Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris ) is an important root rot pathogen of common bean ( Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP ( n = 28) and ∼6% of the MDP ( n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.
The oomycete Pythium comprises one of the most important groups of seedling pathogens affecting soybean. There has been limited research on Pythium spp. pathogenic on soybean in the northern Great Plains. The objectives of this research were to isolate and identify Pythium spp. infecting soybean in North Dakota and to test their pathogenicity. Identification of Pythium spp. was achieved using molecular techniques and morphological features. A total of 26 known Pythium spp. and three unknown species were recovered from soybean seedling roots collected from 125 fields between 2011 and 2012. In 2011, the three most abundant species isolated were P. ultimum, Pythium sp. (unknown; GenBank HQ643777.1), and P. heterothallicum, representing 21, 16, and 12% of 2,675 isolates, respectively. More species and isolates were obtained in 2011, a wet and cool year, compared with 2012, which was dry and warm. The majority of Pythium spp. caused pre-emergence damping-off on soybean with less than 50% emergence in a 2-week test using infested soil at 23°C. In contrast, in the presence of P. orthogonon, P. nunn, or P. rostratifingens there was approximately 80% or greater emergence and most plants survived for several weeks, although lesions were observed on roots. Mortierella spp., a zygomycete, was commonly isolated along with Pythium spp. in 2012, but not in 2011. This is the first report of P. kashmirense, P. minus, P. periilum, P. rostratifingens, P. terrestris, P. viniferum, and P. violae as pathogens of soybean seedlings. In addition, this is the first report of P. kashmirense, P. viniferum, and P. terrestris in the United States.
Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
Aphanomyces euteiches is a destructive soilborne plant pathogen, causing economic losses when adequate to excess soil moisture is available. This oomycete organism survives in the soil for decades and infects and degrades roots of plants from 11 families. Symptoms of Aphanomyces root rot are similar across the major economic hosts alfalfa (Medicago sativa subsp. sativa L.), lentil (Lens culinaris Medik.), and pea (Pisum sativum L.). Initial symptoms include the appearance of grey, water-soaked root tissue. Roots develop a golden-brown color, and lateral roots begin to disintegrate as the disease worsens. In the most severe cases, the entire root system is destroyed and aboveground chlorosis and necrosis are observed. A. euteiches isolation can be successful from both infested soil and infected plant tissue. Macroscopically, colony growth is generally nondescript and white in color. A. euteiches is self-fertile (homothallic) and produces sexual oospores in culture in addition to asexual zoosporangia and zoospores (primary and secondary) on hyphae lacking regular septa (coenocytic). Numerous molecular techniques have been developed for successful A. euteiches detection. A. euteiches can be stored in frozen soil or on agar slants, but viability should be evaluated regularly. Oospores or zoospores have been utilized for inoculation under greenhouse and field conditions; although the generation of a field site using soil infestation techniques can take several seasons of productions of a susceptible crop to be utilized to effectively screen for Aphanomyces root rot.
Background and aims Field pea production is greatly impacted by multiple soil-borne fungal and oomycete pathogens in a complex. The objectives of this research were to 1) identify the soil-borne pathogens associated with field pea in North Dakota and; 2) develop prediction models incorporating the occurrence of the soil-borne pathogen communities, soil edaphic properties and disease incidence. Methods Soil and plants were sampled from 60 field pea fields in North Dakota during 2014 and 2015. Plants (1500 across two years) were rated for both root rot and soil-borne pathogens isolated from roots. Soils were analyzed for edaphic properties. Indicator species analysis was used to identify soil-borne pathogen communities. Logistic regression was used to determine associations and develop prediction models. Results Survey results from 2014 and 2015 indicated that the most prevalent soil-borne pathogens identified in field pea fields were Fusarium spp. and Aphanomyces euteiches. Five soil-borne pathogen communities were identified; three of which had statistically significant associations characterized by (1) Fusarium acuminatum, (3) A. euteiches, and (4) Fusarium sporotrichioides. The occurrence of the three communities were associated with clay content, soil pH, Fe2+, and K+. Disease incidence was associated with the presence of either community 1 or 3 and K+. Conclusions The results generated from this research will contribute to the development of management strategies by providing a soil-borne pathogen community prediction tool.
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