong ^{[2
]}

Feng, Sisi ^{[1
]}

Tang, Jijun ^{[3
]}

Wu, Rongling ^{[1
]}

机构：

[1] Beijing Forestry Univ, Coll Biol Sci & Biotechnol, Natl Engn Lab Tree Breeding, Ctr Computat Biol, Beijing, Peoples R China

[2] Peking Univ, Coll Life Sci, Ctr Bioinformat, Natl Lab Prot Engn & Plant Genet Engn, Beijing 100871, Peoples R China

[3] Univ S Carolina, Dept Comp Sci & Engn, Columbia, SC 29208 USA

来源：

PLOS ONE | 2013年 / 8卷 / 04期

关键词：

EXPRESSED SEQUENCE TAGS; MICROSATELLITE MARKERS; IN-SILICO; GENETIC DIVERSITY; LINKAGE MAP; REPEATS; GENOME; POLYMORPHISM; DESERT; RICE;

D O I：

10.1371/journal.pone.0061337

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Background: Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. Methodology/Principal Findings: A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). Conclusions: The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.

引用

页数：11

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