Category Archives: ORIGINAL ARTICLE

Genome analysis of three isolates of Stemphylium lycopersici differ in their virulence and sporulation ability: Identification of effectors, pathogenesis and virulence factors

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Genome analysis of three isolates of Stemphylium lycopersici differ in their virulence and sporulation ability: Identification of effectors, pathogenesis and virulence factors

Stemphylium lycopersici encodes effectors whose number is unrelated to virulence, which is reduced by protein degradation, and detoxification and redox processes and by the presence of viral double-stranded RNA sequences.


Abstract

Tomato grey leaf spot is a fungal disease that provokes losses in tomato yield. The aim of this work is to analyse genomic differences among three isolates of Stemphylium lycopersici that differ in virulence and sporulation. The bioinformatics analysis led us to predict the identity of putative effectors, pathogenesis and virulence factors. Like the genome of other necrotrophic pathogens, Stemphylium encodes a wide spectrum of effectors, including an ample and diverse array of carbohydrate-degrading enzymes. Interestingly, the number of predicted effectors was unrelated to virulence. Low virulence appeared to be associated with the presence of several double-stranded RNAs from viruses as well as cellular processes related to protein degradation, redox and detoxifying processes and monoterpenes production. This is the first identification of the potential effectors of tomato–S. lycopersici interaction; nonetheless functional studies should be done.

Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm

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Abstract

The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01 and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots), S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192 (root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000, Sobic.001G273000, Sobic.009G013600, and Sobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.

Genome‐wide identification, gene expression and haplotype analysis of the rhomboid‐like gene family in wheat (Triticum aestivum L.)

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Abstract

The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.

In‐field climatic factors driving Sclerotinia head rot progression across different sunflower planting dates

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In-field climatic factors driving Sclerotinia head rot progression across different sunflower planting dates

Local temperature and humidity at different planting dates significantly influence Sclerotinia head rot in sunflower, with temperatures above 27°C suppressing disease progression in the flower head.


Abstract

Sclerotinia head rot, caused by Sclerotinia sclerotiorum, is a major disease limiting sunflower production in tropical and subtropical agroecological zones. Sporadic outbreaks across South Africa have resulted in major losses, yet little is known about the in-field climatic factors driving this infection. Short-interval, staggered plantings have been proposed as a control method for Sclerotinia head rot, which help to limit the number of plants in a susceptible developmental stage during conducive environmental conditions. However, this complicates field management practices, especially if working at the fringes of a planting window due to delayed rains. This study aimed to investigate the effect of planting date on Sclerotinia head rot progression in monthly plantings across the summer period. Artificial mycelial plug inoculations were performed at the R5.9 flowering stage in an open field. Disease establishment, progression and severity were monitored at 3-day intervals for 30 days. We show that disease establishment was delayed by low relative humidity or extreme low temperatures in the January and March planting dates where the first lesions were only observed 6 days post-inoculation. Consistently high temperatures above 27°C also suppressed disease progression and produced low area under the disease progress curve (AUDPC) scores of 75.15 and 29.4 for the October and November planting dates, respectively. These findings suggest that regardless of season or location, selecting a planting date that ensures the sunflower bloom period aligns with the hottest, driest part of the season will probably suppress Sclerotinia head rot in regions with average summer highs above 27°C.

Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α‐linolenic (ω‐3) content in S. hispanica seeds

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Abstract

Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein-coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3-PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω-3 content in oil crops.

Genome‐wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses

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Abstract

Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.

Cryptic sexual reproduction in an emerging Eucalyptus shoot and foliar pathogen

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Cryptic sexual reproduction in an emerging Eucalyptus shoot and foliar pathogen

By using microsatellite and mating-type markers, we elucidated the population biology and likely mode of reproduction of Elsinoe necatrix causing the destructive Eucalyptus scab and shoot malformation epidemic in North Sumatra, Indonesia.


Abstract

Eucalyptus scab and shoot malformation is an emerging disease and a serious threat to the global plantation forestry industry. The disease appeared in North Sumatra (Indonesia) in the early 2010s and the causal agent was recently described as a novel species, Elsinoe necatrix. Nothing is known regarding its possible origin or why it emerged rapidly to cause a serious local epidemic. To investigate its population biology, we developed 15 polymorphic microsatellite markers as well as mating-type markers using genome sequences for two E. necatrix isolates. Isolates of the pathogen were collected from different host varieties at four locations in the Lake Toba region of North Sumatra and characterized using these markers. A high level of genotypic diversity was observed for all populations with little to no genetic differentiation between sampling areas. Discriminant analysis of principal components, genotype networks and analysis of molecular variance all showed a lack of population structure and a high level of gene flow among sampling regions. Mating-type ratios and linkage disequilibrium analyses suggest that sexual recombination is likely to be occurring, although a sexual state has not been found for the pathogen. The results of this study highlight the fact that new genotypes of E. necatrix, probably arising from cryptic sexual recombination, will challenge efforts to manage the disease, and that breeding and selection for tolerance will require substantial host genetic diversity.

