QTL for resistance to root lesion nematode (Pratylenchus thornei) from a synthetic hexaploid wheat source

Key message

A whole genome average interval mapping approach identified eight QTL associated with P. thornei resistance in a DH population from a cross between the synthetic-derived wheat Sokoll and cultivar Krichauff.

Abstract

Pratylenchus thornei are migratory nematodes that feed and reproduce within the wheat root cortex, causing cell death (lesions) resulting in severe yield reductions globally. Genotypic selection using molecular markers closely linked to Pratylenchus resistance genes will accelerate the development of new resistant cultivars by reducing the need for laborious and expensive resistance phenotyping. A doubled haploid wheat population (150 lines) from a cross between the synthetic-derived cultivar Sokoll (P. thornei resistant) and cultivar Krichauff (P. thornei moderately susceptible) was used to identify quantitative trait loci (QTL) associated with P. thornei resistance. The resistance identified in the glasshouse was validated in a field trial. A genetic map was constructed using Diversity Array Technology and the QTL regions identified were further targeted with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. Six significant and two suggestive P. thornei resistance QTL were detected using a whole genome average interval mapping approach. Three QTL were identified on chromosome 2B, two on chromosome 6D, and a single QTL on each of chromosomes 2A, 2D and 5D. The QTL on chromosomes 2BS and 6DS mapped to locations previously identified to be associated with Pratylenchus resistance. Together, the QTL on 2B (QRlnt.sk-2B.1–2B.3) and 6D (QRlnt.sk-6D.1 and 6D.2) explained 30 and 48 % of the genotypic variation, respectively. Flanking PCR-based markers based on SSRs and SNPs were developed for the major QTL on 2B and 6D and provide a cost-effective high-throughput tool for marker-assisted breeding of wheat with improved P. thornei resistance.     

QTL analysis of root-lesion nematode resistance in barley: 1. Pratylenchus neglectus

The root-lesion nematode Pratylenchus neglectus can cause severe losses in barley cultivation. Multiplication rates had been found to vary greatly between different barley accessions. Two winter barley cultivars, Igri and Franka, had been found to differ in their ability to resist this parasite. An existing Igri?×?Franka doubled haploid population was chosen to genetically map resistance genes after artificial inoculation with P. neglectus in the greenhouse and climate chamber. A continuous phenotypic variation was found indicating a quantitative inheritance of P. neglectus resistance. An existing map was enriched by 527 newly developed Diversity Array Technology markers (DArTs). The new genetic linkage map was comprised of 857 molecular markers that cover 1,157?cM on seven linkage groups. Using phenotypic data collected from four different experiments in 3?years, five quantitative trait loci were mapped by composite interval mapping on four (3H, 5H, 6H and 7H) linkage groups. A quantitative trait locus with a large phenotypic effect of 16% and likelihood of odds (LOD) score of 6.35 was mapped on linkage group 3H. The remaining four QTLs were classified as minor or moderate with LOD scores ranging from 2.71 to 3.55 and R ² values ranging from 8 to 10%. The DNA markers linked to the resistance QTLs should be quite useful for marker-assisted selection in barley breeding because phenotypic selection is limited due to time constraints and labor costs.     

Temperature response of root‐lesion nematode (Pratylenchus thornei) reproduction on wheat cultivars has implications for resistance screening and wheat production

The root‐lesion nematode Pratylenchus thornei is a major pathogen of wheat and other field crops, particularly in the northern grain region of sub‐tropical eastern Australia. Research was conducted into the temperature requirements of P. thornei for reproduction on wheat to increase the reliability of selection in resistance tests for wheat breeding. Final population densities (P_f) of P. thornei were determined on four wheat cultivars (Gatcher, GS50a, Potam and Suneca) at fortnightly intervals from 8 to 18 weeks at a range of six soil temperatures (15°C, 20°C, 22.5°C, 25°C, 27.5°C and 30°C) in a glasshouse experiment. Pratylenchus thornei had the highest P_f in the temperature range of 20–25°C on all wheat cultivars at all growth times after sowing, with no nematode reproduction measured at 30°C and very little at 15°C. The wheat cv. GS50a consistently produced lower P_f than cvs Gatcher, Potam and Suneca in the optimum temperature range of 20–25°C. In carrot disc cultures, P. thornei had an optimum temperature of 25°C with little reproduction at 17.5°C and none detectable at 30°C. A standard soil temperature of 23°C was chosen to maximise differences in nematode reproduction between resistant and susceptible wheat genotypes for selection in wheat breeding, and to improve reproducibility among successive experiments. The relationships derived from these experiments will be valuable for simulation of P. thornei reproduction in crop growth models. They also indicate that early sowing of wheat into cool soil (≤15°C) in farmers' fields of the northern grain region should favour wheat growth over nematode reproduction and increase grain yield.     

