QTL mapping for resistance to and tolerance for the rice root-knot nematode, Meloidogyne graminicola

Comprehensive study of tRNA-derived fragments in plants for biotic stress responses

Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum are investigated using in-silico approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study's database is publicly available at http://www.nipgr.ac.in/PbtRFdb .

Identification of a Promising Novel Genetic Source for Rice Root-Knot Nematode Resistance through Markers Associated with Trait-Specific Quantitative Trait Loci

Direct-seeded rice (DSR) is gaining popularity among farmers due to its environmentally safe and resource-efficient production system. However, managing the rice root-knot nematode (RRKN), Meloidogyne graminicola, remains a major challenge in DSR cultivation. Developing genetic resistance is a pragmatic and effective approach compared to using hazardous pesticides. Pusa Basmati 1121 (PB1121) is the most popular Basmati rice variety, but it is highly susceptible to RRKN. In contrast, Phule Radha (PR) has shown highly resistant reaction to RRKN, as reported in our earlier study. We generated an F2:3 population from the cross of PB1121/PR and evaluated it for RRKN resistance-related traits under artificial inoculation conditions. The distribution pattern of traits in the F2:3 population indicated that resistance may be governed by a few major-effect genes and many minor-effect genes. The molecular markers reported to be associated with QTLs governing RRKN resistance traits were used to test in the current population. Although the simple linear regression identified significant associations between the markers and RRKN resistance-associated traits, these associations were spurious as the LOD score was below the threshold limit. This indicates that PR possesses novel genomic regions for resistance to RRKN as it does not possess any of the earlier reported QTLs.

Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions

Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.

Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola

Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima

Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC₁F₁ population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.

Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice

Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F₂ hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.

Novel Lead Compound Discovery from Aspergillus fumigatus 1T-2 against Meloidogyne incognita Based on a Chemical Ecology Study

To replace biohazardous nematicides, there is an ever-increasing need to identify natural product-based agents to contain root-knot nematodes (RKNs) in agriculture. In this chemical ecology study, an antagonistic fungus Aspergillus fumigatus 1T-2, which could cause the formation of withering of the gut and vacuole-like structures in the nematode body, was isolated based on the gradually increased antagonistic interactions between the soil fungi and RKNs. Based on these typical morphological characteristics, a potent nematode-antagonistic compound 2-furoic acid, which had a simple structure, was successfully identified from 1T-2 fermentation broth by liquid chromatography-mass spectrometry (LC-MS). 2-Furoic acid showed effective mortality activity in vitro, of which the LC₅₀ value to Megalaima incognita at 24 h was 37.75 μg/mL. 2-Furoic acid had similar mortality activity to the positive control fosthiazate at 30 μg/mL. Continuous 2-furoic acid exposure had obvious negative influences on both nematode vitality and egg hatchability. Notably, significant variations were observed in nematodes and eggs with 2-furoic acid treatment, which might be induced by novel nematocidal mechanisms. Furthermore, the 1T-2 fermentation broth and 2-furoic acid had significant control efficacy on M. incognita under the greenhouse test-tube assay. Overall, these findings provide valuable insights into the use of 2-furoic acid with biocontrol potential as a preferable lead structure for the development of innovative nematicides.

Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines

Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238-553,648 unique SNPs and 32,395-65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.

Penetration and Development of Meloidogyne Javanica on Four Pistachio Rootstocks and their Defense Responses

Pistachio yield is annually reduced due to root-knot nematode infections. In order to evaluate its resistance to Meloidogyne javanica, three domestic pistachio rootstocks, namely, Badami, Ghazvini and Sarakhs, and a wild pistachio, Baneh (Pistacia atlantica subsp. mutica), were selected. Their response to the nematode infection was evaluated based on different plant and nematode indexes, 120 days post-inoculation (dpi). The penetration and development rate of nematode in roots of these four pistachio rootstocks were evaluated at different time points by acid fuchsin staining. Based on the measured indexes, Badami, Ghazvini, Sarakhs, and Baneh rootstocks ranked as susceptible, moderately resistant, moderately resistant, and resistant, respectively. The penetration rate of second-stage nematode juveniles (J2) into four rootstocks was discussed. The first "midstage" or swollen juveniles appeared at 4 dpi but to a lesser extent in Ghazvini, Sarakhs, and Baneh cultivars. The first females were seen in Badami at 21 dpi, in Ghazvini and Sarakhs at 35 dpi, and in Baneh at 45 dpi. Three types of defense responses were distinguished and characterized in the examined pistachio rootstocks: (i) a hypersensitive response (HR)-like reaction in the cortex in Ghazvini, Sarakhs, and Baneh root tips at 4 dpi and 6 dpi; (ii) an HR response, degrading J2 which induce giant cells in the vascular cylinder of all rootstocks, at 6 dpi and 10 dpi; and (iii) an HR response, degrading females and giant cells in the vascular cylinder of all rootstocks at 15 dpi onward. These observations open new fields of study in breeding programs of this crop.

