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Mutation screening of candidate genes and the development of polymorphic markers residing on chromosome 19q13.3, the progressive familial heart block I gene search areaMakubalo, Zola 03 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2000. / ENGLISH ABSTRACT: Progressive familial heart block type I (PFHBI) is a cardiac ventricular conduction disorder of
unknown cause associated with risk of sudden death, which has been described in several
South African families. Clinically, PFHBI is characterised by right bundle branch block on
ECG, which may progress to complete heart block, necessitating pacemaker implantation.
The disease shows an autosomal dominant pattern of inheritance with evidence of genetic
anticipation. Using genetic linkage analysis, the PFHBI-causative gene was mapped to a 10
eentimorgan (cM) gene-rich area of chromosome (C) 19q13.3, which has, subsequently, been
reduced to 7cM by fine mapping with polymorphic dinucleotide (CA)n short tandem repeat
(STR) markers. Several attractive candidate genes, including muscle glycogen synthase
(GSY 1) and histidine-rich calcium binding protein (HRC), lie within this region.
The aim of the present study was two-fold: 1) to identify and characterise tetranucleotide
(AAAT)n STRs within the PFHBI critical region that could be developed as polymorphic
markers for use in genetic fine mapping and 2) to screen selected regions of GSY 1and HRC,
positional candidate genes, for the presence ofPFHBI-causing mutation(s).
Cosmids harbouring CI9q13.3 insert DNA were screened for the presence of (AAAT)n STRs
by dot blot and Southern blot hybridisation using a radiolabelled (AAAT)lO oligonucleotide
probe. To characterise the harboured (AAAT)n STRs, the positively hybridising fragments
identified by Southern blot were sub-cloned, sequenced and primers designed from the unique
repeat-flanking sequences. These primers were used to genotype the (AAAT)n repeat locus to
assess its polymorphic nature in a panel of unrelated individuals. Alternatively, vectorette
PCR, a rapid method of identifying repeat sequences and obtaining the flanking sequences in
large inserts, was employed to develop polymorphic markers from the positively hybridising
clones. Selected exons of GSY1 and HRC were screened for the presence of potentially
disease-causing mutations by PCR-SSCP analysis and direct sequencing, respectively, in
PFHBI-affected and unaffected family members.
Of the available cosmid clones that gave strong signals on dot blot and Southern blot
hybridisation, three, 29395, 24493 and 20381, were located within the critical PFHBI area
and were used for marker development. An interrupted (AAAT)n repeat motif (n less than 5)
was identified in cosmid 29395, however, the repeat locus was not polymorphic in the tested
population. No (AAAT)n motif, single or repeated was observed in the partial sequence of the sub-cloned fragment of cosmid 24493. Using vectorette peR, no repeated (AAAT)n motif
was identified on sequencing the generated products in either cosmid 24493 or 2038l.
However, diffuse single AAAT motifs were detected in both cosmids. Exons 4, 5, 11, 12 and
16 of GSY 1, containing domains that are conserved across species, and the conserved eterminus-
encoding exons 2-6 of HRC were selected for screening for potential PFHBI-causing
mutation(s). However, no sequence variations were detected.
The interrupted (AAAT)n repeat identified in cosmid 29395 was not polymorphic, which
confirmed reports that complex repeats, especially those containing AAAT motifs of less than
6 repeats, are not polymorphic. One possible explanation for the absence of a repeated AAAT
motif in cosmids 24493 and 20381, which both gave positive hybridisation signals, is that the
low annealing temperature of the AfT -rich repeat-anchored primers used in vectorette peR
may have resulted in transient annealing to the diffuse single AAAT motifs detected on
sequencing. The screened regions of candidate genes GSYI and HRC were excluded from
carrying the disease-causing mutation(s).
The availability of new sequence data generated by the Human Genome Project will influence
future strategies to identify the PFHBI gene. Electronic searches will allow identification of
STR sequences for development of polymorphic markers and gene annotation will allow
selection of new candidate genes for mutation screening. / AFRIKAANSE OPSOMMING:
Sien volteks vir opsomming
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Obsessive-compulsive disorder : defining the role of gene-based variants and immunological factorsKinnear, Craig 03 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2001. / ENGLISH ABSTRACT:
Please see fulltext for abstract / AFRIKAANSE OPSOMMING:
Sien asb volteks vir opsomming
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Investigating candidate genes identified by genome-wide studies of granulomatous diseases in susceptibility to tuberculosis: ANXA11 and the CADM familySalie, Muneeb 12 1900 (has links)
Thesis (MScMedSc (Biomedical Sciences))--University of Stellenbosch, 2010. / Thesis presented in partial fulfilment of the requirements for the degree Master of Medical Science (Human Genetics) at the University of Stellenbosch. / Bibliography / ENGLISH ABSTRACT: The infectious disease tuberculosis (TB) remains the leading cause of death worldwide by a single infectious agent, despite significant advances in biomedical sciences. The idea that host genetics plays a role in the development of disease was proposed by Haldane in 1949. The observation that only 10% of immunocompetent individuals develop disease while others are able to successfully contain it, further suggests that host genetics plays an important role. TB is thus a complex disease, with the causative bacterium, Mycobacterium tuberculosis, host genetic factors and environment all contributing to the development of disease. To date several genes have been implicated in TB susceptibility, albeit with small effect.
Genome-wide association studies (GWAS) offer the means to identify novel susceptibility variants and pathways through their ability to interrogate polymorphisms throughout the genome without being limited by our understanding of the immune processes involved in TB infection and disease progression. TB and sarcoidosis are both granulomatous diseases, and we therefore hypothesized that the genes and their associated variants identified in recent GWAS conducted in West Africa for TB, and Germany for sarcoidosis, could alter susceptibility to TB in the South African Coloured (SAC) population. In the sarcoidosis GWAS, ANXA11 was shown to alter susceptibility to sarcoidosis; whereas in the TB GWAS, CADM1 was found to alter susceptibility to TB.
This study tested the association with TB of 16 polymorphisms in 5 potential TB host susceptibility genes in the SAC population. A well designed case-control study was employed, using the TaqMan® genotyping system to type the various polymorphisms. Any polymorphism that was found to be significantly associated with susceptibility to TB was then subjected to further analysis to determine the functional effect of the polymorphism. Promoter methylation patterns were also investigated in ANXA11 as another mechanism to elucidate its role in TB susceptibility.
A 3’ UTR ANXA11 polymorphism was found to be strongly associated with susceptibility to TB, including 3 haplotypes. The gene expression analysis identified differential transcriptional levels between individual with the different genotypes, with individuals homozygous for the A-allele exhibiting a 1.2-fold increase in gene expression relative to those homozygous for the G-allele. Methylation analysis however found no differences between cases and controls. In addition, 16 novel polymorphisms were also identified, 15 of which occurred in the 3’UTR of ANXA11. The mechanism of action of ANXA11 in TB susceptibility is hypothesised to be in the area of endocytosis, autophagy or apoptosis.
