Location Of Resistance Genes Research Articles

Metagenomic next-generation sequencing-based retrospective investigation of the drug resistance sites of Mycoplasma pneumoniae in children

Objective: To analyze the drug-resistant gene loci of Mycoplasma pneumoniae (MP) using metagenomic next-generation sequencing (mNGS). Methods: From November 2022 to October 2023, 697 clinical samples (including sputum, alveolar lavage fluid and blood) of 686 children with Mycoplasma pneumoniae positive detected by mNGS were retrospectively analyzed. Samples were divided into intensive care unit (ICU) group and non-ICU group, Chi-square test was used to compare groups, and Mann-Kendall trend test was used to analyze the change trend of the detection rate of drug resistance gene loci over time. Results: Of the 697 samples, 164 were from the ICU group and 533 were from the non-ICU group. The detection rate of Mycoplasma pneumoniae resistance gene was 44.3% (309/697), and all detected drug-resistant gene loci of MP were A2063G. The detection rate of Mycoplasma pneumoniae in ICU group was 50.0% (82/164), and the detection rates of Mycoplasma pneumoniae resistance gene loci in sputum, alveolus lavage fluid and blood samples were 75.0% (18/24) and 48.4% (62/128), respectively. The detection rate in sputum was higher than alveolus lavage fluid samples (χ2=5.72,P=0.017). The detection rate of Mycoplasma pneumoniae in non-ICU group was 42.6% (227/533), the detection rate of Mycoplasma pneumoniae resistance gene loci in sputum and alveolar lavage fluid was 40.0% (16/40), 44.3% (201/454), and no detection rate in blood samples (0/12). There was no significant difference in the detection rate of alveolar lavage fluid and sputum (χ2=0.27, P=0.602). From November 2022 to October 2023, the detection rate of submitted samples showed an increasing trend month by month (overall: Z=3.99, ICU inspection group: Z=2.93, non-ICU group: Z=3.01, all P<0.01). Among the bacteria commonly detected with Mycoplasma pneumoniae, Streptococcus pneumoniae accounted for the highest proportion, the detection rate was 15.5% (108/697), and Epstein-Barr virus accounted for the highest proportion of 17.6% (123/697). Conclusions: From November 2022 to October 2023, the detection rate of Mycoplasma pneumoniae drug resistance gene loci showed an increasing trend. The detection rate of drug resistance gene loci in sputum samples of ICU group was higher than alveolus lavage fluid. No new drug resistance site were detected.

Insecticide resistance triggers a reduction of virulence to host‐plant defenses in the brown planthopper

AbstractPlants produce various phytochemicals against herbivory, but phytophagous insects have encountered phytochemicals in the co‐evolutionary history between plants and insects. Selection pressure exerted by phytochemicals triggers a preadaptation to insecticide resistance in insect pests that is due to detoxification systems that are common to phytochemicals and insecticides in the insect's body. We investigated the interaction between the host plant resistance of rice cultivars and the brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). Forty brown planthopper resistance gene loci (BPHs) that are related to phytochemicals in various cultivars of rice inhibit feeding by N. lugens, but this planthopper has developed virulence to resistant rice cultivars possessing some genes. Nilaparvata lugens has also developed resistance to some insecticides as a rapid adaptation to human‐driven selection. We tested the hypothesis that the evolution of insects' resistance to an insecticide is promoted by their encounters with phytochemicals. We compared the virulence of imidacloprid‐resistant and control N. lugens strains toward seven rice cultivars that possess different genes, and we observed that the imidacloprid‐resistant N. lugens had reduced virulence to three rice cultivars, Rathu Heenati (BPH3, BPH17), Babawee (BPH4), and Balamawee (BPH27, three quantitative trait loci), meaning that the development of imidacloprid resistance has a negative impact on the virulence of N. lugens to three cultivars. Our results indicate trade‐offs rather than a co‐relationship between the evolution of insecticide resistance and encounters with host plant defense.