Breeding rice for a changing climate by improving adaptations to water saving technologies

Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.

Meloidogyne graminicola-A Threat to Rice Production: Review Update on Distribution, Biology, Identification, and Management

Simple Summary

New risks to plant health are constantly emerging. Such is the case of the rice root knot nematode Meloidogyne graminicola, adapted to flooded conditions and representing a risk to all types of rice agro-systems. It has been recently detected in Italy and added to the European and Mediterranean Plant Protection Organization (EPPO) Alert List. The presence of this nematode in Europe poses a threat to rice production, as there is a high probability to spread, due to trade activities and climate changes. In view of its importance, an extensive updated review was carried out.

Abstract

Rice (Oryza sativa L.) is one of the main cultivated crops worldwide and represents a staple food for more than half of the world population. Root-knot nematodes (RKNs), Meloidogyne spp., and particularly M. graminicola, are serious pests of rice, being, probably, the most economically important plant-parasitic nematode in this crop. M. graminicola is an obligate sedentary endoparasite adapted to flooded conditions. Until recently, M. graminicola was present mainly in irrigated rice fields in Asia, parts of the Americas, and South Africa. However, in July 2016, it was found in northern Italy in the Piedmont region and in May 2018 in the Lombardy region in the province of Pavia. Following the first detection in the EPPO region, this pest was included in the EPPO Alert List as its wide host range and ability to survive during long periods in environments with low oxygen content, represent a threat for rice production in the European Union. Considering the impact of this nematode on agriculture, a literature review focusing on M. graminicola distribution, biology, identification, and management was conducted.

Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents

Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.

An improved draft genome assembly of Meloidogyne graminicola IARI strain using long-read sequencing

The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.

A rice root-knot nematode Meloidogyne graminicola-resistant mutant rice line shows early expression of plant-defence genes

Resistance to rice root-knot nematode Meloidogyne graminicola in a mutant rice line is suggested to be conferred by higher expression of several genes putatively involved in damage-associated molecular pattern recognition, secondary metabolite biosynthesis including phytoalexins, and defence-related genes. Meloidogyne graminicola has emerged as the most destructive plant-parasitic nematode disease of rice (Oryza sativa L.). Genetic resistance to M. graminicola is one of the most effective methods for its management. A M. graminicola-resistant O. sativa ssp. indica mutant line-9 was previously identified through a forward genetic screen (Hatzade et al. Biologia 74:1197-1217, 2019). In the present study, we used RNA-Sequencing to investigate the molecular mechanisms conferring nematode resistance to the mutant line-9 compared to the susceptible parent JBT 36/14 at 24 h post-infection. A total of 674 transcripts were differentially expressed in line-9. Early regulation of genes putatively related to nematode damage-associated molecular pattern recognition (e.g., wall-associated receptor kinases), signalling [Nucleotide-binding, Leucine-Rich Repeat (NLRs)], pathogenesis-related (PR) genes (PR1, PR10a), defence-related genes (NB-ARC domain-containing genes), as well as a large number of genes involved in secondary metabolites including diterpenoid biosynthesis (CPS2, OsKSL4, OsKSL10, Oscyp71Z2, oryzalexin synthase, and momilactone A synthase) was observed in M. graminicola-resistant mutant line-9. It may be suggested that after the nematode juveniles penetrate the roots of line-9, early recognition of invading nematodes triggers plant immune responses mediated by phytoalexins, and other defence proteins such as PR proteins inhibit nematode growth and reproduction. Our study provides the first transcriptomic comparison of nematode-resistant and susceptible rice plants in the same genetic background and adds to the understanding of mechanisms underlying plant-nematode resistance in rice.

Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding

There is an urgent need to breed dry direct-seeded adapted rice varieties in order to address the emerging scenario of water-labor shortage. The aim of this study was to develop high-yielding, direct-seeded adapted varieties utilizing biparental to multiparental crosses involving as many as six different parents in conventional breeding programs and 12 parents in genomics-assisted breeding programs. The rigorous single plant selections were followed from the F₂ generation onwards utilizing phenotypic selection and quantitative trait locus (QTL)/gene-based/linked markers for tracking the presence of desirable alleles of targeted QTL/genes. In conventional breeding, multiparent lines had significantly higher yields (2,072-6,569 kg ha^-1) than the biparental lines (1,493-6,326 kg ha^-1). GAB lines derived from multiparent crosses had significantly higher (3,293-6,719 kg ha^-1) yields than the multiparent lines from conventional breeding (2,072-6,569 kg ha^-1). Eleven promising lines from genomics-assisted breeding carrying 7-11 QTL/genes and eight lines from conventional breeding with grain-yield improvement from 727 to 1,705 kg ha^-1 and 68 to 902 kg ha^-1, respectively, over the best check were selected. The developed lines may be released as varieties/parental lines to develop better rice varieties for direct-seeded situations or as novel breeding material to study genetic interactions.

More and more of less and less: Is genomics-based breeding of dry direct-seeded rice (DDSR) varieties the need of hour?

Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotype-based breeding.

A method for evaluating root-knot nematode infection in rice using a transparent paper pouch

The root-knot nematode (RKN) Meloidogyne incognita is one of the most economically damaging plant-parasitic nematodes. Molecular studies of the plant-RKN interaction have been vigorously carried out in dicotyledonous model plants, while the host range of M. incognita is wide including monocotyledonous plants. As M. incognita causes quality and yield losses in rice (Oryza sativa L.) cultivated in both upland and irrigated systems, we developed a method to examine the plant-RKN interaction in this model monocotyledonous crop plant. Here, we show that a transparent paper pouch could be used to evaluate nematode infection rates in rice with similar results to that of the traditional soil method. The system using a transparent paper pouch can be used to observe the spatial and temporal distribution of developing galls and can save the space of growth chamber.

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

Tolerance of Plants to Pathogens: A Unifying View

Increasing evidence indicates that tolerance is a host defense strategy against pathogens as widespread and successful as resistance. Since the concept of tolerance was proposed more than a century ago, it has been in continuous evolution. In parallel, our understanding of its mechanistic bases and its consequences for host and pathogen interactions, ecology, and evolution has grown. This review aims at summarizing the conceptual changes in the meaning of tolerance inside and outside the field of phytopathology, emphasizing difficulties in demonstrating and quantifying this trait. We also discuss evidence of tolerance and current knowledge on its genetic regulation, mechanisms, and role in host-pathogen coevolution, highlighting common patterns across hosts and pathogens. We hope that this comprehensive review attracts more plant pathologists to the study of this key plant defense response.

Proteome-Wide Analyses Provide New Insights into the Compatible Interaction of Rice with the Root-Knot Nematode Meloidogyne graminicola

The root-knot nematode Meloidogyne graminicola is an important pathogen in rice, causing huge yield losses annually worldwide. Details of the interaction between rice and M. graminicola and the resistance genes in rice still remain unclear. In this study, proteome-wide analyses of the compatible interaction of the japonica rice cultivar “Nipponbare” (NPB) with M. graminicola were performed. In total, 6072 proteins were identified in NPB roots with and without infection of M. graminicola by label-free quantitative mass spectrometry. Of these, 513 specifically or significantly differentially expressed proteins were identified to be uniquely caused by nematode infection. Among these unique proteins, 99 proteins were enriched on seven Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. By comparison of protein expression and gene transcription, LOC_Os01g06600 (ACX, a glutaryl-CoA dehydrogenase), LOC_Os09g23560 (CAD, a cinnamyl-alcohol dehydrogenase), LOC_Os03g39850 (GST, a glutathione S-transferase) and LOC_Os11g11960 (RPM1, a disease resistance protein) on the alpha-linolenic acid metabolism, phenylpropanoid biosynthesis, glutathione metabolism and plant–pathogen interaction pathways, respectively, were all associated with disease defense and identified to be significantly down-regulated in the compatible interaction of NPB with nematodes, while the corresponding genes were remarkably up-regulated in the roots of a resistant rice accession “Khao Pahk Maw” with infection of nematodes. These four genes likely played important roles in the compatible interaction of rice with M. graminicola. Conversely, these disease defense-related genes were hypothesized to be likely involved in the resistance of resistant rice lines to this nematode. The proteome-wide analyses provided many new insights into the interaction of rice with M. graminicola.

QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite's life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F₂ progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20 and 23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification.