Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India

Abstract

Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Punjab (PB), Rajasthan (RJ) and West Bengal (WB)) of India. The phylogenetic and haplotype analysis showed the presence of thirty haplotypes in all the analyzed populations. The haplotypic diversity in the RJ population (Hd = 0.981) was higher than in the HR (Hd = 0.972), PB (Hd = 0.965) and WB population (Hd = 0.962). Recombination events (Rm = 12) and mutation events (485) were also detected. Analysis of molecular variance (AMOVA) indicated that genetic diversity was exclusively due to the differences within populations. The haplotype network was widely dispersed and not associated with specific populations, as a single common haplotype was not detected. The PB population contained both unique (H9, H10 and H11) and shared haplotypes (27 haplotypes) in a higher number in comparison to other geographical locations. Except for haplotype H22 (contains highly aggressive isolates), there was no specific linkage noticed between the isolate aggressiveness and haplotype. The concatenated sequences of all the three genes demonstrated a low level of genetic differentiation (Fst = -0.014 to 0.02) in the analyzed population. Positive values for the neutrality tests in PB, HR and RJ reveal a balancing selection mechanism behind the FG population structure. The WB population showed both positive and negative values of neutrality indices, indicating the role of both population expansion as well as balancing selection in structuring the FG population.

Keywords: aggressiveness; head scab multi-locus sequence typing; mutation; phylogeny; population structure; recombination.

Figure 1

Typical symptoms of wheat head scab disease (Fusarium graminareum) on wheat spike.

Figure 2

Map showing the sample collection sites in Northern wheat belt of India. N= Number of samples; Distance between two sample collecting states is mentioned over the black line.

Figure 3

Phylogenetic relationship determined by using combined sequence of three gene loci (TUB, TEF and HIS sequences) and neighbor-joining (NJ) method. The percentage of replicate tree in the bootstrap test is 1000 replicates. The evolutionary distances were computed using the Kimura 2-parameter method. All positions containing gaps and missing data were eliminated. The tree was rooted with Diaporthe alleghaniensis strain CBS 495.72 [KC343733.1].

Figure 4

Unrooted maximum parsimony (MP) tree of haplotypes.

Figure 5

Median joining network of different haplotypes of FG population. Size of the circle is related with frequency of haplotypes. Colors indicate the proportion of individuals sampled in different populations within the study area.

Figure 6

Median joining network according to different categories of aggressiveness of FG haplotypes. Size of the circle is related with aggressivity of the haplotypes. Colors indicate the proportion of individuals depicting the same level of the study area. HA: Highly aggressive; MA: Moderately aggressive and LA: Least aggressive.