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 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.

Figure 1

Geographic distribution of 25 wild emmer wheat populations in Israel and Turkey. (A) 22 populations in Israel, and (B) 3 populations in Turkey. Details of the numbered populations are listed in Table 1.

Figure 2

Mantel test showing the relationship of genetic and geographic distances. (A) Relationship between shared-allele distance and geographic distances, and (B) relationship between population differentiation F_ST and geographic distances.

Figure 3

Genetic structure of 25 wild emmer wheat populations from Israel and Turkey. (A) Evolution of the natural logarithm probability of the data against K; (B) Magnitude of ΔK for each K value; (C) Clustering for K = 2 to 4 for the entire set of wild emmer wheat.

Figure 4

Detection of outlier SNPs under the hierarchical structure model using Arlequin 3.5.F_ST: locus-specific genetic divergence among populations; Heterozygosity/1- F_ST: a modified measure of heterozygosity per locus. Loci significant at the 1% level are indicated by red dots.

Figure 5

Chromosomal distribution of 33 outlier loci subjected to positive selection. The codes of mapped loci are shown on the right of each chromosome and the intervals are indicated on the left. Details of codes are presented in Table 5. Candidate loci from known genes of wheat were indicated by *, and these known genes subjected to positive selection were listed after each loci. The number in parentheses at the bottom of each chromosome is the number of EST loci mapped in that chromosome without knowing the exact bin. Only these bins with mapped loci are indicated.

Figure 6

Gene diversity (Nei 1978) profiles of allozyme, RAPD, EST-SSR, SSR, and EST- related SNP loci in 10 wild emmer wheat populations from Israel and Turkey.