Comparison between artificial fire blight shoot and flower inoculations in apple

AbstractFire blight is the most important bacterial disease in apple (Malus × domestica). Owing to the severity of the caused damages, fire blight resistance is an important breeding objective. In the past, various phenotypic screening methods and strategies have been used to identify new sources of fire blight resistance for breeding. In this study, breeding material, modern cultivars and heirloom accessions were phenotyped by artificial inoculation of shoots under greenhouse (n = 273) and flowers under field conditions (n = 20) and genotyped for known resistance genes and quantitative trait loci by using molecular markers. A comparison between the two phenotyping methods was made in relation to the two control varieties ‘Gala Galaxy’ and ‘Enterprise’. The results obtained for the resistance sources FB_MR5, Fb_E and FB_F7 are consistent with previously published data, showing a large effect of the two major resistance genes FB_MR5 (‘Malus × robusta 5’) and Fb_E (‘Evereste’). Genotypes carrying FB_F7 showed greater variation in their resistance levels, but were on average less susceptible than ‘Gala Galaxy’ and genotypes with no known resistance gene or quantitative trait locus (QTLs) in both tests. No correlation was found between the results of 18 genotypes phenotyped with both inoculation methods. The ranking of genotypes according to their flower and shoot fire blight resistance varied between the two methods. However, 11 of the 18 tested genotypes showed no significant difference between the results of the two methods. Additionally, it was found that flower shedding appears to be an important triggered mechanism for flower resistance to fire blight.

Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9

Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust.

Advancements in Research on Prevention and Control Strategies for Maize White Spot Disease.

Maize white spot (MWS), caused by the bacterium Pantoea ananatis, is a serious disease that significantly impacts maize production and productivity. In recent years, outbreaks of white spot disease have resulted in substantial maize yield losses in southwest China. Researchers from various countries worldwide have conducted extensive research on this pathogen, including its isolation and identification, the localization of resistance genes, transmission pathways, as well as potential control measures. However, the information related to this disease remains fragmented, and standardized preventive and control strategies have not yet been established. In light of this, this review aims to comprehensively summarize the research findings on MWS, providing valuable insights into understanding its occurrence, prevention, and control measures in the southwestern and southern regions of China while also mitigating the detrimental impact and losses caused by MWS on maize production in China and across the world.

Prevalence and genetic diversity of multidrug-resistant Salmonella Typhimurium monophasic variant in a swine farm from China.

Salmonella 4,[5],12:i:-, a monophasic variant of S. Typhimurium, has become a global serovar causing animal and human infections since its first emergence in the late 1980's. Several previous studies showed the increasing prevalence of S. 4,[5],12:i:- in China, most of which were from swine with multidrug resistance (MDR) profiles. However, the molecular characteristic and evolution of S. 4,[5],12:i:- in the same swine farm are still unknown. In this study, a total of 54 S. enterica strains were isolated from different fattening pigs aged 1, 3, and 6 months, most of which belonged to S. 4,[5],12:i:-. Whole-genome sequencing revealed that all 45 S. 4,[5],12:i:- strains belonged to ST34 and were further divided into two different ribosomal STs and nine different core-genome STs. Phylogenetic analysis of 286 S. 4,[5],12:i:- strains in China, including 241 from the EnteroBase Salmonella database, revealed the genetic diversity of S. 4,[5],12:i:- and indicated that S. 4,[5],12:i:- in this swine farm might have multiple origins. Three different IncHI2 plasmids carrying various resistance genes were characterized by nanopore sequencing and could be conjugated to Escherichia coli. The colistin resistance gene mcr-1 and ESBLs gene blaCTX - M-14 were co-located on the chromosome of one strain. The dynamic changes in antimicrobial resistance regions and transferability of IncHI2 plasmids, as well as the chromosomal location of resistance genes, facilitated the diversity of the antimicrobial resistance characteristics in S. 4,[5],12:i:-. Since the swine farm is regarded as the important reservoir of MDR S. 4,[5],12:i:-, the prevalence and evolution of S. 4,[5],12:i:- from swine farms to pig products and humans should be continually monitored.

Genetics of Resistance to Leaf Rust in Wheat: An Overview in a Genome-Wide Level

Due to the global warming and dynamic changes in pathogenic virulence, leaf rust caused by Puccinia triticina has greatly expanded its epidermic region and become a severe threat to global wheat production. Genetic bases of wheat resistance to leaf rust mainly rely on the leaf rust resistance (Lr) gene or quantitative trait locus (QLr). Although these genetic loci have been insensitively studied during the last two decades, an updated overview of Lr/QLr in a genome-wide level is urgently needed. This review summarized recent progresses of genetic studies of wheat resistance to leaf rust. Wheat germplasms with great potentials for genetic improvement in resistance to leaf rust were highlighted. Key information about the genetic loci carrying Lr/QLr was summarized. A genome-wide chromosome distribution map for all of the Lr/QLr was generated based on the released wheat reference genome. In conclusion, this review has provided valuable sources for both wheat breeders and researchers to understand the genetics of resistance to leaf rust in wheat.

