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Rinaldo D, Rolland-Sabaté A, Lange D, Pétro D. Varietal and environmental influences on organoleptic and cooking quality of water yam (Dioscorea alata) landraces. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4729-4737. [PMID: 37471517 DOI: 10.1002/jsfa.12873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/08/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Yam is a major staple food that provides both energy (starch) and bioactive compounds. However, there is a lack of knowledge on its cooking quality. We have determined the cooking quality of five varieties of water yam (among those most appreciated by consumers), when they were steamed or boiled. The yams were grown in two contrasting locations with regard to pedoclimatic conditions. RESULTS Ratio of length to mean circumference of the tuber, difficulty to peel, cooking time, color attributes, hardness of steamed pulp, and dry matter (DM) and starch contents significantly varied among varieties. Cooking time and hardness of the cooked pulp, either steamed or boiled, were higher for tubers grown at the drier location, with vertisols, than at the rainy one, with a ferralitic soil. The raw pulp was richer in starch at the rainy location. We found no correlation between either textural properties or DM and the cooking time. A slight (r = 0.44) but significant correlation was recorded between the DM of the raw pulp and the hardness of the steamed product. CONCLUSION We propose a comprehensive multicriteria approach for determination of yam cooking quality, textural properties, color attributes and chemical composition, along with varietal and environmental influences. This approach takes into consideration the complexity of food quality, allows a better understanding of its determinants and provides a basis for useful guidelines for breeders. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Jiang Y, Lu XY, Qin YL, Zhang YM, Shao ZQ. Genome-Wide Identification and Evolutionary Analysis of Receptor-like Kinase Family Genes Provides Insights into Anthracnose Resistance of Dioscorea alata. PLANTS (BASEL, SWITZERLAND) 2024; 13:1274. [PMID: 38732488 PMCID: PMC11085297 DOI: 10.3390/plants13091274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Dioscorea alata, commonly known as "greater yam", is a vital crop in tropical and subtropical regions of the world, yet it faces significant threats from anthracnose disease, mainly caused by Colletotrichum gloeosporioides. However, exploring disease resistance genes in this species has been challenging due to the difficulty of genetic mapping resulting from the loss of the flowering trait in many varieties. The receptor-like kinase (RLK) gene family represents essential immune receptors in plants. In this study, genomic analysis revealed 467 RLK genes in D. alata. The identified RLKs were distributed unevenly across chromosomes, likely due to tandem duplication events. However, a considerable number of ancient whole-genome or segmental duplications dating back over 100 million years contributed to the diversity of RLK genes. Phylogenetic analysis unveiled at least 356 ancient RLK lineages in the common ancestor of Dioscoreaceae, which differentially inherited and expanded to form the current RLK profiles of D. alata and its relatives. The analysis of cis-regulatory elements indicated the involvement of RLK genes in diverse stress responses. Transcriptome analysis identified RLKs that were up-regulated in response to C. gloeosporioides infection, suggesting their potential role in resisting anthracnose disease. These findings provide novel insights into the evolution of RLK genes in D. alata and their potential contribution to disease resistance.
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Affiliation(s)
- Yuqian Jiang
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
| | - Xin-Yu Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China;
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ya-Li Qin
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China;
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Zhu-Qing Shao
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
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Gogile A, Kebede M, Kidanemariam D, Abraham A. Identification of yam mosaic virus as the main cause of yam mosaic diseases in Ethiopia. Heliyon 2024; 10:e26387. [PMID: 38449648 PMCID: PMC10915350 DOI: 10.1016/j.heliyon.2024.e26387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Yam (Dioscorea spp.) is a staple food crop with cultural, nutritional and economic significance for millions of small-scale farmers in sub-Saharan Africa. While various virus-like symptoms such as mosaic and chlorosis are frequently observed in yam fields in Ethiopia, little information is available on the prevalence, distribution, and molecular characteristics of viruses causing these symptoms. The aim of this study was to investigate the incidence and distribution of yam viruses and determine the primary cause of yam mosaic diseases (YMD) in Ethiopia. Both symptomatic (n = 280) and asymptomatic (n = 110) yam leaf samples were collected and tested for potyviruses using ACP-ELISA. In addition, the symptomatic leaf samples were screened for yam mosaic virus (YMV), yam mild mosaic virus (YMMV), and cucumber mosaic virus (CMV) by DAS-ELISA. Subsequently, total RNA was extracted from 130 leaf samples comprising 94 symptomatic and 36 asymptomatic samples representing the different study areas. The representative RT-PCR amplicons (n = 6) were Sanger sequenced. The ACP-ELISA and DAS-ELISA results showed 9.2%, and 12.9% YMV infection, respectively, while the RT-PCR analysis showed 28.5% YMV positivity rate. Both CMV and YMMV were not detected in any of the samples tested. Thus, YMV is confirmed as the primary cause of YMD in Ethiopia. YMV isolates from Ethiopia shared 92-93% nucleotide identity among themselves and 85-99% with other YMV isolates from the GenBank. Phylogenetic analysis revealed that YMV isolates from Ethiopia, South America, and west-central Africa have the most recent common ancestor, while isolates from China and Japan are clustered as sister groups. This study enhances our understanding of YMV's genetic diversity and provides valuable information regarding the first report of YMV in Ethiopia.
