Major Resistance Genes Research Articles

Linking symbioses with intrinsic chemical defences in conifers: Fungal‐mediated resistance against an invasive pathogen

Abstract Invasive pathogens threaten the sustainability of forest ecosystems globally. Trees possess intrinsic pathogen defence mechanisms, including major gene resistance (MGR) and quantitative disease resistance (QDR). Plant‐symbiotic fungi can enhance tree defences, generating far‐reaching ecosystem impacts. However, the specific contributions of various fungal guilds to this symbiont‐mediated resistance remain unclear. In this study, we inoculated six Pinus monticola seedling families exhibiting resistance (MGR or QDR) or high susceptibility to the introduced invasive pathogen Cronartium ribicola, the causative agent of white pine blister rust (WPBR), with endophytic and ectomycorrhizal fungi, either alone or in combination (symbiont treatments), in an open‐air greenhouse study. Over a period of 25 months, we monitored the growth, foliar terpene defences, and disease progression in trees before and after C. ribicola infection and in trees inoculated with the symbionts but never inoculated with C. ribicola. We observed enhanced inducible host defences and evidence of defensive priming in response to symbiont treatments. In WPBR‐free control treatments, differences in pine defences coincided with an increased seedling growth rate. For WPBR‐infected seedlings, symbiont treatments reduced disease symptoms in seedlings with QDR and to a lesser extent in susceptible families, but not in those with MGR. Furthermore, disease symptoms correlated with variations in terpene composition. Synthesis and applications: Interactions with fungal symbionts should be considered when breeding native trees for resistance against invasive pathogens. Our study underscores the capacity of endophytic and ectomycorrhizal fungi to enhance tree growth and defence while also reducing disease symptoms. We also show that fungi can induce long‐lasting changes in conifer foliar terpenes, suggesting potential applications in tree protection from invasive pathogens.

Genomic Epidemiology of Antimicrobial Resistance: Tracking the Global Spread of Resistant Pathogens

The rapid development and spread of antimicrobial resistance have been one of the most prominent health crises globally, which significantly challenges treating infectious diseases. This paper will address the contribution that genomic epidemiology makes to track and understand the global spread of antimicrobial-resistant pathogens. Genomic epidemiology, an area combining pathogen genomics with epidemiological data, allows for an extremely powerful approach in the identification of resistance mechanisms and tracing transmission routes for guiding public health interventions. This review Emphasizes major bacterial pathogens, such as Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae, which harbor major resistance genes: blaCTX-M, mecA, and blaKPC. These genes contribute to the worldwide dissemination of resistance, mainly through mechanisms involving horizontal gene transfer and selective antibiotic pressure. Thus, genomic surveillance, phylogenetic analysis, and bioinformatics approaches allow for the pinpointing of transmission hotspots, mapping of resistance gene distribution, and tracking of emerging resistant strains in real time. It also provides information on how genomic data are being used to improve antimicrobial stewardship programs and inform clinical treatment decisions. Public health responses can further be tailored by recognizing regional resistance patterns, hence enhancing interventions. However, several challenges persist—for example, the need for standardized sharing of data, interpretation of genomic data, and integration of these insights into public health systems, especially in low-resource settings. This abstract highlights the transformative impact of genomic epidemiology in the management of the AMR crisis while emphasizing the continued need for global cooperation, enhanced data infrastructures, and policy initiatives to ensure the effective use of genomic data in public health.

Multi-component resistance responses of melon to zucchini yellow mosaic virus.

A major resistance gene of the melon accession PI414723 to zucchini yellow mosaic virus (ZYMV) is located at the Zym-1 locus on chromosome 2, but the underlying defense mechanisms are poorly understood. The physiological responses and expression of selected genes at Zym-1 were assessed in PI414723 and in the susceptible genotype Védrantais. Viral titers and the expression of genes related to systemic acquired resistance (SAR) were evaluated in inoculated (Inoc) and non-inoculated (Non-Inoc) portions of the cotyledons at 3, 7 and 10 days after inoculation (dai) and in apical leaves at 10 dai. ZYMV was detected in both portions of the cotyledons but not in the apical leaves of PI414723 plants. Also, ZYMV was recovered in a susceptible zucchini only from Inoc portions at 3 dai. By contrast, in Védrantais ZYMV was detected and recovered from all tissues at high concentrations. Starchy local lesions and accumulation of transcripts of the SAR marker genes PR1 and PR4 were also detected in the resistant genotype. Plus, transcripts of one candidate resistance gene analog previously located at Zym-1 and of two melon homologs of restricted tobacco etch virus movement 2 (RTM2) genes located close to Zym-1, accumulated only in PI414723. It is proposed that resistance results from the combined action of the R gene, involved in restricting ZYMV replication after a supposed recognition event and of the RTM genes which impact viral systemic movement to distal apical tissues.

