Liezel Herselman

Genetic variation among Southern African cultivated peanut (Arachis hypogaea L.) genotypes as revealed by AFLP analysis

The amplified fragment length polymorphism (AFLP) technique, employing two different rare cutters, EcoRI and MluI in combination with the frequent cutter MseI, was used to assess genetic diversity and relationships among 21 closely related cultivated Southern African peanut genotypes. A dendrogram was constructed using Jaccards coefficient and the UPGMA clustering method. Low levels of polymorphism (on average 2.78%) were detected. Results indicated that both EcoRI/MseI and MluI/MseIAFLP enzyme combinations efficiently detected polymorphism within closely related cultivated peanut, although the EcoRI/MseI enzyme combination detected more fragments per primer combination (on average 67.8) as opposed to29.7 by the MluI/MseI enzyme combination. All 21 genotypes could be uniquely distinguished from each other with a minimum of three MluI/MseI primer combinations. Genetic data correlated well with known species and pedigree data, dividing the 21 genotypes into two main groups corresponding to the two subspecies of Arachis hypogaea namely fastigiata and hypogaea. Divisions within the two main groups correlated with botanical types and pedigree data. This is the first report where MluI/MseI primer combinations were used on cultivated peanut and also the first successful detection of polymorphisms between closely related cultivated peanut genotypes worldwide.

Characterization of two new Puccinia graminis f. sp. tritici races within the Ug99 lineage in South Africa

Two new races of the wheat (Triticum aestivum L.) stem rust pathogen, representing the fifth and sixth variants described within the Ug99 lineage, were detected in South Africa. Races TTKSP and PTKST (North American notation) were detected in 2007 and 2009, respectively. Except for Sr24 virulence, race TTKSP is phenotypically identical to TTKSF, a commonly detected race of Puccinia graminis f. sp. tritici (Pgt) in South Africa. PTKST is similar to TTKSP except that it produces a lower infection type on the Sr21 differential and has virulence for Sr31. Simple sequence repeat (SSR) analysis confirmed the genetic relationship amongst TTKSF, TTKSP, PTKST and TTKSK (Ug99). TTKSK, PTKST and TTKSF grouped together with 99% similarity, while sharing 88% genetic resemblance with TTKSP. These four races in turn shared only 31% similarity with other South African races. It is proposed that both TTKSP and PTKST represent exotic introductions of Pgt to South Africa.

Genetic comparison of Ug99 with selected South African races of Puccinia graminis f.sp. tritici.

Using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) marker analyses, the genetic structure of selected South African wheat stem rust races was compared with Ug99. SSR analysis divided the population into two distinct groups with 24.5% similarity between them. A local race, UVPgt55 (North American race notation TTKSF), grouped with Ug99 (TTKSK) with a 100% similarity. When AFLP data were included, the same groups were found, but with an increased similarity of 66.7%. Although the SSR data were unable to distinguish between all individual isolates, the AFLP data alone and in combination with the SSR data discriminated between the isolates. The grouping of individual isolates resembled the pathogenicity profile of the different races. On the basis of its similarity with Ug99, it was concluded that UVPgt55 was most probably an exotic introduction into South Africa, whereas the other races specialized locally through mutational adaptation.

A cassava clonal evaluation trial based on a new cassava breeding scheme

Cassava (Manihot esculenta) breeding at the earlier stages so far has been mainly based on a mass phenotypic recurrent selection, as little data is taken. This has resulted in a long breeding cycle and lack of organised information on the breeding values of parental lines used in the breeding programmes. The International Institute of Tropical Agriculture (CIAT) recently initiated a scheme to try and correct this, by introduction of replication and blocking in the clonal evaluation trial (CET) and collection of data on all genotypes at early stages of breeding. The aim of the study was to evaluate a CET using the new breeding scheme. Replicating and blocking of clones improved the accuracy of the data obtained. High broad-sense heritability values, comparable to those at advanced selection stages, were obtained, as environmental effects were minimised. The highest was for harvest index (HI) (0.80), followed by cassava frogskin disease (CFSD) (0.79), dry matter content (DMC) (0.75) fresh and dry root yields (DRY) (0.73), root weight (RtWt) (0.61), number of commercial roots (0.60) and roots per plant (RtPlt) (0.43). DMC, HI and RtWt were identified as important variables in selection and determination of economic yield at early stages of selection.

Yield traits as selection indices in seedling populations of cassava

The cassava breeding scheme currently used is long, because initial stages concentrate mainly on improving yield, with root quality selection following later. To shorten the scheme, yield and root quality should be selected simultaneously, starting at the seedling nursery. In this study, a nursery comprising of eight cassava families and 1885 seedlings developed from parents adapted to three major agro-ecologies, were evaluated for yield related traits in Colombia. Percentage dry matter content (DMC) and harvest index produced similar ranking of the parents. Tuber yield, weight, and number showed potential of increasing yield through conventional breeding. A selection index including fresh root yield, percentage DMC, root weight and roots per plant, with heavier weights being assigned to root weight and roots per plant, should be used.

