Resistant Genotypes Research Articles

A first study of meat-borne enterococci from butcher shops: prevalence, virulence characteristics, antibiotic resistance and clonal relationship.

IntroductionEnterococcus, which used to be thought of as a harmless commensal living in the digestive tract, has now become a highly resistant and highly contagious pathogen that makes nosocomial infections much more common. This study examined enterococci species and their antibiotic resistance phenotypes and genotypes and virulence gene content in Turkish ground beef samples. Methodology A total of 100 ground beef samples were analyzed between May 2020 and May 2021. The isolated strains were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and confirmed using polymerase chain reaction (PCR) after which they were divided into several species using PCR and tested for antibiotic resistance against 19 antimicrobial agents using the disc diffusion method. The genetic similarity analysis, pulsed-field gel electrophoresis (PFGE) was performed. Results A total of 93 isolates in ground beef were identified, comprised of E. faecalis 72.04%; E. hirae- 11.82%; E. casseliflavous- 7.52%; E. faecium- 5.3%; E. gallinarium- 3.23%. The virulence genes observed in Enterococcus species were distributed as follows: gelE 88.1%, ace 53.7%, efaA 40.8%, asaI 19.3%, esp 6.4%, and cylA 1.07%. A high antibiotic resistance was recorded for tetracycline (43.01%), followed by ampicilin (17.2%), and chloramphenicol (13.9%). 17.2% of Enterococcus isolates were multidrug-resistant. The study determined the high prevalence of antibiotic resistance genes, specifically for tet(L) 10 (10.7%), aac(6')Ie-aph(2")-la 3 (3.2%), and ermB 3 (3.2%). The presence of efflux pump genes were identified in 74.1% of Enterococcus isolates. Genetic characterization of 67 E. faecalis isolates by PFGE revealed 41 pulsed-field gel electrophoresis (PFGE) patterns that were grouped into 15 clusters, which presented more than one strain with 100% similarity. Conclusion Isolates obtained from several areas and butchers had comparable patterns of PFGE, suggesting that the presence of circulating E. faecalis poses a potential public health concern in diverse districts. To mitigate the health hazards associated with the contamination of enterococci from raw to cooked meats, it is necessary to enhance the disinfection of butcheries, promote excellent hand hygiene among butchers, and implement appropriate meat storage and handling methods to prevent bacterial development.

Green synthesized silver nanoparticles from Ocimum sanctum: A potent inhibitor of biofilm forming ability and efflux pumps in bacteria causing bovine mastitis

Therapeutic management of mastitis faces significant challenges due to multidrug resistance. In the present study, multi-drug-resistant (MDR) Staphylococcus spp, Klebsiella pneumoniae, and Escherichia coli were isolated from bovine clinical mastitis cases and the phenotypic and genotypic multidrug resistance profiling was carried out. Silver nanoparticles (AgNPs) were biosynthesized using Ocimum sanctum leaf extracts and characterized via UV Vis absorption, Fourier Transform Infrared Spectroscopy, X-ray diffraction studies, Energy dispersive spectroscopy and Electron Microscopy. The determined minimum inhibitory concentration and minimum bactericidal concentration of the AgNPs against the recovered MDR isolates were 62.5 μg/ml and 125 μg/ml respectively. At a concentration of 50 μg/ml, the AgNPs demonstrated biofilm inhibitory activities of 80.35 % for MDR E. coli, 71.29 % for S. aureus and 60.18 % for MDR K. pneumoniae. Post-treatment observations revealed notable differences in biofilm formation across bacterial isolates. Furthermore, AgNP treatment led to significant downregulation of expression of the efflux pump genes acrB, acrE, acrF, and emrB in Gram-negative isolates and norB in Staphylococci isolates. This research underscores the potential for the development of an eco-friendly antimicrobial alternative in the form of green synthesized silver nanoparticles to combat drug resistance offering potential antibiofilm and efflux pump inhibitory activities.

