DNA-based identification of Lentinula edodes strains with species-specific primers

Lentinula edodes is among the five globally cultivated edible mushrooms, which are wood decaying spore bearing Basidiomycetes possessing separate hyphae. Specific identification of this fungus from others in the division Basidiomycota using specific primers enables a fast and accurate detection through polymerase chain reaction (PCR). As a prelude to additional nutritional and sequence characterization research, we have developed a species specific PCR assay for this fungus after screening four primer-pairs and two universal primer pairs. The primer-pair LE1F/R was specific in amplifications of ATCC-defined L. edodes strains and did not amplify DNA from six medicinally and nutritionally important fungal reference strains, Oyster (Pleurotus ostreatus), Maitake (Grifola frondosa), Enoki (Flammulina velutipes), Baby bella (Agaricus bisporus), Porcini (Boletus edulis), and Chanterelle (Cantharellus cibarius). However, amplifications using the universal primers were positive for all six strains. This assay will therefore serve to validate morphology-based identifications of L. edodes strains.Keywords: Lentinula edodes, LE1F/R, species-specific primer

Genetic Resistance to the Reniform Nematode in Cotton

Among major nematode pests of Upland, cotton production is the reniform nematode, which is a serious threat in various cotton-producing regions. The availability of germplasm lines with tolerance or resistance to this menacing pest is a valued asset. To date, various laboratories and research institutions have collaborated to transfer the reniform nematode resistance from wild gene pools of cotton into widely cultivated Upland cotton, which have led to positive results. This chapter focuses on the current status of these introgressions and resistance mechanisms in cotton. In this overview, four major themes are being pursed: (1) tolerance mechanisms in cotton to the reniform nematode, (2) genotype evaluations, (3) introgression of reniform resistance into Upland cotton, and (4) functional analysis of reniform infection in Upland cotton. Genetic resistance in Upland cotton to the reniform nematode is the only practical solution because conventional control measures are the most cost-effective and environmentally sustainable and therefore have been and will be actively pursued. Resistance genes, if successfully introgressed into crop plants from wild relatives, should complement management of the reniform nematode with traditional methods

Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

Cotton is economically and evolutionarily important crop for its fiber. In order to improve fiber quality and yield, and to exploit the natural genetic potential inherent in genotypes, understanding genome structure and function of cultivated cotton is important. In order to achieve this, a functional understanding of bioinformatics resources such as databases, software solutions, and analysis tools is required. But currently, there are very few unified reports on bioinformatics tools and even fewer repositories to access cotton genomic information. Also, resourceful developers and bioinformatics scientists actively addressing complex genomic challenges in cotton genomes are much in need. The primary goal of this chapter is to provide a review of such tools and resources for analyzing the structure and function of the cotton genome with preferential emphasis on this complex and economically important plant species. This discourse begins with a description of concurrent advances in high‐throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources for analysis of: (1) genomes; (2) transcriptomes; (3) small RNAs; and (4) epigenomes. In each section, recent advances in cotton have been discussed. Cotton genome sequencing and annotation efforts are outlined within these sections. This review discusses the availability of genome information of both diploid and tetraploid species that have impelled cotton genome research into the post‐genomics era, opening new avenues for exploring regulatory mechanisms associated with fine‐tuning of gene expression of fiber‐related genes. Finally, the potential impacts of these rapid advances, especially the challenges in handling and analyzing the large datasets are discussed

Evaluation of Preplant Seed Protectants for the Management of Root-Knot Nematode of Okra in Ghana

Root-knot nematode (Meloidogyne incognita) poses a significant threat to okra production, resulting in substantial yield losses. The objectives of this study were to assess the impact of biological seed protectants on the growth and establishment of okra plants and nematode population reduction in soil. Okra seeds were coated with 40% sesame oil, 50% neem oil, 100% citrus oil, velum at 3.8 ml/7l of water, and a control (sterilized distilled water) at different time intervals of 30 min, 60 min, 90 min, and 120 min to determine the germination percentages and vigor. The experimental setup was laid out in a completely randomized design (CRD), with three replications, utilizing a Jacobson table for the germination test. The laboratory results demonstrated significant differences (P<0.05) in germination percentage and vigor index across the different time intervals. Neem oil, citrus oil, and velum exhibited higher germination percentages and vigor indices at all time intervals. Notably, 30-minute time interval proved to be efficient with 100% citrus oil producing 80.33% germination and 965 vigor index and 50% neem oil producing 75% germination and 994 vigor index. Field evaluations revealed citrus at 100% concentrations as seed coating (T5) and neem at 50% concentrations as seed coating (T3), with the highest nematode reductions (90.1% and 90.4%) and least reproductive factors (RFs) of 0.05 and 0.04, respectively, at the Atomic farms. The study has revealed that treating okra seeds with 100% citrus oil and 50% neem oil has the efficacy of reducing nematode reproduction in soil, while enhancing germination and seedling vigor, together with an improvement in growth and yield. Sesame oil has a negative influence on seed germination and vigor and is therefore not recommended as a preplant protectant

