Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea (Pisum sativum)

Aphanomyces euteiches is the most damaging soilborne pea pathogen in France. Breeding of pea resistant varieties combining a diversity of quantitative trait loci (QTL) is a promising strategy considering previous research achievements in dissecting polygenic resistance to A. euteiches. The objective of this study was to provide an overview of the diversity of QTL and marker haplotypes for resistance to A. euteiches, by integrating a novel QTL mapping study in advanced backcross (AB) populations with previous QTL analyses and genome-wide association study (GWAS) using common markers. QTL analysis was performed in two AB populations derived from the cross between the susceptible spring pea variety “Eden” and the two new sources of partial resistance “E11” and “LISA”. The two AB populations were genotyped using 993 and 478 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for resistance to A. euteiches in controlled conditions and in infested fields at two locations. GWAS and QTL mapping previously reported in the pea-Aphanomyces collection and from four recombinant inbred line (RIL) populations, respectively, were updated using a total of 1,850 additional markers, including the markers used in the Eden x E11 and Eden x LISA populations analysis. A total of 29 resistance-associated SNPs and 171 resistance QTL were identified by GWAS and RIL or AB QTL analyses, respectively, which highlighted 10 consistent genetic regions confirming the previously reported QTL. No new consistent resistance QTL was detected from both Eden x E11 and Eden x LISA AB populations. However, a high diversity of resistance haplotypes was identified at 11 linkage disequilibrium (LD) blocks underlying consistent genetic regions, especially in 14 new sources of resistance from the pea-Aphanomyces collection. An accumulation of favorable haplotypes at these 11 blocks was confirmed in the most resistant pea lines of the collection. This study provides new SNP markers and rare haplotypes associated with the diversity of Aphanomyces root rot resistance QTL investigated, which will be useful for QTL pyramiding strategies to increase resistance levels in future pea varieties

Semi-automated genomic DNA extraction from Plant with CyBi®-SELMA 96/1000 μl using NucleoSpin® 96 Plant II Kit

INRA - CyBio Application Noteil s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : REPORTThe CyBi® SELMA 96/1000 μl was used to automate MACHEREY-NAGEL NucleoSpin 96 Plant II technology for plant genomic DNA extraction. The use of a 96-well pipetting head enables a rapid automated procedure while maintaining the purification technology’s highly reliable performance. The result is good yields (1-8 μg species function) of highly purified DNA (A260/280 > 1.8)

Exemple d'extraction semi-automatique d'ADN de végétaux à l'aide du pipeteur CyBi®-Selma 96/1000μL et du kit Nucleospin® 96 Plant II

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Successive legumes tested in a greenhouse crop rotation experiment modify the inoculum potential of soils naturally infested by Aphanomyces euteiches

International audienceThe consequence of 10 successive monocultural cycles involving different legume species/cultivars on the inoculum potential (IP) of soils naturally infested by Aphanomyces euteiches was investigated under greenhouse conditions. The results showed that the IP of a soil naturally infested by A.euteiches can be significantly modified not only by the non-host or host status of crop species but also by the level of resistance of the cultivar. Susceptible species/cultivars (pea, lentil and susceptible cultivars of vetch and faba bean) are very favourable to pathogen multiplication, and continuous cultivation of each of these increased the IP values of a soil with a moderate initial IP (from 1 center dot 9 to 3 center dot 5 after 10 cycles). Conversely, non-host species and resistant cultivars of vetch or faba bean contributed to reducing the IP values of soils irrespective of the initial IP (from 1 center dot 9 to 0 center dot 5 and from 4 to 2, respectively, after 10 cycles). Aphanomyces root rot severity values on the resistant legume species/cultivars were not affected by the successive cultural cycles. This study, which showed that the IP of A.euteiches in soil can be reduced by planting appropriate legume species and cultivars in greenhouse conditions, will be useful for defining better crop successions for legumes

Fine mapping of Ae-Ps4.5, a major locus for resistance to pathotype III of Aphanomyces euteiches in pea

International audienceAphanomyces root rot, caused by Aphanomyces euteiches, is the most important disease of pea (Pisum sativum L.) worldwide. The development of pea-resistant varieties is a major challenge to control the disease. Previous linkage studies identified seven main resistance quantitative trait loci (QTL), including the QTL Ae-Ps4.5 associated with partial resistance in US nurseries infested by the pea pathotype III of A. euteiches. This study aimed to confirm the major effect of Ae-Ps4.5 on A. euteiches pathotype III, refine its interval, and identify candidate genes underlying the QTL. QTL mapping on an updated genetic map from the Puget x 90-2079 pea recombinant inbred line population identified Ae-Ps4.5 in a 0.8-cM confidence interval with a high effect (R-2 = 89%) for resistance to the Ae109 reference strain of A. euteiches (pathotype III) under controlled conditions. However, the QTL mapping did not detect Ae-Ps4.5 for resistance to the RB84 reference strain of A. euteiches (pathotype I). Screening 224-pea BC5F2 plant progeny derived from three near-isogenic lines (NILs) carrying the 90-2079 allele at Ae-Ps4.5 in the Puget genetic background with 26 SNP markers identified 15 NILs showing recombination in the QTL interval. Phenotyping of the recombinant lines for resistance to the Ae109 strain of A. euteiches reduced the QTL to a physical interval of 3.06 Mb, containing 50 putative annotated genes on the Cameor pea genome V1a among which three candidate genes highlighted. This study provides closely linked SNP markers and putative candidate genes to accelerate pea breeding for resistant varieties to Aphanomyces root rot

