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Browsing Plant Sciences by Subject "AFLP"
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Item Open Access Biodiversity in plant, grain and nutritional characteristics of sorghum [Sorghum bicolor (L.) Moench] accessions from Ethiopia and South Africa(University of the Free State, 2010-11) Gerrano, Abe Shegro; Labuschagne, M. T.; Geleta, N.; Van Biljon, A.This study was conducted with the objectives of assessing the genetic diversity of sorghum accessions that were obtained from different geographical locations in Ethiopia, as well as South Africa, using phenotypic traits, AFLP markers, minerals, starch and protein. Twenty phenotypic traits were subjected to ANOVA and highly significant differences were observed for all traits among accessions. Some important characteristics were found to be significantly correlated, which could allow for selection of related secondary characteristics to improve primary characteristics. Cluster analysis grouped accessions into five clusters based on similarity. These results would be useful in a breeding programme for selecting sorghum accessions to improve production. Nine qualitative morphological traits were also analysed using the Shannon Weaver diversity index (H’). The results showed that the average H’ was 0.59. The highest polymorphism was recorded for the glume colour (0.84), while the lowest was recorded in panicle compactness and shape (0.31). This indicated that there was wide variability among accessions studied. The cluster analysis for the qualitative traits also identified accessions based on their similarity and differences based on their genetic distances. Hence, visual selection and measurements of the sorghum attributes in field trials could be used to select the desirable traits and improving yield and stability of the accessions in breeding programmes. AFLP analysis showed high genetic similarity of Ethiopian landraces, as well as breeding material from the Ethiopian and South African sorghum breeding programmes, even though the phenotypical characterisation showed high variability. This indicated the possibility that South African and Ethiopian breeding material may have a common ancestry. The morphological, AFLP and combined morphological and AFLP cluster analysis clearly distinguished between all accessions, even though they were genetically similar. Sorghum kernels were used to determine the mineral, starch and protein composition of the sorghum accessions. The ANOVA of the traits revealed highly significant variation among the accessions studied. Furthermore, PCA grouped accessions according to their similarity/differences in the four quadrants which confirmed that there was variation among them for these nutritional traits. Therefore, there would be potential for selecting accessions for specific mineral and protein content for human consumption, and specific starch and amylose content for industrial use. The sugar content of the stalks also indicated the potential to develop dual sorghum cultivars where both the seed and sugar can be produced from the same plants.Item Open Access Breeding potential of cassava (Manihot esculenta Crantz) in Mozambique(University of the Free State, 2008-05) Da Silva, Anabela Matangue Zacarias; Koen, Elizma; Kanju, Edward EneahEnglish: This study represents the first comprehensive genetic study based on local cultivars of Mozambique. Five cassava (Manihot esculenta Crantz) parents were crossed in a full diallel. The parents and F1 progeny were evaluated for eight agronomical and 17 morphological traits in two consecutive seasons. General combining ability (GCA) was higher than specific combining ability (SCA) for number of roots, root taste, fresh root yield, root pulp hardness and harvest index. Positive heterosis was seen for number of roots, fresh root weight and harvest index. Negative heterosis was present for cassava brown streak virus disease. Harvest index showed high broad sense heritability, which indicated that phenotypic variance was additive. The predictability ratio was close to unity, which confirmed that this trait is highly heritable, and determined by additive gene action. Cassava brown streak root necrosis had SCA effects significantly higher than GCA effects indicating the presence of non-additive genetic effects. A selection index comprised of the most relevant characters was compiled. Amplified fragment length polymorphism (AFLP) analysis showed high genetic similarity among 17 accessions. A total of 425 fragments were produced by eight primer combinations. Mocuba and Nikwaha were the most distinct among the accession and two heterotic groups were suggested. Morphological analysis showed genetic distance ranging from 0.105 to 0.833. The correlation coefficient between AFLP and agronomic clustering was not significant. The AFLP and morphological analysis did not group the accessions according to geographical origin. The principal component analysis provided diversity structure, suggesting the effectiveness of this analysis in genetic diversity studies. The narrow genetic similarity observed, indicates the need to introduce new cassava germplasm.Item Open Access Characterisation and diallel analysis of commercially planted cotton (Gossypium hirsutum L.) germplasm in Tanzania(University of the Free State, 2005-11) Lukonge, Everina Paul; Labuschagne, M. T.; Herselman, L.English: 1. Thirty cotton varieties were studied. Seven parents generated 21 F1 diallel progenies. The main objective was to evaluate genotypes through oil content, fatty acids, morphological and molecular characteristics. Statistical procedures were performed with Agrobase, NCSS and NTYSS computer programmes. Correlation, heterosis, heritability, G x E interaction and stability values were obtained. Stability across four environments was analysed by five stability measures, that of Shukla, Wricke, Lin and Binns, Eberhart and Russell and the AMMI analysis. 