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Affiliation(s)
- Ashebir Gogile
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Wolaita Sodo University, P.O.Box 138, Wolaita Sodo, Ethiopia
| | - Misrak Kebede
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
| | - Dawit Kidanemariam
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Adane Abraham
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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Dentika P, Blazy JM, Alleyne A, Petro D, Eversley A, Penet L. High Genetic Diversity and Structure of Colletotrichum gloeosporioides s.l. in the Archipelago of Lesser Antilles. J Fungi (Basel) 2023; 9:619. [PMID: 37367555 DOI: 10.3390/jof9060619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
Colletotrichum gloeosporioides is a species complex of agricultural importance as it causes anthracnose disease on many crop species worldwide, and strong impact regionally on Water Yam (Dioscorea alata) in the Caribbean. In this study, we conducted a genetic analysis of the fungi complex in three islands of the Lesser Antilles-Guadeloupe (Basse Terre, Grande Terre and Marie Galante), Martinique and Barbados. We specifically sampled yam fields and assessed the genetic diversity of strains with four microsatellite markers. We found a very high genetic diversity of all strains on each island, and intermediate to strong levels of genetic structure between islands. Migration rates were quite diverse either within (local dispersal) or between islands (long-distance dispersal), suggesting important roles of vegetation and climate as local barriers, and winds as an important factor in long-distance migration. Three distinct genetic clusters highlighted different species entities, though there was also evidence of frequent intermediates between two clusters, suggesting recurrent recombination between putative species. Together, these results demonstrated asymmetries in gene flow both between islands and clusters, and suggested the need for new approaches to anthracnose disease risk control at a regional level.
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Affiliation(s)
- Pauline Dentika
- Institut National de Recherche Pour L'Agriculture, L'Alimentation et L'Environnement (INRAE), Research Unit ASTRO, F-97170 Petit-Bourg, Guadeloupe, France
| | - Jean-Marc Blazy
- Institut National de Recherche Pour L'Agriculture, L'Alimentation et L'Environnement (INRAE), Research Unit ASTRO, F-97170 Petit-Bourg, Guadeloupe, France
| | - Angela Alleyne
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, University of the West Indies, Bridgetown BB11000, Barbados
| | - Dalila Petro
- Institut National de Recherche Pour L'Agriculture, L'Alimentation et L'Environnement (INRAE), Research Unit ASTRO, F-97170 Petit-Bourg, Guadeloupe, France
| | | | - Laurent Penet
- Institut National de Recherche Pour L'Agriculture, L'Alimentation et L'Environnement (INRAE), Research Unit ASTRO, F-97170 Petit-Bourg, Guadeloupe, France
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Natural Flora Is Indiscriminately Hosting High Loads of Generalist Fungal Pathogen Colletotrichum gloeosporioides Complex over Forest Niches, Vegetation Strata and Elevation Gradient. J Fungi (Basel) 2023; 9:jof9030296. [PMID: 36983464 PMCID: PMC10058380 DOI: 10.3390/jof9030296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Crop pathogenic fungi may originate from reservoir pools including wild vegetation surrounding fields, and it is thus important to characterize any potential source of pathogens. We therefore investigated natural vegetation’s potential for hosting a widespread pathogenic group, Colletotrichum gloeosporioides species complex. We stratified sampling in different forest environments and natural vegetation strata to determine whether the fungi were found preferentially in specific niches and areas. We found that the fungi complex was fairly broadly distributed in the wild flora, with high prevalence in every study environment and stratum. Some significant variation in prevalence nevertheless occurred and was possibly associated with fungal growth conditions (more humid areas had greater prevalence levels while drier places had slightly lower presence). Results also highlighted potential differences in disease effects of strains between strata components of study flora, suggesting that while natural vegetation is a highly probable source of inoculums for local crops nearby, differences in aggressiveness between vegetation strata might also lead to differential impact on cultivated crops.