Molecular analysis of resistance gene locus to bacterial canker and wilting disease in tomato mutants

The tomato plant is one of the most widely produced vegetables in the world. However, there are several disease factors which limit tomato production. The Clavibacter michiganensis subsp. michiganensis (Cmm) pathogen causes wilting and canker symptoms on the leaves of plants and bird’s eye symptoms on the tomato and then the plants completely die. Development of resistant tomato varieties is prerequisite due to absence of an effective control methods against the bacterial disease. The resistant M3-9 and M3-15 tomato plants have been developed because of mutation from susceptible NCEBR3 tomato seeds with ethyl methanosulfonate (EMS). For each chromosome of the tomato genome, 24 SSR markers were selected from each end of the haploid, 12 tomato chromosomes, and polymorphic differences between susceptible and resistant tomato plants were studied. Polymorphisms were found with SSR13 and SSRB18031 markers located on chromosome 5 with resistant mutants, M3-9, M3-15 and susceptible original NCEBR3 plants. It is envisaged that a resistance gene is located on the 5th chromosome of resistant M3-9 and M3-15 plants. Further fine mapping studies will reveal the location of the resistance gene(s) for controlling bacterial canker and wilting pathogen.

Inheritance and Linkage of Virulence Genes of Puccinia striiformis f. sp. hordei.

Puccinia striiformis f. sp. hordei (Psh) causing barley stripe rust has only recently been known to be heteroecious, for which reason the inheritance of its virulence has not been analyzed. Herein, we selfed a Psh isolate, XZ-19-972, on Berberis aggregata and obtained 53 progenies. The virulence phenotypes (VPs) for these progenies were identified on 11 barley differentials, and their genotypes were assessed with 22 Kompetitive allele specific PCR-single nucleotide polymorphism (KASP-SNP) markers. In total, 18 VPs were detected among progenies, 17 (VP2-VP18) of which, corresponding to 43 isolates, were different from the parental isolate showing VP1. Of the 53 progenies, 8 exhibited increased virulence and 34 decreased virulence. One progeny, belonging to VP18, showed a different virulence formula but without a virulence increase or decrease. The parental isolate and all progenies were avirulent to yrc6 but virulent to yrc7. The parental isolate was heterozygous in terms of avirulence/virulence to nine barley resistance gene loci. KASP-SNP marker analysis identified 36 multilocus genotypes, based on which a linkage map was constructed, with total genetic distance intervals of 516.07 cM, spanning 16 avirulence or virulence loci. Taken together, our results provide important insights into the inheritance and virulence diversity of Psh.

Fecal carriage and clonal dissemination of blaNDM-1 carrying Klebsiella pneumoniae sequence type 147 at an intensive care unit in Lao PDR

ObjectivesCarbapenemase-producing Enterobacterales (CPE) are high priority targets of global antimicrobial surveillance. Herein, we determined the colonization rate of CPE on admission to intensive care units in Vientiane, Lao PDR in August-September 2019.MethodsData regarding clinical conditions, infection control, and antibiotic usage were collected during admission. Rectal swab samples (n = 137) collected during admission were inoculated to selective chromogenic agars, followed by confirmatory tests for extended-spectrum beta-lactamases and carbapenemases. All CPE isolates were sequenced on Illumina (HiSeq2500), reads assembled using SPAdes 3.13, and the draft genomes used to query a database (https://www.genomicepidemiology.org) for resistome, plasmid replicons, and sequence types (ST). Optical DNA mapping (ODM) was used to characterize plasmids and to determine location of resistance genes. Minimum spanning tree was generated using the Bacterial Isolate Genome Sequence database (BIGSdb) and annotated using iTOL.ResultFrom 47 Enterobacterales isolated on selective agars, K. pneumoniae (25/47) and E. coli (12/47) were the most prevalent species, followed by K aerogenes (2/47), K. variicola (1/47), and K. oxytoca (1/47). The overall prevalence of ESBLs was 51.0%; E. coli 83.3% (10/12) and Klebsiella spp. 41.3% (12/29). Twenty percent of the K. pneumoniae (5/25) isolates were carbapenem-resistant, and 4/5 contained the blaNDM-1 gene. All blaNDM-1 isolates belonged to ST147 and were indistinguishable with cgMLST. ODM showed that the blaNDM-1 gene was located on identical plasmids in all isolates.ConclusionThe prevalence of ESBL-producing Enterobacterales was high, while carbapenemases were less common. However, the detection of clonal dissemination of blaNDM-1-producing K. pneumoniae isolates in one of the intensive care units calls for vigilance. Stringent infection prevention and antimicrobial stewardship strategies are highly important measures.