Management of root lesion nematode, Pratylenchus delattrei in crossandra using oil cakes

Selected oil cakes, neem, castor and mahua, were tried independently and in combination with a chemical nematicide (carbofuran 3G) for the management of Pratylenchus delattrei in crossandra under glass house conditions. The neem oil cake was effective compared to other oil cakes used and there was a synergistic effect when the neemcake was coupled with carbofuran 3G in the management of Pratylenchus delattrei. The treatment resulted in better establishment of seedlings, and with increased plant bio-mass and flower yield.     

Yield of maize as influenced by population densities of the root lesion nematode,Pratylenchus zeae

Under field conditions, population density of the root lesion nematode, Pratylenchus zeae in soil and roots of maize cv. Single Hybrid 10 fluctuated throughout its growing season and reached the peak in September, harvest stage of maize. There were negative correlations (r) between the population densities of P. zeae in maize roots and grain yield of maize according to the data collected at all growing seasons.     

Comparative QTL analysis of root lesion nematode resistance in barley

Key message

This study demonstrates for the first time that resistance to different root lesion nematodes ( P. neglectus and P. penetrans ) is controlled by a common QTL. A major resistance QTL ( Rlnnp6H ) has been mapped to chromosome 6H using two independent barley populations.

Abstract

Root lesion nematodes (Pratylenchus spp.) are important pests in cereal production worldwide. We selected two doubled haploid populations of barley (Igri × Franka and Uschi × HHOR 3073) and infected them with Pratylenchus penetrans and Pratylenchus neglectus. Nematode multiplication rates were measured 7 or 10 weeks after infection. In both populations, continuous phenotypic variations for nematode multiplication rates were detected indicating a quantitative inheritance of resistance. In the Igri × Franka population, four P. penetrans resistance QTLs were mapped with 857 molecular markers on four linkage groups (2H, 5H, 6H and 7H). In the Uschi × HHOR 3073 population, eleven resistance QTLs (P. penetrans and P. neglectus) were mapped with 646 molecular markers on linkage groups 1H, 3H, 4H, 5H, 6H and 7H. A major resistance QTL named Rlnnp6H (LOD score 6.42–11.19) with a large phenotypic effect (27.5–36.6 %) for both pests was mapped in both populations to chromosome 6H. Another resistance QTL for both pests was mapped on linkage group 5H (Igri × Franka population). These data provide first evidence for common resistance mechanisms against different root lesion nematode species. The molecular markers are a powerful tool for the selection of resistant barley lines among segregating populations because resistance tests are time consuming and laborious.     

Response of six strawberry (Fragaria x ananassa Duch.) cultivars to the root lesion nematode (Pratylenchus penetrans Filipjev and Schurmanns Stekhoven)