2. Significant differences were observed for oil and fatty acids content. Oil content results revealed an average of 20.23%. The ratio for polyunsaturated:saturated fatty acid was 2:1 and for unsaturated:saturated 3:1. The predominant fatty acids were linoleic, palmitic, oleic, stearic, myristic, palmitoleic, arachidic and behenic. Palmitic fatty acid was high while oleic and stearic fatty acids were low for almost all varieties studied. Oil and fatty acid content were significantly influenced by the environment. CIM 70 and Cyto 12/74 can be selected as parents for increased oleic and stearic fatty acid and Stoneville 506 as a parent for reduced palmitic fatty acid, increased oleic, stearic and linolenic fatty acids in hybridisation. 3. ANOVA results indicated significant differences between varieties for all agronomical characteristics studied, where NTA 93-21 and NTA 93-15 were the best performers almost for all characteristics. Genetic distances for morphological (qualitative characteristics) analysis ranged from 0.18 to 0.80. Two major groups, one including many varieties from Africa and the other including varieties from the USA, were revealed. 4. AFLP analysis showed high genetic similarities (0.85 to 0.98). Varieties were distinguished according to pedigree and origin. The increased genetic similarity observed, indicates the need for the introduction of more diverse cotton material. Comparison of agronomical and AFLP markers for determining genetic diversity indicated that genetic similarities between varieties were low for agronomical compared to AFLP markers. The correlation coefficient between AFLP analysis and agronomical genetic similarities was not significant, 5. Highly significant differences between genotypes over environments were observed and NTA 93-21 crosses outperformed the seven parents for almost all characteristics. The parent Okra leaf performed poorly for many characteristics. Trial sites Ukiriguru followed by Kanziga were high yielding environments. 6. Combining ability analysis results indicated significant variation in GCA estimates among parents for different characteristics. Genotypes having high positive GCA estimates for yield components exhibited negative GCA estimates for fibre quality, excluding NTA 93-21. Some combinations indicated positive and significant SCA effects for seedcotton, boll weight, GOT and lint yield. The GCA/SCA ratios for most of the studied characteristics were larger than one. 7. Correlation among characteristics indicated highly significant positive and negative correlations. The observed high and significant GCA and SCA effects for those characteristics are promising for cotton population improvement. Positive heterosis for boll weight was observed for more than 90% of the combinations. Hybrids with high SCA values presented high values of heterosis. Heritability values for the studied characteristics were moderate to high. 8. The combined ANOVA over four environments indicated significant differences between genotypes and locations for all characteristics. The percentage contribution of location to total variation was high compared to genotype variation except for a few characteristics. Highly significant differences of G x E for lint yield and fibre strength were observed. 9. Three stability procedures (Wricke, Shukla and ASV) identified similar stable genotypes. Eberhart and Russell’s procedure, was in harmony with the above three methods but with some divergence. Cultivar superiority measure deviated from the other four measures. Therefore the procedures of Wricke, Shukla and AMMI can be applied for cotton stability studies.Item Open Access Characterization of cactus pear germplasm in South Africa(University of the Free State, 2007-05) Mashope, Barbara Keitumetse; Labuschagne, M. T.; Swart, W. J.; Herselman, L.English: South Africa hosts one of the largest cactus pear germplasm collections in the world. However, not all the varieties have been fully characterised, and evaluated for fruit quality, nutritional quality for use as fodder, and disease resistance. In this study, 38 South African cactus pear (Opuntia ssp.) varieties were characterised using AFLP markers to circumvent G X E effect on phenotypic characterisation. With the use of nine primer combinations, the varieties were grouped into four main clusters based on 346 fragments (per sample) of which 48% were polymorphic between samples. The dendrograms generated indicated that commercially cultivated varieties were dispersed amongst the different clusters indicating that they represent the genetic diversity within the germplasm. Genotype specific fragments were generated using six primer combinations, allowing the unique identification of nine varieties, three of which are commercially cultivated (Meyers, Roedtan, and Santa Rosa). Varieties that are