Genomic regions associated with resistance to soybean rust (Phakopsora pachyrhizi) under field conditions in soybean germplasm accessions from Japan, Indonesia and Vietnam

Key messageEight soybean genomic regions, including six never before reported, were found to be associated with resistance to soybean rust (Phakopsora pachyrhizi) in the southeastern USA.Soybean rust caused by Phakopsora pachyrhizi is one of the most important foliar diseases of soybean [Glycine max (L.) Merr.]. Although seven Rpp resistance gene loci have been reported, extensive pathotype variation in and among fungal populations increases the importance of identifying additional genes and loci associated with rust resistance. One hundred and ninety-one soybean plant introductions from Japan, Indonesia and Vietnam, and 65 plant introductions from other countries were screened for resistance to P. pachyrhizi under field conditions in the southeastern USA between 2008 and 2015. The results indicated that 84, 69, and 49% of the accessions from southern Japan, Vietnam or central Indonesia, respectively, had negative BLUP values, indicating less disease than the panel mean. A genome-wide association analysis using SoySNP50K Infinium BeadChip data identified eight genomic regions on seven chromosomes associated with SBR resistance, including previously unreported regions of Chromosomes 1, 4, 6, 9, 13, and 15, in addition to the locations of the Rpp3 and Rpp6 loci. The six unreported genomic regions might contain novel Rpp loci. The identification of additional sources of rust resistance and associated genomic regions will further efforts to develop soybean cultivars with broad and durable resistance to soybean rust in the southern USA.

Genomics-Assisted Improvement of Super High-Yield Hybrid Rice Variety "Super 1000" for Resistance to Bacterial Blight and Blast Diseases.

The two-line rice hybrid “Super 1000” (GX24S × R900) represents a major landmark achievement of breeding for super-hybrid rice in China. However, both male parent R900 and hybrid “Super 1000” have an obvious defect of high susceptibility to rice bacterial blight (BB) and blast. Thus, improving disease resistance and maintaining the original high-yield capacity are essential for the sustainable application of “Super 1000.” In this study, the application of closely linked single-nucleotide polymorphism (SNP) markers for foreground selection of dominant resistance gene loci together with genome-wide SNP markers for the background selection rapidly improved the disease resistance of R900 without disturbing its high-yield capacity. A series of improved R900 lines (iR900, in BC2Fn and BC3Fn generations) were developed to stack resistance genes (Xa23+Pi9, Xa23+Pi1+Pi2/9) by marker-assisted backcrossing and field selection for phenotypes, and further crossed with the female line GX24S to obtain improved hybrid variety Super 1000 (iS1000). The genetic backgrounds of iS1000 and “Super 1000” were profiled by using a 56 K SNP-Chip, and results showed that they shared 98.76% of similarity. Meanwhile, evaluation of the field disease resistance showed that the iR900 lines and iS1000 hybrids possess significantly enhanced resistance to both BB and rice blast. Resistance spectrum assays revealed that the iR900 lines and their derived hybrids exhibited high-level resistance to 28 Xoo strains tested, and enhanced resistance to leaf blast at the seedling stage when infected with 38 Magnaporthe oryzae isolates. Between 2019 and 2020, the multi-location field trials across the middle and lower reaches of the Yangtze River were launched and showed that the iS1000 slightly out-yielded than the original variety. In a large-scale demonstration site (6.73 ha, Yunnan, China), the iS1000 achieved 17.06 t/hm2 of yield in 2019. Moreover, the high similarity was observed in main agronomic traits and grain quality when comparing the improved lines/hybrids to original ones (iR900 vs. R900, iS1000 vs. S1000). This work presented a typical genomics-assisted breeding strategy and practice, which involves in directional introgression and rapid stack of multiple disease resistance genes, endowing the super-high-yield hybrid rice variety with holistic disease resistance but without yield penalty.

Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction

BackgroundSoybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21–24 nucleotides) which are endogenously produced by the plant host as part of a general gene expression regulatory mechanisms, but also play roles in regulating plant defense against pathogens. However, miRNA-mediated plant response to SMV in soybean is not as well documented.ResultIn this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1 × Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs profile changes during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. The expression patterns of several miRNAs were validated by quantitative real-time PCR. We also validated the miRNA-target gene interaction by agrobacterium-mediated transient expression in Nicotiana benthamiana.ConclusionWe have identified a large number of miRNAs and their target genes and also functional annotations. We found that multiple miRNAs were differentially expressed in the two lines and targeted a series of NBS-LRR resistance genes. It is worth mentioning that many of these genes exist in the previous fine-mapping interval of the resistance gene locus. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

Identification and phylogenetic analysis of the pathogen of jute anthracnose in China

<p id="C3">Anthracnose is a major fungal disease that seriously affects the yield and quality in jute fiber. Identifying the types of anthracnose pathogens and determining their pathogenicity will help jute disease-resistant breeding and develop elite disease-resistant gene resources. The 92 strains were isolated and purified from samples of diseased jute, which were collected from 7 jute production areas including Fuzhou and Zhangzhou in Fujian Province, Xinyang City in Henan Province, Liu’an City in Anhui Province, Hangzhou City in Zhejiang Province, Nanning City in Guangxi Province, and Changsha City in Hunan Province. The sequence analysis of the rDNA-ITS region showed that 11 out of the 92 strains were typical anthracnose pathogens. Further identification of the phylogenetic tree of the LSU region and morphological characteristics revealed that 10 strains, including ZZ4 and GX19, were <italic>Colletotrichum gloeosporioides</italic>, while the strain of CS3 was <italic>Colletotrichum dematium</italic>. The pathogenicity test of artificial inoculation indicated that there was a significant difference in pathogenicity between <italic>Colletotrichum gloeosporioides</italic> and <italic>Colletotrichum dematium</italic>. These results laid a basis for identification of resistance gene loci and effective controlling of anthracnose in jute.

The prevalence and characterization of ESBL-producing strains of Salmonella enterica circulating in the territory of the Russian Federation (2016–2020)

Objective. To analyze frequency and identify genetic determinants of resistance of non-typhoid Salmonella (NTS) producing extended-spectrum β-lactamase (ESBL) isolated in the Russian Federation over the period 2016 to 2020. Materials and Methods. Salmonella isolates, suspected to ESBL production, were collected by the All-Russia Reference Center of Salmonellosis during the national Salmonellosis surveillance program. Phenotypic resistance was determined by the broth microdilution method using G-I and G-II Mikrolatest®SensiLaTest MIC plates and by the double-disk synergy test. Whole genome sequencing was performed on the NextSeq platform (Illumina, USA), with subsequent de novo genome assembly (SPAdes 3.15.4), identification of plasmid types (MOB-suite v3.0.0), and identification of resistance genes (AMRFinderPlus v3.10.40). Results. Out of 1792 NTS isolates, 22 strains contained bla-genes of molecular classes A and D (blaTEM, blaCTX-M, blaSHV, blaOXA), one strain – AmpC (blaCMY-2) and three strains – combination ESBL of class A and AmpC (blaTEM, blaCMY-2, blaDHA). The frequency of occurrence of ESBL-producing Salmonella is 1.3%, AmpC – 0.2%. Additionally, strains were resistant to other non-β-lactam antibiotics. Six different types of plasmids were identified (IncI, IncFIB, IncC, IncHI2A, IncL/M and IncX1) in studied isolates. It was possible for 17 strains to identify location of resistance genes in plasmids of a certain type. Conclusions. The frequency of occurrence of Salmonella strains producing ESBL and AmpC was 1.45%, which were found in sporadic cases of human diseases, as well as food and environmental objects were sources of isolation. The fact of detection of such strains among various NTC serotypes and a wide range of sources of isolation confirms the relevance of monitoring antimicrobial resistance of Salmonella strains in the future.

Identification of molecular marker linked to resistance gene loci against Indian isolate of Phytophthora capsici L. causing root rot in chilli (Capsicum annuum L.)

Identification of molecular marker linked to resistance gene loci against Indian isolate of Phytophthora capsici L. causing root rot in chilli (Capsicum annuum L.)

