Screening for quantitative resistance to the white potato cyst nematode Globodera pallida

The resistance to Globodera pallida of potatoes bred from Solanum uernei was assessed rapidly in pot tests by counting cysts on the exterior of the root ball. Assessments of resistance made in this way in three consecutive years were reproducible on a ranking basis. There was also a significant agreement in the ranked results of pot and field tests. A more accurate assessment of nematode multiplication rates in the field could be provided by laboratory tests in which temperature, moisture and initial nematode numbers were strictly controlled.     

Mapping QTLs for resistance to the cyst nematode Globodera pallida derived from the wild potato species Solanum vernei

Resistance to the potato cyst nematode (PCN) species Globodera pallida, derived from the wild diploid potato species Solanum vernei, has been investigated. This source of resistance, which is effective against all of the major pathotypes of G. pallida and Globodera rostochiensis, has been assumed to be due to several genetic factors, but it has proved difficult to deploy effectively in breeding strategies for potato cultivars. Diploid and tetraploid potato populations segregating for 'vernei' resistance were analysed. At the tetraploid level, a bulk segregant analysis (BSA) approach was employed and detected AFLP markers linked to a resistance QTL on potato linkage group V. Conventional linkage analysis of a diploid population identified QTL on linkage groups V and IX. A marker linked to a QTL on linkage group V has been converted to a single-locus PCR-based marker, which can be used to detect the presence of the QTL in diploid and tetraploid potato germplasm. Moreover, there is evidence that one of the AFLPs detected by BSA appears to be specific to an introgressed segment of DNA from S. vernei. These results are compared with those obtained from other studies on resistance to the PCN species G. pallida.     

The effect of pyramiding two potato cyst nematode resistance loci to Globodera pallida Pa2/3 in potato

Globodera pallida is a major nematode pest causing severe constraints in many potato production regions worldwide. The most prevalent G. pallida pathotypes are Pa2 and Pa3, which exist in mixed populations referred to as Pa2/3. Due to heterogeneity for avirulence genes within these nematode populations, so far, breeders have failed to identify a single resistance gene source which offers complete resistance. Currently, there are two quantitative trait loci (QTL) available, $ GpaIV_{adg}^{s} $ and Gpa5, conferring partial levels of resistance to G. pallida pathotype Pa2/3. The objective of this research was to pyramid $ GpaIV_{adg}^{s} $ and Gpa5 through marker-assisted selection to investigate whether or not pyramiding provides increased resistance to G. pallida Pa2/3. We developed a population segregating for both resistance QTLs and, using diagnostic genetic markers (Contig237 and HC), we identified groups of individuals from this population containing each individual QTL, both QTLs simultaneously, and neither QTL. These individuals were assessed for their resistance levels against G. pallida Pa2/3 population Chavornay. We demonstrated that individuals carrying both QTLs showed a significant reduction in the number of cysts formed in comparison to genotypes carrying $ GpaIV_{adg}^{s} $ or Gpa5, indicating an additive effect. Overall these results show that MAS-based pyramiding of these QTLs is an effective strategy for breeding cultivars exhibiting very high levels of resistance to G. pallida pathotype Pa2/3.     

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida

Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV_vrn, has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high‐density genome scan. We performed a whole‐genome resequencing of pools of individuals (Pool‐Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population‐specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.     

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis

The resistance gene H1 confers resistance to the potato cyst nematode Globodera rostochiensis and is located at the distal end of the long arm of chromosome V of potato. For marker enrichment of the H1 locus, a bulked segregant analysis (BSA) was carried out using 704 AFLP primer combinations. A second source of markers tightly linked to H1 is the ultra-high-density (UHD) genetic map of the potato cross SH × RH. This map has been produced with 387 AFLP primer combinations and consists of 10,365 AFLP markers in 1,118 bins (). Comparing these two methods revealed that BSA resulted in one marker/cM and the UHD map in four markers/cM in the H1 interval. Subsequently, a high-resolution genetic map of the H1 locus has been developed using a segregating F₁ SH × RH population consisting of 1,209 genotypes. Two PCR-based markers were designed at either side of the H1 gene to screen the 1,209 genotypes for recombination events. In the high-resolution genetic map, two of the four co-segregating AFLP markers could be separated from the H1 gene. Marker EM1 is located at a distance of 0.2 cM, and marker EM14 is located at a distance of 0.8 cM. The other two co-segregating markers CM1 (in coupling) and EM15 (in repulsion) could not be separated from the H1 gene.Communicated by J.G. Wenzel     

The relationship between glycoalkaloids and resistance to the white potato cyst nematode, Globodera pallida in potato clones derived from Solanum vernei

No relationship was found between the degree of resistance to Globodera pallida and total glycoalkaloid content of the roots or tubers of a number of potato clones derived from Solanum vernei × S. tuberosum. Nematode infestation of the roots did not lead to increases in the glycoalkaloid content of susceptible or resistant potatoes.     

Mode of action of fosthiazate used for the control of the potato cyst nematode Globodera pallida

Fosthiazate (Nemathorin 10G Ishihara Sangyo Kaisha Ltd, Japan) is a new nematicide approved for use on potatoes Solanum tuberosum L. in die UK for die control of die potato cyst nematodes Globodera rostochiensis (Woll). Skarbilovich and G. pallida (Stone). Fosdiiazate delayed and suppressed hatch of die potato cyst nematode Globodera pallida in bom in vitro laboratory tests and a glasshouse pot experiment. In vitro hatch was temporarily inhibited by fosdiiazate concentrations above 0.09 μg ml^-1 and increasing me fosdiiazate concentration further prolonged the duration of hatch inhibition. Analysis of fosthiazate soil concentrations, using high-pressure liquid chromatography, during me glasshouse experiment showed mat hatch was suppressed in the soil at concentrations above 0.5 mg kg^-1. Other factors such as the paralysis of hatched nematodes in the soil solution are also involved.     

A major quantitative trait locus for resistance to Potato leafroll virus is located in a resistance hotspot on potato chromosome XI and is tightly linked to N-gene-like markers.

Potato leafroll virus (PLRV) causes one of the most widespread and important virus diseases in potato. Resistance to PLRV is controlled by genetic factors that limit plant infection by viruliferous aphids or virus multiplication and accumulation. Quantitative trait locus (QTL) analysis of resistance to virus accumulation revealed one major and two minor QTL. The major QTL, PLRV.1, mapped to potato chromosome XI in a resistance hotspot containing several genes for qualitative and quantitative resistance to viruses and other potato pathogens. This QTL explained between 50 and 60% of the phenotypic variance. The two minor QTL mapped to chromosomes V and VI. Genes with sequence similarity to the tobacco N gene for resistance to Tobacco mosaic virus were tightly linked to PLRV.1. The cDNA sequence of an N-like gene was used to develop the sequence characterized amplified region (SCAR) marker N127(1164) that can assist in the selection of potatoes with resistance to PLRV.     

The response of eggs of the white potato cyst nematode Globodera pallida to diffusate from potato and mustard roots

Brief exposure of eggs of Globodera pallida to potato root diffusate not only initiated hatching but also caused the majority of unhatched juveniles to respond more rapidly to subsequent treatment with diffusate. Eggs previously exposed to diffusate had a peak hatch after 1 or 2 days compared with 4 days for untreated eggs. Mustard root diffusate prevented hatch, and further stimulation with potato root diffusate was necessary to re-initiate it. Eggs previously treated with potato root diffusate for 24 h were much more sensitive to drought than untreated eggs. These results are discussed in relation to the theory that potato root diffusate alters the permeability of the eggshell as an initial step in the hatching process.     

Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14

A maximum-likelihood QTL mapping method that simultaneously exploits linkage and linkage disequilibrium and that is applicable in outbred half-sib pedigrees is described. The method is applied to fine map a QTL with major effect on milk fat content in a 3-cM marker interval on proximal BTA14. This proximal location is confirmed by applying a haplotype-based association method referred to as recombinant ancestral haplotype analysis. The origin of the discrepancy between the QTL position derived in this work and that of a previous analysis is examined and shown to be due to the existence of distinct marker haplotypes associated with QTL alleles having large substitution effects.     

Identification of RFLP markers linked to the H1 gene conferring resistance to the potato cyst nematode Globodera rostochiensis.

The H1 gene from Solanum tuberosum ssp. andigena confers high levels of resistance to the potato cyst nematode Globodera rostochiensis and is used extensively in potato breeding. Using a dihaploid segregating population, a search was conducted for linkage between this gene and markers on the potato/tomato RFLP map. A total of 60 RFLP markers covering the entire genome were screened on bulk resistant and susceptible segregants. Linkage was indicated for eight markers on chromosome 5. Individual plant analysis placed the closest marker, CD78, at a maximum map distance of 2.7 cM from H1. A molecular marker for the H1 should be useful both as a correlative screening tool for incorporation of resistance into new cultivars and as starting point for map-based cloning of this important gene.     

Localization by restriction fragment length polymorphism mapping in potato of a major dominant gene conferring resistance to the potato cyst nematode Globodera rostochiensis

Summary A major dominant locus conferring resistance against several pathotypes of the root cyst nematode Globodera rostochiensis was mapped on the linkage map of potato using restriction fragment length polymorphism (RFLP) markers. The assessment of resistance versus susceptibility of the plants in the experimental population considered was based on an in vivo (pot) and an in vitro (petri dish) test. By linkage to nine RFLP markers the resistance locus Gro1 was assigned to the potato linkage group IX which is homologous to the tomato linkage group 7. Deviations from the additivity of recombination frequencies between Gro1 and its neighbouring markers in the pot test led to the detection of a few phenotypic misclassifications of small plants with poor root systems that limited the observation of cysts on susceptible roots. Pooled data from both tests provided better estimates of recombination frequencies in the linkage interval defined by the markers flanking the resistance locus.     

Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei

A population of diploid potato (Solanum tuberosum) was used for the genetic analysis and mapping of a locus for resistance to the potato cyst nematode Globodera rostochiensis, introgressed from the wild potato species Solanum vernei. Resistance tests of 108 genotypes of a F₁ population revealed the presence of a single locus with a dominant allele for resistance to G. rostochiensis pathotype Ro1. This locus, designated GroV1, was located on chromosome 5 with RFLP markers. Fine-mapping was performed with RAPD and SCAR markers. The GroV1 locus was found in the same region of the potato genome as the S. tuberosum ssp. andigena H1 nematode resistance locus. Both resistance loci could not excluded to be allelic. The identification of markers flanking the GroV1 locus offers a valuable strategy for marker-assisted selection for introgression of this nematode resistance.Abbreviations BSA bulked segregant analysis - RAPD random-amplified polymorphic DNA - RFLP restriction fragment length polymorphism - SCAR sequence-characterized amplified region     

Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping

A novel and robust method for the fine-scale mapping of genes affecting complex traits, which combines linkage and linkage-disequilibrium information, is proposed. Linkage information refers to recombinations within the marker-genotyped generations and linkage disequilibrium to historical recombinations before genotyping started. The identity-by-descent (IBD) probabilities at the quantitative trait locus (QTL) between first generation haplotypes were obtained from the similarity of the marker alleles surrounding the QTL, whereas IBD probabilities at the QTL between later generation haplotypes were obtained by using the markers to trace the inheritance of the QTL. The variance explained by the QTL is estimated by residual maximum likelihood using the correlation structure defined by the IBD probabilities. Unlinked background genes were accounted for by fitting a polygenic variance component. The method was used to fine map a QTL for twinning rate in cattle, previously mapped on chromosome 5 by linkage analysis. The data consisted of large half-sib families, but the method could also handle more complex pedigrees. The likelihood of the putative QTL was very small along most of the chromosome, except for a sharp likelihood peak in the ninth marker bracket, which positioned the QTL within a region <1 cM in the middle part of bovine chromosome 5. The method was expected to be robust against multiple genes affecting the trait, multiple mutations at the QTL, and relatively low marker density.     

The white potato cyst nematode (Globodera pallida) – a critical analysis of the threat in Britain

Over the last 30 years, there has been an epidemic of the white potato cyst nematode (wPCN, Globodera pallida). It has progressively replaced the yellow species (yPCN, G. rostochiensis) throughout most of England and Wales and is now a widespread problem. As damaging populations of wPCN are enormous (>10⁹ eggs ha^?1), several crops of potato cultivars resistant only to yPCN were required to produce this change. The threat it poses is reflected in an increase in the numbers of soil samples being tested and in nematicide use, which has increased to > 25 000 ha of potatoes being treated annually. Computer modelling shows that current management of wPCN is mostly ineffective and populations will continue to increase. The multiplication rate of wPCN is inversely related to its population density at planting and, because of this, modelling shows that sufficient eggs are likely to survive to enable large populations of wPCN to “rebound” following nematicide treatment. This is supported by recent trial results showing that wPCN population increase was almost as great in nematicides‐treated plots as in the untreated. Modelling also showed that current rotations (typically potatoes once every 5 or 6 years) are too short to prevent wPCN populations from progressively increasing, even when used in conjunction with a nematicide. Similarly, except with avirulent populations, the partially resistant cultivars currently available will not prevent wPCN from increasing. However, as the effectiveness of partially resistant cultivars is independent of population density, they can be very effective when integrated with a nematicide. Unfortunately, only c. 8% of the potato area is planted with partially resistant cultivars, and much of that is in land not known to be infested with wPCN. Consequently, the current epidemic of wPCN is likely to become progressively more serious. However, many farmers are failing to recognise and respond to this threat until it is too late because of the slow rate of increase of wPCN, the difficulties of detecting small populations and the costs of nematicides. To respond to the current epidemic of wPCN, the greatest priority is to have available an increased number of commercially‐attractive partially resistant cultivars.     

The effect of the potato cyst nematode Globodera pallida on in vitro root growth of potato genotypes, differing in tolerance

Roots of eighteen potato genotypes, differing in tolerance of G. pallida, were grown from tuberpieces on agar in Petri dishes. Juveniles of G. pallida were inoculated directly onto root tips. Root length was measured at various times after inoculation. Inoculation reduced root growth within one day. At later stages, genotypes differed strongly in growth of inoculated roots. Between four and seven days after inoculation, growth of inoculated roots was not significantly correlated with growth of untreated roots, and was only poorly correlated with tolerance assessed in the greenhouse or in the field. However, multiple regression analysis revealed that the tolerance of the tested genotypes was associated with both the rate at which they induced hatching and the growth of roots after inoculation. The combination of these two variables accounted for high percentages explained variance.     

The effects of desiccation and root diffusates from potato and mustard on eggs of the white potato cyst nematode Globodera pallida

Following exposures to potato root diftusate of between 6 and 12 h, desiccation killed a proportion of juveniles in eggs of G. pallida and affected the hatching behaviour of survivors. In hatching tests of 9 wk duration, more juveniles hatched in the final wk from cysts, which were soahed and dried alternately for 9 wk than from cysts soaked in tap water for the final 2 wk only. Mustard root diffusate prevented eggs previously stimulated by potato root diffusate from hatching, but it did not alleviate the effects of desiccation.