Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies
Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping met...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1365132/full |
| _version_ | 1797263669668610048 |
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| author | Leah Nandudu Leah Nandudu Samar Sheat Stephan Winter Alex Ogbonna Robert Kawuki Jean-Luc Jannink Jean-Luc Jannink |
| author_facet | Leah Nandudu Leah Nandudu Samar Sheat Stephan Winter Alex Ogbonna Robert Kawuki Jean-Luc Jannink Jean-Luc Jannink |
| author_sort | Leah Nandudu |
| collection | DOAJ |
| description | Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies. |
| first_indexed | 2024-04-25T00:16:41Z |
| format | Article |
| id | doaj.art-68eda9d9ec1748129fa2929ffa0d02e8 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-25T00:16:41Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-68eda9d9ec1748129fa2929ffa0d02e82024-03-13T04:20:47ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-03-011510.3389/fpls.2024.13651321365132Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studiesLeah Nandudu0Leah Nandudu1Samar Sheat2Stephan Winter3Alex Ogbonna4Robert Kawuki5Jean-Luc Jannink6Jean-Luc Jannink7School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United StatesRoot Crops Department, National Crops Resources Research Institute (NaCRRI), Kampala, UgandaPlant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, GermanyPlant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, GermanySchool of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United StatesRoot Crops Department, National Crops Resources Research Institute (NaCRRI), Kampala, UgandaSchool of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United StatesUS Department of Agriculture, Agricultural Research Service (USDA-ARS), Ithaca, NY, United StatesCassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies.https://www.frontiersin.org/articles/10.3389/fpls.2024.1365132/fullcassavafood securityUgandan cassava brown streak virus (UCBSV) titercassava brown streak virus (CBSV)genomics |
| spellingShingle | Leah Nandudu Leah Nandudu Samar Sheat Stephan Winter Alex Ogbonna Robert Kawuki Jean-Luc Jannink Jean-Luc Jannink Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies Frontiers in Plant Science cassava food security Ugandan cassava brown streak virus (UCBSV) titer cassava brown streak virus (CBSV) genomics |
| title | Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies |
| title_full | Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies |
| title_fullStr | Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies |
| title_full_unstemmed | Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies |
| title_short | Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies |
| title_sort | genetic complexity of cassava brown streak disease insights from qpcr based viral titer analysis and genome wide association studies |
| topic | cassava food security Ugandan cassava brown streak virus (UCBSV) titer cassava brown streak virus (CBSV) genomics |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1365132/full |
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