In the Philippines, strawberry is grown only in Benguet Province because of its unique climatic conditions. It has been a lucrative source of income for Benguet farmers and adds to the revenue of Benguet Province. The root lesion nematode, Pratylenchus penetrans is an economically important pest of strawberry in the area. It can cause substantial losses to strawberry growers, both by reducing vegetative plant growth and by reducing strawberry yields. The nematode has a very wide host range and hence, is not readily controlled by crop rotation. An alternative approach which growers may wish to consider trying is planting of strawberry varieties which are either resistant or tolerant to this nematode. The relative susceptibility/tolerance of six strawberry cultivars to the root lesion nematode, P. penetrans was evaluated under greenhouse and field conditions. Inoculation of 500 nematodes/pot did not significantly affect the fresh top weight, fresh root weight, and yield of strawberry cultivars Festival, Whitney, Winterdawn, Earlibrite, and Camarosa. The said cultivars had significantly higher number of nematodes recovered from the roots. On the other hand, the highest strawberry yield was recorded in cv Sweet Charlie, however, this was significantly reduced by nematode inoculation .Surprisingly, the number of nematodes recovered from the roots of this cultivar was significantly the lowest among the cultivars tested. Results of the field experiment showed that strawberry cv Sweet Charlie gave the highest marketable yield which was significantly different from the rest of the cultivars tested. This was followed by Festival, and Earlibrite. On the other hand, Camarosa and Whitney gave significantly lower yield than the above cultivars but significantly higher than Winterdawn. In terms of nematodes recovered from the roots, the highest was noted in Whitney, followed by Sweet Charlie and Earlibrite. The lowest was obtained from Camarosa, followed by Festival and Winterdawn. Based on the results of the greenhouse experiment, Festival, Whitney, Winterdawn, Earlibrite and Camarosa can be considered tolerant while Sweet Charlie was slightly susceptible to P. penetrans. However, based on the field trial, Sweet Charlie, Festival and Earlibrite were tolerant while Whitney, Camarosa and Winterdawn were slightly susceptible.     

A study about geographical distribution of root lesion nematode (Pratylenchus loosi, Loof 1960) in tea gardens at Guilan Province, Iran

Root lesion nematode of tea (Pratylenchus loosi) is one of the most dangerous and distractive pests in all over areas in the world where tea grows. In Iran, this species was one of the quarantine pests that for first time it were separated from the Japan imported tea slips and reported by Maafi (1993). Nowadays it has been distributed in some tea growth areas of Guilan and Mazandaran provinces (North of Iran). In this study, geographical distribution of this pest is reported on some tea growth areas of Guilan province. In order to, 147 samples from root and soil around them were investigated. These samples were gathered from various gardens of Guilan province. They were transferred to nematology lab with suitable temperature and moisture conditions and were stored at 5-10 degrees C until extraction time. Centrifugal methods for nematode extraction from soil (Jenkins, 1964) and from root (Coolen & D'Herde, 1972) were used. The nematode was identified by Handoo & Golden (1989) and Frederick & Tarjan (1989) diagnostic keys. According to this study different infested areas and geographical distribution were detected in Guilan province. Results indicated that many important tea growth areas in Guilan were infested by this nematode. In addition, it seems that it has been distributed during short time.     

High resolution RFLP map around the root knot nematode resistance gene (Mi) in tomato

Summary In the 1940's the root-knot nematode resistance gene (Mi) was introgressed into the cultivated tomato from the wild species, L. peruvianum, and today it provides the only form of genetic resistance against this pathogen. We report here the construction of a high resolution RFLP map around the Mi gene that may aid in the future cloning of this gene via chromosome walking. The map covers the most distal nine map units of chromosome 6 and contains the Mi gene, nine RFLP markers, and one isozyme marker (Aps-1). Based on the analysis of more than 1,000 F₂ plants from four crosses, we were able to pinpoint the Mi gene to the interval between two of these markers — GP79 and Aps-1. In crosses containing the Mi gene, this interval is suppressed in recombination and is estimated to be 0.4 cM in length. In contrast, for a cross not containing Mi, the estimated map distance is approximately 5 times greater (ca. 2 cM).Using RFLP markers around Mi as probes, it was possible to classify nematode resistant tomato varieties into three types based on the amount of linked peruvianum DNA still present. Two of these types (representing the majority of the varieties tested) were found to still contain more than 5 cM of peruvianum chromosome — a result that may explain some of the negative effects (e.g. fruit cracking) associated with nematode resistance. The third type (represented by a single variety) is predicted to carry a very small segment of peruvianum DNA (<2 cM) and may be useful in the identification of additional markers close to Mi and in the orientation of clones during a chromosome walk to clone the gene.     

