Genome‐wide mapping in an international isolate collection identifies a transcontinental erg11/CYP51 promoter insertion associated with fungicide resistance in Leptosphaeria maculans

Genome-wide mapping in an international isolate collection identifies a transcontinental erg11/CYP51 promoter insertion associated with fungicide resistance in Leptosphaeria maculans

Insertion of a remnant transposable element in the promoter region of the erg11/CYP51 demethylase inhibitor (DMI) target gene confers resistance to DMI fungicides worldwide.


Abstract

Fungicide resistance is often conferred through the mutation of genes encoding fungicide targets or proteins that remove fungicides from cells, but mechanisms can vary widely between taxa. Discovering the specific resistance alleles present in pathogen populations is essential for monitoring the evolution and movement of resistant genotypes. In this study, we explored the genomic basis of demethylase inhibitor (DMI) resistance in Leptosphaeria maculans, the main pathogen of the canola crop Brassica napus. Using an international collection of over 200 genome-sequenced isolates, we assayed in vitro sensitivity to the DMI tebuconazole and conducted a genome-wide association study on a variant set including single-nucleotide polymorphisms (SNPs), small indels and structural variants. The main resistance allele identified was a 237 bp remnant transposable element insertion in the promoter of the erg11/CYP51 DMI target gene in a large proportion of isolates from Europe, an allele known to confer DMI resistance in Australia. Several associated loci were identified, none of which are commonly linked to DMI resistance in other phytopathogens. We also found little to no relationship between DMI tolerance and baseline growth rate, suggesting minimal fitness effects of fungicide resistance in these isolates. This study indicates common DMI resistance alleles in L. maculans are shared across continents and erg11/CYP51 coding mutations, which are near-ubiquitous in other fungal pathogens, may not underpin DMI resistance in this species. Furthermore, that resistance occurs frequently in numerous canola-growing regions suggests management is essential for growers.

Applying unoccupied aerial systems to assess genetic gain from mass selection for tembotrione tolerance in sorghum (Sorghum bicolor)

Abstract

The post-emergent herbicide options to control grasses in sorghum have historically been limited. Therefore, a mass selection program was implemented to increase the tolerance of sorghum to the broad-spectrum herbicide tembotrione. The objectives of this study are to determine (i) which observation timing and vegetative indices are most effective in assessing sorghum injury to tembotrione using unoccupied aerial system imagery and (ii) if mass selection can be used to increase the tolerance of sorghum to tembotrione. Using an unoccupied aerial system, several vegetative indices, collected at either 14 or 21 days after tembotrione application, accurately measured sorghum injury. Over four cycles of selection, tembotrione tolerance increased in a linear and consistent manner. This demonstrates that mass selection can be used as a strategy for developing herbicide tolerance in crops. The modest, but steady genetic gain indicates both the quantitative nature of the trait and sufficient heritability to improve it. Given further development, tembotrione-resistant sorghum hybrids could provide an effective means of post-emergent weed control for a range of common weeds.

Evolution of decreased sensitivity to azole fungicides in western European populations of Plenodomus lingam (Phoma stem canker on oilseed rape)

Evolution of decreased sensitivity to azole fungicides in western European populations of Plenodomus lingam (Phoma stem canker on oilseed rape)

Plenodomus lingam (Phoma leaf spot/stem canker) populations in western Europe (Germany, Ireland and the United Kingdom) predominantly contain CYP51 promoter inserts leading to deceased azole (DMI) fungicide sensitivity.


Abstract

Plenodomus lingam (Leptosphaeria maculans) and P. biglobosus (L. biglobosa) are fungi causing Phoma leaf spot/stem canker, an international damaging disease of oilseed rape (Brassica napus) and other brassicas. In Europe, fungicides used for disease management are mainly sterol 14α-demethylase (CYP51) inhibitors (DMIs/azoles); quinone-outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs) are also used. Decreased DMI sensitivity has emerged in Australian and eastern European P. lingam populations and is mediated by CYP51 promoter inserts resulting in target site overexpression. In this study using in vitro sensitivity testing, we report decreased DMI (prothioconazole-desthio, mefentrifluconazole) sensitivity in modern western European P. lingam isolates (collected 2022–2023) compared to older baseline (1992–2005) isolates. Around 85% of modern western European P. lingam isolates collected, for which the CYP51 promoter region was sequenced, carried a promoter insert, but target site alterations were not detected. Six different CYP51 promoter inserts were identified, most commonly a 237 bp fragment of the Sahana transposable element. Inserts were associated with an approximately 3- to 10-fold decrease in sensitivity to the DMIs tested. In contrast to P. lingam, PCR screening revealed CYP51 promoter inserts were absent in modern western European P. biglobosus isolates (2021–2023). Combined data indicate P. lingam isolates lacking an insert were similarly (or slightly more) sensitive to the DMIs tested for P. biglobosus, whereas those carrying an insert were slightly less sensitive than P. biglobosus. No evidence for substantive sensitivity shifts to the QoI (pyraclostrobin) or SDHI (boscalid) fungicides tested was obtained for either Plenodomus species.