Mapping rust resistance in European winter wheat: many QTLs for yellow rust resistance, but only a few well characterized genes for stem rust resistance

Key messageStem rust resistance was mainly based on a few, already known resistance genes; for yellow rust resistance there was a combination of designated genes and minor QTLs.Yellow rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) and stem rust (SR) caused by Puccinia graminis f. sp. tritici (Pgt) are among the most damaging wheat diseases. Although, yellow rust has occurred regularly in Europe since the advent of the Warrior race in 2011, damaging stem rust epidemics are still unusual. We analyzed the resistance of seven segregating populations at the adult growth stage with the parents being selected for YR and SR resistances across three to six environments (location–year combinations) following inoculation with defined Pst and Pgt races. In total, 600 progenies were phenotyped and 563 were genotyped with a 25k SNP array. For SR resistance, three major resistance genes (Sr24, Sr31, Sr38/Yr17) were detected in different combinations. Additional QTLs provided much smaller effects except for a gene on chromosome 4B that explained much of the genetic variance. For YR resistance, ten loci with highly varying percentages of explained genetic variance (pG, 6–99%) were mapped. Our results imply that introgression of new SR resistances will be necessary for breeding future rust resistant cultivars, whereas YR resistance can be achieved by genomic selection of many of the detected QTLs.

Within-plant genetic drift to control virus adaptation to host resistance genes.

Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These PVY populations exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term.

Stomatal penetration: the cornerstone of plant resistance to the fungal pathogen Zymoseptoria tritici

BackgroundSeptoria tritici blotch (STB), caused by the foliar fungus Zymoseptoria tritici, is one of the most damaging disease of wheat in Europe. Genetic resistance against this fungus relies on different types of resistance from non-host resistance (NHR) and host species specific resistance (HSSR) to host resistance mediated by quantitative trait loci (QTLs) or major resistance genes (Stb). Characterizing the diversity of theses resistances is of great importance for breeding wheat cultivars with efficient and durable resistance. While the functional mechanisms underlying these resistance types are not well understood, increasing piece of evidence suggest that fungus stomatal penetration and early establishment in the apoplast are both crucial for the outcome of some interactions between Z. tritici and plants. To validate and extend these previous observations, we conducted quantitative comparative phenotypical and cytological analyses of the infection process corresponding to 22 different interactions between plant species and Z. tritici isolates. These interactions included four major bread wheat Stb genes, four bread wheat accessions with contrasting quantitative resistance, two species resistant to Z. tritici isolates from bread wheat (HSSR) and four plant species resistant to all Z. tritici isolates (NHR).ResultsInfiltration of Z. tritici spores into plant leaves allowed the partial bypass of all bread wheat resistances and durum wheat resistance, but not resistances from other plants species. Quantitative comparative cytological analysis showed that in the non-grass plant Nicotiana benthamiana, Z. tritici was stopped before stomatal penetration. By contrast, in all resistant grass plants, Z. tritici was stopped, at least partly, during stomatal penetration. The intensity of this early plant control process varied depending on resistance types, quantitative resistances being the least effective. These analyses also demonstrated that Stb-mediated resistances, HSSR and NHR, but not quantitative resistances, relied on the strong growth inhibition of the few Z. tritici penetrating hyphae at their entry point in the sub-stomatal cavity.ConclusionsIn addition to furnishing a robust quantitative cytological assessment system, our study uncovered three stopping patterns of Z. tritici by plant resistances. Stomatal resistance was found important for most resistances to Z. tritici, independently of its type (Stb, HSSR, NHR). These results provided a basis for the functional analysis of wheat resistance to Z. tritici and its improvement.

Combining Single-Gene-Resistant and Pyramided Cultivars of Perennial Crops in Agricultural Landscapes Compromises Pyramiding Benefits in Most Production Situations.