Identification of RFLP markers linked to the cereal cyst nematode resistance gene (Cre) in wheat

The cereal cyst nematode (CCN) (Heterodera avenae Woll.) is an economically damaging pest of wheat in many of the worlds cereal growing areas. The development of CCN-resistant cultivars may be accelerated by the use of molecular markers. The Cre gene of the wheat line AUS 10894 confers resistance to CCN. Using a pair of near-isogenic lines (NILs) that should differ only in a small chromosome segment containing the Cre locus, we screened 58 group-2 probes and found two (Tag605 and CDO588) that detect polymorphism between the NILs. Nulli-tetrasomic and ditelosomic lines confirmed that the restriction fragment length polymorphism (RFLP) markers identified were derived from the long arm of wheat chromosome 2. Crosses between AUS 10894 and Spear and the NIL AP and its recurrent parent Prins were used to produce F₂ populations that gave the expected 31 segregation ratio for the resistance gene. Linkage analysis identified two RFLP markers flanking the resistance gene. Xglk605 and Xcdo588 mapped 7.3 cM (LOD=6.0) and 8.4 cM (LOD=6.7), respectively, from the Cre locus.     

Identification of common root-lesion nematode (Pratylenchus thornei Sher et Allen) loci in bread wheat.

Plant parasitic nematodes are a major biotic cause of wheat-yield loss in temperate wheat-growing regions. A major strategy to develop resistance to root-lesion nematodes (RLNs) in wheat is to assess and then exploit their natural genetic variation. This study examines RLN (Pratylenchus thornei) resistance in 1 Middle Eastern landrace (AUS4930 7.2) and 1 synthetic hexaploid wheat, CROC_1/AE.SQUARROSA (224)//OPATA (CROC), using F2 and F9 populations generated by crossing AUS4930 7.2 and CROC with the susceptible cultivar Pastor, and inoculating these crosses with P. thornei in greenhouse trials. Wheat microsatellite markers linked to previously identified quantitative trait loci (QTLs) for resistance to P. thornei and P. neglectus were used to screen both populations. In the AUS4930 7.2 x Pastor population, resistance loci on chromosomes 1B, 2B, and 6D were detected. Similarly, in the CROC x Pastor population, 2 resistance loci, located on chromosomes 1B and 3B, were identified. Interestingly, a resistance locus located on chromosome 6D was not detected. More detailed mapping is required in these 2 populations, developed using new RLN resistance sources, to determine whether the QTLs identified on these chromosomes are the same, are allelic, or are linked to different resistance loci from those previously identified, and to determine whether these 2 sources contain other novel resistance loci.     

Molecular-genetic characterisation of a new nematode resistance gene in wheat

Bread wheat lines introgressed with Aegilops ventricosa chromosomes were evaluated for their resistance to the Australian cereal cyst nematode (CCN, Heterodera avenae) pathotype Ha13. Higher levels of resistance relative to the phenotype of the Cre1 CCN resistance gene in wheat were found in the donor Ae. ventricosa parental lines and chromosome-5N^v substitution or addition lines. The newly identified resistance to pathotype Ha13 on chromosome 5N^v, designated, Cre6, was shown to be independent of the Ae. ventricosa-derived Cre2 gene, effective against several European pathotypes. Another Ae. ventricosa derived gene, Cre5, showed partial resistance to pathotype Ha13. Inhibition of Ha13 female nematode reproduction was ranked in the order Cre6 >Cre1 >CreF≥Cre5. Cre6 was inherited as a single dominant locus. Gene sequences encoding nucleotide-binding sites and leucine-rich repeats (NBS-LRR) from the Cre3 CCN-pathotype Ha13 resistance locus were used as probes to isolate related sequences from one of the donor Ae. ventricosa parents. Related sequences from Ae. ventricosa (71–73% similarity at the amino-acid level to the Cre3-derived sequences) of chromosome 5N^v origin were identified and served as diagnostic molecular markers for the presence of 5N^v. CCN-susceptible plants, found as variants in some of the purported chromosome 5N^v lines, were also found to be missing the diagnostic 5N^v RFLP markers assayed by the NBS-LRR probe. An alloplasmic chromosome-5N^v addition line with Ae. ventricosa cytoplasm in the wheat cultivar, Moisson, background was particularly variable, with 43% CCN-susceptible plants and a corresponding loss of the diagnostic chromosome-5 molecular markers. Received: 26 June 2000 / Accepted: 15 July 2000     