Botryosphaeria dothidea causes stem canker of Idesia polycarpa in China

Botryosphaeria dothidea causes stem canker of Idesia polycarpa in China

This is the first report of Botryosphaeria dothidea as the pathogen of stem canker of Idesia polycarpa based on morphological and molecular characterization and pathogenicity identification.


Abstract

Idesia polycarpa is a woody oil plant with great development and application prospects. However, stem canker disease of I. polycarpa was frequently observed in Henan and Hubei provinces of China in 2020–2022. The seriousness of the disease caused a large number of trees deaths, which affected seedling production and fruit yield, restricting the development of the I. polycarpa industry. We performed isolation, purification and pathogenicity analysis of canker samples. Pathogenicity tests reproduced typical canker disease symptoms on detached branches of I. polycarpa. Based on morphological observations, conidial morphology and phylogenetic analysis of isolates with high similarity to the rDNA internal transcribed spacer (ITS), EF-1α and TUB2 sequences screened in GenBank by BLAST, the pathogen of canker disease on I. polycarpa was identified as Botryosphaeria dothidea. This is the first report of B. dothidea as the pathogen of stem canker of I. polycarpa.

Identification of candidate RXLR effectors from downy mildew of foxtail millet pathogen Sclerospora graminicola and functional analysis of SG_RXLR41

Identification of candidate RXLR effectors from downy mildew of foxtail millet pathogen Sclerospora graminicola and functional analysis of SG_RXLR41

Sixty-two RXLR effectors were identified from Sclerospora graminicola. The screening revealed that SG_RXLR41 suppresses INF1-induced cell death and promotes Phytophthora capsici infection by inhibiting host immune responses.


Abstract

Downy mildew caused by Sclerospora graminicola is a systemic disease that affects the yield and quality of foxtail millet. This obligate biotrophic oomycete manipulates host physiology and immune processes through numerous effectors. A thorough comprehension of effector biology is crucial to unravel disease mechanisms and understand host plant resistance. In this study, bioinformatic analyses revealed 498 potentially secreted proteins in S. graminicola, of which 62 were identified as RXLR effectors; 46 RXLR-encoding genes exhibited upregulated expression during the early stages of infection. To elucidate the functions of these secreted proteins, a heterogeneous expression system was developed using Nicotiana benthamiana. Twenty-one RXLR effectors secreted by S. graminicola were transiently expressed in N. benthamiana, of which four could suppress INF1-triggered cell death. Various defence responses in N. benthamiana were attenuated, including inhibition of defence gene expression, reduction of reactive oxygen species (ROS) accumulation and diminished callose deposition. The expression of SG_RXLR41 also enhanced the growth of Phytophthora capsici on N. benthamiana leaves. These findings indicate that S. graminicola facilitates infection and expansion through the secretion of multiple RXLR effectors, and SG_RXLR41 is an important virulence-related effector that is involved in manipulating plant immunity by suppressing cell death.

Identifying quantitative trait locus and candidate genes for maize (Zea mays L.) plant architecture traits based on segregating populations constructed by high‐generation sister lines

Abstract

Leaf length, width and angle are important traits in the architecture of maize plants. Delving into the genetic mechanisms of these traits is of utmost significance for promoting population yield. In this study, we employed the high-generation sister lines PCU and PCM, which have significant differences in leaf morphological traits, as parental entities for the creation of F2 and F2:3 populations. Through quantitative trait locus (QTL) mapping of the traits in the three ear leaves by ICIM, 55 QTL were obtained, with six stable QTL selected across divergent populations. These QTL had physical spans ranging from 0.34 to 44.8 Mbp. Through gene annotation and qRT-PCR, Zm00001d007382, Zm00001d035965, Zm00001d042777 and Zm00001d020641 were predicted as potential candidates for regulating maize plant architecture. The results of this study lay a foundation for analysing the genetic mechanisms of maize plant architecture traits and cloning-related genes.