A weak association was noted with one of the 5’ UTR polymorphisms of CADM3, which did not hold up to further analysis in the GWAS study, and no functional work was therefore done.
This work facilitates our understanding of the role of host genetics in susceptibility to TB and adds to the growing amount of information available. Proper understanding of the role that host genetics plays in TB susceptibility could result in better treatment regimens and prediction of individuals who are at a greater risk of developing TB, a disease that still kills millions of individuals annually. / AFRIKAANSE OPSOMMING: Tuberkulose is verantwoordelik vir meer sterftes as enige ander aansteeklike siekte, ten spyte van die voortuitgang wat die Biomediese Wetenskappe tans beleef. In 1949 het Haldane voorgestel dat die genetiese samestelling van die gasheer ‘n rol speel in vatbaarheid vir aansteeklike siektes. Vir tuberkulose word hierdie aanname gesteun deur die feit dat slegs 10% van individue wat geïnfekteer word aktiewe simptome ontwikkel, terwyl 90% die siekte suksesvol sal afweer. Tuberkulose is dus ‘n komplekse siekte wat veroorsaak word deur Mycobacterium tuberculosis, maar wat beïnvloed word deur genetiese sowel as omgewingsfaktore. Verskeie gene is al geïdentifiseer wat ‘n rol speel in vatbaarheid vir tuberkulose, tog is hul invloed betreklik klein.
Genoom-wye assosiasiestudies (GWAS) bied unieke geleenthede vir die identifisering van nuwe polimorfismes wat genetiese vatbaarheid kan beïnvloed. Hierdie tegniek kan die hele genoom fynkam, sonder dat enige vooropgestelde idees oor die immuunrespons teen tuberkulose ‘n invloed sal hê. Tuberkulose en sarkoïdose is albei siektes wat die vorming van granulomas veroorsaak. Verskeie gene met hul geassosieerde variante is geïdentifiseer in ‘n onlangse GWAS, wat gefokus het op populasies in Wes-Afrika en Duitsland. Ons hipotese was dat die polimorfismes wat in hierdie studie geïdentifiseer is, ‘n invloed kan hê op genetiese vatbaarheid vir TB in die Suid-Afrikaanse Kleurlingbevolking (SAK). Die sarkoïdose GWAS het bevind dat ANXA11 vatbaarheid vir die siekte beïnvloed, terwyl CADM1 in die tuberkulose GWAS geïdentifiseer is.
Die studie het die assosiasie tussen 16 variante en tuberkulose vatbaarheid ondersoek in die SAK populasie. Die variante strek oor 5 potensiële tuberkulose vatbaarheidsgene. Goedbeplande pasiënt-kontrole assosiasiestudies is gedoen en die polimorfismes is gegenotipeer deur gebruik te maak van die TaqMan® genotiperingsisteem. Enige polimorfisme wat beduidend met tuberkulose geassosieer was, is verder geanaliseer om die moontlike funksionele invloed daarvan te bepaal. Promotormetileringspatrone van ANXA11 is ook geanaliseer, om ‘n addisionele meganisme in tuberkulose vatbaarheidheid te ondersoek.
Na genotipering van die polimorfismes is ‘n 3’ UTR ANXA11 variant geïdentifiseer wat beduidend met tuberkulose vatbaarheid geassosieer was. Drie haplotipes is ook geïdentifiseer. Geenuitdrukkingsanalise het aangedui dat verskille in transkripsie vlakke voorkom in individue met verskillende genotipes. Individue wat homosigoties was vir die A-alleel het ‘n verhoging van 1.2 in geenuitdrukking gehad, relatief tot individue wat homosigoties was vir die G-alleel. Metileringsanalise het egter geen verskil aangedui tussen pasiënte en kontroles nie. Addisioneel, is 16 nuwe variante ontdek, waarvan 15 in die 3’UTR van ANXA11 geleë was. Die meganisme waarmee ANAX11 genetiese vatbaarheid vir tuberkulose beïnvloed, blyk in die area van endositose, apoptose of outofagie, te wees.
‘n Swak assosiasie is gevind vir ‘n 5’ UTR variant van CADM3 en is nie verder opgevolg in die GWAS nie. Gevolglik is geen funksionele studies op hierdie polimorfisme gedoen nie.
Hierdie studie dra by tot ons kennis oor die rol wat die genetiese samestelling van die gasheer speel in vatbaarheid vir tuberkulose. Indien die rol van mensgenetika in tuberkulose vatbaarheid korrek verstaan word, kan behandeling van die siekte verbeter word en kan individue wat ‘n hoër risiko loop om tuberkulose te ontwikkel geïdentifiseer word.
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Predictive value of gene mutations as a diagnostic tool for ART resistance in a Zambian populationMaseko Phiri, Thabiso 12 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2012. / Background: While Selection of reverse transcriptase (RT) mutation has been
reported frequently, protease (PR) mutations on antiretroviral therapy (ART) including
boosted Protease inhibitor (PI) have not been reported as much in Zambia. Affordable
in-house genotyping assays can been used to expand the number of patients receiving
drug resistance geno-typing, which can aid in determining prevalence of RT/PI
emerging mutations.
Methods: A previously published drug resistance genotyping assay was modified and
used to genotype RT and PR genes. 19 patients virologically failing first-line regimen
and 24 failing second-line regimen were studied to determine resistance patterns.
Virological failure was defined as failing to maintain <1000 copies/mL during ART.
Only major and minor RT and PR mutations (IAS-USA 2010) were considered for
analysis. The in-house assay was validated by comparing sequence data of 7 previously
ViroSeq tested samples and 5 randomly selected samples to determine reproducibility.
Results: The in-house assay efficiently amplified all 12 validation samples with the
lowest sample scoring 99.4% sequence homology. The most common RT mutation was
M184V (79% n=19) and (71% n=24) first and second-line respectively. No significant
differences were reported in all the other RT mutations between first-line and secondline
regimens. Drug resistant PI mutations (I54V, M46I and V82A all present 20.8%)
were only found in the second-line regimen and were insignificant, p= 0.0562.
Conclusion: The in-house assays can be used as alternatives for commercial kits to
genotype HIV-1C in Zambia without compromising test quality. The insignificant PI
drug resistant mutations which were found, despite virological failure in patients, could
indicate a possibility of other mutations within the HIV-1 genome that could reduce PI
susceptibility.
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Molecular-genetic analysis of Hirschsprung's disease in South AfricaJulies, Monique G. 03 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2000. / ENGLISH ABSTRACT: Hirschsprung's disease, or aganglionic megacolon, is a common cause of intestinal
obstruction in neonates and is associated with the congenital absence of intrinsic
ganglion cells in the myenteric and submucosal plexuses of the gastrointestinal tract.
The affected area is usually restricted to the distal part of the colon (short segment
disease), but total colonic or intestinal involvement occurs in some patients (long
segment disease).
