Hindawi International Journal of Microbiology Volume 2023, Article ID 8690464, 12 pages https://doi.org/10.1155/2023/8690464 Research Article Seed-Borne Fungi Associated with Diverse Rice Varieties Cultivated in the Western North Region of Ghana Francis Mensah Ackaah,1 Seloame Tatu Nyaku ,2 and Edmund Darkwa1 1West Africa Center for Crop Improvement (WACCI), University of Ghana, PMB 30, Legon, Accra, Ghana 2Department of Crop Science, School of Agriculture, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG44, Legon, Accra, Ghana Correspondence should be addressed to Seloame Tatu Nyaku; stnyaku@ug.edu.gh Received 17 August 2022; Revised 6 January 2023; Accepted 13 January 2023; Published 27 January 2023 Academic Editor: Clemencia Chaves Lopez Copyright © 2023 FrancisMensahAckaah et al.Tis is an open access article distributed under theCreative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rice is amajor staple in the Ghanaian diet. However, its production is constrained by fungal diseases. A survey was conducted in 2018 in three selected districts in the Western North Region of Ghana using a structured questionnaire and face-to-face interaction with 230 farmers to assess their knowledge, perceptions of seed-borne fungal diseases, and management practices. Additionally, fungi associated with farmer’s seeds were isolated and identifed through the Agar and Blotter tests. Findings indicate that 72.7% of the farmers in the selected districts relied on their saved seeds for planting.Tirteen fungal genera were associated with the rice seed samples collected from the three districts. Te Juaboso district had the majority (13) of seed-borne fungi. Te seed samples were categorized into various forms of discolouration, and signifcant diferences (P< 0.05) existed among the seed samples for this parameter. Te AGRA rice, a farmer- saved seed from Juaboso, had the highest level of seed discolouration (41.96%). Fungi identifed to be associated with the dark brown/ brown discolouration of rice seeds were Bipolaris spp., Fusarium spp.,Macrophomina phaseolina and Aspergillus spp. Te only fungus associated with the yellow/pale yellow colour was Bipolaris spp.Te fungi Bipolaris spp., Curvularia spp., and Botryodiplodia spp. were associated with the dark spot discolouration.Alternaria spp., andAspergillus spp. were observed on the greyish white seed discolouration sample. Fungi are associated with rice cultivation and vary according to district and rice variety. A complex of pathogenic and saprophytic fungi therefore infects rice grains both in feld and storage conditions. 1. Introduction a critical component of food security in the twenty-frst century for many nations [5]. Rice is an important food source for more than half of the Rice sufers from several biotic and abiotic agents, world’s population. About 480 million metric tons of milled resulting in heavy losses to farmers. Among the several rice are produced worldwide each year [1]. Consumption of constraints to rice production, diseases caused by fungi, rice is rising swiftly over any other produce in Africa because nematodes, and bacteria cause major economic losses [6–8]. it is seen as a suitable food by the growing urban population Fungi play signifcant roles in reducing the quality of rice [1]. Rice production area harvested and yield were 973,000 seed through their infections [4].Tese pathogens cause seed tonnes, 331,471 ha, and 29,354 hg/ha for the year 2020 [2]. discolouration, seed rot, reduced seed germination, and Ghana spends about $450 million on rice imports to make vigour in seedlings, as well as making the plant weak during up for the shortfall in supply [3].Te husk of rice can be used its early growth period. Fungal diseases that are seed-borne to feed animals as well as used as a source of fuel and in are comparatively challenging to manage because the fungal biochar preparation. In developing countries, rice serves as hyphae get established and becomes dormant [9]. Most crop the most important crop and plays a major role in poverty diseases that are important economically are seed-borne and alleviation and food security attainment [4]. Rice is therefore seed transmitted, including blast disease of rice, bakanae, 2 International Journal of Microbiology loose smut, fag smut, Karnal bunt, and ear cockle of 2.2. Seed Sample Collection. Twelve samples were collected, wheat [10]. comprising farmer-saved seeds and certifed seeds, between Worldwide, about 56 fungal pathogens are reported to November and December, 2018. Te samples comprised infest rice, of which 41 are reported to be seed-borne [11]. three certifed seed samples, eight (8) farmer-saved seed Seed-borne infections in rice cause 50–80% yield losses, (FSS) samples, and one (1) local seed grower seed sample. depending on the agroecology, disease severity, and crop Te samples were made up of the following varieties: AGRA susceptibility [12]. In the Ashanti Region of Ghana, about 20 rice, Bosome mmienu, Kotoko, Mercy, Lapete, and Agya fungal species (16 pathogens and 4 saprophytes) associated Amoah rice (Table 1). Te farmer-saved seed samples of the with rice seeds have been identifed [13]. Te most common AGRA rice were collected from three selected localities fungal species