Publications by authors named "Lyndon D Porter"

14 Publications

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KASP markers reveal established and novel sources of resistance to Pea seed-borne mosaic virus in pea genetic resources.

Plant Dis 2021 Jan 24. Epub 2021 Jan 24.

Vegetable and Forage Crops Research Unit, 24106 N. Bunn Road, Prosser, Washington, United States, 99350;

Pea seed-borne mosaic virus (PSbMV) is both seed-borne and aphid transmitted and can cause economic losses in pea ( L.) production by reducing yield through decreased seed weight and number. The P1 pathotype is especially virulent, affecting this important vegetable crop across the United States and internationally in regions of West Asia, North Africa, Europe, and Australia. Previously, two Kompetitive Allele-Specific PCR (KASP) genotyping markers ( and ) were developed and validated on accessions identifying two PSbMV pathotype P1 resistance alleles in the eukaryotic translation initiation factor gene, . The current study utilized these novel markers to rapidly evaluate 318 genetic resource accessions maintained as part of the USDA National Plant Germplasm System's Pea Single Plant Collection (PSPC). The evaluations also included 58 commercial and other plant introduction (PI) lines that were assessed for the two resistance alleles. All genotyping results were validated in greenhouse assays by confirmation of observable disease symptoms following inoculations and by ELISA. The and alleles were found in 18 accessions from the PSPC, 5 commercial lines, and 14 other PI accessions. A single PSPC accession showed resistance to PSbMV pathotype P1 that is believed to be a novel source of resistance based on sequencing analysis of . Sources of resistance were identified in the PSPC and in commercial cultivars that can be introgressed into breeding lines using traditional techniques to reduce time and cost required to generate germplasm with superior disease-resistant traits.
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http://dx.doi.org/10.1094/PDIS-09-20-1917-REDOI Listing
January 2021

Analysis and Identification of QTL for Resistance to in Pea ( L.).

Front Genet 2020 19;11:587968. Epub 2020 Nov 19.

Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, MT, United States.

White mold caused by is an important constraint to field pea ( L.) production worldwide. To transfer white mold resistance into an adapted background, and study the genetics of the disease, two recombinant inbred line (RIL) populations (PRIL17 and PRIL19) were developed by crossing two partially resistant plant introductions with two susceptible pea cultivars. PRIL17 (Lifter × PI240515), and PRIL19 (PI169603 × Medora) were evaluated for resistance to white mold by measuring lesion expansion inhibition (LEI) and nodal transmission inhibition (NTI) at 3, 7, and 14 days post inoculation (dpi) under controlled environmental conditions. Lesion expansion inhibition percentage (LEIP), survival rate (SR), and area under disease progress curves (AUDPC) were also calculated accordingly. Because of a positive correlation between LEI and NTI with height, short and long internode individuals of each population were analyzed separately to avoid any confounding effect of height to pathogen response. A total of 22 short genotypes demonstrated partial resistance based on at least two Porter's resistance criteria. Only two pea genotypes with partial resistance to white mold (PRIL19-18 and PRIL19-124) had both semi-leafless (afila) and short internode traits. Both the RIL populations were genotyped using genotyping by sequencing (GBS). For PRIL17 and PRIL19, genetic maps were constructed from a total of 1,967 and 1,196 single nucleotide polymorphism (SNP) and spanned over 1,494 cM and 1,415 cM representing seven and nine linkage groups, respectively. A consensus map constructed using data from both populations, had 1,486 unique SNPs over 2,461 cM belonging to seven linkage groups. Inclusive composite interval mapping (ICIM) identified thirteen quantitative trait loci (QTL) associated with white mold resistance traits in both populations. Three of them were co-located with height genes (a morphological trait that reduces infection risk and acts as disease avoidance) and the other ten QTL were associated with two forms of physiological resistance (seven for LEI and three for NTI) with LOD and r ranging from 3.0 to 28.5 and 5.1 to 64.3, respectively. The development of resistance lines, genetic dissection and identification of markers associated will help accelerate breeding efforts for white mold resistance using molecular breeding approaches.
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http://dx.doi.org/10.3389/fgene.2020.587968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710873PMC
November 2020

Chickpea seed rot and damping-off caused by metalaxyl-resistant Pythium ultimum and its management with ethaboxam.

