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Part 1: Document Description
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Citation |
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Title: |
Data: Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America |
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Identification Number: |
doi:10.7910/DVN/H4PDE5 |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2024-09-16 |
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Version: |
2 |
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Bibliographic Citation: |
Ospina Colorado, Jessica Alejandra; Lopez Alvarez, Diana Carolina; Gimode, Winnie Riziki Adu; Wenzl, Peter; Carvajal-Yepes, Monica, 2024, "Data: Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America", https://doi.org/10.7910/DVN/H4PDE5, Harvard Dataverse, V2, UNF:6:ILxU5oEWF+J+qUI7SpwgeA== [fileUNF] |
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Citation |
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Title: |
Data: Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America |
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Identification Number: |
doi:10.7910/DVN/H4PDE5 |
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Authoring Entity: |
Ospina Colorado, Jessica Alejandra (International Center for Tropical Agriculture - CIAT) |
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Lopez Alvarez, Diana Carolina (International Center for Tropical Agriculture - CIAT) |
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Gimode, Winnie Riziki Adu (International Center for Tropical Agriculture - CIAT) |
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Wenzl, Peter (International Center for Tropical Agriculture - CIAT) |
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Carvajal-Yepes, Monica (International Center for Tropical Agriculture - CIAT) |
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Producer: |
International Center for Tropical Agriculture |
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Date of Production: |
2019-08-01 |
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Distributor: |
Harvard Dataverse |
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Distributor: |
International Center for Tropical Agriculture |
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Access Authority: |
Alliance Data Management |
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Depositor: |
Alliance Data Management |
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Date of Deposit: |
2024-07-19 |
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Holdings Information: |
https://doi.org/10.7910/DVN/H4PDE5 |
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Study Scope |
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Keywords: |
Agricultural Sciences, Earth and Environmental Sciences, cassava brown streak disease, genetic resources conservation, disease resistance, ex situ conservation, breeding, Americas, Crops for Nutrition and Health |
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Topic Classification: |
genome-wide association studies |
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Abstract: |
Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases. <br><br> Methodology:DNA was extracted from 234 accessions of Manihot esculenta, conserved at the CIAT genebank, which had previously been phenotyped by an independent group for CBSD resistance. The DNA was sent to DArT P/L for genotyping with DArTseq. Using the generated SNP data, we conducted a diversity analysis, population structure analysis, and genome-wide association study (GWAS) to identify genetic variants associated with CBSD resistance. |
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Time Period: |
2019-08-01-2024-05-01 |
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Date of Collection: |
2019-08-01-2023-05-01 |
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Kind of Data: |
Experimental Data |
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Kind of Data: |
Genomic Data |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
https://www.frontiersin.org/articles/10.3389/fpls.2019.00567/full#supplementary-material |
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Data Access |
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Disclaimer: |
<p>The Alliance of Bioversity International and CIAT (hereinafter "the Alliance"), its partners, and the data authors have exercised utmost care in collecting and compiling the data. However, the data is provided "as is" without any express or implied warranty. Neither the Alliance, its partners, the data authors, nor any relevant funding agencies shall be held liable for any actual, incidental, or consequential damages arising from the use of this data.</p> <p>By utilizing the Alliance Dataverse, users explicitly acknowledge that the data may contain nonconformities, defects, or errors. No warranty is provided that the data will meet users' needs or expectations, nor that all nonconformities, defects, or errors can or will be corrected.</p> <p>Users are responsible for verifying the accuracy and suitability of the data for their intended use. It is strongly recommended that users refer to related publications as a baseline for their analysis whenever possible. This practice serves as an additional safeguard against misinterpretation of the data. Related publications are listed in the metadata section of the respective Dataverse study.</p> |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Carvajal-Yepes, M., Ospina, J. A., Aranzales, E., Velez-Tobon, M., Correa Abondano, M., Manrique-Carpintero, N. C., & Wenzl, P. (2024). Identifying genetically redundant accessions in the world's largest cassava collection. Frontiers in plant science, 14, 1338377. https://doi.org/10.3389/fpls.2023.1338377 |
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Bibliographic Citation: |
Carvajal-Yepes, M., Ospina, J. A., Aranzales, E., Velez-Tobon, M., Correa Abondano, M., Manrique-Carpintero, N. C., & Wenzl, P. (2024). Identifying genetically redundant accessions in the world's largest cassava collection. Frontiers in plant science, 14, 1338377. https://doi.org/10.3389/fpls.2023.1338377 |
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Other Reference Note(s) |
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Sheat, S., Fuerholzner, B., Stein, B., & Winter, S. (2019). Resistance Against Cassava Brown Streak Viruses From Africa in Cassava Germplasm From South America. Frontiers in plant science, 10, 567. https://doi.org/10.3389/fpls.2019.00567 |
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Label: |
01a. readme.xlsx |
|
Text: |
file summarizing files content |
|
Notes: |
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet |