Category Archives: ORIGINAL ARTICLE

Assessment of genetic diversity of latent bacteria in coconut leaves associated with lethal yellowing disease symptoms in Kenya

Posted on by
Assessment of genetic diversity of latent bacteria in coconut leaves associated with lethal yellowing disease symptoms in Kenya

Coconut plants with yellowing disease are infected with bacterial species of economic importance. NGS analysis of samples found 285 OTUs with Actinobacteria as the predominant phylum and Streptomyces as the most abundant genus.


Abstract

Coconut (Cocos nucifera) is an economically important palm tree with diverse applications. However, limited scientific research exists on coconut diseases in the Kenyan coastal region. This cross-sectional study aimed to investigate the genetic diversity of latent bacteria associated with yellowing symptoms in coconut plants along the Kenyan coast. Sixty-two samples with symptoms were collected and their bacterial diversity assessed using culture-independent methods. DNA was extracted from controls and symptomatic samples using the cetyl trimethyl ammonium bromide (CTAB) method. Next-generation sequencing with Illumina MiSeq was used to profile the bacterial communities using amplicons of 16S ribosomal RNA sequences (V4 region). Sequence data were analysed using the Quantitative Insights Into Microbial Ecology 2 (QIIME 2) pipeline. A total of 113,330 reads were obtained, which clustered into 285 Operational Taxonomic Units. Bacterial diversity was highest in Kilifi, followed by Kwale and Lamu, while control samples exhibited low bacterial diversity. Actinobacteria was the predominant phylum across all counties, and Streptomyces was the most abundant genus. Kilifi and Kwale counties were more affected than Lamu. This is a pioneer study that provides insight into the bacterial diversity associated with yellowing disease symptoms in coconut plants in Kenya and will help with future elucidation of the agents causing or exacerbating coconut disease symptoms.

Physiological and hormonal responses of drought‐stressed Eucalyptus seedlings infected with Neofusicoccum kwambonambiense

Posted on by
Physiological and hormonal responses of drought-stressed Eucalyptus seedlings infected with Neofusicoccum kwambonambiense

Water stress increased Eucalyptus globulus predisposition to Neofusicoccum kwambonambiense infection and may also have promoted a change in the lifestyle of the fungus.


Abstract

The contribution of Eucalyptus globulus plantations to timber production for pulp, paper and energy production may be hampered by climate change. It is expected that Eucalyptus productivity may be affected through drought stress and changes to both pathogen distribution/pathogenicity and host–pathogen interactions. The impact of the fungal pathogen Neofusicoccum kwambonambiense on E. globulus, causing cankers and dieback, is well known but the impact of drought on disease development is still understudied. Our aim was to study the effect of drought on N. kwambonambiense infection by inoculating E. globulus plants under well-watered conditions or with water limitation. Non-infected plants for both water regimes were also analysed. Morphophysiological, biochemical and hormonal parameters were assessed 65 days post-inoculation. Inoculation under conditions of water stress decreased water potential and photosynthetic efficiency and increased abscisic acid, jasmonic acid and lipid peroxidation. Water-stressed infected plants also showed higher fungal colonization and external lesion length in comparison with well-watered inoculated plants. Our results indicate that drought increased E. globulus predisposition to N. kwambonambiense infection and may also have promoted a change in the lifestyle of the fungus. Identifying host–pathogen interaction responses under different stress conditions is necessary to provide knowledge for decision-making in the management of forest systems in general and of Eucalyptus production in particular.

Uncovering the hidden hosts: Identifying inoculum reservoirs for Phytophthora pseudosyringae in Nothofagus forests in Chile

Posted on by
Uncovering the hidden hosts: Identifying inoculum reservoirs for Phytophthora pseudosyringae in Nothofagus forests in Chile

First study in the Southern Hemisphere on Phytophthora pseudosyringae life cycle in Nothofagus forests and its first detection in Persea lingue leaves.