Tolerance of wheat cultivars to root‐lesion nematode (Pratylenchus thornei) assessed by normalised difference vegetation index is predictive of grain yield

Tolerant wheat cultivars yield well when sown in fields infested with the root‐lesion nematode Pratylenchus thornei, which is present in 67% of fields in the subtropical grain region of eastern Australia. Wheat breeding programmes require accurate phenotyping to select germplasm with superior tolerance to P. thornei. This study investigated normalised difference vegetation index (NDVI) as a phenotypic tool to predict the tolerance of wheat cultivars on low and high P. thornei population densities. Three, 2‐year field experiments used a resistant and a susceptible wheat cultivar in the first year to develop low and high P. thornei populations. In the second year, 36 wheat cultivars were sown on these plots. A NTech Greenseeker was used to determine the NDVI of each plot at regular times during the season and grain yield was measured at crop maturity. There was an inverse relationship between P. thornei population densities and the NDVI for intolerant wheat cultivars. Regression analysis showed a highly predictive response between the yield tolerance index and NDVI with R² ranging from 0.85 (n = 36) to 0.93 (n = 36) for the three experiments. The area under the disease progress curve with respect to NDVI was highly predictive of yield tolerance (R² = 0.92; n = 36) when there were high populations (9,091 P. thornei/kg), but not when populations were low (578 P. thornei/kg). Tolerant cultivars can be identified by NDVI when sown on soil containing high populations (>2,500 P. thornei/kg) by measurement at approximately 1,000 degree days after sowing. Greenseeker is a valuable tool for wheat breeders to select germplasm with tolerance of P. thornei.     

Mapping of a novel QTL for resistance to cereal cyst nematode in wheat

Cereal cyst nematode (CCN; Heterodera avenae Woll.) is a root pathogen of cereals that can cause severe yield losses in intolerant wheat cultivars. Loci for resistance to CCN, measured by a seedling bioassay, were identified by creating a genetic map based on a Trident/Molineux doubled haploid population of 182 lines. A novel locus accounting for up to 14% of the resistance to CCN was mapped to chromosome 1B of Molineux by association with microsatellite marker loci Xwmc719 and Xgwm140. This locus acts additively with the previously identified CCN resistance loci identified on chromosomes 6B (Cre8) and 2A (Cre5 on the VPM1 segment) in this population to explain 44% of the genetic variance for this major wheat pathogen.     

RFLP markers linked to the root knot nematode resistance gene Mi in tomato

Summary The Mi gene originating from the wild tomato species Lycopersicon peruvianum confers resistance to all major root knot nematodes (Meloidogyne spp.). This single dominant gene is located on chromosome 6 and is very closely linked to the acid phosphatase-1 (Aps-1) locus. Resistance to nematodes has been introgressed into various cultivars of the cultivated tomato (L. esculentum), in many cultivars along with the linked L. peruvianum Aps-1 ¹ allele. By using a pair of nearly isogenic lines differing in a small chromosomal region containing the Mi and Aps-1 loci, we have identified two RFLP markers, GP79 and H6A2c2, which are located in the introgressed L. peruvianum region. Analysis of a test panel of 51 L. esculentum genotypes of various origins indicated that GP79 is very tightly linked to the Mi gene and allows both homozygous and heterozygous nematode-resistant genotypes to be distinguished from susceptible genotypes, irrespective of their Aps-1 alleles. Marker H6A2c2 is linked to the Aps-1 locus and is capable of discriminating between the L. peruvianum Aps-1 ¹ allele and the L. esculentum Aps-1 ³ and Aps-1 ⁺ alleles. In combination, these RFLP markers may provide a powerful tool in breeding tomatoes for nematode resistance.     

Partial sequence of acid phosphatase-1(1) gene (Aps-1(1)) linked to nematode resistance gene (Mi) of tomato.