Although resistant cultivars are valuable in safeguarding crops against diseases, they can be rapidly overcome by pathogens. Numerous strategies have been proposed to delay pathogen adaptation (evolutionary control) while still ensuring effective protection (epidemiological control). For perennial crops, multiple resistance genes can be deployed (i) in the same cultivar (pyramiding strategy); in single-gene-resistant cultivars grown (ii) in the same field (mixture strategy) or (iii) in different fields (mosaic strategy); or (iv) in hybrid strategies that combine the three previous options. In addition, the spatial scale at which resistant cultivars are deployed can affect the plant-pathogen interaction: Small fields are thought to reduce pest density and disease transmission. Here, we used the spatially explicit stochastic model landsepi to compare the evolutionary and epidemiological control across spatial scales and deployment strategies relying on two major resistance genes. Our results, broadly focused on resistance to downy mildew of grapevine, show that the evolutionary control provided by the pyramiding strategy is at risk when single-gene-resistant cultivars are concurrently planted in the landscape (hybrid strategies), especially at low mutation probability. Moreover, the effectiveness of pyramiding compared with hybrid strategies is influenced by whether the adapted pathogen pays a fitness cost across all hosts or only for unnecessary virulence, particularly when the fitness cost is high rather than intermediate. Finally, field size did not affect model outputs for a wide range of mutation probabilities and associated fitness costs. The socioeconomic policies favoring the adoption of optimal resistant management strategies are discussed.

Management and breeding for rust resistance in legumes

AbstractRust diseases are a major concern in legume production worldwide causing heavy losses especially in developing countries that depend on grain legumes as staple food. Fungal species from Uromyces, Phakopsora and Puccinia genera are the main causal agents of the various legume rust diseases. They induce up to 100% yield losses on susceptible cultivars and are emerging as a substantial threat to global food security. Developing durable resistance to rust has thus become a critical breeding objective alongside efforts to improve cultural and disease management practices. This review specifically focuses on the recent advances in understanding and enhancing genetic rust resistance across diverse legume crops. Key topics covered include: (i) the diversity and host range of the rust species affecting legumes; (ii) the disease management strategies from cultural practices to chemical control; (iii) the available screening methods for identifying new sources of resistance; (iv) the genetic basis of resistance, encompassing both major resistance genes and quantitative trait loci; (v) insights into gene regulation and effector molecules leading to legume-rust interactions; and (vi) emerging genomic-assisted breeding techniques that can accelerate the development of durable rust resistance in legumes. Overall, this review highlights the progress made to date and the remaining challenges in sustainably managing rust diseases across diverse legume crops through integrated approaches spanning pathogen biology, advanced phenotyping, genetic resistance, and molecular breeding.

Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat

In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1–57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.

Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines

Main conclusionPM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8.Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.

The Development of Multi-Resistant Rice Restorer Lines and Hybrid Varieties by Pyramiding Resistance Genes against Blast and Brown Planthopper

Rice blast, caused by the fungus Magnaporthe oryzae, and brown planthopper (BPH) infestation are two of the most destructive problems of rice production in China. The development of multi-resistant varieties is widely recognized as the most efficient and environmentally friendly approach to controlling crop diseases and pests. Functional molecular markers (FMMs) have been developed from functional variants in the genic region associated with trait variation, greatly enhancing the efficiency of identifying and pyramiding valuable genes in crop breeding. In this study, two FMMs and a multiplex PCR amplification system were developed for two major broad-spectrum BPH resistance genes, Bph6 and Bph9. With the assistance of FMMs in the multi-resistant rice restorer-line development pipeline, two lines (Huahui7713 and Huahui3006) with blast and BPH resistance were developed by pyramiding three resistance genes Pigm, Bph6 and Bph9. Two new hybrid rice varieties, Weiliangyou7713 and Xuanliangyou3006, derived from Huahui7713 and Huahui3006, have been developed and commercialized in China. Weiliangyou7713 and Xuanliangyou3006 exhibit enhanced resistance to both blast and BPH, while maintaining optimal yield and grain quality. The adoption of Weiliangyou7713 continues to expand, now being cultivated on a large scale, which is promising for its future role in reducing the dependence on chemical fungicides and pesticides in rice production. This suggests that the implementation of Huahui7713 and Huahui3006 in targeted breeding programs could be highly beneficial for developing rice varieties with strong resistance to blast and BPH.

RNA-Seq Bulked Segregant Analysis of an Exotic B. napus ssp. napobrassica (Rutabaga) F2 Population Reveals Novel QTLs for Breeding Clubroot-Resistant Canola.

