Biology subjects

Periyannan, S.

Publications and source records attributed to Periyannan, S..

11 recordsLinked to original sources

bioRxiv2026

Haplotype-based insights into the genetic architecture of net blotch resistance in barley

Net blotch, caused by Pyrenophora teres, is a major constraint to barley production worldwide and occurs as two epidemiologically distinct forms: net form net blotch (NFNB) and spot form net blotch (SFNB). Although numerous resistance loci have been reported in recent years, their genetic relationship remains poorly understood, and the effective deployment of resistance is constrained by the complex genetic architecture of net blotch resistance. In this study, we used a haplotype-based mapping approach to dissect the genetic basis of resistance to NFNB and SFNB in a diverse panel of 950 barley accessions from the Australian Grains Genebank (AGG). Disease responses were evaluated across 13 experiments, and a total of 40 quantitative trait loci (QTL) were identified, including 26 associated with NFNB, 29 with SFNB, and 15 common for both diseases. Most loci co-localized with previously reported QTL, while six putative novel haploblocks highlighted untapped genetic diversity within the AGG collection. Correlation analyses across phenotypic, genetic and haploblock levels revealed a partial but incomplete overlap in resistance mechanisms between NFNB and SFNB. Among the 4,497 haploblocks, approximately 60% of them showed positive local genetic correlations between the two diseases, suggesting shared genomic contributions to resistance. Haplotype composition analysis further identified a resistant haplotype group, mainly comprising accessions of Asian origin, that exhibited high levels of resistance to both forms of net blotch. Through in silico haplotype stacking, we demonstrated the cumulative genetic potential achievable by combining favourable haplotypes. When the breeding objective was to improve resistance to both NFNB and SFNB, dual-disease stacking strategies outperformed single-disease approaches, highlighting the value of prioritising haplotypes with positive pleiotropic effects. Overall, this study provides a comprehensive haplotype-level framework for understanding net blotch resistance and delivers practical insights for breeding barley cultivars with durable and broad-spectrum resistance to both NFNB and SFNB.

plant biology↗

bioRxiv2026

Transcriptomic analysis reveals SnTox8-mediated reprogramming of wheat defence signalling

Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crousis, a necrotrophic fungal pathogen, is the causal agent for septoria nodorum blotch, a major constraint on global wheat production. Pathogen-produced necrotrophic effectors (NEs) that interact with host-sensitivity genes in an inverse gene-for-gene manner, collectively leading to effector-triggered susceptibility (ETS). Here, we investigated the transcriptional responses of two Triticum aestivum L. genotypes, Mace and Lancer, following infiltration with a novel NE, SnTox8. A total of 12,679 unique differentially expressed genes in Mace and 149 in Lancer were detected from transcriptomic analysis. In the SnTox8-sensitive cultivar, Mace, numerous defence-related genes were induced, including protein phosphorylation cascades, reactive oxygen species bursts, calcium signalling, phytohormone modulation, and suppression of photosynthesis, consistent with findings from other ETS models, in which necrotrophic fungal pathogens hijack host defence systems to proliferate. The interaction also activated genes involved in signal transduction, metabolism, membrane modification, and molecular transport, reflecting a coordinated host reprogramming that promotes cellular dysfunction and cell death, thereby facilitating necrotrophic pathogenesis. In contrast, Lancer, an SnTox8-insensitive cultivar, exhibited minimal transcriptional changes with no evidence of effector recognition or downstream defence-related activities. Overall, this study exhibited that SnTox8 manipulates kinase-mediated immune signalling and metabolic reprogramming to convert defence activation into host cell death, revealing a mechanistic basis for ETS in wheat. The identified SnTox8-Snn8-triggered processes were confirmed through additional transcriptome analysis of Mace mutants. Outcomes from this study establish a foundation for identifying, functionally characterising and validating the corresponding host susceptibility gene Snn8.

molecular biology↗

bioRxiv2026

The variable wheat stripe rust effector AvrYr7 evades Yr7 recognition through sequence and expression polymorphisms