A partial amino acid sequence of acid phosphatase-1(1) (apase-1(1)), one of acid phosphatase isozymes of tomato, was identified. This information enabled us to synthesize degenerated primer pools of oligonucleotides for polymerase chain reactions (PCR) using cDNA for poly(A)+ RNA of tomato leaves as a template. As a result, a 135-bp, then a 467-bp PCR product were obtained. Nucleotide sequencing of these two PCR products gave a total of 522-bp sequence that was identified as a part of the Asp-1(1) gene judging from the amino acid sequence deduced from it. Using the 135-bp PCR product as a probe, we detected the restriction fragment length polymorphism (RFLP) in two different lines of tomato by genomic Southern blot analysis. We also did pulsed-field gel electrophoresis (PFGE) and Southern blot analysis to search for suitable fragments to clone into a YAC vector. As a result, a single band with a size that could be cloned into a YAC vector was detected when the genomic DNA was digested with some kinds of restriction enzymes.     

Mapping of the loose smut resistance gene Ut6 in wheat (Triticum aestivum L.)

Loose smut of wheat (Triticum aestivum L.) caused by Ustilago tritici (Pers.) Rostr. can cause considerable yield losses in the absence of appropriate management practices. The use of wheat varieties with loose smut resistance is an efficient and effective control technique. However, the development of commercial wheat lines with resistance to loose smut is time- and labour-consuming. DNA markers linked to loose smut resistance gene(s) would assist the development of loose smut resistant genotypes. The genetics of loose smut resistance was studied in an F5‐derived recombinant inbred line (RIL) population of 94 lines from the cross BW278/AC Foremost. The line AC Foremost is resistant and line BW278 is susceptible to U. tritici race T10. Phenotypic assessment revealed that a single gene, designated Ut6, segregated for resistance to race T10 in the RIL population. A modified bulked segregant analysis identified a microsatellite marker linked to Ut6. A linkage map was developed consisting of linked microsatellite loci and the resistance gene. The loose smut resistance gene Ut6 mapped to the long arm of chromosome 5B. Five microsatellite markers mapped within 6.7 cM of Ut6. The microsatellite markers gpw5029 and barc232 flanked Ut6 at distances of 1.3 and 2.8 cM on the distal and proximal sides, respectively. A diverse set of wheat lines was haplotyped for Ut6 using the linked microsatellite markers gpw5029 and barc232. The haplotype analysis suggested that the microsatellite markers associated with Ut6 will be useful for marker-assisted selection of loose smut resistant wheat lines.     

Comparative RFLP mapping of the chlorotoluron resistance gene (Su1) in cultivated wheat (Triticum aestivum) and wild wheat (Triticum dicoccoides)

Chlorotoluron is a selective phenylurea herbicide widely used for broad-leaved and annual grass weed control in cereals. Variation in the response to chlorotoluron (CT) was found in both hexaploid bread wheat (Triticum aestivum L.) and wild tetraploid wheat (Triticum dicoccoides KöRN.). Here, we describe the comparative mapping of the CT resistance gene (Su1) on chromosome 6B in bread and wild wheat using RFLP markers. In bread wheat, mapping was based on 58 F₄ single-seed descent (SSD) plants of the cross between a genotype sensitive to chlorotoluron, ‘Chinese Spring’ (CS), and a resistant derivative, the single chromosome substitution line, CS (‘Cappele-Desprez’ 6B) [CS (CAP6B). In T dicoccoides, mapping was based on 37 F₂ plants obtained from the cross between the CT-susceptible accession B-7 and the resistant accession B-35. Nine RFLP probes spanning the centromere were chosen for mapping. In bread wheat Su1 was found to be linked to α-Amy-1 (9.84 cM) and Xpsr371 (5.2 cM), both on the long arm of 6B, and Nor2 (2.74 cM) on the short arm. In wild wheat the most probable linkage map was Nor2-Xpsr312-Su1-Pgk2, and the genetic distances between the genes were 24.8cM, 5.3cM, and 6.8cM, respectively. These results along with other published map data indicate that the linear order of the genes is similar to that found in T. aestivum. The results of this study also show that the Su1 gene for differential response to chlorotoluron has evolved prior to the domestication of cultivated wheat and not in response to the development and use of chemicals.