Simulations of multiple breeding strategy scenarios in common bean for assessing genomic selection accuracy and model updating

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Abstract

The aim of this study was to evaluate the accuracy of the ridge regression best linear unbiased prediction model across different traits, parent population sizes, and breeding strategies when estimating breeding values in common bean (Phaseolus vulgaris). Genomic selection was implemented to make selections within a breeding cycle and compared across five different breeding strategies (single seed descent, mass selection, pedigree method, modified pedigree method, and bulk breeding) following 10 breeding cycles. The model was trained on a simulated population of recombinant inbreds genotyped for 1010 single nucleotide polymorphism markers including 38 known quantitative trait loci identified in the literature. These QTL included 11 for seed yield, eight for white mold disease incidence, and 19 for days to flowering. Simulation results revealed that realized accuracies fluctuate depending on the factors investigated: trait genetic architecture, breeding strategy, and the number of initial parents used to begin the first breeding cycle. Trait architecture and breeding strategy appeared to have a larger impact on accuracy than the initial number of parents. Generally, maximum accuracies (in terms of the correlation between true and estimated breeding value) were consistently achieved under a mass selection strategy, pedigree method, and single seed descent method depending on the simulation parameters being tested. This study also investigated model updating, which involves retraining the prediction model with a new set of genotypes and phenotypes that have a closer relation to the population being tested. While it has been repeatedly shown that model updating generally improves prediction accuracy, it benefited some breeding strategies more than others. For low heritability traits (e.g., yield), conventional phenotype-based selection methods showed consistent rates of genetic gain, but genetic gain under genomic selection reached a plateau after fewer cycles. This plateauing is likely a cause of faster fixation of alleles and a diminishing of genetic variance when selections are made based on estimated breeding value as opposed to phenotype.

Comparison of four inoculation methods and three Fusarium species for phenotyping stalk rot resistance among 22 maize hybrids (Zea mays)

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Comparison of four inoculation methods and three Fusarium species for phenotyping stalk rot resistance among 22 maize hybrids (Zea mays)

Needle injection of Fusarium graminearum and assessment of internode proportion are the most promising methods in phenotyping maize genotypes for Fusarium stalk rot resistance in central Europe.


Abstract

Fusarium stalk rot (FSR) is among the most destructive maize diseases causing significant global yield losses. Resistance of 22 maize hybrids to FSR was tested using four inoculation methods in each of two locations in 2021 and 2022. The inoculation methods included needle injection (NI), toothpick method (TM), stick method (SM) and mycelium method (MM), and the inoculated fungi were Fusarium culmorum, F. graminearum and F. temperatum. NI displayed the highest FSR infection among maize hybrids followed by TM and SM. MM showed the least infection. From five stalk rot-related traits, full-length infection and internode proportion, that is, the percentage of visible infection summed up over internodes, captured most of the genetic variation. The latter was the trait with the highest heritability (0.90). No significant (p > 0.05) genotype × method and genotype × fungus interaction variances were observed for any traits. For F. graminearum inoculation, NI showed the highest internode proportion followed by TM and SM, with F. culmorum responding in a similar way. For F. temperatum, TM outranked all other methods. F. graminearum was the most aggressive fungal pathogen compared to F. culmorum and F. temperatum. For phenotyping maize lines with varying degrees of resistance to FSR, we recommend needle injection and internode proportion.

Fine mapping of sterile genes in soybean (Glycine max [L.] Merril.) based on cross populations between multi‐elite parent and sterile lines ms1 and ms6

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Abstract

The male sterile line of soybean is crucial for hybrid seed production, and has allowed significant advancements in soybean germplasm innovation and yield increase in China. In this study, we created two bulks of sterile plants and collected a natural population consisting of 100 elite soybean germplasms. There were significant phenotypic differences between the sterile and natural populations resulting from flowers and pods. The sterile plants exhibited fleshy spherical pods and large black-green leaves in the maturity stage, while the leaves of the fertile plants fell off. After I2-KI staining, the pollen of the sterile line turned light brown and yellow, while the pollen of the fertile line turned black. On the basis of the SNP sequencing results, the sterility genes were located on eight chromosomes. Additionally, they were fine-mapped to 13 regions on six chromosomes using 72 pairs of SSR markers. Five genes involved in auxin response and pollen development were predicted as candidate genes underlying soybean sterility. These candidate genes for soybean sterility will help with gene cloning and functional analysis and accelerate the widespread use of hybrid seed production and yield increase in soybean grown in cool regions.