scholarly journals Comparison of Frequentist and Bayesian Generalized Linear Models for Analyzing the Effects of Fungicide Treatments on the Growth and Mortality of Piper Nigrum

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2524
Author(s):  
Bao V. Q. Le ◽  
Anh Nguyen ◽  
Otto Richter ◽  
Truc T. Nguyen

Foot rot disease poses a devastating threat to pepper agriculture. In Vietnam, conventionally, fungicides are the control methods used against the disease. However, the practical effectiveness of fungicide treatment has yet to be quantitatively assessed. To fill this gap a three-factorial experiment was conducted, the factors of which were fungicide application, soil type, and infection pathway, with plant mortality and plant growth as the target variables. Two of the most common fungicides were chosen, including Agrifos 400 (potassium phosphonate) and Aliette 800WG (fosetyl-Al). The two fungicides were used in multiple treatment plans, with soil drenching selected as the means of controlling foot rot disease on red basalt soil and red basalt soil added with organic matter in a greenhouse experiment. Three-month-old pepper (Piper nigrum) plants were treated with Agrifos (application interval of 10 and 20 days), Aliette (application interval of 30 and 60 days), and a combination of both fungicides at half doses. Pepper plants were infected with the fungus Pythium spp. from soil or by direct inoculation. To assess the effect of fungicides on foot rot mortality and the growth of pepper plants, multiple generalized linear models were set up using frequentist and Bayesian approaches. Generally, both procedures suggest the same conclusions for model selection in terms of the Akaike information criterion (AIC) and the deviance information criterion (DIC). Fungicide type was found to be the main factor that affected the survival of plants. Most of the treatments (except Aliette, with an interval of 60 days) effectively reduced the mortality. The usage of fungicides affected the growth of plants in interaction with soil types. Aliette suppressed the growth of plants, especially on red soil, while Agrifos had no effect on the growth of pepper plants. The combined application of Agrifos and Aliette with half doses proves to be a promising solution for balancing cost and effectiveness in protecting plants against foot rot pathogens without affecting their growth. In our case, under the inhomogeneity of variance and unbalanced samples, the Bayesian inference appeared to be the most useful because of its flexibility in terms of model structure.

2016 ◽  
Vol 44 (2) ◽  
Author(s):  
K.B. Vinitha, M. Anandaraj and R. Suseela Bhai

<p>Foot rot disease caused by <em>Phytophthora capsici</em> in black pepper is the most destructive disease. A total of 82 isolates from the National Repository of <em>Phytophthora</em> at ICAR-Indian Institute of Spices Research were evaluated for their sensitivity to metalaxylmancozeb and also tested for their virulence. Of the 82 isolates studied, 19 (23.2%) were highly sensitive to metalaxyl-mancozeb and six (7.3%) were comparatively insensitive (EC<sub>90</sub> value &gt;40 ppm; range 41.3 to 68.5 ppm). The isolates also varied in the degree of virulence, viz., 34 (41.5%) were highly virulent, 39 (47.6%) moderately virulent, 4 (3.7%) mildly virulent, and 5 (6.1%) non-virulent. There was neither any significant correlation between sensitivity to metalaxyl-mancozeb and virulence nor with the geographical location<strong>. </strong></p>


2019 ◽  
Vol 14 (5) ◽  
pp. 166
Author(s):  
Bahru Rohmah ◽  
Bambang Hadisutrisno ◽  
Dyah Manohara ◽  
Achmadi Priyatmojo

Morphology characters and mating types distribution of Phytophthora capsici from black pepper in Java IslandPepper (Piper nigrum) is one of the most important spice crops in Indonesia.  Recently its production declining due to infection of foot rot disease caused by Phytophthora capsici. This pathogen has two different mating types, namely A1 and A2, in which the presence of opposite two mating types is important for sexual reproduction and formation of oospores. The movement of pepper seedling from one area to another is highly facilitated alteration of  mating type distribution map of P. capsici. The objectives of this research were to determine the morphological characteristics and the spread of mating types of P. capsici in Java. Morphology characters of P. capsici isolates were indicated by variation in sporangial size and shape, as well as types of colony appearance. The length (l) and width (w) of sporangium were in the range of 15.1–76.2 µm and 9.8–44.8 µm, respectively; while the l/w ratio was 1.12–2.27. Mating type assay showed that A2 type was more dominantly found than A1 type. This study found two different mating types present in the same area, i.e. Regency of Pacitan (East Java) and Regency of Sleman (Special Region of Yogyakarta). The findings of this research suggested that it is required more strict control strategy on the mobilization of black pepper seedling particularly in the area where the certain mating type is not found yet so that the emergence of new more virulent genotype of pathogen can be prevented.


