Identification Of Resistance Genes Research Articles

Identification and Molecular Mapping of the Gene YrFL in Wheat Cultivar Flanders with Durable Resistance to Stripe Rust.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most severe diseases of wheat (Triticum aestivum L.) worldwide. Identification and characterization of resistance genes is advantageous to cultivating wheat varieties with durable resistance, which is the most economic and effective strategy to control stripe rust. Flanders, a common wheat cultivar released in France in 1986, confers effective resistance to stripe rust both at the seedling and adult plant stages. To elucidate the genetic basis of resistance in Flanders, F1, F2, and F2:3 generations derived from the cross Mingxian169 × Flanders were evaluated with the most prevalent Chinese Pst race CYR33 at the seedling stage. Inheritance analysis showed that the stripe rust resistance of Flanders was controlled by a single dominant gene, temporarily designated as YrFL. Bulked segregant analysis (BSA) combined with a wheat 660K single-nucleotide polymorphism (SNP) array indicated that polymorphic SNP markers were mainly located in the 0 to 150 Mb on wheat chromosome 5A. One hundred and eleven kompetitive allele-specific PCR (KASP) and 39 simple sequence repeat (SSR) markers on chromosome 5A were used to locate the YrFL. Linkage analysis mapped YrFL with 19 KASP and three SSR markers on wheat chromosome 5AS, and the genetic distances of the closest flanking markers AX108925494 and Xbarc56 to YrFL were 0.6 and 2.0 cM, respectively. Chromosome location, resistance characterization, and molecular marker positions indicated that YrFL is likely a novel stripe rust resistance gene on wheat chromosome 5AS and could be pyramided with other resistance genes to improve resistance in wheat breeding programs.

Fine mapping of two recessive powdery mildew resistance genes from Aegilops tauschii accession CIae8.

Two recessive powdery mildew resistance loci pmAeCIae8_2DS and pmAeCIae8_7DS from Aegilops tauschii were mapped and two synthesized hexaploid wheat lines were developed by distant hybridization. Wheat powdery mildew (Pm), one of the worldwide destructive fungal diseases, causes significant yield loss up to 30%. The identification of new Pm resistance genes will enrich the genetic diversity of wheat breeding for Pm resistance. Aegilops tauschii is the ancestor donor of sub-genome D of hexaploid wheat. It provides beneficial genes that can be easily transferred into wheat by producing synthetic hexaploid wheat followed by genetic recombination. We assessed the Pm resistance level of 35 Ae. tauschii accessions from different origins. Accession CIae8 exhibited high Pm resistance. Inheritance analysis and gene mapping were performed using F2 and F2:3 populations derived from the cross between CIae8 and a Pm susceptible accession PI574467. The Pm resistance of CIae8 was controlled by two independent recessive genes. Bulked segregate analysis using a 55K SNP array revealed the SNPs were mainly enriched into genome regions, i.e. 2DS (13.5-20Mb) and 7DS (4.0-15.5Mb). The Pm resistance loci were named as pmAeCIae8_2DS and pmAeCIae8_7DS, respectively. By recombinant screening, we narrowed the pmAeCIae8_2DS into a 370-kb interval flanked by markers CINAU-AE7800 (14.89Mb) and CINAU-AE20 (15.26Mb), and narrowed the pmAeCIae8_7DS into a 260-kb interval flanked by markers CINAU-AE58 (4.72Mb) and CINAU-AE25 (4.98Mb). The molecular markers closely linked with the resistance loci were developed, and two synthesized hexaploid wheat (SHW) lines were produced. These laid the foundation for cloning of the two resistance loci and for transferring the resistance into common wheat.