recognized included Bipolaris oryzae, Fusa- within a district and bulked as the farmers-saved seed sample rium verticillioides, Fusarium oxysporum, Cercospora sp., from that particular district. Samples of seeds collected from and Curvularia lunata [13, 14]. Farmers who rely on their the various districts were placed into zip-lock bags, labelled, farm-saved seeds are likely to contaminate their subsequent sealed, and sent to West Africa Centre for Crop Improve- seeds for the next planting season in instances where there is ment (WACCI) seed laboratory and the Plant Pathology seed-borne pathogen transmission from the soil. Laboratory at the University of Ghana for seed health tests Tis research was carried out to assess farmers’ and pathogen isolation and identifcation, respectively. knowledge and their perceptions on fungal diseases asso- ciated with rice, and also isolate and identify fungal diseases 2.3.PhysicalQualityAssessment. Physical quality assessment associated with rice production in the Western North Re- was undertaken to separate the pure seeds from the other gion of Ghana. foreign materials, e.g., weed seeds, stones, etc. through physical examination. Samples were thoroughly mixed, and 2. Materials and Methods 500 g of each sample was weighed for the purity, test which 2.1. Field Survey: Assessing Farmers Knowledge on the Fungal was done with the use of a diaphanoscope (Ultra Swift Lite Seed-Borne Diseases of Rice. A feld survey was conducted in System, China). Te samples examined were categorized the selected districts within theWestern North Region, one of into broken/cracked, seeds with hull/husk, spotted seed/ the newly established regions in Ghana. Te selected districts discolored seed, insect damage, and undamaged. All indi- were Sefwi Waiwso Municipal, Juaboso District, and Bodi vidual components were weighed and expressed as a per- District. Te districts were selected based on previous records centage by the weight of the whole component using the within the districts as hotspots for some seed-borne diseases, formula; (weight of component/total weight) ∗ 100. Te namely, “bakanae,” “foot rot,” and “blast [15]. Te selected discoloured seeds were grouped into various colours (dark communities were also based on their popularity for the spot, yellowish/pale yellow brown, and greyish white) using production of rice within the districts. Tese were Bodi a colour chart. (N6.261961 W-2.754935), Afere (N6.315215 W-2.813313), Amoaya, Bokabo, and Asuopiri (N6.303535 W-794272) for 2.4. Germination Test. Te guidelines of the International Bodi district; Boako (N6.394969 W-2.577142), Asafo Seed Testing Association (ISTA) were followed in the ger- (N6.386971 W-2.654035), Datano (N6.244280 W-2.489403), mination test. Te experiment involving the top of paper Afrimkrom (N6.382248 W-2.639918) and Gyampokrom method (TP), involved 100 seeds (25 seeds per plate) rep- (N6.391655 W-2.615335) for Waiwso Municipal and Juaboso licated 3 times for each sample placed on Petri plates and laid (N6.344330 W-2.828550), Nkwanta (N6.381392 W- with moist flter paper. Te petri dishes were covered with 2.840373), Sanyerano, Benchema and Proso-Kofkrom for lids. Te set up was kept in a germination room under Juaboso District. suitable environment (85–90% RH, 25°C). After 10 days, the Between October and December, 2018, a feld survey was seeds and seedlings were evaluated and categorized into conducted using a structured questionnaire to gather in- normal seedlings, abnormal seedlings, hard seeds, fresh formation from the farmers (Supplementary Method). seeds, and dead seeds as a percentage of the seeds examined Farmers were selected randomly as respondents. Te in- as classifed by ISTA. Seedlings that had well developed plant formation gathered included demographics about the parts, including a well-developed rooting system and well- farmers, sources of seeds, production, varieties, disease in- developed green leaves emerging, were classifed as normal cidence, and control, as well as their knowledge on fungal seedlings. Seedlings that lacked one of the essential plant part seed-borne diseases. A printed picture plate of diseases of such as a root or leaf or had other defects were classifed as rice were used to aid the farmers identify and compare abnormal seedlings. Freshly ungerminated seeds were symptoms they observed on their various farms. A sample classifed as hard seeds. Rotten seeds that failed to germinate size of 230 farmers was selected at random for the survey were classifed as dead seeds. (https://wacci.ug.edu.gh/content/francis-mensah-ackaah) Te germination and composition percentages were [16]. Te respondents consisted of 86, 74, and 70 for Bodi calculated based on the average of 100 seeds in 3 replicates district, Juaboso district, and Wiawso municipal, and expressed as a percentage using the formula stated respectively. below. International Journal of Microbiology 3 Table 1: Sources and varieties of seed samples obtained from the three selected districts. District Community Variety Source Datano, Boako, Amprompe AGRA rice Farmer saved seed Wiawso municipal MoFA district ofce AGRA rice Certifed Asafo (NRGP) AGRA rice Local seed grower Juaboso, Nkwanta, Bonsu AGRA rice Farmer saved seed