Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database.

Fang K. Du,Hong Qu,Fang Xu,Rongling Wu,Sisi Feng,Jijun Tang,Jean-Marc Lacape

doi:10.1371/journal.pone.0061337

Fang K. Du, Hong Qu + Show 5 more

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https://doi.org/10.1371/journal.pone.0061337

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Abstract

BackgroundMicrosatellite 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 FindingsA 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).ConclusionsThe 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.

Highlights

Populus euphratica Oliv. (Salicaceae) inhabits semi-arid areas, with a natural distribution ranging from Western China and the Middle East to Spain and Western Morocco
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, Quantitative Trait Locus (QTL), and marker-assisted breeding
More recent studies using Amplified Fragment Length Polymorphism (AFLP) or microsatellite analysis based on polyacrylamide gel electrophoresis (PAGE) with silver staining have provided useful information on its genetics and evolutionary history [8–0]

Summary

Introduction

Populus euphratica Oliv. (Salicaceae) inhabits semi-arid areas, with a natural distribution ranging from Western China and the Middle East to Spain and Western Morocco. It is considered to be salinity and drought tolerant [1]. P. euphratica is a useful model organism for studying salt and drought resistance mechanisms in trees because it can tolerate NaCl concentrations of up to 450 mM [4,5] and mannitol concentrations up to 400 mM [6] in controlled experiments. Partly because of the scarcity of suitable molecular markers, much remains to be learned about the genetic factors responsible for the ability of P. euphratica to cope with various adverse environmental conditions. 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

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