Detecting Locus of Resistance to Scab in Local Apple Varieties in Uzbekistan Using Molecular Genetic Markers

The apple tree (Malus sp.) is the most cultivated plant in the world. Apple orchards cover a large area. scab (Venturia inaequalis) causes significant damage to the economies of many countries that are engaged in the production of apple trees. In Uzbekistan, most of the orchards are apple orchards. The present study includes a molecular genetic analysis of the resistance of local apple cultivars to pathogens Venturia inaequalis in local apple cultivars grown in Uzbekistan and the results of identification of resistance genes. The paper presents the results of molecular genetic analysis of the combination of scab resistance genes (Vf, Vfa1, Vfa2) found in 15% of samples. In 58.7% of the studied samples, a “high level of resistance” to scab was revealed.

POSTULATION OF YR RESISTANCE GENES TO STRIPE RUST IN 12 COMMERCIAL WHEAT CULTIVARS OF RUSSIAN BREEDING

Stripe rust (Puccinia striiformis f. sp. tritici) is a common wheat disease of economic importance in all world wheat production regions. In most of the regions stripe rust causes yield losses of 10-70 %, depending on the time infection occur, host susceptibility, disease development, and the duration of the epidemics. In South Russia even in unfavourable conditions for the pathogen, stripe rust occurred in the region every year, and in some areas there are foci of the disease with of up to 50% severity.
 Phytopathological testing is one of the least expensive and most effective methods for the rapid identification of juvenile resistance genes in varieties against pathogens. It allows to obtain detailed information about the genetics of the host and pathogen in a short time. In the research Yr resistant genes and its combinations were postulated in winter wheat varieties of Russian breeding to North-Caucasus population of stripe rust by this method.
 Purpose of this study was identification of known stripe rust resistance genes in 12 commercial winter wheat cultivars by phytopathological testing.
 Material and methods: The postulation of known resistance genes was carried out in a greenhouse complex (seedling stage) and at the research station (adult plant stage) of the Laboratory of Plant Immunity to Diseases of the Federal Scientific Center for Biological Plant Protection (Krasnodar).
 For postulation, we chose the method by Dubin et al. (1989), based on the comparison of response types of differential cultivars and studied varieties to Pst isolates.
 Results. In 10 out of 12 winter wheat varieties of Russian breeding, 13 stripe rust resistance genes and their combinations were postulated.: Yr3, Yr3a, Yr6, Yr32, Yr2+6, Yr2+9, Yr39+Alp, Yr4+12, Yr4b, Yr3a+4a+H46, YrA, YrSp, YrSU. The following resistance genes have not been identified: Yr2, Yr5, Yr10, Yr10+Mor, Yr24, Yr27, Yr25+32, since no isolates virulent to carriers of these genes were isolated from the North Caucasian population of P. striiformis; and they are highly effective against this population. Highly effective (Yr3, Yr2+9, Yr3a, Yr4+12, Yr3a+4a+H46) resistance genes were identified in the Kurs, Morozko, and Step’ varieties. We note a combination of effective Yr2+6 genes in the Gurt variety.
 In field conditions, high resistance (degree of damage up to 10%) to the North Caucasian population of the stripe rust pathogen was shown by lines and differential cultivars containing the following resistance genes: Yr2, Yr3, Yr8, Yr10, Yr24, Yr25, Yr27, Yr10+Mor, Yr3a, Yr25+32, Yr3a+4a+H46, Yr3с+Min, Yr4+12, Yr7+25, Yr8+19, 8+6+25, YrSp. Due to the low degree of damage, these genes and their combinations are classified as highly effective and can be involved in the breeding process to create new resistant varieties. Varieties containing these genes can also be recommended for breeders and used in production for effective disease control.

Natural variation in Arabidopsis responses to Plasmodiophora brassicae reveals an essential role for Resistance to Plasmodiophora brasssicae 1 (RPB1).