recommended for commercial cultivation in the Mokopane district of the Limpopo Province, based on fruit quality and yield are Gymno Carpo, Malta, Algerian, Morado, Meyers, and Roedtan. These varieties meet the minimum requirements for cactus pear fruit production in South Africa. Nutritional quality evaluation of pruned cladodes from a commercial orchard in the Free State Province indicated that the varieties, Malta, Gymno Carpo, and American Giant ranked the highest in terms of CP content. Varieties that yielded the highest DM content were Messina, Nepgen, and Cross X. Varieties that ranked the highest for OM content were Cross X, Nepgen, and Sicilian Indian Fig. Gymno Carpo and Malta are amongst the varieties recommended for cultivation for fruit, as such they can be used as dual purpose crops for the production of both fodder and fruit. Evaluation for disease resistance indicated a quantitative mode of resistance across all varieties for all three fungal pathogens tested. The most resistant varieties surveyed in this study across all three fungal pathogens were Amersfoort, Meyers, and Algerian. Roly Poly, Direkteur, and Zastron were the more susceptible varieties. Of the three fungal pathogens tested, P. virens was the least affected by the antagonistic activity of the yeast isolates. Isolate 25 (Rhodotorula mucilaginosa) performed well against all three pathogens, whilst the remainder of the isolates displayed inhibition at varying degrees.Item Open Access Genetic variation in Clivia miniata var. citrina(University of the Free State, 2006-06) Gagiano, Anthia; Spies, J. J.; Herselman, L.; Herselman, L.English: The genus Clivia is from the African tribe Haemanthaceae and a member of the family Amaryllidaceae. Clivia is endemic to southern Africa. Yellow Clivia are mutations of the orange-red standard forms that have appeared spontaneously in both wild and garden populations. Yellow Clivia plants are rare and desirable and were described as Clivia miniata var. citrina. Hobbyists from around the world trade in these ornamental plants initiating entire enterprises. Although the yellow form occurs naturally, many yellow clones have arisen through cultivation. Clones passed on from breeder to breeder have acquired different names. For directed breeding purposes in a thriving industry it is important to identify genetically similar plants. The aims of this study were to evaluate existing microsatellites for Clivia miniata var. citrina, to determine if AFLP analysis can distinguish among different plants within the genus Clivia and to determine genetic relatedness between different plants of ‘Vico’, ‘Giddy’ and ‘Natal Yellow’ cultivars. Previous studies done on Clivia include RAPD analysis and SSR analysis for Clivia. Work done in this study presents a first report of AFLP and SSR fingerprint analyses on C. miniata var. citrina. SSR fingerprint analysis revealed that the existing four SSR primer combinations were not applicable for studies on C. miniata var. citrina. AFLP analysis was optimised using a total of 28 EcoRI / MseI primer combinations. Primer combinations were evaluated using six randomly selected Clivia plants based on number of generated fragments, ability to score generated fragments, ability to detect polymorphism and level of polymorphic fragments. Fragments generated using EcoRI+3 primers in combination with Mse+4 primer combinations conformed to the chosen criteria. Primer combinations E-ACC with M-CATC, E-AGC with M-CATC and E-AGC with M-CTGG were selected for further studies on Clivia. AFLP analysis using three preselected primer combinations on 72 Clivia plants was successful in detecting genetic diversity and determining genetic relationships within closely related cultivated Clivia plants. Relatively high levels of genetic diversity (35%), as expected from known pedigree and species data, existed among Clivia plants. Genetic diversity within C. miniata and C. miniata var. citrina plants was high at 27%. Plants available for scrutiny were all genetically distinct. However, based on known pedigree data, names allocated to plants might not be truly representative of the true origin of the plants (e.g. Vico Meristem plants). Material obtained from different breeders could be distinguished at DNA level (e.g. ‘Giddy’ and ‘Natal Yellow’ cultivars). AFLP analysis revealed that different flower coloured plants (Apricot, Blush, Peach, Orange and Yellow) as well as plants from the same geographic areas were distributed together throughout the dendrogram with only a few of a certain colour grouping together. Known Group 1 Yellow and Group 2 Yellow were also present throughout the entire dendrogram, although the majority of known Group 1 Yellow plants grouped together. Clustering of the different species of the genus Clivia agreed with known pedigree data and hybrids included with their parents clustered according to known pedigree data. The phylogenetic relationships of natural populations of C. miniata indicated that all C. miniata plants shared a common ancestor. Clivia miniata from the same geographical area grouped together in the cladogram. More data would be required to prove these observations for all Clivia. Taxonomic status of the C. miniata var. citrina would depend on the monophyly of yellow Clivia plants. Orange flowered forms should be included to determine the validity of the current taxonomic status of these