DNA analysis was performed on samples from 53 unrelated sporadic HSCR patients
to search for mutations in RET proto-oncogene, endothelin-B receptor (EDNRB) and
endothelin-3 (EDN3) genes. The patients were from different ethnic groups in South
Africa, including 29 coloured, 14 white (Caucasian) and 9 black individuals. The
origin of 1 patient was unknown. PCR HEX-SSCP analysis of the RET protooncogene
revealed one previously described (P973L) and five novel mutations
(V202M, E480K, IVS10-2A1G, D771N, IVS19-9Crr), likely to cause or contribute to
the HSCR phenotype. Nine polymorphisms were also identified in the RET protooncogene,
of which four were novel (IVS6+56deIG, IVS13-29Crr, IVS16-38deIG,
X1159) and five previously described (A45, A432, L769, S904, R982). All the mobility
shifts detected in the EDNRB gene represented polymorph isms (A60T, S184, 1187,
V234, L277, IVS3-6Crr, IVS4+3A1G). No sequence variants were identified in the
EDN3 gene. The majority of mutations in the RET proto-oncogene (28.6%) were
identified in coloured patients while no mutations were identified in black patients. A
mutation in RET was identified in two of 14 patients (14%) presenting with HSCR and
Down's syndrome compared to 6 mutations identified in 9 of 39 patients (23%) with only HSCR. The fact that Down's syndrome patients have a high chance of
developing HSCR, implies the involvement of modifier gene(s) in a HSCR/Oown's
syndrome phenotype.
This study demonstrated that, within the South African HSCR patient population, the
RET proto-oncogene is the major susceptibility gene, whereas EDNRB and EDN3
may contribute only to a minority of cases. In 81% of patients no disease-causing
mutation could be identified, which is in keeping with the heterogeneous nature of
HSCR. The identification of mutations in HSCR patients would in future lead to
improved and accurate counselling of South African HSCR patients and their
families. / AFRIKAANSE OPSOMMING: Hirschsprung se siekte (HSCR), ook bekend as aganglionosis megakolon, is 'n
algemene oorsaak van intestinale obstruksie in pasgeborenes en word geassosieer
met die kongenitale afwesigheid van intrinsieke ganglion selle, in die miênteries en
submukosa pleksus van die gastrointestinale kanaal. Alhoewel die aangetaste deel
hoofsaaklik by die distale area van die kolon geleê is (kort segment siekte), kom
totale koloniese of intestinale betrokkenheid ook in sommige pasiënte voor (lang
segment tipe).
Molekulêre ONS analise van 53 nie-verwante Suid Afrikaanse sporadiese HSCR
pasiênte (29 kleurlinge, 14 blankes, 9 swartes en 1 individu van onbekende
oorsprong) is uitgevoer in die RET proto-onkogeen, endoteel-B reseptor (EDNRB) en
endoteel-3 (EDN3) gene. Heterodupleks-enkel string konformasie polimorfisme
(HEX-SSCP) analise van polimerase ketting reaksie (PKR) geamplifiseerde produkte
van die RET proto-onkogeen het gelei tot die identifikasie van vyf nuwe mutasies
(V202M, E480K, IVS10-2A1G, D771N, IVS19-9CIT) en een bekende mutasie
(P973L). Vier nuwe polimorfismes (IVS6+56deIG, IVS13-29Crr, IVS16-38deIG,
X1159) en vyf bekende polimorfismes (A45, A432, L769, S904, R982) is ook
aangetoon. Sewe polimorfismes (A60T, S184, 1187, V234, L277, IVS3-6CIT,
IVS4+3A1G) is in die EDNRB geen geïdentifiseer. Geen veranderinge is in die EDN3
geen waargeneem nie. Die meerderheid mutasies waargeneem in die RET protoonkogeen
is in die kleurling populasie (28.6%) waargeneem, terwyl geen mutasies in
die swart populasie geïdentifiseer is nie. 'n RET mutasie is in twee van 14 (14%)
pasiênte met 'n HSCR en Down's sindroom fenotipe waargeneem, in vergelyking met mutasies geïdentifiseer in 9 van 39 pasiënte (23%) met slegs HSCR. Die algemene
voorkoms van Down's sindroom met HSCR, impliseer die rol van ander gene in die
HSCRI Down's sindroom fenotipe.
Die meerderheid mutasies wat aanleiding gee tot die HSCR fenotipe kom voor in die
RET proto-onkogeen (19%), terwyl slegs polimorfismes in die EDNRB geen
waargeneem is. Geen HEX-SSCP bandpatroon veranderinge is in die EDN3 geen
waargeneem nie. Ongeveer 81% van die Suid Afrikaanse HSCR pasiënte was
mutasie-negatief wat dui op die heterogene aard van die siekte. In die toekoms sal
analise van siekte-verwante mutasies in die RET geen lei tot akkurate diagnose en
verbeterde genetiese voorligting van HSCR in die Suid-Afrikaanse populasie.
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Genetic aspects of pre-eclampsia : mutation screening of the low-density lipoprotein receptor, methylenetetrahydrofolate reductase, prothrombin and factor V candidate genesGebhardt, G. S. 03 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: Pre-eclampsia is a condition unique to pregnancy and primarily affects the maternal
and placental vascular endothelium. It has significant morbidity and mortality
consequences for both mother and infant. Despite global research into the aetiology
of the condition, the cause for this condition remains unknown. Several factors,
including a strong family history of hypertension in pregnancy point to a familial or
genetic component in the pathophysiology of this complication.
The purpose of this research project was to investigate candidate genes implicated in
endothelial damage. Common methylene-tetra-hydrofolate reductase (MTHFR) gene
mutations C677T and A1298C, factor V Leiden mutation R506Q and prothrombin
mutation A20210G were investigated in 50 patients with an uncomplicated pregnancy
outcome (controls) and 350 patients with various clinical manifestations of preeclampsia,
including severe, early onset forms and abruptio placentae. Fasting
homocystein levels were determined biochemically on all participants.
In addition, 126 consecutive pregnant patients were recruited at booking, fasting
lipograms were performed on them as well as mutation screening of 7 common
mutations in the low-density lipoprotein receptor gene. This was correlated with
eventual pregnancy outcome, and those with an uncomplicated outcome were
selected as an additional control group.
A significant association between hyperhomocysteinaemia and early onset severe
pre-eclampsia could be demonstrated. Mutant allele T of the C677T mutation could
be associated with hyperhomocysteinaemia but not with pre-eclampsia whilst mutant
allele C of mutation A1298C demonstrated a significant correlation with diastolic blood pressure. In addition, combined heterozygosity for these mutations may serve
as a marker for abruptio placentae. / ENGLISH ABSTRACT: Pre-eklampsie is 'n hipertensiewe toestand uniek aan menslike swangerskap en dit
affekteer hoofsaaklik die vaskulêre endoteel. Die toestand hou ernstige morbiditeit en
mortaliteit vir beide ma en baba in en na jare se navorsing is die oorsaak van hierdie
toestand steeds onbekend. Epidemiologiese studies toon 'n duidelike familiële
verband aan wat die vermoede laat ontstaan dat daar 'n onderliggende genetiese
aspek tot die ontwikkeling van die siektetoestand is.
