Biology subjects

Hane, J. K.

Publications and source records attributed to Hane, J. K..

3 recordsLinked to original sources

bioRxiv2026

QTL mapping and proteomic profiling of barley: insights into resistance and susceptibility to Pyrenophora teres f. teres

Pyrenophora teres f. teres (Ptt), the causal agent of net form net blotch disease in barley, is an economically important fungal pathogen worldwide. Understanding both host resistance mechanisms and pathogen virulence factors is essential for developing durable net form net blotch resistant barley cultivars. Quantitative trait loci (QTL) mapping was conducted using a cross between two Ptt isolates, one virulent on the barley cultivar Prior and the other being avirulent. A major QTL associated with virulence on Prior was detected on chromosome 5. A progeny isolate possessing this QTL, together with the two parental isolates, was subsequently used in the proteomic analyses. Label-free proteomics was used to quantify in planta the protein profile changes in Prior following inoculations with the virulent and avirulent parental Ptt isolates, and the virulent progeny isolate. Leaf samples were collected at two (D2) and five (D5) days post-inoculation, and proteomic analyses performed to identify proteins associated with host resistance and pathogen virulence. A dataset comprising 2,886 barley proteins and 51 Ptt proteins was analysed. Principal component analysis (PCA) of the barley Prior proteomes revealed distinct clustering based on resistance and susceptibility at D5, while D2 samples formed a separate cluster. The PCA of the Ptt proteomes identified separate clusters, one comprised of the D2 and D5 avirulent parental isolate and another cluster of the virulent isolates at D5 only. Gene ontology analysis of the Prior proteins that were significantly increased in the resistant compared to the susceptible groups revealed functional categories related to protein translation, biosynthesis and chloroplast activities. The proteins that were significantly increased in the susceptible compared to the resistant Prior group were associated with organic acid and carbohydrate metabolism. The proteomic profiles and bioinformatic analysis generated in our study provide novel insights into the molecular basis of resistance and virulence in the barley-P. teres pathosystem. Key messageThis study reveals the first in planta proteomic profiles of both barley and Pyrenophora teres f. teres, identifying unique virulence-associated proteins and host responses linked to resistance and susceptibility.

plant biology↗

bioRxiv2021

Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

The wheat pathogen Parastagonospora nodorum has emerged as a model necrotrophic fungal species with growing genomic resources. Recent population-level pan-genome studies were leveraged to provide novel insights into pathogen evolution and effector-like gene contents relevant to local crop disease outbreaks. In this study, we examined 156 isolates representing a regional population from the Western Australian (WA) wheat-belt region, and 17 internationally sourced isolates. We observed a highly diverse local population, within which were numerous small and highly similar clusters of isolates from hotter and drier regions. Pan-genome assembly and orthologous gene datasets resulted in 3579 predicted effector candidates, 2291 of which exhibited presence-absence variation (PAV) across the population, and 1362 were specific to WA isolates. There was an abundance of mutations (including repeat-induced point mutation (RIP)), distributed in hot-spots within the pan-genomic landscape that were rich in effector candidates. Three characterised effector loci (ToxA, Tox1 and Tox3) were located within sub- telomeric regions of lower diversity, but were nestled within larger high-diversity regions. RIP was widespread across the genome, but non-synonymous RIP-like mutations were strongly selected against. These improved bioinformatic resources for P. nodorum, represent progressive advancements in fungal pan-genomics, with a view towards supporting region- specific surveillance of host-pathogen interactions.

genomics↗

bioRxiv2018

Selective sweeps in populations of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a selective sweep. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking.\n\nWe aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents - Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps.\n\nAmong the 25 isolates, there was evidence for four population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), another consisted of five isolates from Australia and one from Morocco (population 2). A further cluster was made up of Australian isolates, and the single South African isolate appeared to be from a separate population. We found that there was evidence of distinct selective sweeps between population 1 and population 2. Many of these sweeps overlapped genes involved in transcriptional regulation, such as transcription factors. It is possible that distinct populations of S. sclerotiorum from differing global environments have undergone selective sweeps at different genomic loci. This study lays the foundation for further work into investigation of the differing selective pressures that S. sclerotiorum populations are subjected to on a global scale.

genetics↗