Resistance of Sesame (<i>Sesamum indicum L</i>.) Genotypes Against Bacterial Blight (<i>Xanthomonas campestris pv. sesami</i>) in Benishangul Gumuz Region, Northwestern Ethiopia

Bacterial blight poses a significant threat to sesame production in Ethiopia, especially in regions with high rainfall. It causes yield reduction and affects seed quality by inducing premature leaf defoliation. To address these challenges, evaluating existing germplasm for disease resistance is crucial. This study assessed various sesame genotypes for resistance to bacterial blight and their performance in seed yield and seed yield related traits. Seventeen genotypes were evaluated in a randomized complete block design at Kamashi research sub-station. Resistance evaluations were conducted every 14 days from emergence up to 72 days, along with recording seed yield and related agronomic and morphological traits. The mean area under the disease progress curve (AUDPC) varied from 673.86 to 825.01, indicating differing susceptibility levels to disease advancement. Approximately 46.67% of the tested genotypes exhibited lower AUDPC compared to Benishangul-1, a variety specifically developed for its adaptability and resistance for bacterial blight-prone regions. Initially, at 14 and 28 days after emergence (DAE), no noticeable bacterial blight symptoms were observed across the genotypes. However, at 42, 56, and 72 DAE, the average severity index steadily rose to 16.92%, 20.78%, and 27.71%, respectively. This transition from immunity to moderate susceptibility underscores the dynamic nature of disease progression and the significant challenge posed by bacterial blight in later sesame growth stages. Notably, significant differences (P<0.05) were noted in days to 50% flowering, days to 90% maturity, plant height to the first branch, overall plant height, length of the capsule-bearing zone, and seed yield. This comprehensive evaluation offers valuable insights into the genetic diversity to improve crop performance and yield potential.

Patterns of Transmitted Drug Resistance Mutations and HIV-1 Subtype Dynamics in ART-Naïve Individuals in Veneto, Italy, from 2017 to 2024.

This study investigates the prevalence and patterns of transmitted drug resistance mutations (TDRMs) and HIV-1 subtypes among antiretroviral therapy (ART) naïve individuals in Veneto, Italy, from 2017 to 2024. This research aims to understand the dynamic landscape of TDRMs and HIV-1 genetic diversity to inform treatment strategies effectively. We included all adult ART-naïve people with HIV (PWH) from seven infectious disease units in Veneto, Italy. We collected the genotypic resistance testing conducted to predict drug susceptibility and subtype distribution using the Stanford HIVdb algorithm. We included 762 PWH, showing a slight but statistically significant decline in the B subtype among Italian PWH (p = 0.045) and an increase in non-B subtypes among foreigners, though it was not statistically significant (p = 0.333). The most frequent mutations were in Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs), especially in non-B subtypes, with a notable rise from 10.7% in 2017-2019 to 15.5% in 2020-2024. Notably, TDRMs were consistently detected, highlighting an ongoing challenge despite the stable prevalence observed over the years. In addition, the data revealed a concerning rise in mutations against newer drug classes, such as integrase inhibitors. Conclusively, the study underscores the necessity of continuous surveillance of HIV subtypes and resistance patterns to adapt ART regimens optimally. Despite the stable levels of drug resistance, the emergence of resistance against newer drugs necessitates ongoing vigilance and possible adjustment in treatment protocols to enhance clinical outcomes and manage HIV drug resistance effectively.

Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions

Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.

Drug Resistance of Different Mycobacterium tuberculosis Genotypes in the Omsk Oblast, Russia

A total of 397 Mycobacterium tuberculosis strains isolated from newly diagnosed patients with pulmonary tuberculosis in the Omsk region in 2019‒2020 were genotyped. The prevalence of strains of the Beijing genotype (70.8%) was established, in particular of two clusters of the modern sublineage — Central Asian/Russian (46.1%) and B0/W148 (19.1%). Strains of the ancient sublineage of the Beijing genotype were represented by clusters 1071-32 and 14717-15, totaling 4.8%. Compared with other genotypes, B0/W148 cluster and the ancient Beijing sublineage were associated with multidrug resistance (MDR): 93.4% and 94.7%, respectively (P 0.0001). Among representatives of other genetic families (LAM, Ural, T, Haarlem), drug-sensitive strains predominated (75.0%). The circulation of MDR Beijing strains requires molecular epidemiological surveillance in view of their possible wider spread.

