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.     

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.     

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.     

Studies on Anhydrobiosis of Pratylenchus thornei

Large populations of Pratylenchus thornei, a winter pest of cereals, legumes, and potatoes in the northern Negev region of Israel, survive 7-8 months of summer drought and return to full activity at the beginning of the rainy season. To demonstrate that it survives the summer in an anhydrobiotic state, all developmental stages of P. thornei were exposed to gradually reduced relative humidity (RH) using glycerin water solutions. At 97.7% RH the nematodes were coiled and able to survive exposure to 0% RH. About 40% of artificially desiccated nematodes could be reactivated by gradually increasing the humidity to the final water environment. Desiccated nematodes could withstand temperatures up to 40 C. Reactivated individuals showed intestines apparently devoid of reserve materials. Only 3% survived three cycles of desiccation and reactivation. P. thornei reactivated after anhydrobiosis multiplied twice as much within Vicia sativa roots as did fresh nematodes.     

Increased tolerance to the root-lesion nematode Pratylenchus vulnus in mycorrhizal micropropagated BA-29 quince rootstock

The interaction between Glomus intraradices and the root-lesion nematode Pratylenchus vulnus was studied on micropropagated BA-29 quince rootstock during one growing season. Inoculation with G. intraradices significantly increased growth of plants in low P soil and was more effective than P fertilization at increasing top-plant development. In the presence of the nematode, mycorrhizal plants achieved higher values in all growth parameters measured. P. vulnus caused a significant decrease in the percentage of root length colonized by G. intraradices and fewer internal vesicles were formed within the host roots. Enhanced root mass production accounted for the twofold increase in final nematode population recovered from plants with combined inoculations of pathogen and symbiont. Low levels were found of Al, Fe, Mn and Zn in nonmycorrhizal nematode-infected plants in low P soil. G. intraradices-inoculated plants reached the highest foliar levels of N, Ca, Mg, Mn, Cu and Zn. Mycorrhizal plants infected with P. vulnus maintained normal to high levels of Mn, Cu, and Zn. Inoculation with G. intraradices favours quince growth and confers protection against P. vulnus by improving plant nutrition.     

QTL mapping of multiple foliar disease and root-lesion nematode resistances in wheat

A genetic linkage map, based on a cross between the synthetic hexaploid CPI133872 and the bread wheat cultivar Janz, was established using 111 F₁-derived doubled haploid lines. The population was phenotyped in multiple years and/or locations for seven disease resistance traits, namely, Septoria tritici blotch (Mycosphaeralla graminicola), yellow leaf spot also known as tan spot (Pyrenophora tritici-repentis), stripe rust (Puccinia striiformis f. sp. tritici), leaf rust (Puccinia triticina), stem rust (Puccinia graminis f. sp. tritici) and two species of root-lesion nematode (Pratylenchyus thornei and P. neglectus). The DH population was also scored for coleoptile colour and the presence of the seedling leaf rust resistance gene Lr24. Implementation of a multiple-QTL model identified a tightly linked cluster of foliar disease resistance QTL in chromosome 3DL. Major QTL each for resistance to Septoria tritici blotch and yellow leaf spot were contributed by the synthetic hexaploid parent CPI133872 and linked in repulsion with the coincident Lr24/Sr24 locus carried by parent Janz. This is the first report of linked QTL for Septoria tritici blotch and yellow leaf spot contributed by the same parent. Additional QTL for yellow leaf spot were detected in 5AS and 5BL. Consistent QTL for stripe rust resistance were identified in chromosomes 1BL, 4BL and 7DS, with the QTL in 7DS corresponding to the Yr18/Lr34 region. Three major QTL for P. thornei resistance (2BS, 6DS, 6DL) and two for P. neglectus resistance (2BS, 6DS) were detected. The recombinants combining resistance to Septoria tritici blotch, yellow leaf spot, rust diseases and root-lesion nematodes from parents CPI133872 and Janz constitute valuable germplasm for the transfer of multiple disease resistance into new wheat cultivars.     