Die doel van hierdie navorsingsprojek was om gene te ondersoek wat geïmpliseer
word in endoteel skade. Twee algemene mutasies, C677T en A1298C in die MTHFR
geen asook faktor V Leiden R506Q en protrombien A20210G mutasies is ontleed in
50 pasiënte met 'n ongekompliseerde swangerskapsverloop en in 350 pasiënte met
'n swangerskap gekompliseer deur verskillende kliniese manifestasies van die
siekteproses, insluitende vroeë aankoms erge pre-eklampsie en abruptio placentae.
Op alle pasiënte is ook 'n vastende homosistiën vlak biochemies bepaal.
'n Verdere 126 opeenvolgende pasiënte is gewerf tydens hulle eerste besoek aan die
voorgeboortekliniek en vastende lipogramme is op almal uitgevoer. Mutasie sifting vir
7 algemene mutasies in die lae-digtheids lipoproteïen reseptor geen is op hierdie
groep gedoen en die resultaat is met die uiteindelike swangerskapsuitkoms
gekorreleer. Pasiënte met 'n uitkoms ongekompliseer deur hipertensie is gekies om
deel te wees van 'n verdere kontrolegroep.
Daar was 'n betekenisvolle verband tussen hiperhomositiënemie en erge, vroeë
aankoms pre-eklampsie. Die T alleel van die C677T mutasie is geassosieer met
hiperhomosistiënemie maar nie met pre-eklampsie nie. Die C alleel van die A 1298C
mutasie toon 'n betekenisvolle verband met diastoliese bloeddruk. Gekombineerde heterosigositeit vir beide MTHFR mutasies kan 'n moontlike merker vir abruptio
placentae wees.
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Establishing genetic and environmental parameters for ostrich (Struthio camelus domesticus) growth and slaughter characteristicsEngelbrecht, Anel 03 1900 (has links)
Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The ostrich industry is a predominantly quantitative industry; focused mainly on the production of large numbers of slaughter birds for maximum meat and leather yield. Competing in the international market in the current economic environment necessitates a more qualitative approach. Productivity and product quality are aspects that need to be improved in order to stay competitive and economically viable. Genetic parameters for ostrich slaughter traits are lacking, however, and breeding programs are yet to be developed. Data on quantitative and qualitative production and slaughter traits from a commercial ostrich breeding flock was consequently analysed to establish the relative importance of genetic and non-genetic influences on these traits. Genetic and environmental (co)variances as well as estimates of heritability, genetic and phenotypic correlations were estimated for and among the various traits using standard software for multi-trait genetic analyses.
Substantial variation, high and favourable genetic correlations as well as moderate to high heritability estimates were found among, and for distinguished body weight traits of growing ostriches. Heritability estimates of 0.14, 0.22, 0.33, 0.43 and 0.43 for 1-month, 4-month, 7-month, 10-month and 13-month-old ostrich weights were estimated in a five-trait animal model analysis.
All carcass component weight traits, with the exception of the weight of the liver, showed significant genetic variation. No significant maternal permanent environmental variance was evident for these traits. Heritability estimates ranged from 0.21 (for subcutaneous fat weight) to 0.45 (for neck weight) in multi-trait analyses. The only potentially unfavourable correlation was a high genetic correlation between live weight and subcutaneous fat weight, as fat is considered as a waste product in the present system. The heritability estimates for individual muscle weights ranged from 0.14 to 0.43, while the genetic correlation between these weights and pre-slaughter live weight were all positive, ranging from 0.59 to 0.82.
When meat quality traits were analysed it was evident that lightness (L*) and ultimate pH (pHu) showed significant genetic variation, with heritability estimates of 0.37 and 0.42, respectively. L* and pHu were negatively correlated (-0.65 ± 0.19). Since pH is an indicator of various meat quality parameters, it could be considered as an appropriate selection criterion for enhanced meat quality. With the exception of skin grading and crown length, all quantitative and qualitative skin traits showed significant genetic variation. Nodule traits were accordingly moderate to highly heritable. A negative, but favourable, correlation between weight and hair follicle score was ascertained, as hair follicles is a defect that should be selected against.
This study demonstrated that sufficient genetic variation exists for most slaughter traits to allow sustained genetic progress for these traits, should it be desired as part of the overall selection objective. Combining some of the current economically important slaughter traits in a provisional selection index, it was clear that weight and crust skin size contributed most to monetary gain (approximately 54 and 38%, respectively). It was also demonstrated with this simple index that monetary gains in slaughter bird production should be easy to achieve at all levels of production performance and data recording. / AFRIKAANSE OPSOMMING: Die volstruisbedryf is hoofsaaklik ‘n kwantitatiewe bedryf wat meerendeels fokus op die produksie van groot getalle slagvolstruise vir die produksie van vleis en leer. Siende dat die bedryf hoofsaaklik op uitvoere fokus, word aanvaar dat ‘n verandering in strategie na ‘n meer kwalitatiewe benadering nodig is, in ag geneem die huidige ekonomiese situasie en marktoestande. Produktiwiteit sowel as produkgehalte moet in ag geneem word vir die bedryf om lewensvatbaar te bly. Daar is egter ‘n gebrek aan genetiese parameters vir volstruisslageienskappe, terwyl doeltreffende teeltstelsels nog ontwikkel moet word. Data van kwantitatiewe en kwalitatiewe produksie- en slageienskappe is gevolglik van ‘n kommersiële volstruis teeltkudde verkry en ontleed om die relatiewe belang van genetiese en nie-genetiese effekte op die eienskappe te kwantifiseer. Genetiese- en omgewings (ko)variansies, asook beramings van oorerflikheid sowel as genetiese en fenotipiese korrelasies, is vervolgens vir en tussen die onderskeie eienskappe beraam deur van standaard sagteware vir veelvuldige-eienskap genetiese ontledings gebruik te maak.
Aansienlike variasie, hoë en meestal gunstige korrelasies, sowel as matige tot hoë oorerflikhede, is tussen en vir die onderskeie ligaamsgewigte van groeiende volstruise gevind. Oorerflikheidsberamings van 0.14, 0.22, 0.33, 0.43 en 0.43 is vir 1-maand, 4-maande, 7-maande, 10-maande en 13-maande-oue volstruise in ‘n vyf-eienskap dieremodel ontleding gekry.
Alle karkaskomponentgewigte, met die uitsondering van die gewig van die lewer, het betekenisvolle genetiese variasie getoon. Oorerflikheidsberamings het tussen 0.21 (vir onderhuidse vetgewig) en 0.45 (vir nekgewig) gevarieer in veelvuldige-eienskapontledings. Die enigste moontlike ongunstige korrelasie was tussen liggaamsgewig en onderhuidse vetgewig, siende dat vet as ‘n afvalproduk gereken word in die huidige stelsel. Die oorerflikhede van die gewigte van indiwiduele spiere het van 0.14 tot 0.43 gevarieer, terwyl die genetiese korrelsies tussen hierdie gewigte en voorslaggewig deurgaans positief was, met waardes wat van 0.59 tot 0.82 gewissel het.