Comparative transcriptome profiling of resistant and susceptible groundnut (Arachis hypogaea) genotypes in response to stem rot infection caused by Sclerotium rolfsii

AbstractThis study aimed to explore transcriptomic distinctions between resistant (CS‐319) and susceptible (JAL‐42) groundnut (Arachis hypogaea) genotypes exposed to Sclerotium rolfsii infection across different developmental stages. Employing a de novo assembly‐based approach, we analysed the transcriptomic response in these groundnut plants under control and infected conditions at 24, 72 and 120 hours post‐inoculation (hpi). Our RNA‐Seq data yielded a total of 133,900,261 reads, revealing 7796 differentially expressed genes (DEGs). We constructed a gene regulatory network with 59 hub genes, identified 6783 transcription factors and uncovered 88,424 putative markers, including 17,236 simple‐sequence repeats (SSRs), 10,099 single‐nucleotide polymorphisms (SNPs) and 78,332 indels. Notably, the majority of DEGs were upregulated at 24 hpi in the resistant genotype, encompassing diverse functional categories such as pathogenesis‐related genes, defence‐related (R) genes, genes involved in plant–fungus interactions, oxidation–reduction‐related genes, transport, metabolism and proteolysis genes, along with transcription factors (FAR1, B3, GATA, NAC, WRKY, MYBC1 and bHLH), secondary metabolic pathway‐related genes and photosynthesis‐related genes. The up‐regulation of WRKY transcripts, associated with the activation of the jasmonic acid defence signalling pathway, potentially induced systemic acquired resistance (SAR). Conversely, these DEGs exhibited down‐regulation in the susceptible genotype. Furthermore, a total of 17,236 expressed sequence tag (EST)‐SSRs were identified from the unigenes, holding significant potential for advancing plant breeding through marker‐assisted methods, facilitating quantitative trait locus (QTL) mapping and evaluating genetic diversity among genotypes. This study's approach contributes to a more profound understanding of the molecular‐level defence mechanisms involved in the interaction between groundnuts and S. rolfsii.

Phenotypic Assessment of Turkish Wheat Genotypes For slow Yellow Rusting Resistance (Puccinia striiformis f.sp. tritici)

Phenotypic Assessment of Turkish Wheat Genotypes For slow Yellow Rusting Resistance (Puccinia striiformis f.sp. tritici)

Characterization of isoniazid resistance and genetic mutations in isoniazid-resistant and rifampicin-susceptible Mycobacterium tuberculosis in China

BackgroundPatients with tuberculosis resistant to isoniazid but susceptible to rifampicin (Hr-Rs TB) remain a neglected demographic, despite a high disease burden and poor outcomes of these patients. The aim of this study was to investigate the characteristics of isoniazid-resistance-related mutations in Mycobacterium tuberculosis and resistance rates to drugs included in WHO-recommended regimens for Hr-Rs patients. MethodsMycobacterium tuberculosis isolates (n = 4922) obtained from national tuberculosis drug-resistance surveillance were subjected to whole-genome sequencing to identify Hr-Rs strains. The minimal inhibitory concentrations (MICs) were established for the Hr-Rs strains to determine the isoniazid resistance levels. We also identified drug-resistance-associated mutations for five drugs (fluoroquinolones, ethambutol, pyrazinamide, streptomycin, and amikacin) in the Hr-Rs strains. ResultsOf the 4922 strains, 384 (7.8 %) were Hr-Rs. The subculture of seven strains failed, so 377 (98.2 %) strains underwent phenotypic MIC testing. Among the 384 genotypic Hr-Rs strains, 242 (63.0 %) contained the katG Ser315Thr substitution; 115 (29.9 %) contained the -15C>T in the promoter region of the fabG1 gene; and 16 (4.2 %) contained Ser315Asn in the katG gene. Of the 239 strains with the Ser315Thr substitution, 229 (95.8 %) had MIC ≥ 2 µg/mL, and of the 114 strains with the -15C>T mutation, 103 (90.4 %) had 0.25 µg/mL ≤ MIC ≤ 1 µg/mL. The genotypic resistance rates were 0.8 % (3/384) for pyrazinamide, 2.3 % (9/384) for ethambutol and fluoroquinolones; 39.6 % (152/384) of the strains were resistant to streptomycin, but only 0.5 % (2/384) of the strains were resistant to amikacin. ConclusionSer315Thr in katG was the predominant mutation conferring the Hr-Rs phenotype, followed by the fabG1 -15C>T mutation. The combination of rifampicin, pyrazinamide, ethambutol, and levofloxacin should be effective in the treatment of patients with Hr-Rs tuberculosis because the resistance rates for these drugs in China are low.

Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines

The Philippines is a high-incidence country for tuberculosis, with the increasing prevalence of multi- (MDR-TB) and extensively-drug (XDR-TB) resistant Mycobacterium tuberculosis strains posing difficulties to disease control. Understanding the genetic diversity of circulating strains can provide insights into underlying drug resistance mutations and transmission dynamics, thereby assisting the design of diagnostic tools, including those using next generation sequencing (NGS) platforms. By analysing genome sequencing data of 732 isolates from Philippines drug-resistance survey collections spanning from 2011 to 2019, we found that the majority belonged to lineages L1 (531/732; 72.5%) and L4 (European-American; n = 174; 23.8%), with the Manila strain (L1.2.1.2.1) being the most prominent (475/531). Approximately two-thirds of isolates were found to be at least MDR-TB (483/732; 66.0%), and potential XDR-TB genotypic resistance was observed (3/732; 0.4%), highlighting an emerging problem in the country. Genotypic resistance was highly concordant with laboratory drug susceptibility testing. By finding isolates with (near-)identical genomic variation, five major clusters containing a total of 114 isolates were identified: all containing either L1 or L4 isolates with at least MDR-TB resistance and spanning multiple years of collection. Closer inspection of clusters revealed transmission in prisons, some involving isolates with XDR-TB, and mutations linked to third-line drug bedaquiline. We have also identified previously unreported mutations linked to resistance for isoniazid, rifampicin, ethambutol, and fluoroquinolones. Overall, this study provides important insights into the genetic diversity, transmission and circulating drug resistance mutations of M. tuberculosis in the Philippines, thereby informing clinical and surveillance decision-making, which is increasingly using NGS platforms.

Evaluation of the Resistance of Bitter Cucumber (Momordica charantia) to Saline Stress through Physical, Biochemical, and Physiological Analysis

Momordica charantia is a climbing plant often used in traditional medicine to treat a large number of diseases, including diabetes. Salinity is one of the main stressors faced by plants, affecting almost half of irrigated agricultural land and constantly increasing. The aim of this study was to determine the resistance of some bitter cucumber genotypes to salt stress by means of dry matter analysis, chlorophyll a, chlorophyll b, malondialdehyde content, chlorophyll fluorescence, and potassium (K)/silicon (Si) and calcium (Ca)/silicon (Si) atomic ratios. Two varieties of bitter cucumber and three experimental lines were used for the experiment. Treatments with different saline solutions (100 mM of NaCl and 200 mM of NaCl) were applied and compared with an untreated control (0 mM of NaCl). The analyses revealed an increase in the dry matter content of the varieties subjected to salt stress. The Line 4 genotype showed an increase of up to 37.2% compared to the control when treated with 200 mM of NaCl. Following the analysis of the chlorophyll a content, a 38% decrease in its amount compared to the control was observed when treated with 100 mM of saline and 58.6% when treated with 200 mM of NaCl in genotype Line 4. Line 3 showed an increase in the chlorophyll a content compared to the control by 53% in the case of saline treatment with 200 mM. After the analysis of the chlorophyll b content, a 44% decrease was revealed in the case of Line 4 in the variant treated with 100 mM compared to the control and a 61% decrease in the 200 mM NaCl treatment. The highest increase in the concentration of malondialdehyde was recorded in the case of Line 4 in the variant treated with 200 mM of NaCl by 41% compared to the control. The maximum quantum yield of PS II decreased in the treated variants compared to the control plants. The most pronounced difference compared to the control was registered in the case of Line 4, where the treatment with 100 mM of NaCl caused a decrease of 16%, and the treatment with 200 mM caused a decrease of 25%. In the case of the atomic ratio, significant decreases in K and Ca were observed in the NaCl-treated variants. The observed differences between the values obtained for each studied genotype highlight the different degrees of their resistance to salinity.

Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic.