A Cmv2 QTL on chromosome X affects MCMV resistance in New Zealand male mice

NK cell-mediated resistance to viruses is subject to genetic control in humans and mice. Here we used classical and quantitative genetic strategies to examine NK-mediated murine cytomegalovirus (MCMV) control in genealogically related New Zealand white (NZW) and black (NZB) mice. NZW mice display NK cell-dependent MCMV resistance while NZB NK cells fail to limit viral replication after infection. Unlike Ly49H⁺ NK resistance in C57BL/6 mice, NZW NK-mediated MCMV control was Ly49H-independent. Instead, MCMV resistance in NZW (Cmv2) involves multiple genetic factors. To establish the genetic basis of Cmv2 resistance, we further characterized a major chromosome X-linked resistance locus (DXMit216) responsible for innate MCMV control in NZW × NZB crosses. We found that the DXMit216 locus affects early MCMV control in New Zealand F₂ crosses and demonstrate that the NZB-derived DXMit216 allele enhances viral resistance in F₂ males. The evolutionary conservation of the DXMit216 region in mice and humans suggests that a Cmv2-related mechanism may affect human antiviral responses. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Pest Management Approach to the Control of Pratylenchus thornei on Wheat in Mexico

The lesion nematode, Pratylenchus thornei, was clearly demonstrated as a parasite of wheat. It reduced plant stands and stunted plants in the field under the environmental conditions found in Sonora, Mexico. Other soil organisms also may have contributed to the problem. The nematode is widely distributed throughout the wheat-growing region, and may be a problem each growing season. Nematicides controlled the nematode and increased yields, but they were not economical. No resistance was found in existing commercial wheat cultivars. A pest management approach using variety selection, nitrogen fertilizer, planting in cool soil (15 C) and a crop rotation avoiding wheat after wheat was the most practical solution to this problem on a commercial scale.     

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.     

Effects of the root-lesion nematode Pratylenchus vulnus and the mycorrhizal fungus Glomus mosseae on the growth of EMLA-26 apple rootstock

The interaction between Pratylenchus vulnus and the endomycorrhizal fungus Glomus mosseae on the growth of EMLA 26 apple rootstock was studied under shadehouse conditions in the field during the first 6 months of growth. Fresh top weights, fresh root weights, and shoot lengths of mycorrhizal plants with and without P. vulnus were significantly higher than those of nonmycorrhizal plants. Addition of P to non-mycorrhizal controls had little overall effect. Mycorrhizal treatments with the nematode showed a significantly lower amount of nematodes per gram of root than nonmycorrhizal treatments with P. vulnus. Root colonization by G. mosseae was not affected by the presence of the nematode. No nutrient deficiencies were detected in foliar analyses, although low levels of K, A1, and Fe were detected in nematode treatments. The highest levels of S, Mg, Mn and Zn were detected in P. vulnus inoculated plants. Mycorrhizal plants had the highest levels of N, Na, P, K, and Fe. The importance of early mycorrhizal infection of EMLA 26 apple root-stock in the presence of the nematode is discussed.     

Effects of the root-lesion nematode Pratylenchus vulnus and the vesicular-arbuscular mycorrhizal fungus Glomus mosseae on the growth of three plum rootstocks

The effects of Pratylenchus vulnus and the endomycorrhizal fungus Glomus mosseae on growth of Myrobalan 605, Marianna 2624 and San Julian 655-2 plum rootstocks were measured under shadehouse conditions in the field for two growing seasons (1990–91). Shoot dry weights were higher in the majority of the vesicular-arbuscular mycorrhizal (VAM) alone inoculated plants after both growing seasons. Root weights of mycorrhizal Myrobalan and Marianna were higher than root weights of the same rootstocks lacking mycorrhizae, inoculated with P. vulnus, and VAM in combination with the nematode. Mycorrhizal Marianna inoculated with the nematode showed a considerably higher final nematode population in relation to non-inoculated VAM treatments. No correlation was found in the number of nematodes per gram of root between mycorrhizal and non-mycorrhizal treatments. P. vulnus adversely affected the mycorrhizal colonization in Marianna, but not in Myrobalan and San Julian. Marianna appears to be more mycorrhizal dependent than the two other rootstocks.     

Suppression of the root-lesion nematode (Pratylenchus penetrans) in alfalfa (Medicago sativa) by Streptomyces spp.

Strains of Streptomyces were tested for their ability to reduce population densities of the root-lesion nematode (RLN), Pratylenchus penetrans, in roots of alfalfa (Medicago sativa) in growth chamber assays. Previously, these strains were shown to suppress potato scab disease, caused by Streptomyces scabies, in field experiments and to inhibit in vitrogrowth of a wide range of plant-pathogenic fungi and bacteria. Inoculation with Streptomyces at planting significantly reduced RLN population densities in roots of both susceptible and resistant alfalfa varieties grown in either heat-treated or untreated soil. Reductions in RLN population densities were observed 6 weeks after nematode inoculation. Shoot dry matter was not affected by any treatment; root dry weight was reduced in Streptomycesplus nematode treatments compared to the nematode inoculation alone in some experiments but was not affected by Streptomyces when RLN was absent. Mutant strains not producing antibiotics in vitro also reduced RLN population densities in alfalfa roots and all strains maintained high population densities after inoculation into heat-treated soil and on alfalfa roots. These strains may be useful in multi-crop, multi-pathogen management programs to augment genetic resistance to plant diseases.     