Plant Dis 2020 Oct 29. Epub 2020 Oct 29.

USDA-ARS, Grain Legume genetics and Physiology, Pullman, Washington, United States.

Metalaxyl and its isomer mefenoxam have been the primary fungicides used as seed treatments in managing Pythium seed rot and damping-off of chickpea. However, recent outbreaks of seed rot and damping-off of metalaxyl-treated chickpea seeds were found in the dryland agriculture regions of southeastern Washington and northern Idaho. Pythium spp. isolated from rotten seeds and associated soils showed high levels of resistance to metalaxyl. Large proportions (31 to 91%) of Pythium isolates resistant to metalaxyl were detected in areas where severe chickpea damping-off occurred and were observed in commercial chickpea fields over several years. All metalaxyl-resistant isolates were identified as P. ultimum var. ultimum. The metalaxyl resistance trait measured by EC50 values was stable over 10 generations in the absence of metalaxyl, and no observable fitness costs were associated with metalaxyl resistance. Under controlled conditions, metalaxyl treatments failed to protect chickpea seeds from seed rot and damping-off following inoculation with metalaxyl-resistant Pythium isolates. In culture, ethaboxam inhibited mycelial growth of metalaxyl-resistant, as well as metalaxyl-sensitive isolates. Greenhouse and field tests showed that ethaboxam is effective in managing metalaxyl-resistant Pythium. Ethaboxam in combination with metalaxyl is now commonly applied as seed treatments in commercial chickpea production.
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http://dx.doi.org/10.1094/PDIS-08-20-1659-REDOI Listing
October 2020

Identification of f. sp. () Responsive Genes in .

Front Genet 2020 18;11:950. Epub 2020 Aug 18.

Molecular Plant Sciences, Washington State University, Pullman, WA, United States.

(pea) is rapidly emerging as an inexpensive and significant contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogen f. sp. (), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis of interaction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identify -responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes after the challenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis, and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot in . challenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes and the preexisting level of disease-preparedness in the tolerant genotypes.
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http://dx.doi.org/10.3389/fgene.2020.00950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461991PMC
August 2020

Development and Validation of KASP Markers for the Identification of Pathotype P1 Resistance in .

Plant Dis 2020 Jun 9;104(6):1824-1830. Epub 2020 Apr 9.

Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture Agricultural Research Service, Prosser, WA 99350.

As pesticides have become heavily relied on for management of insect pests vectoring economically important pathogens of vegetable crops, development of pathogen-resistant germplasm remains a promising alternative to reduce or eliminate costly and timely chemical inputs. Molecular markers can be used to rapidly identify resistant genotypes to aid breeders in advancing germplasm. This study developed two kompetitive allele-specific PCR (KASP) genotyping markers for rapid screening of genotypes for resistance to pathotype P1 (PSbMV-P1), the most economically devastating strain worldwide. The KASP markers differentiate two PSbMV-P1-resistant allelic variants from susceptible variants. A single nucleotide polymorphism (Resistant 1) and a 3-basepair deletion (Resistant 2) present in either of the two resistant alleles were used for marker design. Forty-four lines previously characterized for resistance to PSbMV were inoculated with PSbMV-P1 in a greenhouse, observed for visual symptoms, assayed for virus susceptibility by enzyme-linked immunosorbent assay (ELISA), and genotyped by KASP marker analysis. The KASP markers were 100% accurate in characterizing PSbMV-P1-susceptible and PSbMV-P1-resistant genotypes when correlated with the ELISA results. The Resistant 1 marker also correlated with resistance to PSbMV pathotypes P2 and P4 completely, making this marker a new advanced tool for breeding programs.
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http://dx.doi.org/10.1094/PDIS-09-19-1920-REDOI Listing
June 2020

Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study.

Int J Mol Sci 2020 Mar 20;21(6). Epub 2020 Mar 20.

USDA-ARS Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164, USA.