2018 ◽  
Vol 40 (3) ◽  
pp. 281-287 ◽  
Author(s):  
Fábio Janoni Carvalho ◽  
Denise Garcia de Santana ◽  
Lúcio Borges de Araújo

Abstract: We compared the goodness of fit and efficiency of models for germination. Generalized Linear Models (GLMs) were performed with a randomized component corresponding to the percentage of germination for a normal distribution or to the number of germinated seeds for a binomial distribution. Lower levels of Akaikes’s Information Criterion (AIC) and Bayesian Information Criterion (BIC) combined, data adherence to simulated envelopes of normal plots and corrected confidence intervals for the means guaranteed the binomial model a better fit, justifying the importance of GLMs with binomial distribution. Some authors criticize the inappropriate use of analysis of variance (ANOVA) for discrete data such as copaiba oil, but we noted that all model assumptions were met, even though the species had dormant seeds with irregular germination.


Biometrika ◽  
2021 ◽  
Author(s):  
Emre Demirkaya ◽  
Yang Feng ◽  
Pallavi Basu ◽  
Jinchi Lv

Summary Model selection is crucial both to high-dimensional learning and to inference for contemporary big data applications in pinpointing the best set of covariates among a sequence of candidate interpretable models. Most existing work assumes implicitly that the models are correctly specified or have fixed dimensionality, yet both are prevalent in practice. In this paper, we exploit the framework of model selection principles under the misspecified generalized linear models presented in Lv and Liu (2014) and investigate the asymptotic expansion of the posterior model probability in the setting of high-dimensional misspecified models.With a natural choice of prior probabilities that encourages interpretability and incorporates the Kullback–Leibler divergence, we suggest the high-dimensional generalized Bayesian information criterion with prior probability for large-scale model selection with misspecification. Our new information criterion characterizes the impacts of both model misspecification and high dimensionality on model selection. We further establish the consistency of covariance contrast matrix estimation and the model selection consistency of the new information criterion in ultra-high dimensions under some mild regularity conditions. The numerical studies demonstrate that our new method enjoys improved model selection consistency compared to its main competitors.


2020 ◽  
Vol 18 (4) ◽  
pp. 173
Author(s):  
CHAERANI CHAERANI ◽  
DYAH MANOHARA

<p>ABSTRAK<br />Penggunaan varietas lada tahan penyakit paling praktis dan efektif<br />untuk menekan serangan Phytophthora capsici, penyebab penyakit busuk<br />pangkal batang (BPB) lada, tetapi varietas lada tersebut belum tersedia.<br />Seleksi dini ketahanan lada dapat dilakukan di laboratorium menggunakan<br />inokulum sporangia atau filtrat biakan P. capsici. Tujuan penelitian ini<br />ialah membandingkan agresivitas inokulum sporangia dengan toksisitas<br />filtrat biakan (FB) P. capsici. Penelitian dilakukan dari bulan Juni sampai<br />September 2009 di laboratorium Biokimia BB Biogen dan Hama dan<br />Penyakit Balittro. Penelitian menggunakan 50 isolat P. capsici dari<br />berbagai daerah pertanaman lada yang diisolasi tahun 1982 sampai 2009.<br />Daun-daun lada yang diambil dari varietas Natar-1 (agak tahan terhadap P.<br />capsici) dan Petaling-1 (rentan terhadap P. capsici) diinokulasi dengan<br />potongan agar mengandung sporangia atau 20 µl FB P. capsici. Percobaan<br />dilakukan secara faktorial (2 varietas × 50 isolat) dengan rancangan acak<br />kelompok dan tiga ulangan. Derajat agresivitas isolat dan toksisitas FB<br />diukur berdasarkan luas bercak nekrotik. Hasil penelitian menunjukkan<br />bahwa agresivitas inokulum sporangia dan toksisitas FB bervariasi antar<br />isolat P. capsici. Bercak nekrotik yang disebabkan oleh inokulum<br />sporangia lebih luas (0,0–2.535,2 mm 2 ) dibandingkan dengan FB (0,7–<br />233,0 mm 2 ). Derajat agresivitas isolat dan toksisitas FB sangat dipengaruhi<br />oleh asal isolat (P&lt;0,0001), tetapi tidak dipengaruhi oleh varietas dan<br />interaksi isolat×varietas (P&gt;0,05). Derajat ketahanan pada varietas tahan<br />Natar-1 diduga tidak berbasis genetik dan tidak berbeda nyata dari varietas<br />rentan Petaling-1 sehingga kedua metode seleksi ketahanan tidak dapat<br />dibedakan keefektifannya. Luas bercak nekrotik yang diinduksi oleh FB<br />tidak berkorelasi nyata dengan yang ditimbulkan oleh inokulum sporangia<br />(R 2 =0,002; P&gt;0,05), sehingga secara umum FB P. capsici tidak dapat<br />digunakan sebagai standar pengujian ketahanan lada. Oleh karena itu<br />masih perlu dikembangkan metode inokulasi yang konsisten untuk seleksi<br />dini ketahanan lada.<br />Kata kunci: lada, penyakit busuk pangkal batang, Phytophthora capsici,<br />agresivitas, filtrat biakan, seleksi dini</p><p>ABSTRACT<br />Resistant varieties are the most practical and effective means to<br />control Phytophthora capsici, the pathogen of foot rot disease of black<br />pepper. However, no resistant cultivars are available. Early selection of<br />black pepper resistance can be performed in laboratory using P. capsici<br />inocula or culture filtrate. The objective of this study was to compare P.<br />capsici isolate aggressiveness with culture filtrate (CF) toxicity. The study<br />was conducted from June until September 2009 at the Biochemistry<br />Laboratory of the Indonesian Center for Agriculutral Biotechnology and<br />Genetic Resources Research and Development and the Plant Pest and<br />Disease Laboratory of the Indonesian Research Institute of Spice and<br />Medicinal Crops. The study used 50 P. capsici isolates collected from<br />various black pepper plantations during 1982 until 2009. Detached leaves<br />of two black pepper cultivars, i.e. moderately resistant cv. Natar-1 and<br />susceptible cv. Petaling-1, were inoculated with agar blocks containing<br />sporangia or 20 µl CF of P. capsici. The experiments were designed as<br />factorial experiments (2 cultivars × 50 isolates) under a randomized<br />completely block design. Isolate aggressiveness and CF toxicity were<br />measured based on the necrotic area of the inoculated leaves. The results<br />from the two inoculation methods showed varying levels of aggressiveness<br />and CF toxicity among isolates. Necrotic lesions incited by sporangial<br />inoculum were more extensive (0.0-2,535.2 mm 2 ) than those induced by<br />CF (0.7-233.0 mm 2 ). Degree of isolate aggressiveness and CF toxicity<br />were significantly affected by origins of isolate (P&lt;0.0001), but not by<br />cultivar and isolate×cultivar interaction (P&gt;0.05). Resistance degree in the<br />moderately resistant cv. Natar-1 was presumably not genetically based and<br />was not different to that in the susceptible cv. Petaling-1, and hence both<br />selecting agents were unable to discriminate resistance level between the<br />two cultivars. Necrotic sizes induced by CF did not well correlate with<br />those incited by sporangial inocula (R 2 =0.002; P&gt;0.05), indicating that CF<br />is generally not suitable to be used as early selection agent of resistant<br />plants. Therefore, further study is justified to find more reliable inoculation<br />method for early detection of resistant black pepper.<br />Key words: black pepper, foot rot disease, Phytophthora capsici,<br />aggressiveness, culture filtrate, early selection in laboratory</p>