Despite the identification of clubroot resistance genes in various Brassica crops our understanding of the genetic basis of immunity to Plasmodiophora brassicae infection in the model plant Arabidopsis thaliana remains limited. To address this issue, we performed a screen of 142 natural accessions and identified 11 clubroot-resistant Arabidopsis lines. Genome-wide association analysis identified several genetic loci significantly linked with resistance. Three genes from two of these loci were targeted for deletion by CRISPR/Cas9 mutation in resistant accessions Est-1 and Uod-1. Deletion of Resistance to Plasmodiophora brassicae 1 (RPB1) rendered both lines susceptible to the P. brassicae pathotype P1+. Further analysis of rpb1 knock-out Est-1 and Uod-1 lines showed that the RPB1 protein is required for activation of downstream defence responses, such as the expression of phytoalexin biosynthesis gene CYP71A13. RPB1 has recently been shown to encode a cation channel localised in the endoplasmic reticulum. The clubroot susceptible Arabidopsis accession Col-0 lacks a functional RPB1 gene; when Col-0 is transformed with RPB1 expression driven by its native promoter it is capable of activating RPB1 transcription in response to infection, but this is not sufficient to confer resistance. Transient expression of RPB1 in Nicotiana tabacum induced programmed cell death in leaves. We conclude that RPB1 is a critical component of the defence response to P. brassicae infection in Arabidopsis, acting downstream of pathogen recognition but required for the elaboration of effective resistance.

Genome-wide QTL mapping for stripe rust resistance in spring wheat line PI 660122 using the Wheat 15K SNP array.

Stripe rust is a global disease of wheat. Identification of new resistance genes is key to developing and growing resistant varieties for control of the disease. Wheat line PI 660122 has exhibited a high level of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 239 recombinant inbred lines (RILs) was developed from a cross between PI 660122 and an elite Chinese cultivar Zhengmai 9023. The RIL population was phenotyped for stripe rust response in three field environments and genotyped with the Wheat 15K single-nucleotide polymorphism (SNP) array. A total of nine quantitative trait loci (QTLs) for stripe rust resistance were mapped to chromosomes 1B (one QTL), 2B (one QTL), 4B (two QTLs), 4D (two QTLs), 6A (one QTL), 6D (one QTL), and 7D (one QTL), of which seven QTLs were stable and designated as QYrPI660122.swust-4BS, QYrPI660122.swust-4BL, QYrPI660122.swust-4DS, QYrPI660122.swust-4DL, QYrZM9023.swust-6AS, QYrZM9023.swust-6DS, and QYrPI660122.swust-7DS. QYrPI660122.swust-4DS was a major all-stage resistance QTL explaining the highest percentage (10.67%-20.97%) of the total phenotypic variation and was mapped to a 12.15-cM interval flanked by SNP markers AX-110046962 and AX-111093894 on chromosome 4DS. The QTL and their linked SNP markers in this study can be used in wheat breeding to improve resistance to stripe rust. In addition, 26 lines were selected based on stripe rust resistance and agronomic traits in the field for further selection and release of new cultivars.

RT-PCR Analysis of Caucasian and Mugla Honey Bees by SNP Markers of Chalkbrood Disease

Two different honey bee subspecies’ genotypes obtained from Ordu, Apiculture Research Institute were analyzed by SNP markers using Real-Time PCR-HRM. Genomic DNA samples analysed with 10 SNP primers those were used for identification of chalkbrood disease resistance genes and two SNP primers those were obtained from honey bee genom sequencing. Result of SNP analyses, four primers (AMB-00858574, AMB-01151447, AMB00631190, AMB-00686140) amplified in Caucasian honey bee and six (AMB-00858574, AMB-00612262, AMB-01151447, AMB-00631190, AMB-00674355, AMB-00686140) primers amplified in Mugla honey bee. Four amplicons are similar for this subspecies. Result of electrophoresis analyses, five primers (AMB00858574, AMB-00612262, AMB-01151447, AMB-00631190, AMB-00686140) form a band in Caucasian honey bee, seven amplicons (AMB-00858574, AMB00612262, AMB-01151447, AMB-00631190, AMB-00902548, AMB-00674355, AMB-00686140) form a band in Mugla honey bee and four amplicons (AMB00858574, AMB-01151447, AMB-00631190, AMB-00686140) similar for this subspecies. As a result of this study, in Caucasian and Muğla honeybee for identification of disease resistance and evaluability as a identification key for this subspecies was emerged the capacity of association of single nucleotide polymorphisms to resistance to chalkbrood in two important honeybee genotypes in country of Apis mellifera using RT-PCR for HRM analysis.

Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance.

Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.

Genetic analysis of stripe rust resistance in the common wheat line Kfa/2*Kachu under a Chinese rust environment.

We mapped a new race-specific seedling stripe rust resistance gene on wheat chromosome 5BL and a new APR locus QYr.hazu-2BS from CIMMYT wheat line Kfa/2*Kachu. Breeding resistant wheat (Triticum aestivum) varieties is the most economical and efficient way to manage wheat stripe rust, but requires the prior identification of new resistance genes and development of associated molecular markers for marker-assisted selection. To map stripe rust resistance loci in wheat, we used a recombinant inbred line population generated by crossing the stripe rust-resistant parent 'Kfa/2*Kachu' and the susceptible parent 'Apav#1'. We employed genotyping-by-sequencing and bulked segregant RNA sequencing to map a new race-specific seedling stripe rust resistance gene, which we designated YrK, to wheat chromosome arm 5BL. TraesCS5B02G330700 encodes a receptor-like kinase and is a high-confidence candidate gene for YrK based on virus-induced gene silencing results and the significant induction of its expression 24h after inoculation with wheat stripe rust. To assist breeding, we developed functional molecular markers based on the polymorphic single nucleotide polymorphisms in the coding sequence region of YrK. We also mapped four adult plant resistance (APR) loci to wheat chromosome arms 1BL, 2AS, 2BS and 4AL. Among these APR loci, we determined that QYr.hazu-1BL and QYr.hazu-2AS are allelic to the known pleiotropic resistance gene Lr46/Yr29/Pm39 and the race-specific gene Yr17, respectively. However, QYr.hazu-2BS is likely a new APR locus, for which we converted closely linked SNP polymorphisms into breeder-friendly Kompetitive allele-specific PCR (KASP) markers. In the present study, we provided new stripe rust resistance locus/gene and molecular markers for wheat breeder to develop rust-resistant wheat variety.

Assessing anthracnose resistance in common bean accessions: identification of resistance genes using SCAR markers against Colletotrichum lindemuthianum

Assessing anthracnose resistance in common bean accessions: identification of resistance genes using SCAR markers against Colletotrichum lindemuthianum

Development of novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance and physical mapping of the resistance gene PmW6RS.

Novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance were developed, and the resistance gene PmW6RS was physically mapped onto 6RS-0.58-0.66-bin corresponding to 18.38Mb in Weining rye. Rye (Secale cereale L., RR) contains valuable genes for wheat improvement. However, most of the rye resistance genes have not been successfully used in wheat cultivars. Identification of new rye resistance genes and transfer of these genes to wheat by developing small fragment translocation lines will make these genes more usable for wheat breeding. In this study, a broad-spectrum powdery mildew resistance gene PmW6RS was localized on rye chromosome arm 6RS using a new set of wheat-rye disomic and telosomic addition lines. To further study and use PmW6RS, 164 wheat-rye 6RS translocation lines were developed by 60Coγ-ray irradiation. Seedling and adult stage powdery mildew resistance analysis showed that 106 of the translocation lines were resistant. A physical map of 6RS was constructed using the 6RS translocation and deletion lines, and PmW6RS was localized in the 6RS-0.58-0.66-bin, flanked by markers X6RS-3 and X6RS-10 corresponding to the physical interval of 50.23-68.61Mb in Weining rye genome. A total of 23 resistance-related genes were annotated. Nine markers co-segregate with the 6RS-0.58-0.66-bin, which can be used to rapidly trace the 6RS fragment carrying PmW6RS. Small fragment translocation lines with powdery mildew resistance were backcrossed with wheat cultivars, and 39 agronomically acceptable homozygous 6RS small fragment translocation lines were obtained. In conclusion, this study not only provides novel gene source and germplasms for wheat resistance breeding, but also laid a solid foundation for cloning of PmW6RS.