In this study, a rutabaga (Brassica napus ssp. napobrassica) donor parent FGRA106, which exhibited broad-spectrum resistance to 17 isolates representing 16 pathotypes of Plasmodiophora brassicae, was used in genetic crosses with the susceptible spring-type canola (B. napus ssp. napus) accession FG769. The F2 plants derived from a clubroot-resistant F1 plant were screened against three P. brassicae isolates representing pathotypes 3A, 3D, and 3H. Chi-square (χ2) goodness-of-fit tests indicated that the F2 plants inherited two major clubroot resistance genes from the CR donor FGRA106. The total RNA from plants resistant (R) and susceptible (S) to each pathotype were pooled and subjected to bulked segregant RNA-sequencing (BSR-Seq). The analysis of gene expression profiles identified 431, 67, and 98 differentially expressed genes (DEGs) between the R and S bulks. The variant calling method indicated a total of 12 (7 major + 5 minor) QTLs across seven chromosomes. The seven major QTLs included: BnaA5P3A.CRX1.1, BnaC1P3H.CRX1.2, and BnaC7P3A.CRX1.1 on chromosomes A05, C01, and C07, respectively; and BnaA8P3D.CRX1.1, BnaA8P3D.RCr91.2/BnaA8P3H.RCr91.2, BnaA8P3H.Crr11.3/BnaA8P3D.Crr11.3, and BnaA8P3D.qBrCR381.4 on chromosome A08. A total of 16 of the DEGs were located in the major QTL regions, 13 of which were on chromosome C07. The molecular data suggested that clubroot resistance in FGRA106 may be controlled by major and minor genes on both the A and C genomes, which are deployed in different combinations to confer resistance to the different isolates. This study provides valuable germplasm for the breeding of clubroot-resistant B. napus cultivars in Western Canada.

Allele mining for blast-resistance gene at Pi5 locus in rice

Rice plays a crucial role in global food security, serving as a staple for more than half of the world's population. Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating fungal diseases, resulting in substantial economic losses in terms of rice yield and grain quality. The resistance provided by individual blast resistance genes tends to become ineffective within a few years of extensive agricultural use due to the rapid evolution of the fungus. Therefore, continuous efforts in resistance breeding in rice are required to enrich the pool of new resistance genes and alleles. A large-scale screening of new blast resistance alleles was conducted across 2000 rice accessions from major rice-producing areas in China. Field trials were employed in two rice uniform blast nurseries located in Enshi and Yichang. Approximately 153 rice accessions showed at least moderate resistance to the rice blast. Sequence-based allele mining was used to identify the allelic variants of major rice blast resistance genes at the Pi5 locus of chromosome 9. Six novel alleles were identified from 64 accessions. Field tests at five locations, including Enshi, Yichang, Lvtian, Taojiang, and Yaan, and greenhouse inoculation using 33 blast strains from Hubei, Hunan, Guangzhou, and Sichuan, were employed to verify the resistance of these six alleles. Three near-isogenic lines (types 2, 4, and 6) were constructed and inoculated with 31 blast isolates from Heilongjiang to evaluate their blast resistance. Furthermore, bulk segregant analysis was used to confirm that Pi5-type2 and Pi5-type6 are dominant alleles in the analyzed populations. These novel alleles expand the allelic series, enriching the genetic resources for rice blast resistance breeding programs, especially in the north of China. Furthermore, they provide valuable insights into the molecular interactions between rice and rice blast.

Screening for disease resistance and profiling the expression of defense-related genes contributing to resistance against bacterial blight (Xanthomonas oryzae pv. oryzae) in rice genotypes

Bacterial Bight profoundly affects global rice-growing regions. Breeding resistant cultivars is a reliable, effective, and eco-friendly way to control bacterial blight. The study was conducted during 2021–2022 to evaluate the resistance of rice genotypes to bacterial blight under glasshouse conditions. A total of 137 rice genotypes were screened for their resistance against two Xanthomonas oryzae pv. oryzae strains (TXO01 and TXO08) using the leaf clipping method. The results revealed diverse disease reactions among the genotypes, with some exhibiting high levels of resistance characterized by hypersensitive reactions and shorter lesion lengths. To further investigate the genetic basis of resistance, we screened moderately resistant and resistant genotypes for major bacterial blight resistance genes, including Xa21, xa5, and xa13, using gene-specific markers. Five genotypes viz., ADT55, CB MAS 13056, CB MAS 13060, CB MAS 13066, and ACM 18234 confirmed the presence of all R genes in a homozygous state, indicating a potentially robust resistance background. In addition, we examined the expression patterns of five defense-related genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways using quantitative real-time PCR (qRT-PCR). The resistant genotypes exhibited significantly elevated expression levels of OsNPR1, OsWRKY45, OsPAL1, OsPR1a, and OsPR10a, ranging from 2 to 20-fold changes compared with the susceptible genotype. In conclusion, our findings suggest that the resistant genotypes not only harbor multiple bacterial blight resistance genes but also manifest up regulated defense responses against Xanthomonas oryzae pv. oryzae, possibly substantiating their elevated level of disease resistance.

