Detection of Resistance, Susceptibility, Tolerance, and Virulence in Plant-Nematode Interactions: Part I-Sedentary Endoparasitic Nematodes

The use of nonhost, tolerant, or resistant plants, to manage plant parasitic nematodes (PPNs), is an appealing, economic, and environmentally friendly agronomic practice, which is effective when precise information on the identification of PPN species and their virulence to target host crops is available. This chapter describes suggested protocols to evaluate the reaction of the most important crops and fruit trees to infestation by the most damaging PPN with sedentary endoparasitic habits, with the aim of assessing resistance and tolerance traits, sources of resistance in progenies from breeding programs, the reaction to nematodes of newly released cultivars, and the virulence of the most noxious PPNs. These protocols consist of classical screening techniques not involving biochemical and molecular analyses. PPN species and genera considered in this chapter include (i) the most important species of root-knot nematodes Meloidogyne spp., including also M. chitwoodi, M. enterolobii, and M. graminicola, and (ii) the cyst-forming nematodes of the genera Globodera and Heterodera, such as the potato cyst nematodes (PCNs) Globodera rostochiensis and G. pallida, and also Heterodera avenae group, H. ciceri, H. glycines, and H. schachtii. Schemes are given to identify virulence groups for most of these nematodes.

Identification of Genetic Resistance to the Crown and Root Rot Caused by Fusarium culmorum and Cereal Cyst Nematode (Heterodera filipjevi) in the Turkish Cereal Varieties

Soilborne pathogens associated with cereals cause significant yield losses throughout the world. Among soilborne pathogens Heterodera filipjevi and Fusarium culmorum are two main destructive causal agents that attack the roots and crowns of cereals and have been reported as the most prevalent species in Türkiye. A total of 245 Turkish cereal varieties consisting of wheat, oat, triticale and rye which were registered between 1931 to 2013; were tested for their resistance to Fusarium culmorum and Heterodera filipjevi. The varieties were screened under controlled and/or field conditions for two successive growing seasons. The bread wheat ‘Murat-1’ was the most resistant variety for both pathogens. The durum wheats ‘Yelken 2000’ and ‘Yılmaz 98’ were found the most promising varieties for resistance to F. culmorum and H. filipjevi, respectively. The triticale ‘Umranhanim’ ranked moderately resistant at adult plant stage while ‘Presto’ and ‘Melez 2001’ were ranked moderately resistant at seedling stage for Fusarium culmorum. The findings of this study are important for the global wheat breeding programs as those genotypes are still being used in crosses for new genotype development.

A GWAS to identify the cereal cyst nematode (Heterodera filipjevi) resistance loci in diverse wheat prebreeding lines

Yield losses because of cereal cyst nematodes could be as high as 92%, causing a bottleneck for wheat production. An integrated approach (application of pesticides, crop rotation, and use of host resistance) is needed to manage this devastating pathogen where resistant cultivars are considered most effective. This necessitates the identification of nematode-resistant sources in the available germplasm. Here, we report on the genetic mapping of nematode resistance in 255 diverse prebreeding lines (PBLs) employing an association mapping strategy. Altogether, seven additive quantitative trait loci (QTL) were identified on chromosomes 1A, 2A, 2B, 2D, 3A, 6B, and 6D explaining a maximum of 9.42% phenotypic variation where at least five QTL (on chromosomes 2A, 2B, 2D, 6B, and 6D) are located on the same chromosomes that harbor the already known nematode resistance genes. Resistant PBLs carried Aegilops squarrosa (436) in their pedigree which could be the possible source of positive alleles. To add to it, better yield performance of the identified nematode-resistant lines under stress conditions indicates that the germplasm can provide both nematode resistance and high-yielding cultivars.

Resistance to Heterodera filipjevi and H. avenae in Winter Wheat is Conferred by Different QTL

The coexistence of cereal cyst nematode (CCN) species Heterodera avenae and H. filipjevi, often involving multiple pathotypes, is a limiting factor for wheat production in China. Some of the known genes for resistance to CCN are not effective against both nematode species, hence complicating breeding efforts to develop CCN-resistant wheat cultivars. Here, we demonstrate that the CCN resistance in wheat cultivar Madsen to both Heterodera spp. is controlled by different genetic loci, both of which originated from Aegilops ventricosa. A new quantitative trait locus (QTL), QCre-ma7D, was identified and localized in a 3.77-Mb genomic region on chromosome arm 7DL, which confers resistance to H. filipjevi. QCre-ma2A on chromosome arm 2AS corresponds to CCN resistance gene Cre5 and confers resistance to H. avenae. This QTL is a new locus on chromosome arm 7DL and is designated Cre9. Three Kompetitive allele-specific PCR markers (BS00150072, BS00021745, and BS00154302) were developed for molecular marker-assisted selection of Cre9 and locally adapted wheat lines with resistance to both nematode species were developed. QCre-ma2A on chromosome arm 2AS corresponds to CCN resistance gene Cre5 and confers resistance to H. avenae. The identification of different loci underlying resistance to H. filipjevi and H. avenae and the development of adapted resistant entries will facilitate breeding of wheat cultivars that are resistant to these devastating nematodes in China.

Genome-wide association study uncovers a novel QTL allele of AtS40-3 that affects the sex ratio of cyst nematodes in Arabidopsis

Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection. Three different susceptibility parameters were examined, with the aim of providing insights into the infection process, the number of females and males present in the infected plant, and the female-to-male sex ratio. GWAS results suggested that variation in sex ratio is associated with a novel quantitative trait locus allele on chromosome 4. Subsequent candidate genes and functional analyses revealed that a senescence-associated transcription factor, AtS40-3, and PPR may act in combination to influence nematode sex ratio. A detailed molecular characterization revealed that variation in nematode sex ratio was due to the disturbed common promoter of AtS40-3 and PPR genes. Additionally, single nucleotide polymorphisms in the coding sequence of AtS40-3 might contribute to the natural variation in nematode sex ratio.