Lentil ( Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.
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http://dx.doi.org/10.3390/ijms21062129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139309PMC
March 2020

Protein, weight, and oil prediction by single-seed near-infrared spectroscopy for selection of seed quality and yield traits in pea (Pisum sativum).

J Sci Food Agric 2020 Jun 9;100(8):3488-3497. Epub 2020 Apr 9.

Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.

Background: Pea (Pisum sativum) is a prevalent cool-season crop that produces seeds valued for their high protein content. Modern cultivars have incorporated several traits that improved harvested yield. However, progress toward improving seed quality has received less emphasis, in part due to the lack of tools for easily and rapidly measuring seed traits. In this study we evaluated the accuracy of single-seed near-infrared spectroscopy (NIRS) for measuring pea-seed weight, protein, and oil content. A total of 96 diverse pea accessions were analyzed using both single-seed NIRS and wet chemistry methods. To demonstrate field relevance, the single-seed NIRS protein prediction model was used to determine the impact of seed treatments and foliar fungicides on the protein content of harvested dry peas in a field trial.

Results: External validation of partial least squares (PLS) regression models showed high prediction accuracy for protein and weight (R = 0.94 for both) and less accuracy for oil (R = 0.74). Single-seed weight was weakly correlated with protein and oil content in contrast with previous reports. In the field study, the single-seed NIRS predicted protein values were within 10 mg g of an independent analytical reference measurement and were sufficiently precise to detect small treatment effects.

Conclusion: The high accuracy of protein and weight estimation show that single-seed NIRS could be used in the dual selection of high-protein, high-weight peas early in the breeding cycle, allowing for faster genetic advancement toward improved pea nutritional quality. © 2020 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.10389DOI Listing
June 2020

Exploring the genetics of lesion and nodal resistance in pea ( L.) to using genome-wide association studies and RNA-Seq.

Plant Direct 2018 Jun 26;2(6):e00064. Epub 2018 Jun 26.

Department of Plant, Soil and Microbial Sciences Michigan State University East Lansing Michigan.

The disease white mold caused by the fungus is a significant threat to pea production, and improved resistance to this disease is needed. Nodal resistance in plants is a phenomenon where a fungal infection is prevented from passing through a node, and the infection is limited to an internode region. Nodal resistance has been observed in some pathosystems such as the pea ( L.)- pathosystem. In addition to nodal resistance, different pea lines display different levels of stem lesion size restriction, referred to as lesion resistance. It is unclear whether the genetics of lesion resistance and nodal resistance are identical or different. This study applied genome-wide association studies (GWAS) and RNA-Seq to understand the genetic makeup of these two types of resistance. The time series RNA-Seq experiment consisted of two pea lines (the susceptible 'Lifter' and the partially resistant PI 240515), two treatments (mock inoculated samples and -inoculated samples), and three time points (12, 24, and 48 hr post inoculation). Integrated results from GWAS and RNA-Seq analyses identified different redox-related transcripts for lesion and nodal resistances. A transcript encoding a glutathione S-transferase was the only shared resistance variant for both phenotypes. There were more leucine rich-repeat containing transcripts found for lesion resistance, while different candidate resistance transcripts such as a VQ motif-containing protein and a myo-inositol oxygenase were found for nodal resistance. This study demonstrated the robustness of combining GWAS and RNA-Seq for identifying white mold resistance in pea, and results suggest different genetics underlying lesion and nodal resistance.
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http://dx.doi.org/10.1002/pld3.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508546PMC
June 2018

Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions.

BMC Plant Biol 2019 Mar 12;19(1):98. Epub 2019 Mar 12.

Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650, Le Rheu, France.

Background: Dry pea production has increased substantially in North America over the last few decades. With this expansion, significant yield losses have been attributed to an escalation in Fusarium root rots in pea fields. Among the most significant rot rotting pathogenic fungal species, Fusarium solani fsp. pisi (Fsp) is one of the main causal agents of root rot of pea. High levels of partial resistance to Fsp has been identified in plant genetic resources. Genetic resistance offers one of the best solutions to control this root rotting fungus. A recombinant inbred population segregating for high levels of partial resistance, previously single nucleotide polymorphism (SNP) genotyped using genotyping-by-sequencing, was phenotyped for disease reaction in replicated and repeated greenhouse trials. Composite interval mapping was deployed to identify resistance-associated quantitative trait loci (QTL).