Host status and reaction of Medicago truncatula accessions to infection by three major pathogens of pea (Pisum sativum) and alfalfa (Medicago sativa)

International audienceDitylenchus dipsaci, the stem nematode of alfalfa (Medicago sativa), Mycosphaerella pinodes, cause of Ascochyta blight in pea (Pisum sativum) and Aphanomyces euteiches, cause of pea root rot, result in major yield losses in French alfalfa and pea crops. These diseases are difficult to control and the partial resistances currently available are not effective enough. Medicago truncatula, the barrel medic, is the legume model for genetic studies, which should lead to the identification and characterization of new resistance genes for pathogens. We evaluated a collection of 34 accessions of M. truncatula and nine accessions from three other species (two from M. italica, six from M. littoralis and one from M. polymorpha) for resistance to these three major diseases. We developed screening tests, including standard host references, for each pathogen. Most of the accessions tested were resistant to D. dipsaci, with only three accessions classified as susceptible. A very high level of resistance to M. pinodes was observed among the accessions, none of which was susceptible to this pathogen. Conversely, a high level of variation, from resistant to susceptible accessions, was identified in response to infection by A. euteiche

Aggressiveness of Diverse French Aphanomyces euteiches Isolates on Pea Near Isogenic Lines Differing in Resistance Quantitative Trait Loci

International audienceAphanomyces root rot is a major disease in many pea growing regions worldwide. Development of resistant varieties is necessary to manage the disease. Near isogenic lines (NILs) carrying resistance alleles at main quantitative trait loci (QTLs) were developed by marker-assisted backcrossing. This study aimed to evaluate the aggressiveness of diverse French isolates of Aphanomyces euteiches on NILs carrying different resistance QTLs. Forty-three A. euteiches isolates from different French pea growing regions were tested for aggressiveness on eight NILs carrying single or combinations of resistance QTLs and two susceptible or resistant control lines, in controlled conditions. Three clusters of isolates, unrelated to geographical origin, were identified, including 37, 56, and 7% of isolates with high, moderate, and low average levels of aggressiveness, respectively. Three groups of pea lines were also identified. The first group consisted of a pea resistant control line, moderately to highly resistant to all of the isolates. The second group included five NILs carrying a major-effect resistance allele at QTL Ae-Ps7.6, with a medium to broad range of effects on the isolates. The third group consisted of three NILs carrying minor-effect resistance alleles, with a narrow range of effects on the isolates. The results suggest that highly aggressive isolates occur naturally, which may be selected by future partially resistant pea varieties carrying QTLs and increase the risk of erosion of QTL effect. QTL pyramiding strategies for a higher level and a broader range of effect of quantitative resistance on A. euteiches populations will be required for breeding for durable pea resistant varieties

Combining polygenic resistance with prophylactic and cultural methods for sustainable management of Aphanomyces root in pea

Combining polygenic resistance with prophylactic and cultural methods for sustainable management of Aphanomyces root in pe

Five Regions of the Pea Genome Co-Control Partial Resistance to D. pinodes, Tolerance to Frost, and Some Architectural or Phenological Traits

International audienceEvidence for reciprocal links between plant responses to biotic or abiotic stresses and architectural and developmental traits has been raised using approaches based on epidemiology, physiology, or genetics. Winter pea has been selected for years for many agronomic traits contributing to yield, taking into account architectural or phenological traits such as height or flowering date. It remains nevertheless particularly susceptible to biotic and abiotic stresses, among which Didymella pinodes and frost are leading examples. The purpose of this study was to identify and resize QTL localizations that control partial resistance to D. pinodes, tolerance to frost, and architectural or phenological traits on pea dense genetic maps, considering how QTL colocalizations may impact future winter pea breeding. QTL analysis revealed five metaQTLs distributed over three linkage groups contributing to both D. pinodes disease severity and frost tolerance. At these loci, the haplotypes of alleles increasing both partial resistance to D. pinodes and frost tolerance also delayed the flowering date, increased the number of branches, and/or decreased the stipule length. These results question both the underlying mechanisms of the joint control of biotic stress resistance, abiotic stress tolerance, and plant architecture and phenology and the methods of marker-assisted selection optimizing stress control and productivity in winter pea breeding

Identification of regions in the pea genome controlling both stress resistance and developmental traits

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