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Plant tissue culture has become one of the fundamental tools of plant science research. It is extensively employed in the production, conservation and improvement of plant resources. The presence of somaclonal variation in populations derived from tissue culture is affecting the use of tissue culture negatively and has remained a major problem. Conversely, it is a source of new desirable clones/variants with better agronomic traits. In this review, we summarize the possible causes, detection methods and desirability of variants. Somaclonal variation is one of the most researched and reviewed topics. Hence, we restricted ourselves to outlining various examples which may be used as important references for researchers who intend to identify and/or characterize somaclonal variants while using tissue culture for research and production. Emphasis is placed on the negative effects of somaclonal variation. However, this review also includes examples of some useful variants generated as a result of somaclonal variation.

Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds’ largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.

Sweet potato is an important world staple with the potential to address hunger and malnutrition. The Agricultural Research Council of South Africa has led sweet potato breeding efforts in the country since 1952 and released several important cultivars. More detailed quality assessments are necessary in addition to general breeding criteria. The present study investigated sweet potato cultivars and elite clones for (1) their nutritional composition; (2) biochemical reaction to drought stress; (3) correlate biochemical reaction to root yield for possible identification of screening methods for drought tolerance in sweet potato. Orange-fleshed cultivars, in particular Bophelo, had superior contents of Fe, Zn, Mg, Ca, Mn, and dietary fiber. Cream-fleshed cultivars, particularly Ndou, were higher in starch and carbohydrate. When sweet potato cultivars were subjected to drought stress, significant changes were noted in most antioxidant enzymes, chlorophyll and proline concentrations, and 13C discrimination. All of these showed significant correlations with root yield. For screening of drought tolerance, the determination of nitrate reductase, proline, and chlorophyll concentrations at 60 days after planting are recommended. Ndou was less affected by drought stress. Bophelo and Ndou, which are gaining popularity on the informal market, have superior nutritional value and are good cultivar choices for food security and addressing malnutrition.

Black wattle (Acacia mearnsii) has great economic value as a commercial source of tannins, timber and a source of firewood for local and international markets. It has been suggested that to maximize the genetic gain of A. mearnsii plantations in South Africa, the gene pool that exist within ICFR needs to be broadened via introduction of new genotypes with diverse traits. In this work, 282 A. mearnsii samples sourced from the ICFR breeding program were genotyped using 11 cross-species SSR markers. Our results showed low to moderate genetic differentiation (FST) among the six breeding subpopulations, with positive inbreeding (FIS) values that could be attributed to an historical inbreeding event. Low levels of relatedness could however indicate some mechanism of inbreeding avoidance. The effects from a recent supplementation of genetic material from two native Australian populations were observed through genetic structuring analyses. Analysis of molecular variance (AMOVA) revealed that significant genetic variation was mainly distributed within populations (75%) and among individuals (23%). The results provide significant information on A. mearnsii population genetic diversity and structure, which can be used for conservation of the current subpopulations and future tree improvement programs.

Cassava (Manihot esculenta Crantz) is an important root crop worldwide. It is adapted to a wide range of environmental conditions, exhibiting differential genotypic responses to varying environmental conditions. The objectives of this study were: (1) to examine the effect of genotype, environment and genotype × environment interaction (GEI) on fresh root yield (FRY) and dry matter content (DMC); and (2) to identify superior genotypes that exhibit high performance for the traits of interest using the genetic tools of additive main effects and multiplicative interaction (AMMI) and genotype stability index (GSI) analysis. Eleven cassava genotypes were evaluated in a randomized complete block design at six trial sites in South Africa. The combined analysis of variance based on AMMI revealed significant genotype, environment and GEI for the traits. The percentage variation due to GEI was higher than the percentage variation due to genotype for FRY, reflecting differential genotypic responses across the experimental sites. The proportion of variance due to genotype variation was larger for DMC. Genotype stability index (GSI) showed that UKF3 (G6), 98/0002 (G2) and P4/10 (G5) were the highest yielding and most stable genotypes for FRY, and 98/0002 (G1), UKF3 (G6) and UKF9 (G11) were the highest yielding and most stable genotypes for DMC. Cultivars 98/0002 and UKF3 were identified as providing high stability with superior fresh root yield and DMC. These genotypes could be recommended to farmers for food, feed and industrial applications without the need for further breeding. The AMMI-2 model clustered the testing environments into three mega-environments based on the winning genotypes for FRY and DMC. Mabuyeni (KwaZulu-Natal), Shatale (Mpumalanga) and Mandlakazi (Limpopo) would be the best testing sites in future cassava-genotype evaluation and breeding programs. This study provides a baseline for a future study on the GEI of cassava varieties, using a larger set of genotypes, factoring in seasonal variation.

DNA fingerprinting is a molecular technique applied to identify genetic differences between plant cultivars or lines and is used for genetic purity testing. The suitability of single nucleotide polymorphism (SNP) panels for the fingerprinting of tetraploid potato were investigated as a new high throughput, objective, and cost-effective method instead of simple sequence repeats (SSRs) and polyacrylamide gel electrophoresis (PAGE). One-hundred and ninety (190) potato cultivars, including various cultivars currently important in South Africa, were genotyped at 500 SNP positions utilising SeqSNP by LGC Biosearch Technologies. An optimal panel of 25 SNP markers was identified that could discriminate between South African potato cultivars on genetic allele dosage. The genotypes of these SNPs were validated on selected potato genotypes using KASP (Kompetitive Allele Specific PCR) SNP assays. A database of SNP genotype profiles was compiled for all the entries of the germplasm database. The panel of 21 successful SNPs accurately identified the unique potato cultivars in the database. The KASP SNP assays of the successful SNP panel are therefore available for potato DNA fingerprinting as new germplasm, or purity test requests are submitted to ARC-VIMP. This panel provides an objective method for assigning putative cultivar identity to unknown samples submitted for fingerprinting.