Benchemaa, Nkatieso, Proso-Kof krom Kotoko Farmer saved seed Juaboso Nkatieso, Proso-Kof Krom Agyamoah Farmer saved seedProso-Kof krom Mercy Farmer saved seed Proso-Kof krom Bossome mmienu Farmer saved seed MoFA district ofce AGRA rice Certifed Afere, Aferewaa Amoaya AGRA rice Farmer saved seed Bodi Aferewaa Lapete Farmer saved seed MoFA district ofce AGRA rice Certifed Total number of germinated seeds X 100 Germination percentage(%) � . (1) Total number of seeds plated After the seed germination evaluation, the percentages of the various categories were calculated by the formula;   Total number component X 100Composition percentage(%) � . (2) Total number of seeds plated 2.5. Seed Health Test. Two methods (Agar test and Blotter at 25 + 2°C. After the incubation period, pathogens were test), were employed for the seed health testing following the morphologically identifed based on the colony’s colour, International Seed Testing Association [17]. shape, and size. A compound microscope (Ultra Swift Lite System, China) was then used to examine and confrm the 2.6. Blotter Test. Hundred seeds each of the various samples pathogens on the basis of growth of mycelium and other were randomly selected and surface sterilized with 2% so- fruiting bodies, spore shape and size as described in the dium hypochlorite (NaOCl2). Filter papers were moistened technical bulletin on seed-borne diseases and seed health and placed in petri plates. One hundred (100) seeds, in testing of rice [18]. Unknown cultures were grown on Agar batches of 10 seeds, were arranged per plate and replicated 3 media for improved growth to aid identifcation. times. Te seeds in the plates were in incubated for 7–8 days Number of infected seeds by individual fungal X 100 Percentage prevalence of individual fungi � . (3) Total number of seeds plated 2.7. Agar Method. Potato Dextrose Agar (PDA) enhanced saprophytes grow rapidly on the media, which mostly axenic fungal growth for further identifcations after usage of prevents the growth of important pathogens of interest. Te the incubation method. Five (5 g) powdered agar was mixed seeds were then plated and incubated for 7–8 days at with 100ml of water and stirred. It was then autoclaved for 25 + 2°C. After the incubation period, pathogens were 15–20minutes, after which it was cooled to about 50°C. Te morphologically identifed based on the colony’s color, Agar was then transferred into the petri-dishes, which so- shape, and size. A compound microscope (Ultra Swift Lite lidifed in about 20minutes. Antibiotics and amoxicillin, System, China) was then used to examine and confrm the were added to the Agar to inhibit the growth of bacteria. pathogens on the basis of growth of mycelium and other After the solidifcation phase, the seeds were surface ster- fruiting bodies, spore shape and size as described in the ilized with sodium hypochlorite in order to eliminate any technical bulletin on seed-borne diseases and seed health form of contamination as well as saprophytic organisms.Te testing of rice [18]. 4 International Journal of Microbiology 2.8. Determination of Percentage Incidence of Fungi on Table 2: Percent distribution of varieties of rice cultivated by Samples Collected from theTree SelectedDistricts. Te seeds farmers in the three rice growing districts. infected by fungi were counted for each sample, divided by Varieties of rice Number of farmers Percentage the total number of seeds plated, and multiplied by 100% to AGRA 191 83.0 determine the percent incidence. Lapete 26 11.3 Jasmine 5 2.2 2.9. Fungi Associated with Discolored Seeds. Hundred (100) Agyamoah 4 1.7Mercy 2 0.9 seeds each from the six varieties were sampled and critically Bossom mmienu 1 0.4 examined. Te seeds were grouped according to their col- Kotoko 1 0.4 ours. Te discoloured seeds were grouped into diferent Total 230 100.0 categories and plated using the blotter method. Te diferent categories were dark spot, brown/dark brown, yellow/pale yellow, and greyish white. 3.2.2. Seedling Rot. Seventy-three (73) farmers representing 31.7% of the farmers responded they observed symptoms of seedling rot, however, 157 farmers (68.3%) indicated they 2.10. Data Analysis. Te IBM SPSS STATICSTICS 22 was did not observe any seedling rot symptoms. used to analyze the feld survey data. Fungal pathogen count data were subjected to analysis of variance (ANOVA), and the means were separated using the least signifcant dif- 3.2.3. Seedling Blight. Over seventy percent (73.5%) of the ference (LSD) at a 5% probability level, in GenStat Statistical farmers had observed seedling blight before, as shown to Package (12th Edition). them on a picture plate. About 26.5% responded that they had not observed any symptoms of seedling blight in their 3. Results felds. 