Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava
The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 mill...
| Autores principales: | , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2012
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/35257 |
| _version_ | 1855542469909807104 |
|---|---|
| author | Ferguson, Morag E. Hearne, Sarah Jane Close, T.J. Wanamaker, S. Moskal, W.A. Town, C.D. Young, J. de Marri, P.R. Rabbi, Ismail Y. Villiers, Etienne P. de |
| author_browse | Close, T.J. Ferguson, Morag E. Hearne, Sarah Jane Marri, P.R. Moskal, W.A. Rabbi, Ismail Y. Town, C.D. Villiers, Etienne P. de Wanamaker, S. Young, J. de |
| author_facet | Ferguson, Morag E. Hearne, Sarah Jane Close, T.J. Wanamaker, S. Moskal, W.A. Town, C.D. Young, J. de Marri, P.R. Rabbi, Ismail Y. Villiers, Etienne P. de |
| author_sort | Ferguson, Morag E. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 million people. Here, expressed sequence tags (ESTs) were generated from five drought stressed and well-watered cassava varieties. Two cDNA libraries were developed: one from root tissue (CASR), the other from leaf, stem and stem meristem tissue (CASL). Sequencing generated 706 contigs and 3,430 singletons. These sequences were combined with those from two other EST sequencing initiatives and filtered based on the sequence quality. Quality sequences were aligned using CAP3 and embedded in a Windows browser called HarvEST:Cassava which is made available. HarvEST:Cassava consists of a Unigene set of 22,903 quality sequences. A total of 2,954 putative SNPs were identified. Of these 1,536 SNPs from 1,170 contigs and 53 cassava genotypes were selected for SNP validation using Illumina’s GoldenGate assay. As a result 1,190 SNPs were validated technically and biologically. The location of validated SNPs on scaffolds of the cassava genome sequence (v.4.1) is provided. A diversity assessment of 53 cassava varieties reveals some sub-structure based on the geographical origin, greater diversity in the Americas as opposed to Africa, and similar levels of diversity in West Africa and southern, eastern and central Africa. The resources presented allow for improved genetic dissection of economically important traits and the application of modern genomics-based approaches to cassava breeding and conservation. |
| format | Journal Article |
| id | CGSpace35257 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace352572024-08-27T12:27:43Z Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava Ferguson, Morag E. Hearne, Sarah Jane Close, T.J. Wanamaker, S. Moskal, W.A. Town, C.D. Young, J. de Marri, P.R. Rabbi, Ismail Y. Villiers, Etienne P. de animal breeding research crops The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 million people. Here, expressed sequence tags (ESTs) were generated from five drought stressed and well-watered cassava varieties. Two cDNA libraries were developed: one from root tissue (CASR), the other from leaf, stem and stem meristem tissue (CASL). Sequencing generated 706 contigs and 3,430 singletons. These sequences were combined with those from two other EST sequencing initiatives and filtered based on the sequence quality. Quality sequences were aligned using CAP3 and embedded in a Windows browser called HarvEST:Cassava which is made available. HarvEST:Cassava consists of a Unigene set of 22,903 quality sequences. A total of 2,954 putative SNPs were identified. Of these 1,536 SNPs from 1,170 contigs and 53 cassava genotypes were selected for SNP validation using Illumina’s GoldenGate assay. As a result 1,190 SNPs were validated technically and biologically. The location of validated SNPs on scaffolds of the cassava genome sequence (v.4.1) is provided. A diversity assessment of 53 cassava varieties reveals some sub-structure based on the geographical origin, greater diversity in the Americas as opposed to Africa, and similar levels of diversity in West Africa and southern, eastern and central Africa. The resources presented allow for improved genetic dissection of economically important traits and the application of modern genomics-based approaches to cassava breeding and conservation. 2012-03 2014-04-14T10:55:40Z 2014-04-14T10:55:40Z Journal Article https://hdl.handle.net/10568/35257 en Limited Access Springer Ferguson, M.E., Hearne, S.J., Close, T.J., Wanamaker, S., Moskal, W.A., Town, C.D., Young, J. de, Marri, P.R., Rabbi, I.Y. and Villiers, E.P. de. 2012. Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava. Theoretical and Applied Genetics 124(4): 685 - 695 |
| spellingShingle | animal breeding research crops Ferguson, Morag E. Hearne, Sarah Jane Close, T.J. Wanamaker, S. Moskal, W.A. Town, C.D. Young, J. de Marri, P.R. Rabbi, Ismail Y. Villiers, Etienne P. de Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title | Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title_full | Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title_fullStr | Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title_full_unstemmed | Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title_short | Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava |
| title_sort | identification validation and high throughput genotyping of transcribed gene snps in cassava |
| topic | animal breeding research crops |
| url | https://hdl.handle.net/10568/35257 |
| work_keys_str_mv | AT fergusonmorage identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT hearnesarahjane identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT closetj identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT wanamakers identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT moskalwa identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT towncd identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT youngjde identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT marripr identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT rabbiismaily identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava AT villiersetiennepde identificationvalidationandhighthroughputgenotypingoftranscribedgenesnpsincassava |