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Open Access Research article

SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors

Jing Ren12, Liang Chen1, Daokun Sun1, Frank M You34, Jirui Wang3, Yunliang Peng5, Eviatar Nevo6, Avigdor Beiles6, Dongfa Sun7, Ming-Cheng Luo3* and Junhua Peng18*

Author Affiliations

1 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan, Hubei 430074, China

2 Graduate University of Chinese Academy of Sciences, Beijing 100049, China

3 Department of Plant Sciences, University of California, Davis, CA 95616, USA

4 Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB R3T 2M9, Canada

5 Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China

6 Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel

7 College of Plant Science & Technology, Huazhong Agricultural University, Wuhan Hubei 430071, China

8 Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA

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BMC Evolutionary Biology 2013, 13:169  doi:10.1186/1471-2148-13-169

Published: 13 August 2013

Abstract

Background

Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers.

Results

In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed.

Conclusions

Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.

Keywords:
Triticum dicoccoides; SNP marker; Adaptive genetic diversity; Population structure; Natural selection