3.1. Farmers’ Knowledge andPerception onFungal Seed-Borne Diseases of Rice, Varieties of Rice Cultivated and Storage 3.2.4. Respondents Perceptions of the Causes of Diseases. Practices Employed About (25%) of farmers indicated pathogens solely caused diseases on their farms, and 24% indicated both pathogens 3.1.1. Farmers’ Knowledge on Varieties of Rice Cultivated in and soilborne organisms as major causes of diseases. Twenty the Study Area. All the farmers interviewed had knowledge percent (20%) of the respondents reported soil-borne or- about the varieties of rice they cultivated. Tey were able to ganisms caused diseases in their farms. However, 9% did not provide the names of the varieties they cultivated. Seven know the causes of diseases in their felds, and 6% reported varieties were mostly cultivated by the farmers: AGRA, seed-borne diseases were the causes of diseases on “Jasmine,” “Lapete,” “Bossom mmienu,” “Mercy,” their farms. “AgyaAmoah” and “Kotoko.” Te varieties “Bossom mmienu” and “Kotoko” were cultivated by 0.4% of farmers (Table 2). Out of the 230 farmers, 191 representing 83%, 3.2.5. Assessment of Physical Quality of Seeds. All seed cultivated AGRA, followed by the local rice variety, “Lapete,” samples examined had some percentages of undamaged which was cultivated by twenty-six farmers (11.3%). Five seeds, cracked or broken seeds, and discoloured seeds farmers (2.2%) cultivated “Jasmine” rice variety, four (Table 3). Tere were signifcant diferences (P< 0.05) farmers cultivated “Agyamoah” rice variety and two farmers among undamaged seeds. Te least undamaged seeds cultivated “Mercy.” Only one farmer cultivated each of (93.1%) were the “Bossome mmienu” seeds. Te AGRA FSS “Bossom mmienu,” and “Kotoko” rice cultivars. rice seed sample collected from Juaboso had the least un- damaged (50.21%) seeds. Seed discolouration was observed on seed samples ob- 3.1.2. Source of Seeds for Planting. Forty-three percent (43%) tained from farmers as they saved seeds. Tere were sig- of the respondents planted their saved seeds, 28.3% of the nifcant diferences (P< 0.05) among the seed samples farmers planted certifed seeds obtained directly from var- regarding seed discolouration. Te AGRA rice sample col- ious MoFA ofces (Crops Services Department), and 28.7% lected as Farmer-saved seed from Juaboso, had the highest used both farmer-saved and certifed seeds. level of seed discoulouration (41.96%). Other seed varieties “Lapete” and “Mercy” had seed discolouration values 3.2. Recognition of Diseases (39.73% and 38%), respectively. Tere were signifcant diferences (P< 0.05) among the seed samples for broken/ 3.2.1. Rice Blast. One hundred and seventy-nine (179) cracked seeds. Te seed sample obtained from MoFA ofce, farmers, representing 77.8% of the respondents, reported Juaboso and NRGP had the least percentage (2.81% and that they have observed symptoms of blast at various stages 2.91%) of broken/cracked seeds respectively. Te highest of rice production. However, 51 farmers (22.2%) indicated percentages (7.91% and 7.83%) of broken seeds were on the they did not observe any symptoms of blast on their “Mercy” rice seed sample and the AGRA rice variety, rice seeds. respectively. International Journal of Microbiology 5 Table 3: Categories of seed types and their percentages collected from three districts. Damaged Source Sample Undamaged Total Cracked/broken Discoulored Agra Wiawso 58.20 7.82 33.98 100.00 Certifed (MOFA) Agra Juaboso 78.31 2.81 18.88 100.00 AGRA BODI Mofa 81.08 3.12 15.80 100.00 Local seed producer Agra Nrgp 58.13 2.91 38.96 100.00 Agra Wiawso Fss 68.10 4.17 27.73 100.00 Agra Juaboso Fss 50.21 7.83 41.96 100.00 Agra Bodi Fss 62.31 3.89 33.80 100.00 Farmer saved seeds (FSS) Mercy Juaboso 54.09 7.91 38.00 100.00Kotoko Juaboso 89.06 2.98 7.96 100.00 Agyamoah Juaboso 71.32 4.01 24.67 100.00 “Bosomme Mmienu” 93.12 3.58 3.30 100.00 Lapete Bodi 55.89 4.38 39.73 100.00 LSD 4.09 0.44 2.24 P< 0.05 0.001 0.001 0.001 3.2.6. Germination Test and Seedling Evaluation of Rice 3.3.2. Fungi Associated with the Rice Seed Samples Collected Samples Collected from Tree Districts. Te local rice seed from the Tree Selected Districts. All seed samples collected sample, “Bossome mmienu,” collected from farmers in from the three selected districts had various seed-borne fungi at Juaboso performed better and had a high germination score diferent levels of infection (Table 6). Tirteen fungi in total (94.67%) of normal seedlings. Tere were signifcant were associated with the rice seed samples collected. Six out of (P< 0.05) diferences among the seed samples with regards the thirteen fungi identifed were saprophytic, and seven were to germination percentages (Table 4). Te sample with the pathogenic. Some the saprophytes were Aspergillus favus, lowest germination rate was the AGRA rice variety collected Asperfllus niger, Mucor spp., Penicillium spp., and Rhizopus from farmers in the Bodi district. spp. All the seed samples collected scored high levels of sap- Comparing the AGRA rice varieties, the samples taken rophytes. Not all the fungi identifed were present on all the fromMoFA ofces that were certifed seeds performed better seed samples collected from the diferent districts. Te Juaboso in terms of germination than the farmer saved seeds. Tere district scored the highest number of fungi identifed (Table 6) were signifcant diferences among them. AGRA rice sample whiles the Bodi district scored the lowest number of fungi collected fromWiawso scored highest among the AGRA rice associated with rice seeds. In the Bodi district, Aspergillus niger samples with 93.33% normal seedlings followed by the scored the highest frequency of fungi infection (28.25%) fol- AGRA rice variety collected from farmers in the