Introductory paragraphWheat provides about 20% of total dietary calories worldside1. Wheat diseases, including wheat stripe (yellow) rust, cause billions of dollars in losses each year2. Wheat stripe (yellow) rust is caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst) which is best controlled by fungicide application and disease resistant wheat cultivars3. To-date, there are over 80 catalogued and >10 cloned yellow rust resistance genes (Yr genes)4. Yet our knowledge of corresponding avirulence (Avr) genes lags far behind5-8. The absence of cloned Avrs reflects Psts complex genome and the lack of robust transformation and genetic systems3. Recent advances in generating high-quality genome assemblies and the development of wheat defense assays have addressed these challenges9-11. Here we clone AvrYr7 which is recognized by Yr712. We further identify six additional alleles of AvrYr7 that escape recognition due to non-synonymous genetic variations, transposable element activity, missense mutation, and expression polymorphism. These findings provide critical insights into virulence evolution in one of the worlds most important wheat pathogens.

plant biology↗

bioRxiv2025

A conserved stripe rust effector elicits variable resistance responses in wheat

Plant resistance (R) and pathogen avirulence (Avr) gene interactions are central to pathogen recognition and disease resistance in crops. Functional characterisation of recognised Avr effectors of Puccinia striiformis f. sp. tritici (Pst) lags other key fungal pathogens of wheat. Here, we used a wheat protoplast-based screen to identify Avr/R interactions via the proxy of effector-induced defence responses in a set of diverse wheat cultivars. We identified an Avr candidate, termed AvrPstB48, that triggers defence responses in 16 out of 24 cultivars tested. AvrPstB48 is hemizygous, and the Pst genome carries four divergent paralogs within a gene cluster. Analysis of these paralogs revealed partial redundancy in their ability to activate wheat defences and enabled us to identify a single amino acid in AvrPstB48 that is necessary but not sufficient for defence activation. Notably, the activation of defence signalling by AvrPstB48 in protoplasts did not directly correlate with disease outcomes. Whole-plant infection assays revealed that some cultivars which exhibited strong defence activation in the protoplast assay are susceptible to the Pst isolate Pst104E137A- from which AvrPstB48 is derived. Comparison of infection dynamics of two wheat cultivars that differ in their AvrPstB48 recognition capacity revealed a delay in disease progression in the recognising cultivar Avocet S compared to the non-recognising cultivar Morocco. While correlative only, our observations, combined with other recent reports, support a recognize-then-suppress model of plant-pathogen interaction where disease outcomes are driven not only by simple Avr/R interactions but also by pathogen effectors that suppress defence signalling downstream of effector recognition.

plant biology↗

bioRxiv2024

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Phased telomere to telomere (T2T) genome assemblies are revolutionising our understanding of long hidden genome biology "dark matter" such as centromeres, rDNA repeats, inter-haplotype variation, and allele specific expression (ASE). Yet insights into dikaryotic fungi that separate their haploid genomes into distinct nuclei is limited. Here we explore the impact of dikaryotism on the genome biology of a long-term asexual clone of the wheat pathogenic fungus Puccinia striiformis f. sp. tritici. We use Oxford Nanopore (ONT) duplex sequencing combined with Hi-C to generate a T2T nuclear-phased assembly with >99.999% consensus accuracy. We show that this fungus has large regional centromeres enriched in LTR retrotransposons, with a single centromeric dip in methylation that suggests one kinetochore attachment site per chromosomes. The centromeres of chromosomes pairs are most often highly diverse in sequence and kinetochore attachment sites are not always positionally conserved. Each nucleus carries a unique array of rDNAs with >200 copies that harbour nucleus-specific sequence variations. The inter-haplotype diversity between the two nuclear genomes is caused by large-scale structural variations linked to transposable elements. Nanopore long-read cDNA analysis across distinct infection conditions revealed pervasive allele specific expression for nearly 20% of all heterozygous gene pairs. Genes involved in plant infection were significantly enriched in ASE genes which appears to be mediated by elevated CpG gene body methylation of the lower expressed pair. This suggests that epigenetically regulated ASE is likely a previously overlooked mechanism facilitating plant infection. Overall, our study reveals how dikaryotism uniquely shapes key eukaryotic genome features.