Tydens die ontleding van vleisgehalte eienskappe was dit duidelik dat ligtheid (L*) en uiteindelike pH (pHu) genetiese variasie getoon het, met oorerflikheidsberamings van onderskeidelik 0.37 en 0.42. L* en pHu was negatief gekorreleerd op die genetiese vlak (-0.65 ± 0.19). Aangesien pH ‘n aanduiding is van verskeie vleisgehalteparameters, kan dit moontlik as ‘n indirekte seleksie-kriterium vir verbeterde vleisgehalte gesien word. Alle kwantitatiewe en kwalitatiewe veleienskappe het genetiese variasie getoon, met die uitsondering van velgradering en kroonlengte. Knoppie-eienskappe van die veerfollikels op die vel was ooreenstemmend matig tot hoog oorerflik. ‘n Negatiewe, maar gunstige, genetiese korrelasie is tussen liggaamsgewig en haarfollikelpunt beraam, siende dat haarfollikels ‘n defek is waarteen daar geselekteer moet word. Hierdie studie dui op voldoende genetiese variasie vir die meeste slageienskappe om voldoende genetiese vordering te verseker indien dit verlang sou word. Somminge van hierdie eienskappe wat tans van ekonomiese belang is, is vervolgens in ‘n voorlopige seleksie-indeks gekombineer. Dit was duidelik dat liggaamsgewig en velgrootte die meeste tot monetêre vordering bygedra het (onderskeidelik ongeveer 54 en 38%). Dit is vervolgens aangetoon dat monetêre vordering maklik haalbaar behoort te wees op alle vlakke van produksieprestasie en data-aantekening.
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Molecular investigation into regulatory regions of the LDLR gene involved in lipoprotein metabolismScholtz, C. L.(Charlotte Latitia) January 2001 (has links)
Thesis (PhD) -- University of Stellenbosch, 2001. / ENGLISH ABSTRACT: The advent of the new millennium saw the complete sequencing of the entire human genome.
Only approximately 30 000 genes, much less than was initially predicted, have been identified
to be responsible for the genetic diversity in humans. This discovery has prompted a shift in
the approach to disease research, since one gene can be involved in numerous diseases. This
phenomenon seems to be especially true for the low-density lipoprotein receptor (LDLR)
gene. Various substances beside sterols can induce transcription of the LDLR gene.
Non-communicable diseases (e.g. hypertension) are common in the developing world and
contribute significantly to mortality rates. The fmding that a promoter variant (-175 g~t) in
the LDLR gene is associated with elevated diastolic blood pressure may explain the
phenomenon of high LDL-cholesterollevels in hypertensive individuals. Studies have
demonstrated that the lowering of cholesterol, especially LDL-cholesterol, can reduce the
incidence of hypertension. The -175 g~t variant is located in a newly described cis-acting
regulatory element which contains a putative binding site for Yin Yang (YY)-l and also
demonstrates great homology to the cAMP response element (CRE) which bind the Ca2+-
dependent transcription factor, CRE binding protein (CREB). The fact that Ca2+ can induce
transcription of the LDLR gene may, at least in part, explain the association between the -
175g~t variant and elevated diastolic blood pressure.
Cholesterol is important for various processes, such as apoptosis, maintenance of cellular
membranes and immune function. The -59 c-ot mutation in repeat 2 of the LDLR gene
abolishes binding of the sterol regulatory element binding protein(SREBP) to the SRE-l site.
SREBP is proteolytically activated during apoptosis by two caspases (CPP32 and Mch3) to induce cholesterol levels. Our results imply that the -59C/T mutation, in repeat 2 of the LDLR
gene promoter, may inhibit apoptosis under normal immunological conditions.
Atherosclerosis can be considered an immunological disease, since various humoral and
cellular immune processes can be detected throughout the course of the disease. The fmding
that certain lipoproteins can protect against infection by binding and lysing of pathogens, or
competing with pathogens for cellular receptors, prompted the investigation into the potential
role of variation in the LDLR gene promoter in immune function. A significant difference in
allelic distribution was detected between asymptomatic HIY -infected subjects and fast
progressors for the -124 c-ot variant (P=O.006), shown to increase (~160%) transcriptional
activity of the LDLR gene. Of relevance to this particular study is the fact that human
herpesvirus (HHV) 6 can transactivate CD4 promoters through a partial CRE site. It has been
shown that the CREB and YYl can regulate viral and cellular promoters, and these
transcription factors can potentially bind to the LDLR promoter at the FP2 site.
The mutation enrichment in the LDLR gene promoter seen in the South African Black and
Coloured population groups can possibly provide insight into the pathogenesis of various
diseases. This could also potentially, provide novel targets for treatment, since manipulation
of cholesterol levels may affect the pathogenesis of various diseases. / AFRIKAANSE OPSOMMING: Die volledige DNA volgorde bepaling van die mensgenoom is voltooi vroeg in die nuwe
millennium. Slegs ongeveer 30 000 gene is geidentifiseer, heelwat minder as wat in die
verlede voorspel is, wat verantwoordelik is vir die genetiese diversiteit in die mens. Hierdie
ontdekking het gelei tot 'n verandering in die benadering van navorsing ten opsigte van
siektes, aangesien een geen 'n rol by verskeie siektes kan speel. Hierdie gewaarwording blyk
veral waar te wees vir die lae digtheids lipoproteien reseptor (LDLR) geen. Verskeie stimuli,
buiten sterole, kan transkripie van die LDLR geen inisieer.
Verskeie siektes soos hipertensie is algemeen in die ontwikkelende wereld, en dra by tot die
hoe mortaliteit syfers. Die bevinding dat 'n promoter variant in die LDLR geen (-175g-H)
geassosieer is met verhoogde diastoliese bloeddruk, kan moontlik verhoogde lipiedvlakke in
hipertensiewe individue verklaar. Studies het aangetoon dat die verlaging van cholesterol,
veral LDL-cholesterol, die voorkorns van hipertensie kan verlaag. Die -175 g~t variant is
gelee in 'n cis-regulerende element wat na bewering 'n bindingsetel vir die Yin Yang (YY)-l
transkripsie faktor bevat asook sterk homologie met die cAMP respons element (CRE) toon,
wat bind aan die Ca2
+_ afhanklike transkripie faktor, CRE bindings proteiene (CREB). Die feit
dat Ca2+ transkripsie van die LDLR geen kan inisieer, kan dalk tot 'n mate, 'n verklaring bied
vir die assosiasie tussen die -175 (g~t) variant en verhoogde diastoliese bloeddruk.
Cholesterol is noodsaaklik vir verskeie prosesse soos apoptose, die instandhouding van
selmembrane sowel as immuun funksies. Die -59 c-ot mutasie in die sterol regulerende
element 1 (SRE-l) van die LDLR geen vernietig binding van die sterol regulerende element
bindingsprotei'en (SREBP) aan SRE-l. SREBP word proteolities geaktiveer tydens apoptose deur twee kaspases (CPP32 en Mch3) om cholesterolvlakke te induseer. Ons resultate
impliseer dat die -59C/T mutasie, in herhaling-2 van die LDLR-geen promoter, apoptose kan
inhibeer onder normale immunologiese toestande.
