Genetic Diversity and Population Structure Reveal Cryptic Genetic Variation and Long Distance Migration of Puccinia graminis f. sp. tritici in the Indian Subcontinent

Abstract

Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of wheat worldwide since time immemorial. Several wheat stem rust outbreaks have been reported worldwide including India. Approximately 7 mha wheat area in central and peninsular India is highly vulnerable to stem rust epidemics. In this study, a repository of 29 single genotype uredospore pathotypes, representing five geographical regions, was characterized by investigating their virulence phenotype and simple sequence repeat (SSR) genotypes using 37 reproducible polymorphic SSR markers, 32 of which had ≥ 0.50 polymorphic information content (PIC) value. Virulence phenotypes were used to evaluate the virulence frequency (VF) and construct a hypothetical evolutionary hierarchy of these pathotypes. We projected seven lineages to explain the evolutionary pattern of the Pgt population. The VF of these pathotypes ranged between 0% and 100%. The virulence-based neighbor-joining (NJ) cluster analysis grouped Pgt pathotypes into five virulence groups. Likewise, five molecular groups were categorized using molecular genotypes. The molecular grouping was supported by principal coordinate analysis (PCoA), which revealed 25% of the cumulative variance contributed by the first two axes. Analysis of molecular variance (AMOVA) revealed 8 and 92% of the variation among and within the populations, respectively. The Mantel test confirmed a positive but weak correlation (R2 = 0.15) between virulence phenotypes and SSR genotypes. The highest and lowest values of different genetic diversity parameters (Na, Ne, I, He, uHe, and %P) revealed maximum and minimum variability in the Pgt population from Maharashtra and Uttar Pradesh, respectively. The population structure analysis clustered 29 Pgt pathotypes into two subpopulations and an admixture. Our results demonstrated that there was significant genetic diversity among Pgt pathotypes resulting from their long-distance dispersal ability complemented by gene flow. These findings provide insights into the virulence patterns, genetic variations, and possible evolution of Pgt pathotypes, which would support strategic stem rust resistance breeding.

Virulence and genetic analysis of Puccinia graminis tritici in the Indian sub-continent from 2016 to 2022 and evaluation of wheat varieties for stem rust resistance

“…The molecular grouping of Pgt pathotypes, generated through unweighted neighbor-joining (NJ) cluster analysis in DARwin 6.0.14, corroborated, up to some extent, virulence-based grouping of these pathotypes, which was in agreement with our previous findings (Prasad et al, 2022). Pathotypes 21, 21-1, and 21A-2;11 and 11A;117 and 117-6;and 40A, 40-2, and 40-3, sharing almost matching avirulence/virulence structure as reported previously (Prasad et al, 2018;Prasad et al, 2022), were clustered in one MG/subgroup (Figure 4). Such an association of virulence phenotypes and SSR genotypes among P. triticina (Wang et al, 2010) and P. striiformis tritici (Hovmoller et al, 2002) isolates is also reported, which is not uncommon if the genes responsible for virulence/pathogenicity are extensively distributed in pathogen genome (Ordonez and Kolmer, 2009).…”

“…The availability of Sr31 and other known and unknown Sr genes in recently developed wheat varieties, effective against all known pathotypes of stem rust in India and neighboring countries, accompanied by poor rainfall and a significant reduction in relative humidity over the years could have hampered the survival and infection rate of the natural population of Pgt and, therefore, poor stem rust incidence (Ayliffe et al, 2008;Prank et al, 2019). As revealed previously (Prasad et al, 2018;Prasad et al, 2022), the Pgt population reported from India and Nepal remained avirulent to Sr7a, Sr26, Sr27, Sr31, Sr32, Sr33, Sr39, Sr40, Sr43, SrTmp, and SrTt3 to date. Some of these genes, for instance, Sr26, have been found to be effective against the Pgt population including Ug99 globally.…”

“…Such an association of virulence phenotypes and SSR genotypes among P. triticina (Wang et al, 2010) and P. striiformis tritici (Hovmoller et al, 2002) isolates is also reported, which is not uncommon if the genes responsible for virulence/pathogenicity are extensively distributed in pathogen genome (Ordonez and Kolmer, 2009). The comprehensive evolutionary pattern of all these Pgt pathotypes and others reported from the Indian sub-continent is already discussed previously (Prasad et al, 2022). Lower genetic diversity among Pgt pathotypes may be attributed to the clonal multiplication and long-distance migratory nature of the pathogen in the Indian sub-continent (Wingen et al, 2013).…”

“…Such interactions could result from the presence of some additional unknown effective Sr gene other than Sr24, which might impede pathotypes 34-1 and 40-1 from establishing compatible interactions with these varieties (Dakouri et al, 2013). The Indian population of Pgt possesses very low virulence frequencies on Sr31, Sr24, and Sr30 (Prasad et al, 2022), which are among 12 Sr genes postulated in 39 varieties (Table 4), and therefore, these varieties could be targeted for skillful gene deployment. Generally, Sr2, Sr5, Sr6, Sr7a, Sr7b, Sr8a, Sr8b, Sr9b, Sr9e, Sr11, Sr12, Sr13, Sr17, Sr21, Sr24, Sr25, Sr30, and Sr31 are frequently occurring Sr genes in Indian wheat varieties.…”

“…A set of 100 Puccinia spp.-specific SSR markers designed previously (Karaoglu et al, 2013;Prasad et al, 2017;Prasad et al, 2018;Savadi et al, 2020), synthesized in Agile Life Science Technologies (New Delhi, India), were used for genotyping 14 Pgt pathotypes. Thirty-seven markers (Supplementary Table 1), identified as polymorphic in our earlier study (Prasad et al, 2022), were selected to characterize Pgt pathotypes. Each 20 ml of the polymerase chain reaction (PCR) reaction mixture contained 25 ng of template DNA, 800 mM of dNTPs, 1X PCR buffer (10 mM Tris, pH 9.0, and 50 mM KCl), 1.5 mM MgCl 2 , 0.5 U Taq polymerase (HiMedia Laboratory Pvt.…”