Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat.

Prem Lal Kashyap,Poonam Jasrotia,Ravi Shekhar Kumar,Gyanendra Pratap Singh,Devendra Pal Singh,Rahul Tripathi,Sudheer Kumar

doi:10.3389/fmicb.2019.01072

Prem Lal Kashyap, Poonam Jasrotia + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2019.01072

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Abstract

Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (IA = 1.169) and standardized index of association (rBarD = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (Fst = 0.012). Recombination (Rm = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.

Highlights

Loose smut caused by the basidiomycete fungus Ustilago segetum (Pers.) Roussel tritici Jensen (UST), is one of the most serious diseases on wheat (Triticum aestivum L.) globally
Phylogenetic analysis of RPB2 gene from 112 isolates turn out from different wheat growing zones showed that they are related to each another and divergent from the isolate reported from Canada (Figure 1)
Analysis of the sequences of the RPB2 gene loci in the 112 isolates by DnaSP version 5.10 identified a total of 98 haplotypes (Table 1)

Summary

Introduction

Loose smut caused by the basidiomycete fungus Ustilago segetum (Pers.) Roussel tritici Jensen (UST), is one of the most serious diseases on wheat (Triticum aestivum L.) globally. The disease is favored by moist and cool climate during anthesis (Quijano et al, 2016). This fungus converts the spike floral tissues to fungal teliospores, causing yield losses equivalent to the percent smutted spikes (Green et al, 1968; Singh, 2018). Wilcoxon and Saari (1996) documented that the fungus can result in reductions of 5–20 per cent profit at an infection level of 1–2 per cent. Nielsen and Thomas (1996) reported 15–30% annual yield losses as a result of UST infection

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