Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance
The development of molecular technologies for breeding tetraploid brachiaria interspecific hybrids (Urochloa spp.) was limited by its ploidy, the lack of a tetraploid Urochloa reference genome and the consequent drawback of using only simplex markers to construct linkage maps. However, the current i...
| Autores principales: | , , , , |
|---|---|
| Formato: | Informe técnico |
| Lenguaje: | Inglés |
| Publicado: |
Bioversity International and the International Center for Tropical Agriculture
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/126112 |
| _version_ | 1855517838727446528 |
|---|---|
| author | Espitia, Paula A. Hernández, Luis Miguel Ryan, Camilla Vega, Jose J. de Jauregui, Rosa |
| author_browse | Espitia, Paula A. Hernández, Luis Miguel Jauregui, Rosa Ryan, Camilla Vega, Jose J. de |
| author_facet | Espitia, Paula A. Hernández, Luis Miguel Ryan, Camilla Vega, Jose J. de Jauregui, Rosa |
| author_sort | Espitia, Paula A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The development of molecular technologies for breeding tetraploid brachiaria interspecific hybrids (Urochloa spp.) was limited by its ploidy, the lack of a tetraploid Urochloa reference genome and the consequent drawback of using only simplex markers to construct linkage maps. However, the current increasing availability of open-source tools for genomic data in polyploid species has broadened the genetic resources that are available for the breeding of these forages. Using RAD sequencing data from a multiparenting mapping population, a new fully resolved genome of U. decumbens and phenotypical scoring for tolerance and antibiosis to Aeneolamia varia, we designed a bioinformatics pipeline to construct genetic maps that allow us to identify QTL associated with resistance to this spittlebug species. The next steps are to test different software and techniques for each phase in the pipeline, control the quality of the outputs and deliver accurate results from the phenotypic and genotypic data association. |
| format | Informe técnico |
| id | CGSpace126112 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Bioversity International and the International Center for Tropical Agriculture |
| publisherStr | Bioversity International and the International Center for Tropical Agriculture |
| record_format | dspace |
| spelling | CGSpace1261122025-12-08T10:29:22Z Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance Espitia, Paula A. Hernández, Luis Miguel Ryan, Camilla Vega, Jose J. de Jauregui, Rosa computer software pest resistance bioinformatics urochloa hemiptera cercopidae bioinformática programas de ordenador The development of molecular technologies for breeding tetraploid brachiaria interspecific hybrids (Urochloa spp.) was limited by its ploidy, the lack of a tetraploid Urochloa reference genome and the consequent drawback of using only simplex markers to construct linkage maps. However, the current increasing availability of open-source tools for genomic data in polyploid species has broadened the genetic resources that are available for the breeding of these forages. Using RAD sequencing data from a multiparenting mapping population, a new fully resolved genome of U. decumbens and phenotypical scoring for tolerance and antibiosis to Aeneolamia varia, we designed a bioinformatics pipeline to construct genetic maps that allow us to identify QTL associated with resistance to this spittlebug species. The next steps are to test different software and techniques for each phase in the pipeline, control the quality of the outputs and deliver accurate results from the phenotypic and genotypic data association. 2022-12 2022-12-20T14:00:00Z 2022-12-20T14:00:00Z Report https://hdl.handle.net/10568/126112 en Open Access application/pdf Bioversity International and the International Center for Tropical Agriculture Espitia, P.A.; Hernández, L.M.; Ryan, C.; de Vega, J.; Jauregui, R. (2022) Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance. Cali (Colombia): Alliance of Bioversity International and CIAT. 3 p. |
| spellingShingle | computer software pest resistance bioinformatics urochloa hemiptera cercopidae bioinformática programas de ordenador Espitia, Paula A. Hernández, Luis Miguel Ryan, Camilla Vega, Jose J. de Jauregui, Rosa Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title | Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title_full | Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title_fullStr | Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title_full_unstemmed | Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title_short | Developing a bioinformatics pipeline for Urochloa spp. mapping population: from RAD sequencing data to identification of QTL for spittlebug resistance |
| title_sort | developing a bioinformatics pipeline for urochloa spp mapping population from rad sequencing data to identification of qtl for spittlebug resistance |
| topic | computer software pest resistance bioinformatics urochloa hemiptera cercopidae bioinformática programas de ordenador |
| url | https://hdl.handle.net/10568/126112 |
| work_keys_str_mv | AT espitiapaulaa developingabioinformaticspipelineforurochloasppmappingpopulationfromradsequencingdatatoidentificationofqtlforspittlebugresistance AT hernandezluismiguel developingabioinformaticspipelineforurochloasppmappingpopulationfromradsequencingdatatoidentificationofqtlforspittlebugresistance AT ryancamilla developingabioinformaticspipelineforurochloasppmappingpopulationfromradsequencingdatatoidentificationofqtlforspittlebugresistance AT vegajosejde developingabioinformaticspipelineforurochloasppmappingpopulationfromradsequencingdatatoidentificationofqtlforspittlebugresistance AT jaureguirosa developingabioinformaticspipelineforurochloasppmappingpopulationfromradsequencingdatatoidentificationofqtlforspittlebugresistance |