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Rinaldo D, Sotin H, Pétro D, Le-Bail G, Guyot S. Browning susceptibility of new hybrids of yam (Dioscorea alata) as related to their total phenolic content and their phenolic profile determined using LC-UV-MS. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dentika P, Ozier-Lafontaine H, Penet L. Weeds as Pathogen Hosts and Disease Risk for Crops in the Wake of a Reduced Use of Herbicides: Evidence from Yam ( Dioscorea alata) Fields and Colletotrichum Pathogens in the Tropics. J Fungi (Basel) 2021; 7:jof7040283. [PMID: 33918581 PMCID: PMC8069099 DOI: 10.3390/jof7040283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
The transition toward sustainable agriculture requires rethinking cropping systems in the light of less intensive and chemically reliant practices. Weed management is one of the target practices to evolve cropping systems with decreased impact on the environment. While softened management will lead to increased weeds/crops coexistence, it is of importance to assess the relative benefits and drawbacks of new practices. Among the potential drawbacks of weeds/crops coexistence, disease risk may increase if weeds are hosting pathogens. In this study, we assessed the potential of weeds for hosting pathogenic generalist fungi known to translate into disease in crops. We first describe prevalence in fields after harvest and relate prevalence to species characteristics and communities. Then, we directly test the idea that weeds serve as inoculums sources during cropping with a natural experiment. This study highlights variation in host skill among feral weeds for Colletotrichum species, including potential congeneric sub-specialization on different weeds within communities. Last, prevalence within fields was more correlated to focal crop inoculation rates compared to local weed load, but there was a significant correlation effect with prevalence on weeds in the vicinity of fields, suggesting that weeds are mediating disease levels at the local scale, too. Results pointed to the importance of weed host skill in disease risk yet open the door to the potential control of pathogens via targeted weed management.
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Frézal L, Jacqua G, Neema C. Adaptation of a Fungal Pathogen to Host Quantitative Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:1554. [PMID: 30429860 PMCID: PMC6220312 DOI: 10.3389/fpls.2018.01554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/03/2018] [Indexed: 05/29/2023]
Abstract
Impact of host quantitative resistance on pathogen evolution is still poorly documented. In our study, we characterized the adaptation of the pathogenic fungus Colletotrichum gloeosporioides, to the quantitative resistance of its host, the water yam (Dioscorea alata). Genetic and pathogenic diversities of C. gloeosporioides populations were specified at the field scale. We used nuclear markers to describe fungal population structuring within and between six fields of three cultivars differently susceptible to the fungus. Strain aggressiveness was then quantified in the laboratory through cross-inoculation tests. The high level of genetic diversity and significant linkage disequilibrium revealed a significant influence of clonal reproduction in the C. gloeosporioides evolution. The recorded fungal migration between fields was weak (evidence for a dispersion mode via tubers rather than splashing dispersal), which provides the first molecular evidence for limited C. gloeosporioides migration via yam tuber exchanges. C. gloeosporioides's populations are adapted to their host resistance. The aggressiveness of the fungal clones seems to have evolved toward an accumulation of components specific to each host cultivar. Despite the remaining marks of adaptation to the former widely cultivated host, adaptation to current cultivars was clearly depicted.
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Affiliation(s)
- Lise Frézal
- INRA-URPV, Guadeloupe, France
- CNRS – ENS – INSERM, Institut de Biologie de l’Ecole Normale Supérieure, Paris, France
| | | | - Claire Neema
- UMR BGPI, Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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Penet L, Briand S, Petro D, Bussière F, Guyader S. Data on microsatellite markers in Colletotrichum gloeosporioides s.l., polymorphism levels and diversity range. Data Brief 2017; 12:644-648. [PMID: 28540357 PMCID: PMC5432675 DOI: 10.1016/j.dib.2017.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/12/2017] [Accepted: 05/04/2017] [Indexed: 12/01/2022] Open
Abstract
Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2-29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.
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Affiliation(s)
- Laurent Penet
- INRA, UR1321, ASTRO Agrosystèmes tropicaux, F‐97170, Petit‐Bourg (Guadeloupe) France
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