Interaction between the root-lesion nematode Pratylenchus vulnus and the mycorrhizal association of Glomus intraradices and Santa Lucia 64 cherry rootstock

The effects of the interaction between Pratylenchus vulnus and the endomycorrhizal fungus Glomus intraradices on growth and nutrition of Santa Lucia 64 cherry rootstock was studied under microplot conditions during one growing season. Fresh top weight, and stem diameter of mycorrhizal plants and high P treatments with and without P. vulnus were significantly higher than those of non-mycorrhizal plants. The lowest shoot length and fresh root weights were recorded in nematode inoculated plants in low P soil. Mycorrhizal infection did not affect the number of nematodes per gram of root in plants infected with P. vulnus. In the presence of the nematode, internal spore production by G. intraradices was significantly reduced. No nutrient deficiencies were detected through foliar analysis, although low levels of Ca, Mn and Fe were detected in nematode treatments. Mycorrhizal plants achieved the highest values for N, P, S, Fe, and Zn, whereas high P treatments increased absorption of Ca and Mn. Early mycorrhizal infection of Santa Lucia 64 cherry rootstock by G. intraradices confers increased growth capacity in the presence of P. vulnus.     

Effects of preplant inoculation of apple (Malus domestica Borkh.) with arbuscular mycorrhizal fungi on population growth of the root-lesion nematode,Pratylenchus penetrans

Six species of arbuscular mycorrhizal (AM) fungi (Glomus aggregatum, G. clarum, G. etunicatum, G. intraradices, G. mosseae and G. versiforme) were evaluated, in three greenhouse experiments, for their effects on reproduction of the root-lesion nematode, Pratylenchus penetrans, and growth of Ottawa 3 apple rootstock. Glomus mosseae increased total dry weights of nematode-inoculated and non-inoculated rootstock in all three greenhouse experiments, and G. intraradices increased dry weights in two of three greenhouse experiments. Plants inoculated with G. mosseae generally supported fewer P. penetrans per gram of root than plants inoculated with other AM fungi, but did not differ significantly from the controls in any greenhouse experiment. Colonization of roots by AM fungi was reduced by P. penetrans at initial inoculum densities greater than 250 nematodes/L soil. In field trials, preplant inoculation with either G. intraradices or G. mosseae increased rootstock growth and leaf concentrations of P, Mg, Zn and Cu in fumigated plots but not in non-fumigated plots, indicating that colonization by native AM fungi in non-fumigated plots may have been sufficient for adequate nutrient acquisition. The abundance of vesicles and arbuscules was greater in roots of plants inoculated with AM fungi before planting than in roots of non-inoculated plants, in both fumigated and non-fumigated plots. P. penetrans per gram of root and per 50 ml soil were significantly lower for G. mosseae- inoculated plants than for non-inoculated plants in fumigated soil but not in non-fumigated soil.     

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Whole‐genome sequencing‐based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next‐generation sequencing (NGS)‐based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR‐01 and CPR‐02. Eleven QTLs in CPR‐01 and six QTLs in CPR‐02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR‐01 using conventional biparental mapping approach were used to compare the efficiency of NGS‐based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR‐01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS‐based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR‐02 population. This study demonstrated the efficiency of NGS‐based BSA as a rapid and cost‐effective method to identify QTLs associated with ascochyta blight in chickpea.     

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.     

A locus on barley chromosome 5H affects adult plant resistance to powdery mildew

Adult plant resistance against plant pathogens is of interest as a means to achieve durable resistance. Prior to this research, the barley lines CLE210 (from Uruguay) and Denar (from the Czech Republic) had been reported to exhibit adult-plant resistance against powdery mildew. Here, populations of doubled haploid lines from crosses of these lines with the susceptible cultivar Baudin were evaluated for powdery mildew resistance in field experiments. Using linkage maps constructed from genotyping-by-sequencing (GBS) data, it was determined that differences in resistance were largely attributable to a region on the long arm of chromosome 5H (5HL). Therefore, KASP^? assays were developed based on GBS tag sequences mapped on that chromosome, providing more reliable genetic maps. In each population, a large-effect QTL was mapped on 5HL. As no sequence variation was detected between CLE210 and Denar in this region of 5HL, the two sources of resistance may be identical by descent in the QTL region and carry the same resistance gene. Marker assays from the QTL region were evaluated on a panel of barley lines, providing information that breeders could use to select assays for use in marker-assisted selection.     

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.