Results: Three QTL were identified using three disease reaction criteria: root disease severity, ratios of diseased vs. healthy shoot heights and dry plant weights under controlled conditions using pure cultures of Fusarium solani fsp. pisi. One QTL Fsp-Ps 2.1 explains 44.4-53.4% of the variance with a narrow confidence interval of 1.2 cM. The second and third QTL Fsp-Ps3.2 and Fsp-Ps3.3 are closely linked and explain only 3.6-4.6% of the variance. All of the alleles are contributed by the resistant parent PI 180693.

Conclusion: With the confirmation of Fsp-Ps 2.1 now in two RIL populations, SNPs associated with this region make a good target for marker-assisted selection in pea breeding programs to obtain high levels of partial resistance to Fusarium root rot caused by Fusarium solani fsp. pisi.
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http://dx.doi.org/10.1186/s12870-019-1699-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417171PMC
March 2019

Pythium Species Associated with Damping-off of Pea in Certified Organic Fields in the Columbia Basin of Central Washington.

Plant Dis 2016 May 24;100(5):916-925. Epub 2016 Feb 24.

Washington State University Mount Vernon NWREC.

Organic vegetable production accounted for 19% of the total organic acreage in Washington State in 2013, with 1,700 ha of certified organic vegetable pea. However, production is challenged constantly with the threat of poor emergence after planting due to damping-off caused by Pythium spp. A survey of Pythium spp. in organic vegetable production areas of the semiarid Columbia Basin of central Washington was carried out in fall 2009 to identify species associated with damping-off during early spring planting. Of 305 isolates baited from soil sampled from 37 certified organic fields, 264 were identified to 16 Pythium spp. by sequencing the internal transcribed spacer region of ribosomal DNA. A soil DNA-CFU regression curve was developed using real-time quantitative polymerase chain reaction assays for each of the three predominant pathogenic species (Pythium abappressorium, the P. irregulare complex, and P. ultimum var. ultimum) found in soil sampled from the 37 fields. The P. irregulare complex, P. abappressorium, and P. ultimum var. ultimum were detected in 57, 78, and 100% of the fields sampled, respectively. A regression analysis was used to determine that P. ultimum var. ultimum ranged from 14 to 332 CFU/g of soil in the 37 fields, the P. irregulare complex ranged from 25 to 228 CFU/g of soil, and P. abappressorium DNA was below the quantifiable limit. In summary, P. ultimum var. ultimum was the most prevalent pathogenic Pythium sp. detected in certified organic fields in the semiarid Columbia Basin of central Washington but multiple Pythium spp. may be associated with damping-off in cool and wet, early spring planting conditions.
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http://dx.doi.org/10.1094/PDIS-07-15-0774-REDOI Listing
May 2016

Characterization and Pathogenicity of Rhizoctonia and Rhizoctonia-Like spp. From Pea Crops in the Columbia Basin of Oregon and Washington.

Plant Dis 2015 May;99(5):604-613

Professor, Washington State University Mount Vernon Northwestern Washington Research & Extension Center, Mount Vernon 98273.