Marker assisted detection of TYLCV and late blight resistance in tomato (Solanum lycopersicum)

Marker assisted breeding relies on the identification of genetic loci linked to desirable genes/alleles and is beingutilized for selecting desirable traits including disease resistance in a wide variety of crops. The tomato (Solanumlycopersicum L.) production worldwide has lately been threatened by outbreaks of tomato yellow leaf curl virustransmitted by the whitefly (Bemisia tabaci) and late blight caused by oomycete pathogen Phytophthora infestans(Mont.) de Bary. Resistance genes against both pathogens are available and widely used in tomato breeding throughoutthe world. Molecular markers for resistance alleles greatly enhance selection of resistant plants. For effective breedingprogramme, the validation of markers linked to resistance genes in tomato was carried out for tomato improvement.For this purpose, available markers for the tomato yellow leaf curl disease resistance gene loci Ty-2, Ty3, Ty3a andlate blight resistant loci Ph3 were validated. The assay correctly predicted the genotypes of tomato breeding linesharbouring resistance allele at each loci. Further a multiplex assay was also standardized to simultaneously detectthe presence of resistant/susceptible alleles at Ty2,Ty3 and Ty3a loci. The present study carried out in the Division ofVegetable Science, ICAR-IARI, New Delhi, demonstrates the feasibility of combining two SCAR markers (TG0302and P6-25) for detecting simultaneously three important resistance gene loci in tomato genotypes and thereby improvingthe cost and efficiency of the assay.

Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean.

Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-ud to reflect this change; (v) bc-ud alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-ud is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.

Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses.

In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici, has reemerged as a major threat to wheat cultivation. The stem rust (Sr) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare, which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum, which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Prevalence of Cefotaxime-Resistant Escherichia coli Isolates from Healthy Cattle and Sheep in Northern Spain: Phenotypic and Genome-Based Characterization of Antimicrobial Susceptibility.

In order to estimate herd-level prevalence of extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)- and carbapenemase-producing commensal Escherichia coli in ruminants in the Basque Country (northern Spain), a cross-sectional survey was conducted in 2014 to 2016 in 300 herds using selective isolation. ESBL-/AmpC-producing E. coli was isolated in 32.9% of dairy cattle herds, 9.6% of beef cattle herds, and 7.0% of sheep flocks. No carbapenemase-producing E. coli was isolated. Phenotypic antimicrobial susceptibility determined by broth microdilution using EUCAST epidemiological cutoff values identified widespread coresistance to extended-spectrum cephalosporins and other antimicrobials (110/135 isolates), particularly tetracycline, sulfamethoxazole, trimethoprim, and ciprofloxacin. All isolates were susceptible to tigecycline, imipenem, meropenem, and colistin. The genomes of 66 isolates were sequenced using an Illumina NovaSeq 6000 and screened for antimicrobial resistance determinants against ResFinder and PointFinder. The plasmid/chromosomal locations of resistance genes were predicted with PlasFlow, and plasmid replicons were identified using PlasmidFinder. Fifty-two acquired resistance genes and point mutations in another four genes that coded for resistance to 11 antimicrobial classes were identified. Fifty-five genomes carried ESBL-encoding genes, blaCTX-M-14 being the most common, and 11 carried determinants of the AmpC phenotype, mostly the blaCMY-2 gene. Additionally, genes coding for β-lactamases of the CTX-M group 9 were detected as well as the sporadic presence of blaSHV-12, blaCMY-4, and a point mutation in the ampC promoter. Only a bovine isolate coharbored more than one ESBL/AmpC genetic determinant (blaCTX-M-14 and a mutation in the ampC promoter), confirming its ESBL- and AmpC β-lactamase-producing phenotype. Most ESBL/AmpC genes were located in IncI1 plasmids, which also carried a great variety of other antimicrobial resistance genes.IMPORTANCE Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing E. coli isolates have emerged in recent years as some of the fastest spreading antimicrobial resistance determinants in humans and food-producing animals, becoming a concern for animal and public health. This study provided insight into the prevalence of cefotaxime-resistant E. coli in cattle and sheep in the Basque Country and the associated genetic determinants of antimicrobial resistance. These constituted an important contribution to the limited repository of such data for cattle in the region and for sheep worldwide. Antimicrobial susceptibility testing by phenotypic and molecular methods is key in surveillance programs to enhance early detection of resistance development, monitor resistance trends, and provide guidance to clinicians in selecting the adequate therapy.