Deep Learning for Anthracnose Diagnosis in Turnip Leaves

Fungal diseases in plants are extremely pressing issues in the agricultural industry, threatening global food security by reducing crop yields and quality. Traditional approaches to disease diagnosis and management have failed to recognize symptoms when they first appear. Leaves of the turnip, a plant of high agricultural value, has been especially affected by the fungal disease Anthracnose. Therefore, this study aimed to develop a novel convolutional neural network that can identify turnip leaves with early symptoms of Anathrosce blight. The model had 4 convolutional blocks and was trained on a custom dataset of 1,470 images, randomly split into 60% train, 20% validation, and 20% test. To compare how the CNN model fared with other machine learning algorithms, a support vector machine(SVM) model was developed and trained with the same image dataset. The CNN model’s accuracy 98.75% compared to the SVM model’s 80.50% accuracy. These results validate the efficacy of the CNN model to accurately identify infected turnip leaves and demonstrate that it can be implemented into a practical disease diagnosis system. Future studies are warranted to improve the model through means such as k-fold cross validation as well as apply the model architecture to other crops and diseases.

First Report of Alternaria japonica Causing Black Spot of Turnip in Spain

Turnip (Brassica rapa subsp. rapa L.) is an annual vegetable crop cultivated for consumption of its succulent root. In July 2011, symptoms consisting of leaf spots 1 to 8 mm in diameter with a dark brown color surrounded by a yellow halo and black sunken lesions in the swollen storage root were observed in production areas in Alicante Province in east-central Spain. Disease incidence was approximately 20% in fields of about 3 ha where infection was highest. Symptomatic leaves and roots collected from turnip cv. Virtudes-Martillo in three affected fields were surface disinfected with 0.5% NaOCl for 2 min, and small fragments from necrotic lesions were plated on potato dextrose agar (PDA) amended with 0.5 g streptomycin sulfate per liter. Alternaria colonies were consistently isolated from affected leaves and roots after 7 days of incubation at 24°C, and were transferred to V-8 with autoclaved turnip cv. Virtudes-Martillo leaves. Two isolates from leaves and two isolates from roots were included in the study. Plates were incubated for 15 days at 24°C with an 8-h fluorescent light period and a 12-h dark period for morphological examination. Conidia produced in culture were mostly solitary or in short chains of 2 to 3 spores, beakless, ovoid to ellipsoid, and light brown. Conidia were 32 to 78 × 13 to 24 μm, with 3 to 7 transverse septa and 1 to 2 longisepta. Aggregated hyphal chains of dark, thick-walled ornamented cells distinctive of Alternaria japonica Yoshii (3) were observed. The 5.8S, ITS2, and 28S ribosomal RNA (rRNA) regions were amplified using the primers ITS3 and ITS4 (4) and sequenced from DNA extracted from the isolate designated as IVIA-A070, obtained from turnip leaves cv. Virtudes-Martillo in Alicante Province (GenBank Accession No. JX983044). The sequence had 100% identity (total score 302, 73% coverage) with that of A. japonica strain ATCC 13618 (2) (AY376639). Pathogenicity tests were performed twice on two 3-month-old plants of turnip cv. Virtudes-Martillo and cv. Blanco-Globo, and cabbage (B. oleracea var. capitata L.) cv. Brunswick. Plants were inoculated by spraying a conidial suspension of the isolate IVIA-A070 (10 ml/plant, 104 conidia/ml water) using manual pressure sprayer. Two plants of each host sprayed with sterile distilled water were used as controls in each experiment. Plants were covered with black plastic bags and incubated in a growth chamber for 48 h at 25°C. Leaf spots similar to those observed in affected plants in the field were visible on all turnip and cabbage plants 4 days after inoculation with the fungus. No symptoms were observed on control plants. Fungal colonies morphologically identified as A. japonica were reisolated from leaf lesions on inoculated turnip and cabbage plants, but not from asymptomatic leaves of control plants. Based on these results, the disease was identified as black spot of turnip caused by A. japonica. In Spain, black spot of brassicas was previously associated only with A. brassicae (Berkeley) Saccardo and A. brassicicola (Schw.) Wiltshire (1). References: (1) P. Melgarejo et al. Patógenos de Plantas Descritos en España. MARM-SEF, Madrid, 2010. (2) B. M. Pryor and R. L. Gilbertson. Mycol. Res. 104:1312, 2000. (3) E. G. Simmons. Alternaria: An Identification Manual. CBS Fungal Biodiversity Centre, Utrecht, 2007. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.