Hunting for sources of durable resistance in crop cultivar evaluation data: The case of wheat yellow rust in France

AbstractCultivar resistance is a major asset for the management of crop diseases and can play an important role in agroecological transition. However, the wide deployment of a reduced number of resistance genes can lead to a rapid adaptation of pathogen populations and to a loss of resistance efficiency. The objective of this study was to characterize and discuss different trajectories of adult plant ratings for resistance to yellow rust in French wheat cultivars between 1963 and 2018. Among 719 cultivars assessed for at least 2 years, 590 cultivars showed no variation in their resistance scores, despite a mean of 4.3 years and up to 33 years of assessment. A set of descriptive variables was computed in order to compare the evolution of resistance score of 129 cultivars that experienced resistance variation. We applied a principal component analysis and a hierarchical clustering on principal components to this subdataset to constitute clusters corresponding to different cultivar profiles. Clusters C1 and C2 had small resistance variations (1–2 points on a 1–9 scale); Cluster C3 had long assessment durations and several small drops in resistance score and could be associated with quantitative resistance erosion; Cluster C4 included major drops in resistance score (4–5 points), often associated with known breakdowns of major resistance genes. Cases of limited drops in resistance score as a known resistance gene was broken down suggest the presence of efficient adult plant resistance. We discuss the use of information extracted from this dataset and methods to further explore sources of resistance to yellow rust present in French cultivars.

A cluster of putative resistance genes is associated with a dominant resistance to sunflower broomrape.

The HaOr5 resistance gene is located in a large genomic insertion containing putative resistance genes and provides resistance to O. cumana, preventing successful connection to the sunflower root vascular system. Orobanche cumana (sunflower broomrape) is a parasitic plant that is part of the Orobanchaceae family and specifically infests sunflower crops. This weed is an obligate parasitic plant that does not carry out photosynthetic activity or develop roots and is fully dependent on its host for its development. It produces thousands of dust-like seeds per plant. It possesses a high spreading ability and has been shown to quickly overcome resistance genes successively introduced by selection in cultivated sunflower varieties. The first part of its life cycle occurs underground. The connection to the sunflower vascular system is essential for parasitic plant survival and development. The HaOr5 gene provides resistance to sunflower broomrape race E by preventing the connection of O. cumana to the root vascular system. We mapped a single position of the HaOr5 gene by quantitative trait locus mapping using two segregating populations. The same location of the HaOr5 gene was identified by genome-wide association. Using a large population of thousands of F2 plants, we restricted the location of the HaOr5 gene to a genomic region of 193kb. By sequencing the whole genome of the resistant line harboring the major resistance gene HaOr5, we identified a large insertion of a complex genomic region containing a cluster of putative resistance genes.

Combining Ability Analysis and Genetic Studies of Stripe Rust Resistance in Bread Wheat Genotypes

A set of eighteen F1 and F2 experimental crosses were grown in a randomized complete block design (RCBD) with three replications. From lines, TD-1 was on top by showing greater and significant general combining ability (GCA) effects for maximum number characters including grain yield in both (F1 and F2) populations, while tester Benazir remained exceptional by showing higher and significant specific combining ability (GCA) effects for majority traits including grain yield in F1 and F2 populations, as a result, both parents would contribute significantly to the improvement of the bread wheat. Regarding the SCA effects in F1 population, the hybrids TD-1 × Pakistan-2013, TJ-83 × Benazir, and NIA-Sundar × NIA-Sarang and from F2 populations, the crosses TD-1 × Benazir, TJ-83 × Benazir, Kiran-95 × NIA-Sarang and NIA-Amber × Pakistan-2013 expressed desirable and maximum SCA effects for number of traits including grain yield, thus may be preferred in future wheat breeding programs. Disease reaction on selected 18 F2 populations was performed, the introgression stripe rust resistance showed single dominant gene. The genetic analysis reported the involvement of major genes for stripe rust resistance. These findings could be used to grow high-yielding wheat lines that could have a profitable yield in stripe rust-prone areas.

