HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants
Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular m...
| Autores principales: | , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/155331 |
| _version_ | 1855516726254370816 |
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| author | Ongom, P.O. Ajibade, Y.A. Mohammed, S.B. Dieng, I. Fatokun, C. Boukar, O. |
| author_browse | Ajibade, Y.A. Boukar, O. Dieng, I. Fatokun, C. Mohammed, S.B. Ongom, P.O. |
| author_facet | Ongom, P.O. Ajibade, Y.A. Mohammed, S.B. Dieng, I. Fatokun, C. Boukar, O. |
| author_sort | Ongom, P.O. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication.
Methods
HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays).
Results
The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets.
Conclusions
This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain. |
| format | Journal Article |
| id | CGSpace155331 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1553312025-12-08T10:29:22Z HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants Ongom, P.O. Ajibade, Y.A. Mohammed, S.B. Dieng, I. Fatokun, C. Boukar, O. quality assurance quality control hybrids single nucleotide polymorphisms Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication. Methods HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays). Results The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets. Conclusions This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain. 2024 2024-10-14T09:12:04Z 2024-10-14T09:12:04Z Journal Article https://hdl.handle.net/10568/155331 en Open Access application/pdf MDPI Ongom, P.O., Ajibade, Y.A., Mohammed, S.B., Dieng, I., Fatokun, C. & Boukar, O. (2024). HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants. Genes, 15(10): 1252, 1-13. |
| spellingShingle | quality assurance quality control hybrids single nucleotide polymorphisms Ongom, P.O. Ajibade, Y.A. Mohammed, S.B. Dieng, I. Fatokun, C. Boukar, O. HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title | HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title_full | HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title_fullStr | HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title_full_unstemmed | HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title_short | HybridQC: A SNP-Based quality control application for rapid hybridity verification in diploid plants |
| title_sort | hybridqc a snp based quality control application for rapid hybridity verification in diploid plants |
| topic | quality assurance quality control hybrids single nucleotide polymorphisms |
| url | https://hdl.handle.net/10568/155331 |
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