Screening Selected Solanum Plants as Potential Rootstocks for the Management of Root-Knot Nematodes (Meloidogyne incognita)

Root-knot nematodes (RKNs) (Meloidogyne spp.) represent agricultural pest of many economic crops, including tomatoes and potatoes. They advance a complex parasitic relationship with roots of tomato plants leading to modification of host structural and physiological functions in addition to significant yield loss. Resistance in solanaceous plants to RKNs has been identified and associated with the possession of Mi gene. The reaction of four Solanum rootstocks (S. aethiopicum L., S. macrocarpon L., S. lycopersicum L.“Mongal F1,” and S. lycopersicum L. “Samrudhi F1”) was evaluated in pots and in a natural Meloidogyne spp.-infested field in a two-year trial (2015–2016), to identify RKN-resistant rootstock(s), which can be utilized in tomato grafting as a management measure against these nematodes. A rootstock’s reaction to RKNs was assessed using root gall scores (GSs), egg count/g of root, and reproductive factors (Rfs) at the end of 6 and 12 weeks after transplanting (wat) in infested fields, respectively. Solanum macrocarpon, S. aethiopicum, and Mongal F1 showed tolerant responses with reduced root galling and low to high reproductive factors in pot and field experimentation. Although Samrudhi F1 was resistant in both pot and field trials and consistently decreased nematode root galling (<1.00) and reproduction (Rf < 1.00), it failed to significantly increase yield, as compared with the highest yield obtained by the tolerant rootstock, Mongal F1 (870.3 and 1236.6 g/plant, respectively). Evaluation of the four rootstocks against four (0, 500, 1,000, and 5000) RKN inocula levels (Juveniles) showed no significant differences among the growth parameters (fresh and dry shoot and root weights). Root-knot nematode-susceptible tomato varieties, for example, Pectomech F1, a popular tomato variety in Ghana, can be grafted onto the RKN-resistant and RKN-tolerant rootstocks for increased yields

Pathogenicity of Meloidogyne incognita and Fusarium oxysporum f. sp. vasinfectum on Growth and Yield of Two Okra Varieties Cultivated in Ghana

The interaction of the fungus, Fusarium oxysporum f. sp. vasinfectum (FOV), and the nematode, Meloidogyne incognita, on wilt disease on “Essoumtem” and Clemson spineless okra varieties, was examined in pot and field experiments from September 2016 to June 2017, in the University of Ghana farms. Four-week-old “Essoumtem” and Clemson spineless seedlings for pot experiment and one-week-old “Essoumtem” and Clemson spineless seedlings for field experiment were inoculated with fungus, Fusarium oxysporum, and nematode, Meloidogyne incognita. The individual, simultaneous, and sequential inoculation of second stage juveniles (at 1000 J2/kg soil) of Meloidogyne incognita and Fusarium oxysporum (1.1 × 106 cells/kg soil) resulted in significant reduced plant growth parameters (plant height, plant girth, chlorophyll content, fresh and dry shoot weights, and fresh and dry root weights). Maximum suppression in plant growth parameters was observed in plants that received NF21 (Fusarium oxysporum inoculated 21 days after Meloidogyne incognita on okra) and F21 (fungus inoculated 21 days after seedling emergence) treatments for pot and field experiments, respectively. The least suppression of plant growth parameters was observed in separate inoculations of the two pathogens for both pot and field experiments. Maximum suppression in yield parameters was observed in okra plants that received NF21 and F21 treatments for pot and field experiments, respectively. Minimal yield suppression was observed for individual inoculations (N and F treatments) in both pot and field experiments. The highest severity of wilt disease was observed on okra plants that received NF21 and F21 treatment in both pot and field experiments. Plants in control plots had higher yields and the least wilt incidences (0.0%)

