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

Jing Ren; Liang Chen; Daokun Sun; Frank M. You; Jirui Wang; Yunliang Peng; Eviatar Nevo; Avigdor Beiles; Dongfa Sun; Ming Cheng Luo; Junhua Peng

doi:10.1186/1471-2148-13-169

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

Jing Ren, Liang Chen, Daokun Sun, Frank M. You, Jirui Wang, Yunliang Peng, Eviatar Nevo, Avigdor Beiles, Dongfa Sun, Ming Cheng Luo, Junhua Peng

Department of Evolutionary and Environmental Biology

Research output: Contribution to journal › Article › peer-review

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 F _ST-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.

Original language	English
Article number	169
Journal	BMC Evolutionary Biology
Volume	13
Issue number	1
DOIs	https://doi.org/10.1186/1471-2148-13-169
State	Published - 2013

Bibliographical note

Funding Information:
The authors are greatly indebted to the two anonymous reviewers for their critical, helpful and constructive comments on this manuscript. We also sincerely thank Ms. Robin Permut, English editor in the Institute of Evolution at University of Haifa, for her professionally editing the manuscript. This work was supported by the China National Science Foundation (NSFC) Grant Nos. 31030055 and 30870233, China National Special Program for Development of Transgenic Plant & Animal New Cultivars (Development of transgenic quality wheat germplasm with soft & weak gluten, and Development of transgenic wheat new cultivars with resistance against rust diseases and powdery mildew), Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project Grant No. KSCX2-YW -Z-0722, the CAS Strategic Priority Research Program Grant No. XDA05130403, the “973” National Key Basic Research Program Grant No. 2009CB118300, and the Ancell Teicher Research Foundation for Genetics and Molecular Evolution.

Keywords

Adaptive genetic diversity
Natural selection
Population structure
SNP marker
Triticum dicoccoides

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/1471-2148-13-169

Cite this

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title = "SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors",

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 F ST-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 = "Adaptive genetic diversity, Natural selection, Population structure, SNP marker, Triticum dicoccoides",

author = "Jing Ren and Liang Chen and Daokun Sun and You, {Frank M.} and Jirui Wang and Yunliang Peng and Eviatar Nevo and Avigdor Beiles and Dongfa Sun and Luo, {Ming Cheng} and Junhua Peng",

note = "Funding Information: The authors are greatly indebted to the two anonymous reviewers for their critical, helpful and constructive comments on this manuscript. We also sincerely thank Ms. Robin Permut, English editor in the Institute of Evolution at University of Haifa, for her professionally editing the manuscript. This work was supported by the China National Science Foundation (NSFC) Grant Nos. 31030055 and 30870233, China National Special Program for Development of Transgenic Plant & Animal New Cultivars (Development of transgenic quality wheat germplasm with soft & weak gluten, and Development of transgenic wheat new cultivars with resistance against rust diseases and powdery mildew), Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project Grant No. KSCX2-YW -Z-0722, the CAS Strategic Priority Research Program Grant No. XDA05130403, the “973” National Key Basic Research Program Grant No. 2009CB118300, and the Ancell Teicher Research Foundation for Genetics and Molecular Evolution.",

year = "2013",

doi = "10.1186/1471-2148-13-169",

language = "English",

volume = "13",

journal = "BMC Evolutionary Biology",

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AU - Ren, Jing

AU - Chen, Liang

AU - Sun, Daokun

AU - You, Frank M.

AU - Wang, Jirui

AU - Peng, Yunliang

AU - Nevo, Eviatar

AU - Beiles, Avigdor

AU - Sun, Dongfa

AU - Luo, Ming Cheng

AU - Peng, Junhua

N1 - Funding Information: The authors are greatly indebted to the two anonymous reviewers for their critical, helpful and constructive comments on this manuscript. We also sincerely thank Ms. Robin Permut, English editor in the Institute of Evolution at University of Haifa, for her professionally editing the manuscript. This work was supported by the China National Science Foundation (NSFC) Grant Nos. 31030055 and 30870233, China National Special Program for Development of Transgenic Plant & Animal New Cultivars (Development of transgenic quality wheat germplasm with soft & weak gluten, and Development of transgenic wheat new cultivars with resistance against rust diseases and powdery mildew), Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project Grant No. KSCX2-YW -Z-0722, the CAS Strategic Priority Research Program Grant No. XDA05130403, the “973” National Key Basic Research Program Grant No. 2009CB118300, and the Ancell Teicher Research Foundation for Genetics and Molecular Evolution.

PY - 2013

Y1 - 2013

N2 - 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 F ST-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.

AB - 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 F ST-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.

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KW - Natural selection

KW - Population structure

KW - SNP marker

KW - Triticum dicoccoides

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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