Cassava is an important starchy root crop grown globally in tropical and subtropical regions. The ability of cassava to withstand difficult growing conditions and long-term storability underground makes it a resilient crop, contributing to food and nutrient security. This study was conducted to evaluate the performance and adaptability of exotic cassava cultivars across different environments in South Africa and to recommend genotypes for cultivation. A total of 11 cassava cultivars were evaluated at six on-farm sites, using a randomized complete block design with three replications. There were highly significant (p < 0.001) variations between genotypes, environments, and their interaction for all yield and yield-related traits studied. This indicates the need to test the genotypes in multiple environments before effective selection and commercialization can be undertaken. MSAF2 and UKF4 showed the overall best performances for most of the traits, whilst UKF9 (49.5%) and P1/19 (48.5%) had the highest dry matter yield. UKF4 (102.7 t ha−1) had the highest yield and greatest root yield stability across environments. MSAF2 did not perform consistently across environments because it was highly susceptible to cassava mosaic disease (CMD). MSAF2 could be used as a donor parent to generate novel clones with large numbers of marketable roots, and high fresh root yields, if the other parent can provide effective resistance to CMD. Based on genotype and environmental mean, Mabuyeni (KwaZulu-Natal), Mandlakazi (Limpopo), and Shatale (Mpumalanga) were found to be better environments for cassava cultivation and testing. This study is a pioneer in cassava research using multiple environments in South Africa. It provides baseline information on the performance of currently available cassava clones, their adaptation to multiple sites, the identification of suitable test sites, and information on current genetic resources for a future breeding program.

Africa has the largest diversity of the genus Hypoxis, accounting for 61% of the current globally accepted taxa within the genus, including some endemic species. Using Hypoxis hemerocallidea as a case study, this review addresses the conservation concerns arising from the unsustainable, wild harvesting of a number of Hypoxis species. Hypoxis hemerocallidea is one of the wild-harvested, economically important, indigenous medicinal plants of southern Africa, with potential in natural product and drug development. There are several products made from the species, including capsules, tinctures, tonics and creams that are available in the market. The use of H. hemerocallidea as a “cure-all” medicine puts an important harvesting pressure on the species. Unsustainable harvesting causes a continuing decline of its populations and it is therefore of high priority for conservation, including a strong case to cultivate the species. Reviewing the current knowledge and gaps on cultivation of H. hemerocallidea, we suggest the creation of a platform for linking all the stakeholders in the industry.

At low concentrations, smoke–water (SW) and smoke-derived karrikinolide (KAR 1 ) are compounds with potential cytokinin and auxin-like activity. Their roles on the growth, photosynthetic pigment and phenolic contents of micropropagated ‘Williams’ bananas were investigated in comparison with meta -topolin ( m T). Explants were cultured on modified Murashige and Skoog basal media supplemented with either SW (1:125; 1:250; 1:500; 1:1,000; 1:2,000 dilutions) or KAR 1 at four concentrations ranging from 4.8 × 10 −22 to 3.3 × 10 −12  M. After 42 days, growth parameters were measured while the photosynthetic pigments and phenolic contents were quantified using spectrophotometric methods. Chlorophyll a, b and total carotenoid contents were significantly enhanced by KAR 1 (4.8 × 10 −22  M) and SW (1:125 and 1:1,000 dilutions). The pigments in KAR 1 -treated plantlets were approximately two-fold to three-fold higher than those in the control and m T-treated plants, respectively. Total phenolic content was highest with KAR 1 at 1.0 × 10 −19  M in the leaves and 7.8 × 10 −17  M in the roots. Furthermore, KAR 1 -treated plants at 1.0 × 10 −19  M yielded the highest level of total phenolics (leaves) and proanthocyanidins (roots). At 1:500 dilutions, SW stimulated the highest total flavonoid content in the leaves across all the treatments. Combining m T with either SW (1:500) or KAR 1 (4.8 × 10 −22  M) significantly increased the quantity of secondary metabolites. However, the growth parameters and pigment contents were not improved. Based on the significant role of photosynthetic pigments and phenolic compounds on the defense and survival strategies of plants, current findings will have practical significance for important processes such as acclimatization and survival of micropropagated plants. These results are also demonstrating the potential of SW and KAR 1 as an eliciting agent for secondary metabolite production.

Since the discovery of topolins as naturally occurring aromatic cytokinins (CKs), they have emerged as genuine alternatives to the long serving CKs such as benzyladenine, zeatin and kinetin in plant tissue culture (PTC). Globally, the past 15 years has witnessed a surge in the use of topolins and their derivatives in research laboratories. Topolins, especially the meta-topolin and its derivatives have been employed for culture initiation, protocol optimization and for counteracting various in vitro induced physiological disorders in many species. Evidence from various studies indicate the rising popularity and advantages (although not universal for all species) of topolins compared to other CKs. In this review, we assess the use of topolins in PTC with emphasis on their metabolism, structure–activity relations and effect on morphogenesis in vitro. In addition, the review provides a detailed list of species that have been used to study the effect of topolins in comparison with other CKs, the growth parameters affected and recommended concentrations are also provided.