groups.Item Open Access The improvement of leaf rust resistance in selected bread wheat lines(University of the Free State, 2002-11) Craven, Maryke; Pretorius, Z. A.; Labuschagne, M. T.; Prins, R.English: The objective of this study was not only to improve leaf rust (caused by Puccinia triticina) resistance in selected wheats (Triticum aestivum L.), but to focus on durability as well as agronomic acceptability of resistant lines. This was achieved by traditional breeding techniques as well as with the use of AFLP analysis. Seven bread wheat lines were obtained from ARC-Small Grain Institute (SGI) where they were developed. Six leaf rust resistance sources were obtained from the University of the Free State. The breeding strategy focused on creating lines that contained both seedling and adult plant resistance genes. Lr34 was chosen as the adult plant resistance source as it is an important gene due to its durability and interaction with other leaf rust resistance genes. It is also an easy gene to follow as it is associated with leaf tip necrosis. In an attempt to create genotypes that will remain durable, four seedling leaf rust resistance genes (Lr21, Lr32, Lr36 and Lr41) were each combined with Lr34 in the seven SGI backgrounds. By combining seedling and adult plant genes, and selecting only the lowest infection types throughout all phases of testing, a significant shift in the leaf rust resistance of the population occurred. Greenhouse evaluations of plant architecture and agronomic performance of lines containing both a seedling gene and Lr34, indicated that individual plants, similar or better than the original SGI parent, had been selected. Several of these selections can therefore be incorporated in larger, mainstream breeding programmes. It is, however, imperative that the agronomic and quality value of selections be determined under field conditions. More efficient manipulation of an undesignated Lr gene was also attempted. This gene, which originates from T. monococcum, was incorporated in certain bread wheat lines and cultivars. Since the gene is characterized by an immune response to South African pathotypes of leaf rust, it is considered valuable in terms of rust resistance. However, its single gene nature implies it will not remain durable and that it has to be protected in complex resistance gene combinations. To achieve this, linked molecular markers are needed. In this study a putative AFLP marker for leaf rust resistance was generated by S12/M14 and S12/M44 using pooled DNA. Analysis of individual plants from which the DNA bulks were constructed indicated that the marker might not be closely linked to the Lr gene of interest. Validation in three additional backgrounds revealed several instances of recombination between the marker and the gene, emphasising the need to do a proper linkage study. Should the linkage distance be acceptable, the marker might still be useful as it proved to be polymorphic in five different wheat backgrounds. The linkage distance is also needed before the intensive effort to clone and convert the AFLP band to a more user-friendly STS marker will be considered.Item Open Access Morphological and genetic characterisation of mango (Mangifera indica L.) varieties in Mozambique(University of the Free State, 2010-05) Mussane, Cecilia Ruth Bila; Van Biljon, A.; Herselman, L.English: Mango (Mangifera indica L.) belongs to the Anacardiaceae family. Consumption is increasing worldwide due its their nutritional value that is rich in vitamins A and C, potassium, β-carotene, fibre as well as proteins. Mangoes are economically important for Mozambique because of suitable climatic conditions and international market opportunities. This study compared morphological and AFLP characterisation of 30 mango varieties from the Umbeluzi research station, including some commercial varieties: “Keitt”, “Kent”, “Haden”, “Sensation” and “Ruby”. Morphological characterisation using IPGRI descriptors were divided into quantitative (23 characteristics) and qualitative (58 characteristics) data. The total variation was lower using quantitative (89.4% similarity) than qualitative data (60% similarity). The combined quantitative and qualitative dendrogram had 63% similarity and clustered varieties in three subgroups based on high fruit weight, high Brix content and low fruit weight. AFLP characterisation used seven primer combinations, generating 207 data points and detecting 74.9% polymorphism with an average of 30 fragments per primer combination. The total variation was low (72.49% similarity) and the dendrogram showed two main groups subdivided in five subgroups based on low fruit weight, dwarfness and low Brix content, high fruit weight and roundish fruit shape. The combined morphological and AFLP dendrogram was more accurate in clustering varieties based on geographic origin within the country and from outside. The dendrograms presented in the study will help breeders to select parents for crosses. PCA results confirmed the pattern of clustering of varieties based on fruit weight and Brix/acidity ratio. It is recommended to extend the study to include, the entire collection at Umbeluzi and to include morphological data, considering pest and diseases resistance characterisation, as well as genetic and cytological analysis. A study of genotype x environment interactions done over years should be undertaken in future.