2020 ◽  
Vol 8 (2) ◽  
pp. 51
Author(s):  
Ni'matuljannah Akhsan ◽  
Albert Patangke

The Malonan-1 variety is a pepper plant originating from East Kalimantan which has become a national superior pepper. This pepper contains around 2,35% essential oil, oleoserin 11,23% and piperine 3,82% and tolerance to stem rot disease. Preliminary survey results in the village of Batuah, Kutai Kartanegara District, East Kalimantan, it was found that the stem rot disease in Malonan-1 pepper, therefore it is necessary to conduct research to find out how much the intensity of the stem rot disease at this time and identify fungi that cause stem rot rot disease in pepper plants. This research was conducted for 5 months starting from January to May 2019. The research location was in Batuah Village, Loa Janan Subdistrict, Kutai Kartanegara District and in the Plant Disease Pest Laboratory, Faculty of Agriculture, Mulawarman University. Research includes activities in the field and in the laboratory. The activity in the field is a direct survey of eight pepper farmer groups and calculating the intensity of the disease. Also carried out samples of symptomatic stem rot disease to be brought to the laboratory. Activities in the laboratory are the preparation of tools and materials to isolate samples of pepper plants. The isolated fungal colonies were purified and then idenfied and continued with Koch's postulate. The average intensity of stem rot disease at the current Lada plant in Batuah village is 14,58% (mild), the highest intensity in the Young Lada farmer group is 26,52% and the lowest intensity in the Beringin Jaya Farmer group is 4.3%. Based on the results of isolation, the root disease of the pepper plant (Piper nigrum L) in Batuah Village, Loa Janan District, Kutai Kartanegara Regency is Phytophthora capsici L. 


2017 ◽  
Vol 12 (5) ◽  
pp. 178
Author(s):  
Halim Halim ◽  
Mariadi Mariadi ◽  
La Karimuna ◽  
Rachmawati Hasid

Stem rot or foot rot disease caused by Phytophthora capsici is known as an important constraint on pepper cultivation. Research was conducted to determine the effect of arbuskula mycorhizal fungi (AMF) on incidence of foot rot disease of pepper seedlings.  The experiment was done in the net house and arranged using completed randomized design with 6 treatments, i.e. (1) soil infested by P. capsici (TPC) as negative control treatment, (2) sterilized soil (TS) as positive control treatment, (3) TPC with 5 g of AMF, (4) TPC with 10 g AMF, (5) TPC with 15 g AMF, and (6) TPC with 20 g AMF.   Observation involved plant height, number of shoots, disease incidence, the percentage of AMF infection on the roots of pepper plants, and pepper plants dependence on AMF. The results showed that the application of AMF at a dose of 20 g per 10 kg of soil effectively suppressed incidence of foot rot disease and improve plant growth


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