Lower respiratory tract infections (LRTIs) are the fourth leading cause of death worldwide, among which Escherichia coli (E. coli) pneumonia is considered a rare phenomenon. Treatment options for LRTIs have become limited, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-EC), which are usually resistant to other groups of antimicrobials as well. The aim of our study was to compare the phenotypic resistance profiles and genotypes of ESBL-EC isolates associated with LRTIs before (pre-COVID-19) and during (COVID-19) the COVID-19 pandemic. All isolates were screened for antimicrobial resistance genes (ARGs) and virulence-associated genes (VAGs) and assigned to phylogenetic groups, sequence types and clonal groups by PCR. During the pandemic, a significantly lower proportion of ciprofloxacin-, levofloxacin- and trimethoprim-sulfamethoxazole-resistant ESBL-EC isolates was retrieved from lower respiratory tract (LRT) samples. PCR-based genotypization revealed greater clonal diversity and a significantly lower proportion of isolates with blaTEM, aac(6')-Ib-cr and qacEΔ1 genes. In addition, a higher proportion of isolates with the integrase gene int1 and virulence genes sat and tsh was confirmed. The lower prevalence of fluoroquinolone resistance and greater genetic diversity of ESBL-EC isolated during the COVID-19 period may have been due to the introduction of new bacterial strains into the hospital environment, along with changes in clinical establishment guidelines and practices.

First line of defence: Eucalyptus leaf waxes influence infection by an aggressive fungal leaf pathogen.

Leaf epicuticular waxes provide important anatomical and chemical defences against fungi that infect leaves. In this study we analysed the leaf wax composition of Eucalyptus grandis × Eucalyptus urophylla hybrids with contrasting susceptibilities to Teratosphaeria leaf blight (TLB) caused by Teratosphaeria destructans, one of the most important foliar diseases of Eucalyptus. The Eucalyptus cuticular wax was extracted from non-inoculated and inoculated genotypes with different levels of susceptibility to TLB and analysed by gas chromatography-mass spectrometry. The results showed that a triterpenoid, cycloartenol (CAS), was abundant in a resistant genotype and that hexanedioic acid content increased in the resistant genotypes in response to T. destructans infection. In contrast, palmitic acid was significantly more abundant in the inoculated highly susceptible genotype. In-vitro and in-planta T.destructans spore germination assays with pure compounds, showed that CAS and hexanedioic acid significantly inhibited spore germination. Application of these two compounds to the leaves of a susceptible host also significantly increased resistance to infection. In contrast, palmitic acid promoted spore germination and, when applied to the leaves of a resistant genotype, increased colonization by the pathogen. This is the first study providing insights into differences in the leaf wax composition of hosts with different levels of susceptibility to T. destructans. It also showed that leaf wax compounds can modulate spore germination and, ultimately, host resistance to infection.

Evaluation of effectiveness resistance genes in wheat genotypes using marker-assisted selection for stripe rust resistance breeding”

Stripe rust, induced by Puccinia striiformis f. sp. tritici, is the most harmful and prevalent disease in temperate regions worldwide, affecting wheat production areas globally. An effective strategy for controlling the disease involves enhancing genetic resistance against stripe rust, achieved through Egyptian breeding efforts not previously conducted on wheat genotypes. The resistance level to stripe rust in thirty-eight wheat genotypes was assessed using marker-assisted selection methods. The investigation suggests that wheat breeding programs can utilize slow-rusting Yr genes, which are effective resistance genes, to develop novel genotypes with stripe rust resistance through marker-assisted breeding. Based on the four disease responses of the wheat genotypes under investigation, the results categorized the genotypes into three groups. The first group included resistant genotypes, the second group exhibited a slow-rusting character with the lowest disease symptom rates, and the last group displayed the highest disease characteristics rates throughout the three seasons, comprising fast-rusting genotypes. The rust-resistant genes identified were Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr29, Yr30, and Yr36. Genes Yr26, Yr30, and Yr36 were present in all genotypes. Genotypes Misr3, Misr4, Giza168, Giza167, Giza170, Giza171, Gemmeiza9, and Gemmeiza10 carried the Yr9 gene. Only one genotype, Sids13, was found to have the Yr17 gene. Genes Yr18 and Yr29 were identified in Sids14, Giza168, Giza170, Gemmeiza9, and Gemmeiza10. However, none of the wheat genotypes showed the presence of Yr5, Yr10, or Yr15. Several backcrossing generations were conducted to introduce the Yr5 and Yr10 genes into susceptible genotypes (Misr1, Misr2, and Gemmeiza11). These genotypes are cultivated globally and are known for producing high-quality flour, making them of great importance to farmers. The study demonstrates significant potential for enhancing wheat genotypes for stripe rust resistance and increased production.

Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D

The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.

Quantifying the resistance of Australian wheat genotypes to Pratylenchus thornei based on a continuous metric from a factor analytic linear mixed model

Genetic resistance to the parasitic root-lesion nematode, Pratylenchus thornei, is one of the main management strategies cereal growers can use to minimise the impact of nematodes on winter cereal cropping. Screening of genotypes in the presence of P. thornei populations must provide reliable resistance measures that are realised under field conditions. Adoption of the latest statistical methodologies can help to better differentiate between resistant and susceptible genotypes. In this study, post-harvest P. thornei population densities were measured from a collection of 17 field experiments, with varying starting P. thornei population densities, conducted between 2011 and 2018 in locations across the northern grain growing region of eastern Australia. The experiments primarily consisted of wheat genotypes. The post-harvest P. thornei population densities were analysed across multiple environments in a linear mixed model framework, with a factor analytic structure used to model genotype by environment (G ×\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ imes$$\\end{document} E) interaction effects exclusively for wheat genotypes. In general, genetic correlations between environments were found to be high, indicating limited G ×\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ imes$$\\end{document} E interaction for resistance to P. thornei. Post-processing of results using the factor analytic selection tools (FAST) method provided a measure of the overall performance for each wheat genotype, as well as a stability measure reflecting the consistency of the resistance status across environments. The FAST method quantified genotype resistance on a continuous scale, better reflecting the nature of genetic resistance based on a quantitative variable such as nematode population density, and provided a statistically robust and informative means of aiding selection decisions for resistance to P. thornei.

Comparative Transcriptome Analysis of Resistant and Susceptible Genotypes of Isabgol (Plantago ovata) During Interactions with Peronospora plantaginis, the Causal Agent of Downy Mildew Disease

Comparative Transcriptome Analysis of Resistant and Susceptible Genotypes of Isabgol (Plantago ovata) During Interactions with Peronospora plantaginis, the Causal Agent of Downy Mildew Disease

Identification of new sources of resistance against late leaf spot disease of groundnut using molecular and field screenings

ABSTRACT Late leaf spot (LLS), caused by the fungus Nothopassalora personata, is an important foliar disease in groundnut (Arachis hypogaea L.) production. The present study used previously reported three single nucleotide polymorphism (SNP) markers to screen a set of groundnut germplasm and compared them with phenotypic values of three hotspot locations. The results indicated that marker-identified genotypes had LLS-resistant or moderately resistant phenotypes. About 56% of the phenotypically confirmed genotypes were confirmed with the SNP genotype. Some of the phenotypically resistant genotypes were not confirmed with marker genotypes, indicating some other quantitative trait locus (QTL) responsible for the LLS resistance might have been involved. The findings in this study are relevant to future LLS resistance breeding programs.

Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism.

Tomato (Solanum lycopersicum) is a major horticultural crop of high economic importance. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild relative of cultivated tomato, has been utilized as breeding material for S. lycopersicum. In the present study, it is the first time that an in-depth analysis has been conducted for these two specific introgression lines (ILs), IL6-2 and IL6-3 (S. lycopersicum X S. pennellii), which were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA) revealed diverse molecular mechanisms that can potentially be implicated in the host's defense response and the establishment of resistance. The identified DEGs were mostly up-regulated in response to broomrape parasitism and play crucial roles in various processes different from strigolactone regulation. Our findings indicate that, in addition to the essential role of strigolactone metabolism, multiple cellular processes may be involved in the tomato's response to broomrapes. The insights gained from this study will enhance our understanding and facilitate molecular breeding methods regarding broomrape parasitism. Moreover, they will assist in developing sustainable strategies and providing alternative solutions for weed management in tomatoes and other agronomically important crops.

Field Evaluation of Sugarcane Genotypes for Resistance to Leaf Scald Disease in China

Field Evaluation of Sugarcane Genotypes for Resistance to Leaf Scald Disease in China