The effect of genotype, location and season on cassava starch extraction

When cassava is harvested too early, it often leads to reduction in yield, while delayed harvest leads to development of woody and fibrous tuberous roots, and reduction in starch content. The optimum harvest time is not known. The objectives of this study were to determine the effect of genotype, location and season on starch extraction in order to find an optimum harvest regime for cassava, and to find the best parameter for monitoring starch levels in cassava tuberous roots. Results showed that genotypic effect was large for starch weight, starch extraction rate on fresh weight basis, and root dry matter content. This suggested that high starch weights could be realised by selection of suitable varieties for starch extraction. It was found that cassava harvesting and starch extractions should be done between October and November since the highest starch extraction rates were achieved during that period, and drying of the extracted starch using the open air method was fast and convenient. The results also suggested that starch levels can efficiently be monitored using starch extraction rate on fresh root weight basis. Starch content on fresh root basis and root dry matter content can also be used to determine the optimum time to harvest cassava for starch extraction but were inferior to starch extraction on fresh root weight basis.

Relationships between heterosis, genetic distances and specific combining ability among CIMMYT and Zimbabwe developed maize inbred lines under stress and optimal conditions

Genetic characterisation of breeding lines is of great importance as it enables breeders to maximise heterosis in hybrid combinations as well as in the breeding material. In this study 10 Department of Research and Specialist Services and 13 Centre for the Improvement of Maize and Wheat inbred lines were crossed using a North Carolina II mating scheme and were genotyped using 1,129 single nucleotide polymorphic (SNP) markers. The resultant 72 single cross hybrids together with eight different local checks were evaluated across seven locations in Zimbabwe in the 2009/2010 and 2010/2011 seasons. SNP markers yielded a total of 2,258 alleles and a moderate genetic diversity and polymorphic information content of 0.32 and 0.258, respectively. Clustering of lines did not relate to available pedigree information. Significant positive correlations were recorded for specific combining ability with mid parent heterosis (MPH), high parent heterosis (HPH) and per se performance of hybrids. However, correlations of genetic distances with heterosis under drought conditions were too low to be of predictive value. The HPH and MPH also showed significant positive associations along with high coefficients of determination with per se performance of hybrids, especially under drought.

Introgression of genes for dry matter content from wild cassava species

Cassava cultivars often have poor resistance to biotic stresses and lack good quality traits. Wild species of cultivated crops have frequently been used as an important source of genetic diversity. Cassava breeders are becoming increasingly interested in incorporating genes of wild relatives. In 2000 the International Center for Tropical Agriculture (CIAT) initiated a programme to introgress genes for several root yield and quality traits from wild cassava relatives into its germplasm collection. The objectives of this study were to evaluate one resulting inter-specific cross with high variability for dry matter content (DMC) and to assess the effect of such a cross on other yield related traits. Crossing of the elite cultivar MTAI 8 to the wild relative Manihot tristis increased the percentage DMC above the normal average of about 35%, with percentage DMC ranging from 34.39 to 42.73. The crosses, however, were accompanied by some detrimental effects, most noticeable the reduction in harvest index (HI). It is apparent that when selecting for DMC, caution should be taken and HI and fresh root yield should be monitored. Regression analysis singled root weight, percentage DMC and fresh root yield out as the most important contributors to dry root yield. Principal component analysis indicated that root weight, roots per plants and DMC contributed most to storage root yield.

Genetic diversity analysis of kenaf (Hibiscus cannabinus L.) using AFLP (amplified fragment length polymorphism) markers

Nineteen kenaf genotypes from Cuba, Taiwan, the USA, El Salvador, Guatemala, Russia, Spain and Indonesia, and three wild types collected in South Africa were analysed for genetic diversity using AFLP analysis. All could be uniquely distinguished from one another, but only a low level of genetic diversity was present. The most distinct accession, Guatemala 4, was 85% similar to all other accessions. The accessions clustered more or less according to known pedigree and/or origin. Two of the three wild types (Hibiscus cannabinus c and H. cannabinus a) clustered separately from the commercial and Russian accessions. One of the wild types, H. cannabinus b clustered with some of the commercial accessions. Commercial accessions in the first subgroup all originated from central and North America, and surrounding islands (Cuba and El Salvador). The Russian accessions are all grouped together. The second subgroup was the only group that contained accessions from different geographical origins.

Diallel analysis of provitamin A carotenoid and dry matter content in cassava (Manihot esculenta Crantz)

Global efforts are underway to biofortify cassava (Manihot esculenta Crantz) with provitamin A carotenoids to help combat dietary vitamin A deficiency afflicting the health of more than 500 million resource-poor people in Sub-Saharan Africa. To further the biofortification initiative in Uganda, a 6×6 diallel analysis was conducted to estimate combining ability of six provitamin A clones and gene actions controlling total carotenoid content (TCC), dry matter content (DMC) in cassava roots and other relevant traits. Fifteen F1 families generated from the diallel crosses were evaluated in two environments using a randomized complete block design. General combining ability (GCA) effects were significant for TCC and DMC, suggesting the relative importance of additive gene effects in controlling these traits in cassava. On the other hand, non-additive effects were predominant for root and shoot weight. MH02-073HS, with the highest level of TCC, was the best general combiner for TCC while NASE 3, a popular white-fleshed variety grown by farmers in Uganda, was the best general combiner for DMC. Such progenitors with superior GCA effects could form the genetic source for future programs targeting cassava breeding for TCC and DMC. A negative correlation was observed between TCC and DMC, which will require breeding strategies to combine both traits for increased adoption of provitamin A cassava varieties.