Aterosklerose kan beskou word as 'n immunologiese siekte, aangesien verskeie humorale en
sellulere immuun prosesse deur die verloop van die siekte waargeneem kan word. Die feit dat
Iipoproteiene beskermend kan wees teen infeksies, deur binding en lisering van virusse of
kompeteer met patogene vir sellulere reseptore, het aanleiding gegee tot 'n ondersoek na die
potensiele rol van variasies in die promoter area van die LDLR geen in immuun funksie.
Betekenisvolle verskille in alleel verspreiding vir die -124c~t variant (P=0.006) is
waargeneem tussen asimptomatiese MIV -geinfekteerde pasiente en individue met vinnige
siekte progressie. In vitro studies het voorheen getoon dat die -124c~t 'n verhoging in LDLR
geen transkripsie (160%) tot gevolg het. Dit is noemenswaardig dat 'n vroee studie getoon het
dat die mens like herpesvirus-6 (MHV6) transaktivering van die CD4 promoters deur 'n
gedeeltelike CRE bindingsetel kan bewerkstellig. Beide CREB en YYl kan virus en sellulere
promotors reguleer, en hierdie transkripsie faktore toon bindingshomologie met die FP2
element van die LDLR promotor
Die mutasie verryking van die LDLR geen promoter soos waargeneem in Suid Afrikaanse
Swart en Kleurling populasies, kan moontlik lig werp op die patogenese van verskeie
siektetoestande. Hierdie bevindinge kan potensieel nuwe teikens vir behandeling identifiseer,
aangesien manipulasie van cholesterolvlakke 'n effek mag he op die patogenese van verskeie
siektes.
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The development and characterisation of grapevine virus-based expression vectorsDu Preez, Jacques 03 1900 (has links)
Thesis (PhD (Genetics))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Grapevine (Vitis vinifera L.) is a very important agricultural commodity that needs to be
protected. To achieve this several in vivo tools are needed for the study of this crop and the
pathogens that infect it. Recently the grapevine genome has been sequenced and the next
important step will be gene annotation and function using these in vivo tools. In this study the
use of Grapevine virus A (GVA), genus Vitivirus, family Flexiviridae, as transient expression
and VIGS vector for heterologous protein expression and functional genomics in Nicotiana
benthamiana and V. vinifera were evaluated. Full-length genomic sequences of three South
African variants of the virus (GTR1-1, GTG11-1 and GTR1-2) were generated and used in a
molecular sequence comparison study. Results confirmed the separation of GVA variants into
three groups, with group III (mild variants) being the most distantly related. It showed the
high molecular heterogeneity of the virus and that ORF 2 was the most diverse. The GVA
variants GTG11-1, GTR1-2 and GTR1-1 were placed in molecular groups I, II and III
respectively. A collaboration study investigating the molecular divergence of GVA variants
linked to Shiraz disease (SD), described two interesting GVA variants of group II, namely
GTR1-2 and P163-M5 (Goszczynski et al., 2008). The group II variants were found to be
closely linked to the expression of SD. GTR1-2 was isolated from a susceptible grapevine
plant that never showed SD symptoms (Goszczynski 2007). The P163-M5 variant that
resulted in exceedingly severe symptoms in N. benthamiana and is that used as SD positive
control by the grapevine industry, was found to contain a 119 nt insert within the native
ORF2. Comparative analysis performed on the complete nt and aa sequences of group II GVA
variants suggested that the components in the GVA genome that cause pathogenicity in V.
vinifera are more complex (or different) to those that cause pathogenicity in N. benthamiana.
The three South African variants (GTR1-1, GTG11-1 and GTR1-2) were assembled into fulllength
cDNA clones under control of CaMV 35S promoters. After several strategies were
attempted, including a population cloning strategy for GTR1-2, none of the clones generated
were able to replicate in N. benthamiana plants. A single amino acid substitution at position
13 (Tyr/Y Cys/C) in ORF 5 of the GTR1-2 cDNA clone was shown to abolish or reduce
replication of the virus to below a detectable level. Two infectious clones of Israeli variants of
GVA (T7-GVA-GR5 and T7-GVA118, obtained from M. Mawassi) were brought under
control of a CaMV 35S promoter (35S-GVA-GR5 and 35S-GVA118). Both clones were
infectious, able to replicate, move systemically and induce typical GVA symptoms after
agroinfiltration in N. benthamiana. These Israeli clones served as backbone for further experiments in characterisation of transient expression and VIGS vectors. The use of GVA as
gene insertion vector (35S-GVA118) and gene exchange vector (35S-GVA-GR5-
ORF2+sgMP) in N. benthamiana and V. vinifera was compared. The gene insertion vector,
35S-GVA118 was based on the full-length GVA genome. The gene exchange vector, 35SGVA-
GR5- ORF2+sgMP, was constructed in this study by elimination of ORF 2 and
insertion of a sgMP and unique restriction sites to facilitate transgene insertion. In N.
benthamiana both vectors showed similar GUS expression levels and photobleaching
symptoms upon virus-induced NbPDS silencing. In V. vinifera limited GUS expression levels
and VIGS photobleaching symptoms were observed for the gene insertion vector, 35SGVA118.
No GUS expression was observed for the gene exchange vector 35S-GVA-GR5-
ORF2+sgMP in this host. As for silencing, one plant, agroinfiltrated with 35S-GVA-GR5-
ORF2-VvPDS+sgMP, developed photobleaching symptoms in 3 systemic infected leaves
after 4 months. This study showed that GVA can be used as gene insertion and gene exchange
vector for expression and VIGS in N. benthamiana, but in grapevine its use is limited to
expression and silencing of genes in the phloem tissue. It is also the first report that ORF 2 of
GVA is not needed for long distance movement in grapevine.
To investigate the possible role of the P163-M5 119 nt insertion and the GVA ORF 2 (of
unknown function), in expression of symptoms in plants, ORF 2 of a 35S-GVA-GR5 cDNA
clone was removed and subsequently substituted by the corresponding ORFs of four South
African GVA variants. Upon agro-infiltration into N. benthamiana leaves, all chimaeric GVA
constructs were able to move systemically through the plant. At this stage no correlation
could be found between severity of symptoms, the presence of the P163-M5 insert and the
specific GVA ORF 2 present in the chimaeras, indicating that other factors in the viral
genome or the host plant probably play a crucial role.
This study contributed to the pool of available in vivo tools for study and improvement of the
valuable grapevine crop. It also opened several exciting research avenues to pursue in the near
future. / AFRIKAANSE OPSOMMING: Wingerd (Vitis vinifera L.) is ‘n baie belangrike landboukundige gewas wat beskerm moet
word. Om die rede word verskeie in vivo gereedskap vir die bestudering van die
wingerdplant, en die patogene wat dit infekteer benodig. Die wingerd genoom se volgorde is
bepaal en dus is die volgende logiese stap om die gene te annoteer en funksie daaraan toe te
skryf. In hierdie studie is die gebruik van Grapevine virus A (GVA), genus Vitivirus, familie
Flexiviridae, as tydelike uitdrukking- en virus-geinduseerde geenuitdowingsvektor vir
heteroloë proteïen uitdrukking en funksionele genoomstudies in Nicotiana benthamiana en V.