Wiawso lowed byMacrophomina spp. (23.65%) while Aspergillus favus Municipality (89.67%). Te AGRA rice sample collected scored the least frequency of infection with 5.95%. from farmers in the Wiawso municipal was the only FSS In the Juaboso District, Aspergillus favus scored the sample which performed better than the MoFA sourced highest frequency of fungi infection at 19.42%, followed by samples. Te AGRA rice seed sample collected from farmers Aspergillus niger, 12.38%.Collectotricum spp. scored the least in the Bodi district performed worst in terms of germination, frequency of infection at 1.92%. Aspergillus favus scored the scoring 62.33% of normal seedling germination. Tere were highest frequency of infection in the Wiawso District, fol- signifcant (P< 0.05) diferences among the abnormal seed lowed by Curvularia spp. (Table 6). percentages of the various samples. Te AGRA sample collected from the Wiawso Farmers and the Mercy rice seed sample collected from the Juaboso had the lowest per- 3.3.3. Frequency of Fungi Associated with the Diferent Rice centages (4%) of abnormal seedlings. Seed Varieties Sampled in the Selected Districts. Te varietyAGRA scored the highest prevalence of fungi followed by the variety “Bossomme mmienu” (Table 7). Te variety Mercy 3.3. Seed Health scored the least number of fungi infections with only fve fungi reported to be associated with the Mercy rice seed 3.3.1. Prevalence of Seed-Borne Fungi Using Diferent Iden- sample. All thirteen fungi identifed were reported to be tifcation Methods. Tirteen fungi were identifed, com- associated with the AGRA rice seed variety. Aspergillus prising of twelve genera (Table 5). Eight fungi were identifed favus, Aspergillus Niger, Rhizopus spp., and Penicillium spp. using the blotter method. Te Blotter test could not support were associated with all the rice seed varieties sampled. Te the growth of some fungi. Aspergillus niger, Aspergillus favus, “Mercy” rice variety had the highest prevalence of Asper- Fusarium spp., Penicillium spp., Rhizopus spp., Mucor spp., gillus niger, whiles “Agyamoah” rice variety had the highest Macrophomina phaseolina, and Bipolaris oryzae were iden- prevalence rate of Aspergillus favus. Bipolaris oryzae was tifed by both the Agar and Blotter tests. Pyricularia spp., observed on only three varieties: AGRA, “Agyamoah,” and Trichoderma spp., Botryodiplodia spp., Curvularia spp., and “Bossomme mmienu,” with 13.77%, 9.59%, and 7.36%, re- Collectitrocum spp.were identifed only through the Agar test. spectively. Te “Agyamoah” rice variety had the highest 6 International Journal of Microbiology Table 4: Percent categorization of the various components of the evaluation of germination test into normal, abnormal, fresh, and dead seeds in the three selected districts. Source Seed sample Normal seedlings Abnormal seedlings Fresh seeds Dead seeds Agra Wiawso 93.33 4.27 1.20 1.20 Certifed (MOFA) Agra Juaboso 83.00 10.27 0.00 6.73 Agra Bodi 81.33 11.93 2.20 4.54 Local seed producer Agra 75.00 9.83 2.73 12.44 Agra wiawso 89.67 4.00 2.00 4.33 Agra Juaboso 74.00 13.33 3.63 9.04 Agra Bodi 62.33 5.83 4.83 27.01 Farmer saved seeds Mercy Juaboso 91.33 4.00 1.87 2.80Kotoko Juaboso 89.00 5.00 0.00 6.00 Agyamoah Juaboso 80.67 9.20 2.80 7.33 “Bosomme Mmienu” 94.67 1.67 0.70 2.96 Lapete Bodi 80.67 11.2 0.33 7.80 LSD 7.59 1.17 1.17 1.32 P< 0.05 0.001 0.001 0.001 0.001 Table 5: Fungi isolated and identifed using diferent methods (blotter and agar). Fungi identifed Blotter Agar Aspergillus Niger ∗∗ ∗∗ Aspergillus favus ∗∗ ∗∗ Fusarium spp. ∗ ∗∗ Trichoderma spp. − ∗ Macrophomina phaseolina ∗ ∗ Rhizopus spp. ∗ ∗∗ Bipolaris oryzae ∗ ∗∗ Botryodiplodia spp. − ∗ Curvularia spp. − ∗ Pyricularia spp. − ∗ Penicillium spp. ∗∗ ∗∗ Collectotricum spp. − ∗ Mucor spp. − ∗ ∗∗Frequency above 50%, ∗frequency below 50%, —fungi not observed. Table 6: Frequency of fungi on rice seeds samples collected from the three selected districts. Fungi identifed Bodi Juaboso Wiawso Aspergillus Niger ++ ++ ++ Aspergillus favus + ++ ++ Fusarium spp. ++ + ++ Trichoderma spp. + + − Macrophomina phaseolina ++ + + Rhizopus spp. ++ + ++ Bipolaris oryzae − + + Botryodiplodia spp − + − Curvularia spp − ++ ++ Pyricularia spp + + ++ Penicillium spp + + + Collectotricum spp − + − Mucor spp − + + − � not present, +� incidence below 10%, ++� incidence between 11–30%, +++� incidence above 30%. NB: +� low prevalence, ++�moderate prevalence, +++� high prevalence. prevalence rate of Bipolaris oryzae. Curvularia spp. was 3.3.4. Frequency of Fungi Infection of the Variety AGRA in identifed on only two rice varieties. Pyricularia spp. was the Selected Districts. Eleven (11) out of the thirteen fungi identifed on the Kotoko rice variety and the AGRA rice identifed were observed on the AGRA rice seeds. Te Bodi variety at 19.91% and 4.09% frequency of occurrence, re- farmer-saved seed sample had the highest number of fungi spectively (Table 7). associated with the seeds however the AGRA Farmer Saved International Journal of Microbiology 7 Table 7: Fungi identifed on rice seed varieties collected from the three selected districts tested by the blotter method. Agra Lapete Mercy Bossome Mmienu Agyamoah Kotoko Aspergillus Niger +++ +++ +++ +++ +++ +++ Aspergillus favus ++ + + + +++ ++ Fusarium spp. ++ ++ ++ ++ − ++ Trichoderma spp + − − + − + Macrophomina phaseolina ++ − − + + − Rhizopus spp. ++ +++ ++ + ++ + Bipolaris oryzae ++ − − + +++ − Botryodiplodia spp ++ − − − − − Curvularia spp ++ − − − +++ − Pyricularia spp + ++ − − ++ ++ Penicillium spp + + + + + + Collectotricum spp + − − − − − Mucor spp + − + − + − − � not present, +� incidence below 10%, ++� incidence between 11–30%, +++� incidence above 30%. NB: +� low prevalence, ++�moderate prevalence, +++� high prevalence. seeds from Wiawso District had the least number of fungi varieties, the local varieties, for example, Lapete was also an associated with the seeds, mainly saprophytes; Aspergillus early maturing variety and resistant to pest and diseases. favus, Aspergillus niger, and Rhizopus spp. However, this Tey explained that the local varieties were able to withstand was the only AGRA rice sample which had Pyricularia spp. harsh weather conditions such as drought, pests and associated with it (Table 8). fooding compared to the newly improved varieties, even though the improved varieties give higher yields. In a study by Marfo et al. [20] rice varieties such as “AgyaAmoah,” 3.3.5. Discolored Seeds and Associated Fungi. Fungi cause “Mercy,” “Bosome Mmiensa,” “Bosome Nnan,” “Kotoko,” seed discolouration in varying forms. Fungi which had dark “Abankora,” and “Sikamo” were grown by farmers in the brown/brown discolouration of rice seeds were Bipolaris Western Region. However, the preferred variety was “Agya oryzae, Fusarium spp., Macrophomina spp. and Aspergillus Amoah” because of the following characteristics: yield spp. (Table 9). However, only Bipolaris oryzaewas associated (45%), grain size (17%), and early maturity (16%). with the yellow/pale yellow colour. Bipolaris oryzae, Cur- vularia spp., Fusarium spp., and Botryodiplodia spp., were associated with the dark spot discolouration. Alternaria spp. 4.2. Source of Seeds for Planting. Majority of the farmers andAspergillus spp. were identifed on the greyish white seed interviewed (70%) use their saved seeds for planting in the discolouration sample. next season, and about 28% of them used certifed seeds.Te farmers used their own saved seeds because, they did not have access to certifed seeds easily, some also preferred to 4. Discussion use their saved seeds because of lower costs. Some farmers however indicated there were no diferences between their 4.1. Knowledge of Farmers on Varieties of Seeds Cultivated. saved seeds and the certifed seeds. Tose who used certifed Majority of the farmers interviewed planted Agra rice fol- seeds obtained their seeds from the district agriculture of- lowed by Lapete, a local rice variety. “Bossom mmienu” and fces, few agro input shops, and NGOs. Te percentage of “Kotoko” varieties were cultivated by only 0.4% of the re- farmers (28%) using certifed seeds relatively increased spondent. AGRA rice was the mostly used variety by the compared to percent of farmers listed in the literature study farmers constituting 83%. Tis is as a result of various (11%) [19]. Tis was because certifed seeds were obtained Programs and projects enrolled by the Government of from MoFA under the Planting for Food and Jobs (PFJ). Ghana through the Ministry of Food and Agriculture and Farmer-saved seeds were the main source of seeds for the other institutions such as Ghana Rice Interprofessional farmers in the three districts. Over 70% of rice farmers Body. In a previous study by Ragasa et al. [19], increased use depend on their saved seeds for subsequent seasons, espe- of certifed seeds was encouraged through projects initiated cially in the sub-Saharan Africa where most farmers do not by the Government of Ghana and or Development Agencies. buy certifed seeds, because of high prices [21]. Tose who Te Planting for Food and Jobs under MOFA was a major used farmer-saved seeds and local varieties acquired their fagship program introduced by the Government of Ghana seeds in the form of seed exchange, gifts, and from the local in 2017 to promote the use of the AGRA rice variety. In spite market. of all these interventions, some farmers still preferred to use local farmer-saved seeds. A rice variety “Agya Amoah” which was introduced to the farmers in the selected districts 4.3. Rice Seed Storage and Storage Practices of Farmers in the back in 1987 was still in use by some farmers. Te farmers Tree Selected Districts. Majority of the farmers (96.1%) in indicated that, even though there were programs and pro- the three districts stored their seeds at home under ambient jects to enhance the use of certifed seeds and improved temperatures in nylon bags and jute sacks. About 2.6% of the 8 International Journal of Microbiology Table 8: Comparison of the fungal infection of samples of the variety AGRA collected from diferent sources (MoFA, farmer-saved seeds (FSS) and NRGP) in the three selected district. Agra Wiawso MoFA Agra Wiawso FSS Agra Wiawso NRGP Agra Juaboso MOFA Agra Juaboso FSS Agra Bodi FSS Agra Bodi MOFA Aspergillus Niger ++ +++ ++ ++ ++ +++ + Aspergillus favus +++ + +++ +++ +++ +++ +++ Fusarium spp. ++ − ++ − ++ ++ ++ Trichoderma spp. − − − − − ++ + Macrophomina phaseolina ++ − ++ − − ++ − Rhizopus spp ++ ++ ++ ++ − ++ ++ Bipolaris oryzae ++ − +++ − ++ ++ − Botryodiplodia spp ++ − ++ − − ++ − Curvularia spp +++ − − − + +++ − Pyricularia spp. − + − − − − − Penicillium spp − − − − − − Collectotricum spp − − − − − − − Mucor spp − − + − + − − − � not present, +� incidence below 10%, ++� incidence between 11–30%, +++� incidence above 30%. NB: +� low prevalence, ++�moderate prevalence, +++� high prevalence. International Journal of Microbiology 9 Table 9: Percentage of seed-borne fungi associated with various discolouration types in the rice seed samples collected from the three selected districts. Type of Pathogens associated discolouration Bipolaris oryzae Curvularia spp. Fusarium spp. Alternaria spp. Macrophomina spp. Botryodiplodia spp. Aspergillus spp. Dark brown/brown Agra 39 0 41 0 7 0 18 Agyamoah 48 0 33 0 5 0 5 Kotoko 12 0 19 0 9 0 9 Mercy 29 0 9 0 18 0 11 Lapete 31 0 18 0 12 0 3 Bossom Mmienu 5 0 41 0 15 0 3 Yellow/pale yellow Agra 31 0 0 0 0 0 0 Agyamoah 28 0 0 0 0 0 0 Kotoko 5 0 0 0 0 0 0 Mercy 11 0 0 0 0 0 0 Lapete 9 0 0 0 0 0 0 Bossom Mmienu 5 0 0 0 0 0 0 Dark spot Agra 19 27 11 0 0 5 0 Agyamoah 21 8 8 0 0 8 0 Kotoko 8 9 10 0 0 11 0 Mercy 11 4 0 0 0 19 0 Lapete 9 18 0 0 0 8 0 Bossom Mmienu 6 3 0 0 0 7 0 Greyish white Agra 0 0 5 16 0 0 0 Agyamoah 0 0 8 21 0 0 3 Kotoko 0 0 6 9 0 0 2 Mercy 0 0 3 11 0 0 3 Lapete 0 0 11 18 0 0 1 Bossom Mmienu 0 0 8 5 0 0 0 10 International Journal of Microbiology farmers stored their seeds in a warehouse operated either by year. Inadequate storage facility inhibited storage for rela- a private individual or MoFA, and 1.3% of the respondents tively longer periods. Most of farmers did all year-round stored their seeds in cold storage. Most farmers in de- farming (two to four times a year), therefore will need seeds veloping countries, e.g., Ghana, store their seeds under for planting frequently. In the Ashanti region, 48% of rice ambient conditions where temperature and moisture farmers stored their seeds beyond six months [13]. Tose content vary. who stored their seeds for longer periods were likely to Te 1.3% of farmers who stored their seeds in cold storage attract more pathogens. Depending on the storage condi- explained they were advised by some agricultural ofcers to do tion, there quality of seeds reduced with increasing storage so. Tey usually stored seeds of new varieties introduced to duration [24]. them by agricultural ofcers. Tey stored their seeds in their home refrigerators usually only for a season at temperatures below 10°C. Te warehouse storage was managed by a private 4.4. Farmers Perception of Occurrence of Some Important Rice individual who stored assorted products for a fee payable Diseases. Farmers had little knowledge about seed-borne monthly. Tey were usually rice mill operators who stored diseases during a focal group discussion session. An average farmers’ seeds for them. Te majority of farmers who stored of about 60% of the farmers reported to have observed their seeds in nylon and jute sacks followed the traditional various symptoms of the seed-borne diseases. Te majority practice of storing produce.Tey stored them either in the store of the farmers (77.8%) observed symptoms of blast at various rooms or kitchens without measuring temperature and relative stages; 73.5% observed seedling blight whiles only 30% humidity (RH) of the storage environments. Te practice of observed seedling rot. In a previous study, the majority of seed storage in these locations may afect the seed quality and farmers interviewed in the Greater Mwea region of Kenya increase the development of pathogens on the rice seeds. Te were aware of the occurrence of rice diseases for e.g., rice bags for storing seeds may not be properly sealed allowing blast disease [25]. From the survey conducted, farmers ig- seeds to be exposed to moisture and other environmental nored symptoms of the various seed-borne diseases when factors, which enhance growth ofmicroorganisms on the seeds. these appeared during storage or on the felds. Tose who Rice with a high moisture content >21% increases rice dis- observed the symptoms of diseases perceived various causes coloration from temperatures 10°C to 40°C as storage period of the diseases. About 50% of the farmer-perceived diseases progresses. Tere is a higher expression of discoloration pat- were caused by pathogens, and few of them attributed the terns on rice seeds stored at the high temperatures for e.g., 40°C causes of the diseases to the source of seeds, soil, and insects. compared to storage at lower temperatures [22]. Most rice Farmers in some selected districts in Ghana paid much farmers in Ghana lack moisture meters to determine the attention to the symptoms of diseases. Te farmers made moisture content of their seeds and this together with storage observations of symptoms of seed-borne diseases such as environments with high temperatures >10°C results in mold rice blast, and they associated the symptoms with being development and discoloration of their seeds. In the study by caused by pathogens [15]. Similarly, rice farmers in Burkina [22] the total discoloured kernel area increased with increasing reported diseases as a major constraint to rice production storage moisture content (MC), temperature, and storage and were aware of the causes of the diseases [26]. duration, with about 100% discolouration observed at 16weeks at 40°C storage temperature. 