Identification of inducible clindamycin resistance gene in Streptococcus agalactiae isolates colonizing pregnant women in Suez Canal University Hospitals

Identification of inducible clindamycin resistance gene in Streptococcus agalactiae isolates colonizing pregnant women in Suez Canal University Hospitals

Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane

Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane and other grass crops. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait in sugarcane is largely unexplored. Here, a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane panel. Nine single-nucleotide polymorphisms (SNPs) explained up to 29.9% of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy, precision, recall, and F1 scores (the harmonic mean of precision and recall). Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane, explaining why this major resistance source has not been identified in this crop. Finally, using sugarcane RNA-Seq data, markers associated with resistance to SCMV were annotated, and a gene coexpression network was constructed to identify the predicted biological processes involved in resistance. This network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis, and the regulation of transcription and translation in resistance to SCMV. These results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance.

Genome wide association study for stripe rust resistance in elite spring bread wheat genotypes (Triticum aestivum L.) in Morocco

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases affecting wheat (Triticum aestivum L.) worldwide. Developing and deploying resistant cultivars is the most cost-effective and environmentally friendly method of combating this disease. However, because the pathogen continues to mutate, resistance genes are quickly overpowered by newly virulent Pst races, requiring the continuous identification and introduction of resistance genes to create resistant wheat varieties. To identify closely linked markers for possible use in marker-assisted selection a genome-wide association study was conducted using rust data at adult plant stages for 200 elite spring bread wheat genotypes and 13151 SNP markers. Stripe rust resistance was evaluated under rainfed conditions at the ICARDA Merchouch station in Morocco during the 2019–2020 and 2020–2021 crop seasons. The genotypes were classified into five distinct categories based on the coefficient of infection (CI), 18 genotypes were highly resistant, while 42 were moderately resistant (21%), additionally, 73 were intermediate (37%), while 26 were moderately susceptible (13%), and the remaining 41 genotypes highly susceptible. Thirteen markers were associated with stripe rust resistance through GWAS analysis using a general linear model. Four of these markers for adult plant resistance (Kukri c8390 1515, CAP7 c5481 96, Excalibur c35203 334, and BS00017187 51) on chromosomes 1B, 5B, 3B, and 7B, correspondingly, are of particular importance and could be used for marker-assisted selection to pyramid rust resistance genes in wheat breeding programs.

Identification of Antimicrobial Resistance in Faecal Microbes from Wild Dugongs (Dugong dugon)

Estuarine and coastal waters are areas of potential concern for antimicrobial resistance because of the discharge of wastewater from sewage treatment plants and the run-off from urban and agricultural lands. Herein, we evaluate the antimicrobial resistance profiles in bacteria from dugongs (Dugong dugon), mammals that inhabit and feed in shallow coastal regions and, thus, are vulnerable to encountering water and sediment contaminated by human activities. Bacterial isolates were cultured from fresh faeces of four wild dugongs, as well as from one sediment sample from a dugong foraging ground in Queensland, Australia. Ten bacterial isolates underwent phenotypic antimicrobial susceptibility testing using disc diffusion and minimum inhibitory concentration testing, and genotypic resistance and virulence gene identification through whole genome sequencing. Four Staphylococcus warneri isolates and one Bacillus cereus isolate from dugong faeces were resistant to penicillin, with two S. warneri isolates also displaying resistance to trimethoprim. Four Escherichia coli isolates were all resistant to ampicillin. Resistance genes, including fosB, BcII, dfrC, blaZ, and mdfA, were identified in the isolates cultured from dugong faeces with two virulence genes (gad and lpfA) identified in all E. coli isolates. Lysinibacillus sphaericus cultured from the marine sediment and B. cereus from dugong faeces displayed phenotypic multidrug resistance (across categories of non-extended spectrum cephalosporins, penicillins and beta-lactamase inhibitors, and clindamycin; and for L. sphaericus, phosphonic acids). These results demonstrate the role that dugongs can play as a sentinel species for antimicrobial resistance in the coastal waters across their range, which includes both disturbed urban and rural regions.