Abstract

Mortality of Nothofagus trees in native forests in Chile has been observed for more than 30 years. Phytophthora pseudosyringae was identified as the causal agent of partial defoliation and bleeding cankers on Nothofagus obliqua and N. alpina. Nevertheless, to improve the conservation of natural resources it is crucial to determine potential native hosts that may act as inoculum reservoirs. Two N. obliqua stands were visited and all native plant species with symptoms resembling those caused by Phytophthora spp. were examined. Seven isolates from cortical and foliar tissues were isolated and subsequentially identified as P. pseudosyringae. Pathogenicity tests were carried out on eight species from a native forest. P. pseudosyringae caused cankers in N. obliqua, N. dombeyi and Persea lingue. Under natural conditions, no symptoms were detected on leaves of Cryptocarya alba, N. dombeyi, N. obliqua or Peumus boldus, but lesions were formed in inoculation assays under a controlled environment, suggesting that these species may act as hosts. Leaf necrosis in P. lingue was observed in both natural and controlled conditions. P. pseudosyringae can sporulate on lesions of C. alba, N. dombeyi and N. obliqua leaves. In Sophora macrocarpa, sporulation was observed both on asymptomatic tissues and on lesions. The frequent association of S. macrocarpa in the understorey of Nothofagus spp. strengthens the putative role of S. macrocarpa as an inoculum reservoir for epidemic events in Nothofagus. This is the first study carried out in the Southern Hemisphere on the life cycle of P. pseudosyringae in native Nothofagus forests.

Levan differentially primes barley defence against infections by Fusarium graminearum, Rhizoctonia solani and Pyricularia oryzae

Posted on by
Levan differentially primes barley defence against infections by Fusarium graminearum, Rhizoctonia solani and Pyricularia oryzae

Levan could induce distinct pathways in response to different pathogens.


Abstract

The widespread use of pesticides poses significant challenges to the safety of agricultural products and the ecological environment. Levan-type fructans have the ability to act as an induced resistance stimulus, enhancing plant disease resistance, which aligns with the principles of green development. This study showed that levan polysaccharide, produced by Halomonas smyrnnensis levansucrase, could induce the resistance of barley to Fusarium graminearum much better than inulin-type fructans or low-molecular-weight chitosan oligosaccharide. Three different application methods of levan, namely seed soaking, leaf spraying or their combination, all decreased the necrotic areas caused by F. graminearum and Rhizoctonia solani. When inoculated with F. graminearum, the content of hydrogen peroxide, proline or jasmonic acid and the activities of peroxidase and ascorbate peroxidase in levan-treated barley were higher than those in the control. In contrast, when inoculated with R. solani, the hydrogen peroxide content and peroxidase activity in levan-treated leaves showed a faster induction than the control at the early priming and the content of proline and methyl salicylate was higher than that of the control. Thus, levan induces distinct pathways in response to different pathogens.

Phylogeny and taxonomy of five species associated with apricot canker in Beijing, China

Posted on by
Phylogeny and taxonomy of five species associated with apricot canker in Beijing, China

Morphology, phylogeny and pathogenicity analyses on Cytospora leucostoma, Phaeobotryon rhois and Diplodia gallae and two new species (C. huairouensis and C. prunina) from apricots in China identified the first two as pathogens.


Abstract

Apricot (Prunus armeniaca) is an economically important fruit tree in Beijing, China. However, canker diseases have become one of the main threats to apricot production. In the present study, a field survey was conducted in apricot orchards in Beijing and the disease incidence of apricots was surveyed (75.7%). Thirty fungal strains were isolated from branches of apricots. Five species were identified through multilocus phylogenetic (rDNA internal transcribed spacer [ITS], large subunit [LSU] and tef1-a for Botryosphaeriales; ITS, act, rpb2, tef1-a and tub2 for Cytospora) and morphological analyses, including two new species (Cytospora huairouensis and C. prunina) and three known species (C. leucostoma, Diplodia gallae and Phaeobotryon rhois). C. leucostoma and P. rhois were identified as the causal agents of canker of apricot by pathogenicity tests conducted on 3-year-old plants in the greenhouse. The current study contributed to a theoretical basis for predicting the potential risk of apricot canker in Beijing, China.

Wheat stripe mosaic virus from Brazil and South Africa evolved as distinct subpopulations with low genetic variability

Posted on by
Wheat stripe mosaic virus from Brazil and South Africa evolved as distinct subpopulations with low genetic variability

Phenotyping and sequencing reveal that wheat stripe mosaic virus (WhSMV) in Brazil is genetically homogeneous constituting a distinct subpopulation, more variable than the South African population.