Vinifera getoets. Vollengte genoomvolgordes van drie Suid-Afrikaanse variante van die virus
(GTR1-1, GTG11-1 en GTR1-2) is gegenereer en in ‘n molekulêre volgorde vergelyking
studie gebruik. Resultate het die verdeling van GVA variante in drie groepe, waar groep III
die verste verwant is, bevestig. Dit het ook gewys dat die virus ‘n baie hoë molekulêre
heterogeniteit het en dat oopleesraam 2 (ORF 2) die mees divers is. ‘n Samewerking studie
waar die molekulêre diversiteit van GVA variante, gekoppel aan Shiraz siekte (SD),
ondersoek is, is twee interessante variante van groep II beskryf, naamlik GTR1-2 en P163-M5
(Goszczynski et al., 2008). Groep II variante is vooraf gevind om nou verwant te wees aan die
ontwikkeling van SD in wingerd. Die GTR1-2 variant is uit ’n vatbare wingerd plant, wat
nooit SD-simptome vertoon het nie, geïsoleer (Goszczynski et al., 2007). In die ORF 2 van
die P163-M5 variant, wat simptome van die ergste graad in N. benthamiana geïnduseer het, en
ook deur die industrie as betroubare SD-positiewe kontrole gebruik word, is ’n 119 nt
invoeging gevind. Die vergelykende analise wat uitgevoer is, het daarop gedui dat die
determinante van patogenisiteit in die GVA genoom moontlik meer kompleks kan wees in V.
vinifera as in N. benthamiana. Die drie Suid-Afrikaanse variante (GTR1-1, GTG11-1 en
GTR1-2) is in afsonderlike vollengte cDNA klone, onder beheer van CaMV 35S promotors,
aanmekaargesit. Nadat verskeie kloneringstrategieë, insluitend ’n populasie kloneringstrategie
vir die GTR1-2 kloon, gebruik is, het geen een van die cDNA klone die vermoë besit om in
N. benthamiana te repliseer nie. ’n Enkele aminosuur substitusie in posisie 13
(Tyr/Y Cys/C) in ORF 5 van die GTR1-2 kloon, het die replisering van die virus tot laer as
’n opspoorbare vlak verlaag. Twee infektiewe klone van Israeliese GVA variante (T7-GVAGR5
en T7-GVA118, verkry van M. Mawassi) is onder beheer van ‘n CaMV 35S promotor
geplaas (35S-GVA-GR5 and 35S-GVA118). Beide klone het na agro-infiltrasie in N.
benthamiana plante gerepliseer, sistemies beweeg en tipiese GVA simptome geinduseer.
Hierdie twee klone het as raamwerk gedien vir verdere eksperimente in karakterisering van tydelike uitdrukkings- en VIGS vektore. Die gebruik van GVA as geen-insvoegingsvektor
(35S-GVA118) en geen-vervangingsvektor (35S-GVA-GR5- ORF2+sgMP) is in N.
benthamiana en V. vinifera vergelyk. Die geen-invoegingsvektor 35S-GVA118, was op die
vollengte GVA genoom gebasseer. Die geen-vervangingsvektor 35S-GVA-GR5-
ORF2+sgMP, was in hierdie studie gekonstrueer. Dit is gemaak eerstens deur eliminasie van
ORF 2 in die 35S-GVA-GR5 kloon, en tweedens deur die invoeging van ’n subgenomiese
promotor van die beweginsproteïen (sgMP) en unieke beperkings-ensiemsetels om klonering
van transgene te fasiliteer. Beide vektore het in N. benthamiana vergelykbare GUS
uitdrukkingsvlakke en fotobleikende simptome getoon na virus-geinduseerde NbPDS
uitdowing. In V. Vinifera is beperkte GUS uitdrukkingsvlakke en VIGS fotobleikende
simptome opgemerk met die geen-invoegingsvektor, 35S-GVA118. Geen GUS uitdrukking is
in hierdie gasheerplant met die geen-vervangingsvektor opgemerk nie. Slegs een wingerdplant
het fotobleikende simptome, na 4 maande in 3 sistemies geïnfekteerde blare gewys, na agroinfiltrasie
van die 35S-GVA-GR5- ORF2-VvPDS+sgMP konstruk. Hierdie studie het
bevestig dat GVA as geen-invoeging en geen-vervangingsvektor, vir heteroloë proteïenuitdrukking
en VIGS, in N. benthamiana gebruik kan word, maar dit blyk of die gebruik
daarvan in wingerd meer tot die floeëm weefsel beperk is. Hierdie studie wys vir die eerste
keer dat ORF 2 nie nodig is vir langafstand beweging van die virus in wingerd nie.
Om die moontlike rol van die P163-M5 119 nt invoeging en die GVA ORF 2 (met onbekende
funksie), in die uitdrukking van simptome in plante te ondersoek, is ORF 2 van die 35SGVA-
GR5 cDNA kloon verwyder en daaropvolgens vervang met die ooreenstemmende
ORFs van vier Suid-Afrikaanse GVA variante. Na agro-infiltrasie in N. benthamiana blare,
het al die chimeras die vermoë gehad om te repliseer, sistemies te beweeg en simptome te
induseer. Geen korrelasie kon gevind word tussen die graad van simptome, die
teenwoordigheid van die P163-M5 insersie en die spesifieke GVA ORF 2 teenwoordig in die
chimeras nie, wat dus daarop dui dat ander faktore in die virusgenoom of die gasheerplant `n
moontlike belangrike rol kan speel.
Hierdie studie het bygedrae tot die beskikbare poel van in vivo gereedskap vir die bestudering
en verbetering van die kosbare wingerdgewas. Dit het ook talle interessante
navorsingsgeleenthede oopgemaak om in die nabye toekoms te betree.
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Genetic mapping of gray leaf spot resistance genes in maizeLehmensiek, Anke 12 1900 (has links)
Thesis (PhD)--Stellenbosch University, 2000. / ENGLISH ABSTRACT: Gray leaf spot (GLS) of maize, caused by the fungus Cercospora zeae-maydis,
can reduce grain yields by up to 60% and it is now recognized as one of the most
significant yield-limiting diseases of maize in many parts of the world. The most
sustainable and long-term management strategy for GLS will rely heavily on the
development of high-yielding, locally adapted GLS resistant hybrids.
Molecular markers could be useful to plant breeders to indirectly select for genes
affecting GLS resistance and to identify resistance genes without inoculation and
at an early stage of plant development. Only two studies in the USA have
examined quantitative trait loci (QTL) association with GLS resistance.
