Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping
Dissertation (MSc)--University of Pretoria, 2014.
Saved in:
| Other Authors: | |
|---|---|
| Format: | Thesis |
| Language: | English |
| Published: |
University of Pretoria
2015
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613527433281536 |
|---|---|
| access_status_str | Open Access |
| author2 | Crampton, Bridget Genevieve |
| author_browse | Crampton, Bridget Genevieve |
| author_facet | Crampton, Bridget Genevieve |
| collection | Thesis |
| dc_rights_str_mv | © 2014 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Dissertation (MSc)--University of Pretoria, 2014. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/43200 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:34.018Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/43200 Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping Crampton, Bridget Genevieve nngoepe@gmail.com Rees, David Jasper G. Odeny, D.A. (Damaris) Ngoepe, Nare UCTD Dissertation (MSc)--University of Pretoria, 2014. Advances in next generation sequencing technologies have enabled researchers to do in depth genome studies. The steadily decreasing cost of sequencing has made it possible to conduct a Genotyping-by-Sequencing (GBS) approach both in plants and animals. A reliable and efficient genotyping protocol is crucial for studying and understanding the genetics and genomics of sorghum. The current work aimed at investigating the applicability of Genotyping-by-Sequencing techniques in a sorghum mapping population generated between sweet stem and grain sorghum parents. Two methods of Genotyping-by-Sequencing, whole genome shotgun (WGS) and restriction-site associated DNA (RAD) methods were used to examine the sorghum genome in this study. A total of 921 031 and 3 119 variants (SNPs and INDELs) were identified in WGS and RAD sequencing approaches respectively using CLC Genomics Workbench 6.0.1. The Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) pipeline identified a total of 2 701 814 and 17 012 in the WGS and the RAD sequencing approach respectively. The TASSEL pipeline identified 1 456 253 and 3 435 variants from the two parents in the WGS and the RAD sequencing approach respectively. The results revealed the RAD method as the better Genotyping-by-Sequencing approach for large populations and Trait Analysis by aSSociation, Evolution and Linkage as the best data analysis tool as it discovered more variations than CLC Genomics Workbench. The development of a precise and inexpensive Genotyping-by-Sequencing protocol serves as a robust framework to which sorghum populations can be characterized. These results will contribute towards genetic mapping of the markers and subsequent identification of quantitative trait loci (QTLs) governing different traits of interest contributing towards breeding for feedstock varieties that are optimized for biofuel production from sorghum. lk2014 Genetics MSc Unrestricted 2015-01-19T12:11:14Z 2015-01-19T12:11:14Z 2014/12/12 2014 Dissertation Ngoepe, N 2014, Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping, MSc Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/43200> M14/9/197 http://hdl.handle.net/2263/43200 en © 2014 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | UCTD Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title | Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title_full | Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title_fullStr | Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title_full_unstemmed | Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title_short | Genotyping-by-sequencing of sweet-stem and grain sorghum for linkage mapping |
| title_sort | genotyping by sequencing of sweet stem and grain sorghum for linkage mapping |
| topic | UCTD |
| url | http://hdl.handle.net/2263/43200 |