Abstract

Wheat stripe mosaic virus (WhSMV) is the causal agent of soilborne wheat mosaic disease (SBWMD) in Brazil, which is a serious threat to wheat production in the southern part of the country. WhSMV also occurs in Paraguay and South Africa. The virus is soilborne, transmitted by Polymyxa graminis, and management strategies are mainly based on genetic resistance. Variation in the reaction (type and severity of symptoms) of cultivars has been reported depending on the region and/or year of cultivation, leading wheat breeding programmes to test their materials in several locations, which increases costs and is time-consuming. One hypothesis is that this variation in symptoms is a result of the genetic variability of WhSMV. We assessed the genetic variability and population structure of WhSMV infecting wheat in Brazil and South Africa. In field experiments conducted in different locations in southern Brazil, a consistent reproducibility of symptoms was observed in a set of cultivars, and molecular analysis showed a low degree of genetic variability of the Brazilian viral population. The hypothesis that the variation in SBWMD symptoms in Brazil is due to genetic variability of the virus was thus rejected. Comparison of the Brazilian and South African WhSMV isolates indicated that they comprise distinct subpopulations and that the Brazilian subpopulation is more variable than the South African subpopulation. The lower genetic variability of the South African subpopulation suggests genetic stability or a recent emergence of WhSMV in that region.

Identification of SSR markers linked to new fertility restoration trait in sorghum (Sorghum bicolor (L.) Moench) for A4 (maldandi) male sterile cytoplasm

Posted on by

Abstract

Identification of markers associated with fertility restoration (Rf) genes is essential because they can streamline the breeding of new CMS lines and production of commercial hybrid seeds. Therefore, in the present study, F2 populations (M31-2A × DSMR 8) was utilized to identify markers linked to Rf loci on maldandi (A4) cytoplasm through bulk segregant analysis (BSA). The F2 population was analysed for seed set percentage. Chi-square (χ2) analysis showed that the fertility restoration trait followed expected digenic ratio. By BSA, simple sequence repeats (SSRs) markers, namely, Xtxp 34 and Xtxp 69 located on chromosome 3 and SB 3956 and Xtxp 312 located on chromosome 7, showed clear polymorphism between two groups of fertile and sterile bulks. The genomic region harbouring Rf locus on chromosome 3 (2.61 Mbp) predicted to encode five pentatricopeptide repeat (PPR) genes whereas, on chromosome 7, the gene SORBI_3007G047400 predicted to encode MYB (myeloblastosis) domain containing proteins. These predicted genes could be the candidate for restoring fertility on A4 cytoplasm. This finding will be fundamental in the production and rapid selection of novel restorer lines.

Multivariate analysis of the effects of weather variables on white rust epidemics and yield reduction of mustard over multiple growing seasons

Posted on by
Multivariate analysis of the effects of weather variables on white rust epidemics and yield reduction of mustard over multiple growing seasons

Present work illustrates the relevance of weather variables in predicting multiple epidemiological variables, and of multiple disease variables as predictors of actual crop yield.


Abstract

Three shrinkage regression and two machine-learning approaches were evaluated to derive models for the prediction of epidemiological characteristics of white rust of mustard, using data from 112 epidemics in the field. Four epidemiological characteristics were considered: (a) crop age at first appearance of disease, (b) crop age at highest disease severity, (c) highest disease severity in a growing season and (d) area under disease progress curve (AUDPC), along with (e) crop yield to measure the effects of disease on crop performance. We developed models using weather indices to predict these variables using five different approaches: ANN, Elastic Net, LASSO, random forest and ridge regression. One model was developed for each sowing date corresponding to each dependent variable. Two hundred different models were developed. All models performed well at the calibration stage for most of the five variables at all sowing dates. However, at the validation stage, ANN-derived models outperformed (R 2val ~ 1.00, nRMSEV ~0.00 and MBEV ~0.00 in most cases) the three shrinkage regression-derived models in predicting all five variables. Predictions by random forest- and LASSO-derived models were acceptable for AUDPC and crop yield. Evaluation metrics (including R 2val, nRMSEV and MBEV) suggested that ENET- and ridge-derived models do not perform satisfactorily, whereas ANN-derived models yielded reliable results and thus generate robust predictions. The present work constitutes a systematic effort to compare modelling methods for disease and yield prediction and illustrates the relevance of weather variables in predicting multiple epidemiological variables, and of multiple disease variables as predictors of actual crop yield.

Genomic‐wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids

Posted on by

Abstract

Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis-acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co-expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2-domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.

Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

Posted on by

Abstract

Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.