genomics↗

bioRxiv2024

Stacking haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance

Wheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8% and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.

plant biology↗

bioRxiv2022

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley (Hordeum spp.). The barley leaf rust resistance locus Rph7, located on the short arm of chromosome 3H, confers defence at all growth stages and was previously shown to have unusually high sequence and haplotype divergence. Earlier, four candidate genes for Rph7 were reported and, despite an in-depth comparative sequence analysis and haplotypic characterisation, the causal gene could not be resolved. Here, we successfully cloned Rph7 utilising a fine mapping approach in combination with an RNA-Seq based expression analysis. We identified three up-regulated and pathogen-induced genes with presence/absence variation (PAV) at this locus. Sequence analysis of chemically induced Rph7 knockout mutant lines identified multiple independent non-synonymous variants, including a premature stop codon in a single non-canonical resistance gene that encodes a 302-amino acid protein. Progeny from four independent transgenic lines segregated for the expected avirulent Rph7 infection type in response to several avirulent P. hordei pathotypes, however, all plants were susceptible to a single virulent pathotype confirming the specificity. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor, as it shares structural similarity to ANAC019 from Arabidopsis, with a C-terminal BED domain. A global gene expression analysis suggests Rph7 is involved in the activation of basal defence.

genetics↗

bioRxiv2022

Extensive somatic nuclear exchanges shape global populations of the wheat leaf rust pathogen Puccinia triticina

Non-sexual processes such as somatic nuclear exchange are postulated to play a role in the diversity of clonally reproducing dikaryotic rust fungi but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage is derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveal that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.

genomics↗

bioRxiv2021

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

BackgroundMost animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false positive signals. ResultsWe generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30-40 times using HiFi sequencing is required for phasing of the leaf rust genome (~0.7% heterozygosity) and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. ConclusionsThis first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.

genomics↗

bioRxiv2020

Ancient BED-domain-containing immune receptor from wild barley confers widely effective resistance to leaf rust

Leaf rust, caused by Puccinia hordei is a devastating fungal disease affecting barley (Hordeum vulgare subsp. vulgare) production globally. Race-specific resistance (R) genes have been deployed widely; however, their durability is often compromised due to the rapid emergence of virulent P. hordei races, prompting the search for new sources of broad-spectrum resistance. Here we report on the cloning of Rph15, a broadly effective resistance gene derived from the wild progenitor Hordeum vulgare subsp. spontaneum. We demonstrate using introgression mapping, mutation and complementation that Rph15 encodes a coiled-coil nucleotide-binding leucine-rich repeat (NLR) protein with an integrated Zinc-finger BED (ZF-BED) domain. The allelic variation at the Rph15 locus was assessed using barley exome capture data that traced its origin to the western region of the Fertile Crescent bordering Jordan and Israel. To unravel the genetic relationship of two other leaf rust resistance genes (Rph14 and Rph16) mapped at similar locus on chromosome 2H, we re-sequenced the Rph15 gene from the near-isogenic line for Rph15 (Bowman+Rph15) and the two donor accessions of Rph14 (PI 584760) and Rph16, (PI 405292, Hs 680). Both whole genome and Sanger sequencing confirmed that Hs 680 carried Rph15, while Rph14 in PI 584760 was an independent locus. A perfect diagnostic KASP marker was developed and validated to permit efficient introduction of Rph15 into cultivated barley.

plant biology↗

bioRxiv2018

Resistance gene discovery and cloning by sequence capture and association genetics

Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes1, 2 and pathogens can rapidly evolve to overcome R genes when deployed singly3. Introducing multiple cloned R genes into crops as a stack would avoid linkage drag and delay emergence of resistance-breaking pathogen races4. However, current R gene cloning methods require segregating or mutant progenies5-10, which are difficult to generate for many wild relatives due to poor agronomic traits. We exploited natural pan-genome variation in a wild diploid wheat by combining association genetics with R gene enrichment sequencing (AgRenSeq) to clone four stem rust resistance genes in <6 months. RenSeq combined with diversity panels is therefore a major advance in isolating R genes for engineering broad-spectrum resistance in crops.

genomics↗