Genotype × Environment Interaction and Stability Analysis of Selected Cassava Cultivars in South Africa.

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.

On-Farm Multi-Environment Evaluation of Selected Cassava (Manihot esculenta Crantz) Cultivars in South Africa.

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.

Analysis of the Nutritional Composition and Drought Tolerance Traits of Sweet Potato: Selection Criteria for Breeding Lines.

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.

Potato Cultivar Identification in South Africa Using a Custom SNP Panel.

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.

Advances in Genetic Analysis and Breeding of Cassava (Manihot esculenta Crantz): A Review.

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.

Genetic diversity and population structure of six South African Acacia mearnsii breeding populations based on SSR markers.

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.

A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop.

Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internationally traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies, we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.

Endogenous cytokinin profiles of tissue-cultured and acclimatized 'Williams' bananas subjected to different aromatic cytokinin treatments.

Endogenous cytokinin (CK) levels of in vitro-cultured and greenhouse-acclimatized 'Williams' bananas treated with six aromatic CKs were quantified using UPLC-MS/MS. The underground parts had higher endogenous CK levels than the aerial parts. Control plantlets had more isoprenoid CKs while the aromatic-type CKs were predominant in all other regenerants. Following acclimatization of the control and 10 µM CK regenerants, there was a rapid decline in both isoprenoid and aromatic CK in the greenhouse-grown plants. Apart from the control and 6-(3-Methoxybenzylamino)-9-tetrahydropyran-2-ylpurine (MemTTHP) treatment with higher level of isoprenoid CK, aromatic CK remain the predominant CK-type across all CK treatments. The most abundant CK forms were meta-topolin (mT) and benzyladenine (BA) in the micropropagated and acclimatized plants, respectively. Micropropagated plantlets had cis-Zeatin (cZ) as the major isoprenoid CK-type which was in turn replaced by isopentenyladenine (iP) upon acclimatization. On a structural and functional basis, 9-glucoside, a deactivation/detoxicification product was the most abundant and mainly located in the underground parts (micropropagation and acclimatization). The results establish the wide variation in metabolic products of the tested aromatic CKs during micropropagation and acclimatization. The findings are discussed with the possible physiological roles of the various CK constituents on the growth and development of banana plants.

Antioxidant and phenolic acid profiles of tissue cultured and acclimatized Merwilla plumbea plantlets in relation to the applied cytokinins.

Merwilla plumbea (Lindl.) Speta is an important medicinal plant widely used in traditional medicine. We evaluated the effect of five cytokinins [benzyladenine (BA), 2-isopentenyladenine (2iP), meta-topolin (mT), meta-topolin riboside (mTR), and meta-methoxy-9-tetrahydropyran-2-yl-topolin (MemTTHP)] on the level of phenolic acids and antioxidant activity of M. plumbea during the tissue culture and acclimatization stages. Two cytokinins (mT and mTR) significantly improved the antioxidant activity of tissue culture plantlets while the control plantlets were better after acclimatization. Using UPLC-MS/MS, the levels of hydroxybenzoic and hydroxycinnamic acid derivatives (phenolic acids) varied significantly during tissue culture and acclimatization, depending on the cytokinin and plant part analyzed. Vanillic acid (24.9 µg g⁻¹) detected in underground parts of tissue culture plants supplemented with BA was the most abundant phenolic acid detected. The current findings indicate that the phytochemicals together with the bioactivity during in vitro propagation of M. plumbea is influenced by the cytokinin type used and the stage of plant material collection.

Physiological responses and endogenous cytokinin profiles of tissue-cultured 'Williams' bananas in relation to roscovitine and an inhibitor of cytokinin oxidase/dehydrogenase (INCYDE) treatments.

The effect of supplementing either meta-topolin (mT) or N(6)-benzyladenine (BA) requiring cultures with roscovitine (6-benzylamino-2-[1(R)-(hydroxymethyl)propyl]amino-9-isopropylpurine), a cyclin-dependent kinase (CDK) and N-glucosylation inhibitor, and INCYDE (2-chloro-6-(3-methoxyphenyl)aminopurine), an inhibitor of cytokinin (CK) degradation, on the endogenous CK profiles and physiology of banana in vitro was investigated. Growth parameters including multiplication rate and biomass were recorded after 42 days. Endogenous CK levels were quantified using UPLC-MS/MS while the photosynthetic pigment and phenolic contents were evaluated spectrophotometrically. The highest regeneration rate (93 %) was observed in BA + roscovitine while mT + INCYDE plantlets produced most shoots. Treatment with BA + roscovitine had the highest shoot length and biomass. Although not significant, there was a higher proanthocyanidin level in BA + roscovitine treatments compared to the control (BA). The levels of total phenolics and flavonoids were significantly higher in mT + roscovitine treatment than in the mT-treated regenerants. The presence of roscovitine and/or INCYDE had no significant effect on the photosynthetic pigments of the banana plantlets. Forty-seven aromatic and isoprenoid CKs categorized into nine CK-types were detected at varying concentrations. The presence of mT + roscovitine and/or INCYDE increased the levels of O-glucosides while 9-glucosides were higher in the presence of BA. Generally, the underground parts had higher CK levels than the aerial parts; however, the presence of INCYDE increased the level of CK quantified in the aerial parts. From a practical perspective, the use of roscovitine and INCYDE in micropropagation could be crucial in the alleviation of commonly observed in vitro-induced physiological abnormalities.

The role of meta-topolins on the photosynthetic pigment profiles and foliar structures of micropropagated 'Williams' bananas.

The effect of five topolins (meta-Topolin=mT; meta-Topolin riboside=mTR; meta-Methoxy topolin=MemT; meta-Methoxy topolin riboside=MemTR and 6-(meta-methoxy)-9-(tetrahydropyran-2-yl)-topolin=MemTTHP) on the photosynthetic pigments and leaf structures of micropropagated 'Williams' bananas was compared with the commonly used benzyladenine (BA). Surface-decontaminated explants were cultured for 70 d on modified Murashige and Skoog (MS) basal medium and supplemented with 10, 20 or 30µM cytokinins (CKs). At 10 d intervals, the photosynthetic pigments were quantified via spectrophotometric methods for 7 cycles. Generally, the maximum pigment content was attained between 40 and 50 d. The control plantlets had the highest pigment content (1150µg/g FW). Among the CKs, 10µM MemTTHP generally had the best pigment stimulatory effect at the same period. After 40 d, scanning electron microscopy (SEM) of the foliar surface showed that the stomata density was highest in 10µM MemTTHP-treated and lowest in 10µM MemTR-treated plantlets. The stomatal structure and pore area also varied with the type and concentration of CK added. Generally, prolonging culture duration as well as increasing CK concentrations reduced the pigment content. However, the drastic breakdown in chlorophyll pigments beyond 50 d was slightly inhibited by the presence of mT, mTR, MemTTHP and BA compared to the control. The CK-treated plantlets at equimolar concentration had comparable chlorophyll a/b and total chlorophyll/carotenoid ratios after 10 d; probably as an adaptive measure. At the end of the current study, 10µM mT and mTR plantlets remained green as reflected by the higher total chlorophyll/carotenoid ratio as well as by the visual observations. A well-developed photosynthetic apparatus enhances the survival of in vitro plantlets during the acclimatization stage. Current findings provide some insight into the role of meta-topolins on photosynthetic parameters in vitro, which inevitably partly contributed to the better acclimatization capability of meta-topolin-regenerants.