Identification and molecular characterisation of Colletotrichum species from avocado, citrus and pawpaw in Ghana

Owing to previous identifications based solely on morphological characteristics, the identity of the causal agents of anthracnose disease of pawpaw and avocado in Ghana is in doubt. In addition, the pathogen has not been identified previously on citrus. In this study, isolates of the pathogen were obtained from anthracnose lesions on avocado and pawpaw, and atypical anthracnose lesions on citrus. The isolates were identified using PCR with speciesspecific primers, complemented by phylogenetic analysis of nucleotide sequences of the internal transcribed spacer region and partial glyceraldehyde-3-phosphate dehydrogenase gene. The pathogenicity of the isolated fungi was determined on detached matured fruits. All isolates, including those isolated from citrus, were identified as Colletotrichum gloeosporioides from the expected 480 bp PCR products amplified by PCR. The phylogenetic analysis showed that isolates from avocado and pawpaw were C. siamense, rather than C. gloeosporioides, whereas isolates from citrus were C. gloeosporioides sensu stricto. The pathogens were able to induce disease only on wounded mature fruits.Keywords: Colletotrichum gloeosporioides sensu stricto, Colletotrichum siamense, glyceraldehyde-3-phosphate dehydrogenase, internal transcribed spacer regio

Principal Component Analysis and Molecular Characterization of Reniform Nematode Populations in Alabama

U.S. cotton production is suffering from the yield loss caused by the reniform nematode (RN), Rotylenchulus reniformis. Management of this devastating pest is of utmost importance because, no upland cotton cultivar exhibits adequate resistance to RN. Nine populations of RN from distinct regions in Alabama and one population from Mississippi were studied and thirteen morphometric features were measured on 20 male and 20 female nematodes from each population. Highly correlated variables (positive) in female and male RN morphometric parameters were observed for body length (L) and distance of vulva from the lip region (V) (r = 0.7) and tail length (TL) and c′ (r = 0.8), respectively. The first and second principal components for the female and male populations showed distinct clustering into three groups. These results show pattern of sub-groups within the RN populations in Alabama. A one-way ANOVA on female and male RN populations showed significant differences (p ≤ 0.05) among the variables. Multiple sequence alignment (MSA) of 18S rRNA sequences (421) showed lengths of 653 bp. Sites within the aligned sequences were conserved (53%), parsimony-informative (17%), singletons (28%), and indels (2%), respectively. Neighbor-Joining analysis showed intra and inter-nematodal variations within the populations as clone sequences from different nematodes irrespective of the sex of nematode isolate clustered together. Morphologically, the three groups (I, II and III) could not be distinctly associated with the molecular data from the 18S rRNA sequences. The three groups may be identified as being non-geographically contiguous

Grafting for sustainable management of Fusarium wilt disease in tomato production in Ghana

Fusarium wilt disease limits tomato production, especially in Ghana. In managing the Fusarium wilt disease, two rootstocks (Solanum torvum and Solanum macrocarpon) were used in grafting experiments. Plant growth, yield, disease severity and incidence of both grafted plants, and non-grafted plants were evaluated in a pot experiment and also under a naturally infected open field condition at Berekum. During the early stage (14 days after inoculation) under artificial inoculation conditions, grafted plants exhibited higher photosynthetic rates (10.41 μmol−2s−1) compared to the non-grafted plants (8.36 μmol−2s−1). Under naturally infested field conditions, chlorophyll content and photosynthetic rate of non-grafted plants decreased. Solanum lycopersicum grafted onto S. macrocarpon and S. torvum were moderately susceptible (20%–40%) to Fusarium oxysporum. However, the non-grafted plants were highly susceptible (50%–100%). Yield from the pot experiment for S. lycopersicum grafted onto S. macrocarpon was significantly higher (453.1 g/plant), compared to S. lycopersicum grafted onto S. torvum (350.3 g/plant) and the non-grafted plant (205 g/plant). However, in naturally infected field, the grafted plants increased in fruit yield compared to the non-grafted tomato plants. Solanum macrocarpon and S. torvum as rootstocks offered resistance against F. oxysporum and showed significantly lower disease progression, than the non-grafted plants (P < 0.05). This study revealed that grafting is an effective tool for the management of Fusarium wilt disease and for tomato growth and yield improvement