Amino acid permease 6 modulates host response to cyst nematodes in wheat and Arabidopsis

Cyst nematodes are plant parasites that cause significant crop loss in wheat and other crops. Infective juveniles invade roots and induce syncytial feeding structures as the only source of nutrients throughout their life. A previous genome-wide association study in wheat identified amino acid permease 6 (TaAAP6) to be linked to susceptibility to the cereal cyst nematode Heterodera filipjevi. To characterise the role of AAP6 during nematode parasitism, we analysed the expression of TaAAP6 and the Arabidopsis orthologue AtAAP6. TaAAP6 was found to be highly expressed in nematode-infected roots of susceptible wheat, whereas it was not upregulated in nematode-infected roots of resistant accessions. AtAAP6 was also found to be highly upregulated in nematode-induced syncytia compared with non-infected roots. Infection assays with an AtAAP6 knock-out mutant revealed reduction in developing females, female size, and size of female-associated syncytia, thus indicating the importance of AAP6 in cyst nematode parasitism.

Morphological and molecular characterisation of Heterodera filipjevi (Madzhidov, 1981) from the Slovak Republic

Cysts, males and juveniles from a population of Heterodera filipjevi found on sports-ground turf in Trnava, Slovak Republic, in 2016 are described based on morphology and morphometrics. The identity of species of juveniles extracted from cysts was subsequently determined and confirmed by PCR-RFLP and sequencing. Morphologically, cysts, juveniles and males from the Slovak Republic are similar to paratypes from Tajikistan. The results of the phylogenetic analysis of the ITS rRNA gene sequences confirmed the species identification and phylogenetic relationship of H. filipjevi with other Heterodera species. Of interest, this analysis showed the close similarity between the Slovakian (KY349106) and Chinese (KU896216) samples, which differed by a single nucleotide and clustered together. To our knowledge, this is also the first report of H. filipjevi from the Slovak Republic, thus increasing the total number of cyst nematode species of the Heterodera genus known to occur in the country to a total of 15 species.

Genetic variation of bread wheat accessions in response to the cereal cyst nematode, Heterodera filipjevi

Bread wheat, Triticum aestivum, produces large edible grains and is consumed by 75% of the world’s populations. Cereal cyst nematodes have a global distribution and cause significant economic yield losses in many countries. Therefore, there is an urgent need to identify new resistance sources. In this study, the genetic diversity of 43 wheat accessions in response to cereal cyst nematode, Heterodera filipjevi Isfahan pathotype, was assessed using a simple sequence repeat (SSR) marker. Seven primers were used, out of which five primers showed polymorphisms. Alleles per primer varied from one to three per locus (mean 2.85). The highest and lowest polymorphic information content of 0.81 and 0.44 (mean 0.66) were related to Xgwm 3012DL and Xgwm147, respectively. Genetic similarity was 29-88% between accessions. SSR analysis divided the accessions into five main groups. Resistant cultivars ‘Bam’ and ‘Behrang’ possessed both Cre1 and Cre8 resistant genes. The Cre3 and Cat genes were partially sequenced in five cultivars of different responses to H. filipjevi. The nucleotide sequences were compared to Cre3 and Cat homologues, indicating 93-100% and 86-92% homology, respectively. The MEGA program showed highest similarity of Cre3 and Cat genes amplified with the resistance gene analogues (RGA14) in the wheat and Cat3-A1 gene in ‘Carnamah’. This research showed that SRR markers could efficiently verify genetic diversity between wheat accessions, and the known resistance genes (Cre genes) against the cereal cyst nematodes could not control the H. filipjevi Isfahan pathotype populations, except the Cre1 gene.

Phenotype and Cellular Response of Wheat Lines Carrying Cre Genes to Heterodera avenae Pathotype Ha91

The cereal cyst nematode (CCN, Heterodera avenae), a major limiting factor for wheat production worldwide, is widespread in most wheat-growing regions in China. Accordingly, screening and characterization of resistant (R) wheat sources against H. avenae are very important. In this study, we screened 51 wheat lines, collected from the International Wheat and Maize Improvement Center (CIMMYT), carrying various Cre genes (Cre1, Cre2, Cre3, Cre5, Cre7, Cre8, CreR, and Pt). From that screen, we identified one immune (M) cultivar (with no adult females produced) and five resistant cultivars (with fewer than five females) to H. avenae pathotype Ha91. The Cre3 gene conferred the most effective resistance against H. avenae pathotype Ha91 in both field and greenhouse assays. Conversely, the Cre1 and CreR genes conferred the poorest effective resistance. Using Pluronic F-127 gel and a staining assay, juvenile nematodes invading wheat roots were observed, and nematode development was analyzed. Compared with R and M roots, those of the susceptible (S) wheat cultivar Wenmai19 were more attractive to H. avenae second-stage juveniles (J2s). We observed the retardation of nematode development in R cultivars and tiny white female cysts protruding from the R cultivar VP1620. Nematodes in M roots either disintegrated or remained J2s or third-stage juveniles (J3s) and failed to complete their life cycle. Molting was also suppressed or delayed in R and M genotypes. For both S and R cultivars, syncytia were characterized by cell wall perforations and dense cytoplasm in hypertrophied syncytium component cells. Syncytial size increased gradually with nematode development in S cultivars. Moreover, an incompatibility reaction occurred in M wheat roots: the syncytium was disorganized, exhibiting disintegration and condensed nuclei. These sources of genetic resistance against CCN can potentially be planted in severely infested fields to reduce economic loss or can be used for introgression in breeding.

Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant-pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.