4.5. Knowledge of Seed Borne Diseases. Majority of the re- Over 98% of the farmers did not treat their seeds spondents (87%) had observed the incidence of seed-borne (farmer-saved or certifed) before storage. Farmers who did diseases. Tey responded that they were aware of the fact not treat their seeds said, thorough drying under the sun that diseases “sit in the seeds.” Tirteen (13%) of the re- enhanced the prolonged storage of their seeds. Tose who spondents did not have any knowledge on seed-borne treated their seeds before storage used various insecticides diseases. In one study by Kihoro et al. [25] in Kenya, they such as Akate Master and Lambda. Tese insecticides were reported that 98% of rice farmers had knowledge about rice used because they believed any poisonous chemical will be blast, a seed-borne disease. efective in controlling any kind of infection or pathogen. Out of those who had knowledge about seed-borne dis- Te chemicals used by the farmers for treating their seeds eases, 50% treated their seeds with diferent kinds of chemicals were also used on other crops, for e.g., cocoa. Rice seed before planting. Tose who treated their seeds used any coating with for example Trichoderma spp., has been found chemical they perceived to be poisonous for e.g., Akate to be very useful in maintaining the seed quality and tol- Master, Lamda, and Dusband. Tose who did not treat their erance to biotic and abiotic stress [23]. seeds before planting relied on the sun as a treatment to Most of the farmers did not really observe changes as- control seed-borne diseases [13]. Rice farmers in Bangladesh, sociated with their seeds during storage.Tey did not bother treated their seeds with hot water, as well as selected fungi- to check for these changes until planting. However, 61% of cides (Bavistin 50 WP, Dithane M 45 and neem extract) [27]. farmers in the Ashanti region of Ghana observed changes associated with rice seeds during storage, they usually ob- served pest infestation during storage as reported [13]. 4.6. Detection and Identifcation of Seed-Borne Fungi on the Most of the farmers stored their seeds for three to fve Rice Samples Collected from the Tree Selected Districts. months. Only few of them stored up to 12months. Farmers Te current study identifed thirteen fungi to be associated in the three districts did not store their seeds beyond one with the rice seeds (Table 5). In a previous study, rice seeds International Journal of Microbiology 11 were associated with 20 fungi in the Ashanti Region. Among employed by the farmers. Tere is therefore the need to these, the following were not identifed in the current study, elucidate the biochemical basis of rice discoloration and the there were Alternaria padwickii, Alternaria spp.,, Cercospora relationship with specifc microorganisms. Tis will enable spp., Curvularia lunata, Curvularia pallescens, Fusarium development of microbe-specifc interventions against rice verticillioides, F. oxysporum, F. pallidoroseum, F. solani, discolouration. Nigrospora oryzae, Phoma spp., Sarocladium oryzae, and Stemphylium spp. Trichoderma spp., Macrophomina pha- Data Availability seolina, Botrydiplodia spp., and Pyricularia spp. identifed in our isolations were absent in those of Asamoah [13]. Similar Te authors confrm that the data supporting the fndings of fungi as identifed in the current study have been identifed this study are available within the article. on rice in Ghana [15, 28, 29]. Mucor spp. identifed in this study, was recently isolated from rice seeds in Kenya [27]. In Conflicts of Interest another study, Nustugah et al. [15] identifed Bipolaris oryzae, Pyricularia spp. and Magnaporthe spp. to be present Te authors declare that they have no conficts of interest or in Ghana in the northern region and upper east regions of personal relationships that could have appeared to infuence Ghana. Te absence of Magnaporthe oryzae from our study the work reported in this paper. sites, confrms the absence of rice blast disease caused by these fungi in farmers’ felds in the current study. Rice seed- Acknowledgments borne fungi such as Bipolaris oryzae, Cercospora sp., Col- Te authors thank theWorld Bank for providing a bursary to letotrichum sp., Curvularia lunata, and Curvularia pallescens support research for FMA. have been reported [30, 31]. Te high prevalence of storage fungi such as Aspergillus favus and Aspergillus niger on all Supplementary Materials rice seed samples was an indication that the seeds were stored under high temperature, and had high moisture Data survey sheet included under the Supplementary content. High temperature and moisture at storage have Method. (Supplementary Materials) been found to decrease germination of seeds of soy and maize as well as increasing the infection of Aspergillus favus. References Te high prevalence of storage fungi such as Aspergillus spp. have been reported to be associated with high moisture [1] USDA, “World Agricultural Production,” 2018, https://www. content [32]. Te high prevalence of storage fungi may also fas.usda.gov/data/world-agricultural-production. cause seed rotting. 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