Genotype by environment interaction (GxE) is the tendency of the phenotypic performance of two or more plant genotypes in one environment to not be predictive of their relative performance in another environment. To discover the importance of GxE in this region, a large set of USDA and commercial hybrids were tested in the regions of practical significance to sunflower production in order to produce recommendations regarding mega-environments for yield and oil. Rank changes for oil content occurred among hybrids and two common factors accounted for 68.6% of the total GxE variation. Breeding programs testing pre-commercial hybrids in multiple environments for oil content could be beneficial. Yield covariates for lodging, bird damage, and disease were significant but occurred in different locations with variable severity each year making it difficult to divide the growing region into mega-environments for yield.

Sunflower (Helianthus annuus L.) is one of the most important oil crops in South Africa and genetic improvement for grain yield and oil-content was initiated in the country in the early 1970s. Commercial production of sunflower in South Africa is done under natural rainfall conditions in areas where frequencies of drought are high hence the requirement for drought tolerant cultivars. An assessment of the genetic gains in seed and oil yield achieved since 1970, the effects of re-cycling inbred lines and strategies for developing drought tolerant sunflower cultivars has not been done for South African sunflower breeding programmes. Two data-sets were used for the genetic gain studies: side-by-side evaluation of historical and current sets of popular cultivars in the same environment under one set of trial management practices; and yield trends in commercial farmers’ fields based on annual production estimates. The estimated relative genetic gain for seed yield based on side-by-side trials was 1.5% year−1 and the relative gain in seed yield per year under commercial production was 1.9% year−1. The contribution of new cultivars to total seed yield progress in sunflower were 56.3% for the period 1970 to 1989; 23.9% from 1990 to 2009 and the mean over the four decades under consideration from 1970 to 2009 was 41.6%. Quantifying the usefulness of inbred lines in advanced cycle plant breeding was done using four base breeding populations based on: phenotypic or genetic variability; heterosis; and combining ability. Significant genetic variation was evident for seed yield and oil yield while genetic variability for oil content was low. Genetic advance (GA%), with a 10% selection intensity, was high for seed yield and oil yield for each of the four populations ranging from 36-42% and 38-43%, respectively. The GA% for oil content was low ranging from 1.3% to 5.1% indicating the need to introgress high oil content germplasm in the present breeding populations in advanced cycle pedigree breeding. Founder parent heterosis (FPH), mid-standard heterosis (MSH) and high standard heterosis (HSH) indicated that some new testcross hybrids from the advanced cycle pedigree breeding populations were performing better than their founder parents in hybrid combination as well as the standard commercial hybrid checks. From variance component analysis, general combining ability (GCA) was predominant over specific combining ability (SCA) for seed and oil yields indicating that superior hybrids can be identified based on positive and significant GCA effects of the female lines. For oil content, SCA was predominant over GCA indicating that it would be best to select for specific hybrids combinations with high oil content rather than selecting female lines with high GCA effects. Variable moisture conditions characterise the sunflower production environments in South Africa. Breeding for such environmental conditions requires a combination of strategies including use of secondary traits and developing appropriate test environments. Three secondary traits, head diameter, stem diameter and stay green canopy which are easy to measure in the field were evaluated for their appropriateness for selecting for drought tolerance under three moisture conditions: random stress environments (RSE), managed drought stress environments (MSE) and well watered nonstress environments (NSE). Type A genetic correlations indicated that stay green canopy (SG) had the potential to be used as secondary trait to indirectly improve oil yield under the three moisture conditions. The indirect selection efficiency (ISE) for SG using genetic correlations based on H2 were 0.79, 0.82 and 0.78 in the RSE, MSE and NSE, respectively, while that using genetic correlation based on h2 were 0.67, 0.98, and 0.93 in the RSE, MSE and NSE, respectively. In both cases selection in the MSE had the highest efficiency using genetic correlations based on either H2 or h2. Estimates of indirect selection based on type B genetic correlations indicated that indirect selection for oil yield (OY) in the MSE and NSE for the target RSE was as effective as direct selection of OY in the RSE based on additive genetic correlations of 0.96 obtained in both selection environments. Overall, the results from the exploratory drought tolerance study should inform the development of breeding strategies to improve drought tolerance and associated yield stability of sunflower cultivars grown in South Africa and associated environments. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

This study compared DNA based SSR markers with total seed protein markers, used to evaluate genetic diversity of sunflower. The multiplex-ability, cost effectiveness and applicability of microsatellites as molecular markers for a genetic diversity study were investigated and evaluated based on pedigree data of the sunflower germplasm. A solution for oil and fat interference in ultrathin iso-electric focusing gels was investigated, in order to make imaging and interpretation easier and clearer. Total protein analysis was utilized for the determination of genetic diversity on the same inbred material used for the DNA analysis. Finally a correlation is made between the data obtained on DNA vs Protein compared with phenotype and expected pedigree data. A set of 73 SSR markers with known mapped positions were utilized to determine genetic similarity in a group of sunflower inbred lines. Cluster analysis of genetic similarity revealed an excellent correlation with the breeding background and source information obtained from breeders on all inbred lines used in this study. Cluster analysis gave a clear differentiation between B and R-lines, showing clearly defined heterotic groups of the proprietary set of inbred lines. The most outstanding single-locus SSR markers in the set used for this study were identified and used as a core set. Multiplex assays were designed and optimized for the most cost and time effective method for rapid variety identification. The selected markers produced robust PCR products, amplified a single locus each, were polymorphic among the elite inbred lines and supplied a good, genome-wide framework of completely co-dominant, single-locus DNA markers for molecular breeding. The use of a fluorescent-tailed primer technique resulted in a considerable cost saving. Furthermore, the SSR markers can be multiplexed through optimization, in order to avoid undesirable primer-primer interactions and non-specific amplification. First stage iso-electric focusing of total protein extracts were used to analyze sunflower looking at genetic purity and genetic variety verification on diverse sunflower germplasm. Severe visual interference was visible on most seed storage protein extracts of sunflower. This interference was visible as a distortion in the gel matrix on the anodal end of the gel, and caused important proteins to denature in the presence of heightened field strength and the absence of a uniform matrix. Adjustment of the extraction solutions removed this interference. Total protein profiles were generated with the use ultrathin layer iso-electric focusing (UTLIEF) to assess the level of genetic diversity on the same set of sunflower lines used for the SSR analysis. Finally, the genetic diversity of the sunflower germplasm was analysed by comparing proteomic, genomic and pedigree data from the same germplasm. A total of 295 alleles were amplified with a set of 73 SSR markers with known mapped positions. These were utilized to determine the genetic relatedness of a group of B-lines and R-lines of sunflower. In parallel, a total of 68 protein bands were visualized using protein samples of two types of seed storage proteins derived from exactly the same sunflower lines. Cluster analysis clearly differentiated between the B-lines and R-lines, identifying defined heterotic groups of this proprietary set of lines. The comparison of DNA and protein data for the application of genetic diversity studies is analysed, as well as the general comparison on the use of the two different molecules as markers. / Thesis (Ph.D)-University of KwaZulu-Natal, Pietermaritzburg, 2008.