Isolates of Rhizoctonia and Rhizoctonia-like spp. (n = 179) were baited selectively from soil and plant samples collected from irrigated pea crops in the semiarid Columbia Basin of Oregon and Washington from 2011 to 2013, and characterized to species, subspecies, and anastomosis groups (AG) based on sequences of the internal transcribed spacer region of ribosomal DNA. Rhizoctonia solani comprised 76% of all isolates, and included isolates of AG 4 (31% of all isolates), AG 2-1 (18%), AG 3 (10%), AG 8 (8%), AG 5 (5%), AG 10 (3%), and AG 9 (1%). The isolates of Ceratobasidium spp. (20%) comprised four AGs: AG K (11%), AG A (6%), AG I (2%), and AG I-like (1%). Waitea circinata isolates (4%) comprised two subspecies: W. circinata var. circinata (approximately 4%) and W. circinata var. zeae (<1%). Repeated pathogenicity tests of isolates of the 10 most frequently detected AGs and subspecies on 'Serge' pea at 15°C revealed that R. solani AG 2-1 caused the greatest reduction in pea emergence, followed by R. solani AG 4. R. solani AG 4 caused the most severe root rot, stunting, and reduction in pea seedling biomass, followed by isolates of AG 2-1. R. solani AG 8 did not affect emergence, plant height, and total biomass compared with noninoculated control plants; however, root rot caused by isolates of AG 8 was ranked the third most severe among isolates of the 10 Rhizoctonia subgroups, after that caused by isolates of AG 4 and AG 2-1. Isolates of other AGs and subspecies were either weakly virulent or nonpathogenic on pea. The most common AGs (AG 4 and AG 2-1) detected in pea fields in the Columbia Basin were also the most virulent. In a growers' pea crop grown for seed ('Prevail') planted 5 days after herbicide application and incorporation of a preceding winter wheat crop, severe stunting caused by Rhizoctonia spp. resulted in an average 75% yield loss within patches of stunted plants. In contrast, the yield of processing pea from a green pea crop of Serge did not differ significantly for plants sampled within versus outside patches of stunted plants; however, plants within patches were significantly more mature. In the Prevail seed crop, a greater frequency of R. solani AG 8 was detected than AG 2-1 or AG 4 from within patches of stunted plants, indicating that isolates of AG 8 may be associated with the root rot complex in some pea crops in the Columbia Basin.
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http://dx.doi.org/10.1094/PDIS-08-14-0803-REDOI Listing
May 2015

Complex patterns of speciation in cosmopolitan "rock posy" lichens--discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota).

Mol Phylogenet Evol 2011 Jun 1;59(3):587-602. Epub 2011 Apr 1.

Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA.

A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan "rock posy" lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi.
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http://dx.doi.org/10.1016/j.ympev.2011.03.020DOI Listing
June 2011

Survival of Phytophthora infestans in Surface Water.

Phytopathology 2004 Apr;94(4):380-7

ABSTRACT Coverless petri dishes with water suspensions of sporangia and zoospores of Phytophthora infestans were embedded in sandy soil in eastern Washington in July and October 2001 and July 2002 to quantify longevity of spores in water under natural conditions. Effects of solar radiation intensity, presence of soil in petri dishes (15 g per dish), and a 2-h chill period on survival of isolates of clonal lineages US-8 and US-11 were investigated. Spores in water suspensions survived 0 to 16 days under nonshaded conditions and 2 to 20 days under shaded conditions. Mean spore survival significantly increased from 1.7 to 5.8 days when soil was added to the water. Maximum survival time of spores in water without soil exposed to direct sunlight was 2 to 3 days in July and 6 to 8 days in October. Mean duration of survival did not differ significantly between chilled and nonchilled sporangia, but significantly fewer chilled spores survived for extended periods than that of nonchilled spores. Spores of US-11 and US-8 isolates did not differ in mean duration of survival, but significantly greater numbers of sporangia of US-8 survived than did sporangia of US-11 in one of three trials.
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http://dx.doi.org/10.1094/PHYTO.2004.94.4.380DOI Listing
April 2004

Development of codominant simple sequence repeat, single nucleotide polymorphism and sequence characterized amplified region markers for the pea root rot pathogen, Aphanomyces euteiches.

J Microbiol Methods 2007 Oct 9;71(1):82-6. Epub 2007 Aug 9.

Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA.

Three kinds of genetic markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs) and sequence characterized amplified regions (SCARs) were developed from Aphanomyces euteiches. Of 69 loci tested, seven SSR, two SNP and two SCAR markers were codominantly polymorphic. These codominant markers and dominant markers described herein will facilitate population genetic and evolutionary studies of this important plant pathogen.
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http://dx.doi.org/10.1016/j.mimet.2007.08.001DOI Listing
October 2007