The aim of this study was to map GLS resistance genes in a resistant Seed Co
LTD, Zimbabwean inbred line. Molecular markers linked to the GLS resistance
QTL were identified by using the amplified fragment length polymorphism (AFLP)
technique together with bulked segregant analysis. Eleven polymorphic AFLP
fragments were identified and converted to sequence-specific PCR (polymerase
chain reaction) markers. Eight of the 11 converted AFLP markers were added to
the maize marker database of the University of Stellenbosch.
Five of the 8 converted AFLP markers were polymorphic between the resistant
and the susceptible parent. They were amplified on the DNA of 230 plants of a
segregating F2 population and linkage analysis was performed with
MAPMAKER/EXP. Two linkage groups consisting of two markers each, with a
linkage distance of 10.4 cM (LOD 22.83) and 8.2 cM (LOD 55.41) between the
two markers, were identified. QTL mapping with MAPMAKER/QTL confirmed the
presence of QTL in both linkage groups. Two publicly available recombinant inbred families (Burr et a/., 1988) were used
to localize the converted AFLP markers on the genetic map of maize. The QTL,
which were identified with the AFLP markers, were mapped to chromosomes 1
and 5. Another AFLP marker was mapped to chromosome 2 and a further to
chromosome 3.
To obtain more precise localizations of the QTL on chromosomes 1 and 5,
sequence-tagged site markers and microsatellite markers were used. The
markers were amplified on the DNA of the 230 plants of the F2 population and
linkage analysis was performed with MAPMAKER/EXP. The order of the markers
was in agreement with the UMC map of the Maize Genome Database. Interval
mapping using MAPMAKERlQTL and composite interval mapping using QTL
Cartographer were performed. The QTL on chromosome 1 had a LOD score of
21 and was localized in bin 1.05/06. A variance of 37% was explained by the
QTL. Two peaks were visible for the QTL on chromosome 5, one was localized in
bin 5.03/04 and the other in bin 5.05/06. Both peaks had a LOD score of 5 and
11% of the variance was explained by the QTL.
To test the consistency of the detected QTL, the markers flanking each QTL
were amplified on selected plants of two F2 populations planted in consecutive
years and regression analysis was performed. Both the QTL on chromosome 1
and the QTL on chromosome 5 were detected in these populations. Furthermore,
the presence of a QTL on chromosome 3 was confirmed with these populations.
A variance of 8 -10% was explained by the QTL on chromosome 3.
In this study, a major GLS resistance QTL was thus mapped on chromosomes 1
and two minor GLS resistance QTL were mapped on chromosomes 3 and 5
using a resistant Seed Co LTD, Zimbabwean inbred line. Markers were identified
which could be used in a marker-assisted selection program to select for the GLS
resistance QTL. / AFRIKAANSE OPSOMMING: Grys blaarvlek (GBV) van mielies, veroorsaak deur die swam Cercospora zeaemaydis,
kan graanopbrengs met tot 60% verlaag en word beskou as een van die
vernaamste opbrengs-beperkende siektes wêreldwyd. Die toepaslikste
langtermyn stragtegie vir GBV beheer sal wees om plaaslike mieliebasters met
hoë opbrengs en GBV weerstand te ontwikkel.
Molekulêre merkers kan nuttig deur plantetelers gebruik word om
weerstandsgene te selekteer. Seleksie is moontlik in die afwesigheid van
inokolum en op 'n vroeë stadium van plant ontwikkeling. Slegs twee vorige
studies (in die VSA) het kwantitatiewe-kenmerk-Iokusse (KKL), vir GBVweerstand
ondersoek.
Die doel van hierdie studie was om die GBV weerstandsgene in 'n
weerstandbiedende ingeteelde lyn (Seed Co BPK, Zimbabwe) te karteer.
Molekulêre merkers gekoppel aan die GBV weerstands KKL is geïdentifiseer
deur gebruik te maak van die geamplifiseerde-fragmentlengte-polimorfisme-
(AFLP-) tegniek en gebulkte-segregaat-analise. Elf polimorfiese merkers is
geïdentifiseer en omgeskakel na volgorde-spesifieke PKR (polimerase
kettingreaksie) merkers. Agt van die elf omgeskakelde AFLP-merkers is by die
mieliemerker databasis van die Universiteit van Stellenbosch gevoeg.
Vyf van die 8 omgeskakelde AFLP-merkers was polimorfies tussen die bestande
en vatbare ouers. Hulle is geamplifiseer op die DNA van 230 plante van 'n
segregerende F2-populasie en is gebruik in 'n koppelingstudie met
MAPMAKER/EXP. Twee koppelingsgroepe, elk bestaande uit twee merkers, met
onderskeidelik koppelingsafstande van 10.4 eM (LOD 22.83) en 8.2 eM (LOD
55.41) tussen die merkers, is geïdentifiseer. KKL-kartering het getoon dat KKL in
albei koppelingsgroepe aanwesig is. Twee kommersieël beskikbare, rekombinant-ingeteelde families (Burr et aI.,
1988) is gebruik om die omgeskakelde AFLP-merkers op die mielie genetiese
kaart te plaas. Die KKL wat met die AFLP-merkers geïdentifiseer is, is gekarteer
op chromosome 1 en 5. 'n Verdere AFLP-merker is op chromosoom 2 gekarteer
en 'n ander op chromosoom 3.
Ten einde die KKL op chromosome 1 en 5 meer akkuraat te karteer, is volgordege-
etikeerde en mikrosatelliet merkers gebruik. Die merkers is geamplifiseer op
die DNA van die 230 plante van die F2-populasie en koppelings-analises is
uitgevoer. Die volgorde van die merkers was dieselfde as die van die UMC-kaart
in die Mielie Genoom Databasis. Interval kartering met MAPMAKER/QTL en
komposiet interval kartering met QTL Cartographer is uitgevoer. Die KKL op
chromosoom 1 het 'n LOD-telling van 21 gehad en is in bin 1.05/06 geplaas. Die
KKL was verantwoordelik vir 37% van die variansie. Twee pieke was
onderskeibaar vir die KKL op chromosoom 5, een in bin 5.03/04 geleë en die
ander in bin 5.05/06. Elke piek het 'n LOD-telling van 5 gehad en die twee KKL
was verantwoordelik vir 11% van die variansie.
Om die herhaalbaarheid van die effek van die KKL te toets is die merkers naaste
aan elke KKL geamplifiseer op geselekteerde plante van twee F2-populasies wat
in opeenvolgende jare geplant is. Regressie analise is op die data gedoen. Beide
die KKL op chromosoom 1 en die KKL op chromosoom 5 kon in hierdie
populasies geïdentifiseer word. Verder kon die aanwesigheid van 'n verdere KKL
op chromosoom 3 in hierdie populasies bevestig word. Laasgenoemde KKL was
verantwoordelik vir 8-10% van die totale variansie.
In hierdie studie is daar dus 'n hoof GBV-weerstands KKL gekarteer op
chromosoom 1 en twee kleiner GBV-weerstands KKL gekarteer op chromosome
3 en 5. Merkers is geïdentifiseer wat moontlik in merker-gebaseerdetelingsprogramme
gebruik kan word om plante te selekteer wat die GBVweerstands
KKL het.
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