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Hasan M, Gani R, Rashid DMRA, Tarin TK, Kamara R, Mou MY, Rabbi SF. Comprehensive smart smartphone image dataset for plant leaf disease detection and freshness assessment from Bangladesh vegetable fields. Data Brief 2024; 56:110775. [PMID: 39221011 PMCID: PMC11363486 DOI: 10.1016/j.dib.2024.110775] [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: 06/15/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Bangladesh's agricultural landscape is significantly influenced by vegetable cultivation, which substantially enhances nutrition, the economy, and food security in the nation. Millions of people rely on vegetable production for their daily sustenance, generating considerable income for numerous farmers. However, leaf diseases frequently compromise the yield and quality of vegetable crops. Plant diseases are a common impediment to global agricultural productivity, adversely affecting crop quality and yield, leading to substantial economic losses for farmers. Early detection of plant leaf diseases is crucial for improving cultivation and vegetable production. Common diseases such as Bacterial Spot, Mosaic Virus, and Downy Mildew often reduce vegetable plant cultivation and severely impact vegetable production and the food economy. Consequently, many farmers in Bangladesh struggle to identify the specific diseases, incurring significant losses. This dataset contains 12,643 images of widely grown crops in Bangladesh, facilitating the identification of unhealthy leaves compared to healthy ones. The dataset includes images of vegetable leaves such as Bitter Gourd (2223 images), Bottle Gourd (1803 images), Eggplants (2944 images), Cauliflowers (1598 images), Cucumbers (1626 images), and Tomatoes (2449 images). Each vegetable class encompasses several common diseases that affect cultivation. By identifying early leaf diseases, this dataset will be invaluable for farmers and agricultural researchers alike.
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Affiliation(s)
- Mahamudul Hasan
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
| | - Raiyan Gani
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
| | | | - Taslima Khan Tarin
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
| | - Raka Kamara
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
| | - Mahbuba Yasmin Mou
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
| | - Sheikh Fajlay Rabbi
- Department of Computer Science and Engineering, East West University, Aftabnagar, Dhaka, Bangladesh
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Kaelin CB, McGowan KA, Hutcherson AD, Delay JM, Li JH, Kiener S, Jagannathan V, Leeb T, Murphy WJ, Barsh GS. Ancestry dynamics and trait selection in a designer cat breed. Curr Biol 2024; 34:1506-1518.e7. [PMID: 38531359 PMCID: PMC11162505 DOI: 10.1016/j.cub.2024.02.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/10/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats. The mean proportion of leopard cat DNA in the Bengal breed is 3.48%, lower than predicted from breed history, and is broadly distributed, covering 93% of the Bengal genome. Overall, leopard cat introgressions do not show strong signatures of selection across the Bengal breed. However, two popular color traits in Bengal cats, charcoal and pheomelanin intensity, are explained by selection of leopard cat genes whose expression is reduced in a domestic cat background, consistent with genetic incompatibility resulting from hybridization. We characterize several selective sweeps in the Bengal genome that harbor candidate genes for pelage and color pattern and that are associated with domestic, rather than leopard, cat haplotypes. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies glitter, a trait desired by breeders that affects hair texture and light reflectivity.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - John M Delay
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Chen Y, Miao L, Li X, Liu Y, Xi D, Zhang D, Gao L, Zhu Y, Dai S, Zhu H. Comparative Transcriptome Analysis between Resistant and Susceptible Pakchoi Cultivars in Response to Downy Mildew. Int J Mol Sci 2023; 24:15710. [PMID: 37958694 PMCID: PMC10649052 DOI: 10.3390/ijms242115710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Downy mildew caused by the obligate parasite Hyaloperonospora brassicae is a devastating disease for Brassica species. Infection of Hyaloperonospora brassicae often leads to yellow spots on leaves, which significantly impacts quality and yield of pakchoi. In the present study, we conducted a comparative transcriptome between the resistant and susceptible pakchoi cultivars in response to Hyaloperonospora brassicae infection. A total of 1073 disease-resistance-related differentially expressed genes were identified using a Venn diagram. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these genes were mainly involved in plant-pathogen interaction, plant hormone signal transduction, and other photosynthesis-related metabolic processes. Analysis of the phytohormone content revealed that salicylic acid increased significantly in the resistant material after inoculation with Hyaloperonospora brassicae, whereas the contents of jasmonic acid, abscisic acid, and 1-aminocyclopropane-1-carboxylic acid decreased. Exogenous salicylic acid treatment also significantly upregulated Hyaloperonospora brassicae-induced genes, which further confirmed a crucial role of salicylic acid during pakchoi defense against Hyaloperonospora brassicae. Based on these findings, we suggest that the salicylic-acid-mediated signal transduction contributes to the resistance of pakchoi to downy mildew, and PAL1, ICS1, NPR1, PR1, PR5, WRKY70, WRKY33, CML43, CNGC9, and CDPK15 were involved in this responsive process. Our findings evidently contribute to revealing the molecular mechanism of pakchoi defense against Hyaloperonospora brassicae.