Report of Bacterial Leaf Spot on Collards and Turnip Leaves in Ohio

In 2000, circular water-soaked lesions typical of bacterial leaf spot were observed on leaves of collards (Brassica oleracea L. var. viridis) throughout commercial fields in northwest Ohio. Light brown, rectangular, water-soaked lesions were observed on turnip leaves (Brassica rapa L.). Bacterial streaming from lesions on both crops was observed microscopically. Cream colored, fluorescent colonies were isolated from diseased tissues on Pseudomonas F medium, and eight representative colonies (four from collards and four from turnip) were selected and purified. Fatty acid methyl ester analysis was performed on all of the isolates. Two from collards and two from turnip were identified as Pseudomonas syringae pv. maculicola (mean similarity index = 0.82 [MIDI Inc., Newark, DE]). DNA extracts from pure cultures of the P. syringae pv. maculicola strains were used as template in a polymerase chain reaction (PCR) assay with primers derived from the region of the coronatine gene cluster controlling synthesis of the coronafacic acid moiety found in P. syringae pv. tomato and P. syringae pv. maculicola (CorR and CorF2) (D. Cuppels, personal communication). DNA from P. syringae pv. tomato strain DC3000 and P. syringae pv. maculicola strain 88–10 (2) served as positive controls, while water and DNA from Xanthomonas campestris pv. vesicatoria strain Xcv 767 were used as negative controls. The expected 0.65-kb PCR product was amplified from three of four strains (two from turnip and one from collards) and the positive control DNA, but not from the negative controls. Pathogenicity tests were performed twice on 6-week-old turnip (‘Forage Star’, ‘Turnip Topper’, ‘Turnip Alamo’, ‘Turnip 7’), collard (‘Champion’) and mustard (Brassica juncea L. ‘Southern Giant Curl’) seedlings using the three PCR-positive strains. Premisted seedlings were spray-inoculated separately with each of the three strains (2 × 108 CFU/ml, 5 ml per plant) and a water control. Greenhouse temperatures were maintained at 20 ± 1°C. For both tests, all strains caused characteristic lesions on all of the crucifer cultivars within 5 days after inoculation; the control plants did not develop symptoms. To satisfy Koch's postulates, one of the turnip strains was reisolated from ‘Turnip Topper’ plants, and the collard strain was reisolated from ‘Champion’ plants. The three original and two reisolated strains induced a hypersensitive response in Mirabilis jalapa L. and Nicotiana tabacum L. var. xanthia plants 24 h after inoculation with a bacterial suspension (1 × 108 CFU/ml). The original and reisolated strains were compared using rep-PCR with the primer BOXA1R (1). The DNA fingerprints of the reisolated strains were identical to those of the original strains. To our knowledge, this is the first report of bacterial leaf spot on commercially grown collards and turnip greens in Ohio. References: (1) B. Martin et al. Nucleic Acids Res. 20:3479, 1992. (2) R. A. Moore et al. Can. J. Microbiol. 35:910, 1989.

Expression of the gum Operon Directing Xanthan Biosynthesis in Xanthomonas campestris and Its Regulation In Planta

The gum gene cluster of Xanthomonas campestris pv. campestris comprises 12 genes whose products are involved in the biosynthesis of the extracellular polysaccharide xanthan. These genes are expressed primarily as an operon from a promoter upstream of the first gene, gumB. Although the regulation of xanthan synthesis in vitro has been well studied, nothing is known of its regulation in planta. A reporter plasmid was constructed in which the promoter region of the gum operon was fused to gusA. In liquid cultures, the expression of the gumgusA reporter was correlated closely with the production of xanthan, although a low basal level of β-glucuronidase activity was seen in the absence of added carbon sources when xanthan production was very low. The expression of the gumgusA fusion also was subject to positive regulation by rpfF, which is responsible for the synthesis of the diffusible signal factor (DSF). The expression of the gumgusA fusion in bacteria recovered from inoculated turnip leaves was maximal at the later phases of growth and was subject to regulation by rpfF. These results provide indirect support for the operation of the DSF regulatory system in bacteria in planta.

Tubular structures in developing plastids of three dicotyledonous species

Tubular structures were observed in the developing plastids of the meristematic regions of spinach, beet, and turnip leaves. These structures were located near the plastid periphery, were frequently in contact with the plastid envelope and (or) the internal plastic membranes, usually had a near-perpendicular orientation with their associated membranes, and were decorated with a distinct striated coating. Based on the high degree of structural similarity, it was suggested that these tubules represent a unique class of plastid inclusions with a common specialized function. A detailed examination of the spinach plastids provided evidence that the tubules are membranous structures and that the tubular lumen is confluent with that of the plastid envelope and also some internal plastidial compartments. It was also shown that the membranes of the tubules differed from the other plastidial membranes in that they were thinner and only lightly stained by osmium – potassium ferrocyanide postfixation. Key words: tubular, structures, developing, plastids, dicots.