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Analysis of maize germplasm relationships using RAPD and microsatellite markers
Thesis (MScAgric)--Stellenbosch University, 1996.
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Stellenbosch : Stellenbosch University
2012
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| _version_ | 1867613845793538048 |
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| access_status_str | Open Access |
| author | Anderssen, Irma Lindsay |
| author2 | Retief, A. E. |
| author_browse | Anderssen, Irma Lindsay Retief, A. E. |
| author_facet | Retief, A. E. Anderssen, Irma Lindsay |
| author_sort | Anderssen, Irma Lindsay |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 1996. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/54970 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:42:37.450Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/54970 Analysis of maize germplasm relationships using RAPD and microsatellite markers Anderssen, Irma Lindsay Retief, A. E. Warnich, L. Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics & Institute of Plant Biotechnology. Corn -- Genetics Corn -- Breeding Corn -- Germplasm resources UCTD Thesis (MScAgric)--Stellenbosch University, 1996. ENGLISH ABSTRACT: Random amplified polymorphic DNA (RAPD) and microsatellite markers are widely used for estimating genetic relationships of crop germplasm. The aim of this study was to compare these genetic markers for the assessment of genetic diversity and relationships among forty two (42) elite inbred maize lines used in South African breeding programmes. Four arbitrary decamer primers were used for RAPD analysis and the reaction conditions were optimised to ensure reproducibility. The amplification products were resolved on 1.4% agarose gels, stained with ethidium bromide and visualised by UV illumination. A total of 15 reproducible polymorphic RAPD fragments were generated, with sizes ranging from 400 to 3000 bp, and scored across the maize lines. All polymerase chain reactions (PCR) were carried out in duplicate using DNA from two plants of each maize line as templates. The same DNA samples used for RAPD analysis of the 42 maize lines were used as templates for microsatellite analysis. PCR products were resolved on 6% denaturing polyacrylamide gels after end-labelling the forward primer, in each case, with [y-32P]. Gels were dried and exposed to X-ray film. The four microsatellite markers detected a total of 40 alleles ranging in size from 60 to 160 bp. Both RAPD and microsatellite analysis revealed a high level of polymorphism among the inbred maize lines. The computer package RAPDistance (Armstrong et al., 1994) was used for the statistical analysis of data. A main database, consisting of 12 maize lines, was created independently for RAPD and microsatellite data. Genetic similarity estimates (Jaccard coefficient) between pairs of lines were calculated to create distance matrices in order to determine the nearest and most distant neighbour of each line. The remaining thirty maize lines were then compared with those in the main database. This option was used to determine which lines in the main database represented their nearest and most distant neighbours. Cluster analysis was performed and genetic relationships were expressed as dendrograms. Several similarities between the respective comparative analyses were observed. Furthermore, dendrograms showing the genetic relationships among 12 and 42 maize lines, based on data obtained from both RAPD and microsatellite polymorphisms, revealed similar groupings of maize lines as was observed in RAPD and microsatellite analysis. Results indicate that RAPD and microsatellite markers are suitable for estimating genetic relationships among closely related maize lines. This will be of considerable help to maize breeders as RAPD and microsatellite data, in conjunction with other information on the maize lines, could be used to facilitate the choice of individuals to cross in hybrid combinations in good order to maximise the expression of heterosis in the hybrid progeny. AFRIKAANSE OPSOMMING: Lukraak geamplifiseerde polimorfiese DNA (LAPD) en mikrosatelliet merkers word algemeen gebruik om genetiese verwantskappe tussen gewasse te bepaal. Die doel van hierdie studie was om hierdie genetiese merkers te vergelyk vir die bepaling van genetiese diversiteit en verwantskappe tussen 42 elite ingeteelde mielielyne, wat in Suid-Afrikaanse teelprogramme gebruik word. Vier 10-basis inleiers met arbitrere volgordes is gebruik vir LAPD analise. Reaksie kondisies is ge optimiseer om herhaalbare resultate te verseker. Die amplifikasie produkte is geskei op 1.4% agarose gels, gekleur met ethidium bromied en gevisualiseer deur gebruik te maak van UV lig. Vyftien herhaalbare polimorfiese fragmente is gegenereer en geevalueer in al die mielielyne. Die groottes van die fragmente het gewissel van 400 tot 3000 bp. Alie polimerase ketting reaksies (PKR) is in duplikaat uitgevoer deur gebruik te maak van DNA van twee plante van elke lyn. Dieselfde DNA monsters wat gebruik is vir LAPD analise is ook gebruik vir mikrosatelliet analise. Die 5'➔ 3' inleier is aan die 5' kant gemerk met [y-32P] en die PKR produkte is geskei op 6% denaturerende poliakrielamied gels. Allele is gevisualiseer deur die gel bloot te stel aan X straal film. Die vier mikrosatelliet merkers het 'n totaal van 40 allele getoon waarvan die groottes gewissel het van 60 tot 160 bp. Beide LAPD en mikrosatelliet merkers het 'n hoe vlak van genetiese variasie tussen die mielielyne getoon. Die RAPDistance rekenaar pakket (Armstrong et al., 1994) is gebruik vir die statistiese analise van data. 'n Hoof databasis, bestaande uit 12 mielielyne, is onafhanklik geskep vir elk van die LAPD en mikrosatelliet data. Genetiese gelyksoortigheidsberamings (Jaccard se koeffisient) tussen pare lyne is bereken en genetiese afstandsmatrikse is geskep sodat bepaal kon word watter lyne die naaste en verste verwant is aan mekaar. Die oorblywende dertig mielielyne is daarna met die in die hoof databasis vergelyk om vas te stel watter van die 12 lyne die naaste en verste verwant is van elk van die 30 lyne. Groepsanalise is uitgevoer en genetiese verwantskappe tussen lyne is uitgedruk as dendrogramme. Verskeie ooreenkomste tussen die onderskeie vergelykende analises is waargeneem. Verder is beide LAPD en mikrosatelliet polimorfismes as data gebruik om dendrogramme van 12 en 42 mielielyne te genereer. Ooreenstemmende mielielyn groeperings is waargeneem tussen hierdie dendrogramme en die LAPD- en mikrosatelliet-gebasseerde dendrogramme. Resultate toon dat LAPD en mikrosatelliet merkers gebruik kan word om verwantskappe tussen naby verwante mielielyne te bepaal. Mielietelers sal hierdie inligting, tesame met ander inligting in verband met die lyne, kan gebruik om hulle te help besluit watter individue in hibried kombinasies gekruis moet word om maksimum uitdrukking van heterose te verseker. Masters 2012-08-27T11:36:50Z 2012-08-27T11:36:50Z 1996 Thesis http://hdl.handle.net/10019.1/54970 en_ZA Stellenbosch University 112 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Corn -- Genetics Corn -- Breeding Corn -- Germplasm resources UCTD Anderssen, Irma Lindsay Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title | Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title_full | Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title_fullStr | Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title_full_unstemmed | Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title_short | Analysis of maize germplasm relationships using RAPD and microsatellite markers |
| title_sort | analysis of maize germplasm relationships using rapd and microsatellite markers |
| topic | Corn -- Genetics Corn -- Breeding Corn -- Germplasm resources UCTD |
| url | http://hdl.handle.net/10019.1/54970 |
| work_keys_str_mv | AT anderssenirmalindsay analysisofmaizegermplasmrelationshipsusingrapdandmicrosatellitemarkers |