Introgression of OsAP47 by marker-assisted selection enhanced resistance against southern rice black-streaked dwarf virus disease

Southern rice black-streaked dwarf virus disease (SRBSDVD) is the most destructive viral disease in rice. In order to breeding resistant cultivars, Insertion-Deletion (InDel) markers were developed linked to OsAP47, the first isolated major resistance gene against SRBSDVD. Marker-assisted selection (MAS) was conducted to introduce this gene into the commercial variety. A rice line carrying homozygous resistance allele of OsAP47 was selected and named Kanghei No. 201 (KH201). Evaluated by artificial inoculation, KH201 showed significantly higher resistance than the recurrent parent Suxiu No.867 (SX867). And no significant differences were detected for KH201 in the yield-related components, including spikelets per panicle (SPP), ripened grains per panicle (RGPP), 1000-grain weight (TGW) and panicles per square meter (PPSM), leading to stable theoretical yield. The results indicated that introgression of OsAP47 improved rice resistance and can avoid yield losses produced by SRBSDVD. KH201 was demonstrated as a resistance material that could be used in rice breeding.

Genome-Wide Association Study Reveals Polygenic Architecture for Limber Pine Quantitative Disease Resistance to White Pine Blister Rust.

Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study. Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over 4 years postinoculation. To reveal the genomic architecture contributing to QDR-related traits, a set of genes related to disease resistance with genome-wide distribution was selected for targeted sequencing for genotyping of single-nucleotide polymorphisms (SNPs). The genome-wide association study revealed a set of SNPs significantly associated with quantitative traits for limber pine QDR to white pine blister rust, including number of needle spots and stem cankers, as well as survival 4 years postinoculation. The peaks of marker-trait associations displayed a polygenic pattern, with genomic regions as potential resistant quantitative trait loci, distributed over 10 of the 12 linkage groups (LGs) of Pinus. None of them was linked to the Cr4-controlled major gene resistance previously mapped on LG08. Both normal canker and bole infection were mapped on LG05, and the associated SNPs explained their phenotypic variance up to 52%, tagging a major resistant quantitative trait locus. Candidate genes containing phenotypically associated SNPs encoded putative nucleotide-binding site leucine-rich repeat proteins, leucine-rich repeat-receptor-like kinase, cytochrome P450 superfamily protein, heat shock cognate protein 70, glutamate receptor, RNA-binding family protein, and unknown protein. The confirmation of resistant quantitative trait loci broadens the genetic pool of limber pine resistance germplasm for resistance breeding.

High-resolution mapping of Ryd4Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum

Key messageWe mapped Ryd4Hb in a 66.5 kbp interval in barley and dissociated it from a sublethality factor. These results will enable a targeted selection of the resistance in barley breeding.Virus diseases are causing high yield losses in crops worldwide. The Barley yellow dwarf virus (BYDV) complex is responsible for one of the most widespread and economically important viral diseases of cereals. While no gene conferring complete resistance (immunity) has been uncovered in the primary gene pool of barley, sources of resistance were searched and identified in the wild relative Hordeum bulbosum, representing the secondary gene pool of barley. One such locus, Ryd4Hb, has been previously introgressed into barley, and was allocated to chromosome 3H, but is tightly linked to a sublethality factor that prevents the incorporation and utilization of Ryd4Hb in barley varieties. To solve this problem, we fine-mapped Ryd4Hb and separated it from this negative factor. We narrowed the Ryd4Hb locus to a corresponding 66.5 kbp physical interval in the barley ‘Morex’ reference genome. The region comprises a gene from the nucleotide-binding and leucine-rich repeat immune receptor family, typical of dominant virus resistance genes. The closest homolog to this Ryd4Hb candidate gene is the wheat Sr35 stem rust resistance gene. In addition to the fine mapping, we reduced the interval bearing the sublethality factor to 600 kbp in barley. Aphid feeding experiments demonstrated that Ryd4Hb provides a resistance to BYDV rather than to its vector. The presented results, including the high-throughput molecular markers, will permit a more targeted selection of the resistance in breeding, enabling the use of Ryd4Hb in barley varieties.