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Affiliation(s)
- Yaosong Chen
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 201418, China
| | - Liming Miao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Xiaofeng Li
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Yiwen Liu
- Institute of Agricultural Science and Technology Information, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Dandan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Dingyu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Lu Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Yuying Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 201418, China
| | - Hongfang Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (Y.C.)
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Ali MA, Zhang F, Guan J, Ma Y. Editorial: Genetic and epigenetic regulation of disease resistance in horticultural plants. Front Genet 2023; 14:1277571. [PMID: 37732320 PMCID: PMC10507395 DOI: 10.3389/fgene.2023.1277571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Feng Zhang
- Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jiantao Guan
- Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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Wu Y, Zhang B, Liu S, Zhao Z, Ren W, Chen L, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Han F, Zhang Y. A Whole-Genome Assembly for Hyaloperonospora parasitica, A Pathogen Causing Downy Mildew in Cabbage ( Brassica oleracea var. capitata L.). J Fungi (Basel) 2023; 9:819. [PMID: 37623590 PMCID: PMC10456066 DOI: 10.3390/jof9080819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Hyaloperonospora parasitica is a global pathogen that can cause leaf necrosis and seedling death, severely threatening the quality and yield of cabbage. However, the genome sequence and infection mechanisms of H. parasitica are still unclear. Here, we present the first whole-genome sequence of H. parasitica isolate BJ2020, which causes downy mildew in cabbage. The genome contains 4631 contigs and 9991 protein-coding genes, with a size of 37.10 Mb. The function of 6128 genes has been annotated. We annotated the genome of H. parasitica strain BJ2020 using databases, identifying 2249 PHI-associated genes, 1538 membrane transport proteins, and 126 CAZy-related genes. Comparative analyses between H. parasitica, H.arabidopsidis, and H. brassicae revealed dramatic differences among these three Brassicaceae downy mildew pathogenic fungi. Comprehensive genome-wide clustering analysis of 20 downy mildew-causing pathogens, which infect diverse crops, elucidates the closest phylogenetic affinity between H. parasitica and H. brassicae, the causative agent of downy mildew in Brassica napus. These findings provide important insights into the pathogenic mechanisms and a robust foundation for further investigations into the pathogenesis of H. parasitica BJ2020.
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Affiliation(s)
- Yuankang Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Bin Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Shaobo Liu
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Zhiwei Zhao
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Wenjing Ren
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Li Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
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Mourou M, Raimondo ML, Lops F, Carlucci A. Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1033. [PMID: 36903895 PMCID: PMC10005080 DOI: 10.3390/plants12051033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.
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Affiliation(s)
- Marwa Mourou
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | | | | | - Antonia Carlucci
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
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Sheng X, Yu H, Wang J, Shen Y, Gu H. Establishment of a stable, effective and universal genetic transformation technique in the diverse species of Brassica oleracea. FRONTIERS IN PLANT SCIENCE 2022; 13:1021669. [PMID: 36311069 PMCID: PMC9597678 DOI: 10.3389/fpls.2022.1021669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Brassica oleracea is an economically important species, including seven cultivated variants. Agrobacterium-mediated transformation of B. oleracea crops, mainly via hypocotyl and cotyledon, has been achieved in the past. However, previously established transformation methods showed low efficiency, severe genotype limitation and a prolonged period for transformants acquisition, greatly restricting its application in functional genomic studies and crop improvement. In this study, we have compared the shoot regeneration and genetic transformation efficiency of hypocotyl, cotyledon petiole and curd peduncle explants from twelve genotypes of cauliflower and broccoli. Finally, an Agrobacterium-mediated transformation method using curd peduncle as explant was established, which is rapid, efficient, and amenable to high-throughput transformation and genome editing. The average genetic transformation efficiency of this method is stable up to 11.87% and was successfully implemented in twelve different genotypes of cauliflower and broccoli and other B. oleracea crops with low genotype dependence. Peduncle explants were found to contain abundant cambial cells with a strong cell division and shoot regeneration ability, which might be why this method achieved stable and high genetic transformation efficiency with almost no genotype dependence.
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Harnessing adult-plant resistance genes to deploy durable disease resistance in crops. Essays Biochem 2022; 66:571-580. [PMID: 35912968 PMCID: PMC9528086 DOI: 10.1042/ebc20210096] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.
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