Identification of candidate genes for rust resistance in asparagus

Identification of candidate genes for rust resistance in asparagus

Identification of resistance genes in the framework of veterinary monitoring

Real-time polymerase chain reaction (PCR-PT) was used to examine 263 environmental samples from animal and poultry facilities, as well as faeces, to determine the genetic determinants of resistance to five classes of antimicrobials such as tetracyclines (tetA, tetO, tetM) fluoroquinolones (qnrS, qnrB) cephalosporins, penicillins (CTX-M-1, CTX-M-9, CMY), polymyxins (mcr-1). 95% of samples tested for AMR showed the presence of resistance genes associated with resistance to at least two classes of these broad-spectrum antibiotics. The level of detection of resistance markers to tetracyclines and fluoroquinolones was the highest. The detection of genetic markers of resistance to most antimicrobials has the following ascending order: sheep → horse → goat → cattle → pig → poultry. Our studies correlate with a trend towards more antimicrobial use in pigs and poultry than in cattle.In samples from environmental objects, the identification of genetic determinants of resistance was comparable to the detection in samples from animals only in poultry houses. In faecal samples, resistance genes were detected two to three times more often than in environmental samples.The study showed which resistance markers are common in the fecal microbiome and environmental samples, and the relative amount and frequency of detection of these markers can serve as a risk assessment parameter for the further spread of antibiotic resistance.

Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants.

Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.

Transposon Polymorphism and Its Potential Impacts on Brown Planthopper (Nilaparvata lugens Stål) Resistance in Rice (Oryza sativa L.)

The brown planthopper (BPH) is a major pest in rice cultivation, significantly affecting both yield and quality; accordingly, exploring and utilizing anti-herbivory genes to enhance rice’s inherent resistance to BPH can be an effective strategy for mitigating infestation. The effects of transposon insertion polymorphisms (TIPs) on rice’s resistance to insect pests have not been reported. In this study, through the identification of transposon insertion sites in susceptible and resistant rice varieties, a total of six possible candidate insect resistance genes were potentially located. Among them, a segment of the LTR/Copia transposon insertion was verified in the promoter of LOC_Os04g02720, which carries a cis-acting element binding site in rice involved in the abscisic acid reaction. Quantitative analysis showed a significant difference of the gene expression between insect-resistant and insect-susceptible varieties (p < 0.05). This study provides insights into the functional analysis of transposons and population transposon polymorphisms, whereas the identification of candidate insect resistance genes offers a theoretical foundation for the development of insect-resistant rice varieties.

Evolution of NLR genes in genus Arachis reveals asymmetric expansion of NLRome in wild and domesticated tetraploid species

Arachis hypogaea is an allotetraploid crop widely grown in the world. Wild relatives of genus Arachis are the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genus Arachis and performed their comparative genomics among four diploids (A. duranensis, A. ipaensis, A. cardenasii, A. stenosperma) and two tetraploid (wild: A. monticola and domesticated: A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified from A. cardenasii, A. stenosperma and A. duranensis, A. hypogaea, A. monticola and A. ipaensis respectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome of A. monticola exhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case of A. hypogaea probably due to distinct natural and artificial selection pressure. In addition, diploid species A. cardenasii revealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure. A. cardenasii and A. monticola can be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genus Arachis to identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security.