Quadrat soil pollen signal reflects plant important values in forests and shrublands from subtropical China

Pollen analysis, a crucial tool in botany and ecology for examining historical biotic dynamics, has elicited debate owing to its complex link with vegetation. The challenge lies in discerning the ecological significance of pollen data. In this study, we conducted detailed quadrat surveys on Jinhua Mountain, subtropical China, analyzing topsoil pollen to determine whether pollen signals accurately reflect key ecological components in the forests and shrublands. We performed direct comparisons between pollen and plant compositions and calculated pollen percentages and plant Important Values (IVs) for each quadrat. The results indicate greater homogeneity in pollen composition across the study area compared to plant composition, particularly in the high percentage of Pinus pollen. However, distinct plant communities exhibited significantly different pollen compositions, as evidenced by the multi-response permutation test. This divergence aligns with variations in the dominant plant species across different communities. There were significant correlations between pollen percentages and plant IVs, with correlation coefficients of 0.55 (p < 0.001) at the quadrat level and 0.78 (p < 0.001) at the taxon level. These results support the utility of pollen analysis for representing ecologically significant values in subtropical Chinese forests and shrublands. Such correlations might also be extrapolated to pollen-based paleoecological studies.

The modified activity of prolyl 4 hydroxylases reveals the effect of arabinogalactan proteins on changes in the cell wall during the tomato ripening process

Arabinogalactan proteins (AGPs) are proteoglycans with an unusual molecular structure characterised by the presence of a protein part and carbohydrate chains. Their specific properties at different stages of the fruit ripening programme make AGPs unique markers of this process. An important function of AGPs is to co-form an amorphous extracellular matrix in the cell wall-plasma membrane continuum; thus, changes in the structure of these molecules can determine the presence and distribution of other components. The aim of the current work was to characterise the molecular structure and localisation of AGPs during the fruit ripening process in transgenic lines with silencing and overexpression of SlP4H3 genes (prolyl 4 hydroxylase 3). The objective was accomplished through comprehensive and comparative in situ and ex situ analyses of AGPs from the fruit of transgenic lines and wild-type plants at specific stages of ripening. The experiment showed that changes in prolyl 4 hydroxylases (P4H3) activity affected the content of AGPs and the progress in their modifications in the ongoing ripening process. The analysis of the transgenic lines confirmed the presence of AGPs with high molecular weights (120–60 kDa) at all the examined stages, but a changed pattern of the molecular features of AGPs was found in the last ripening stages, compared to WT. In addition to the AGP molecular changes, morphological modifications of fruit tissue and alterations in the spatio-temporal pattern of AGP distribution at the subcellular level were detected in the transgenic lines with the progression of the ripening process. The work highlights the impact of AGPs and their alterations on the fruit cell wall and changes in AGPs associated with the progression of the ripening process.

Significant correlation between leaf vein length per unit area and stomatal density: evidence from Red Tip and Chinese photinias

The vascular veins in photosynthetic leaves play an important role in transporting water and sugars throughout the plant body, and their venation pattern and vein density determine the hydraulic efficiency of the leaf. Likewise, stomatal density (SD) can influence photosynthetic gas exchange. However, the correlation between leaf vein density and SD is seldom reported. Herein, we examined 16 leaves from the hybrid Photinia × fraseri and 16 leaves from one of its parents, P. serratifolia, to explore the correlation between leaf vein density and SD. For each leaf, equidistant lamina quadrats were excised along two longitudinal transects (one along the midrib and another along the leaf margin). For each quadrat, micrographs of 1.2 mm × 0.9 mm stomatal imprints, and 2.51 mm × 1.88 mm micrographs of leaf veins were used to measure total vein area per leaf unit area (VAA) and total vein length per unit area (VLA), as indicators of leaf vein density, to determine the correlation between SD and leaf vein density. For each taxon, there was no significant correlation between SD and VAA, but there was a significant correlation between SD and VLA. The data indicate that SD is not positively correlated with VAA but positively correlated with VLA for both the hybrid and the parent species. This study indicates that future work should focus on the relationships between SD and total vein length per unit area rather than on total leaf vein area per unit area within and across species.