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Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), poses a threat to wheat production in South Africa (SA). The locally developed winter wheat cultivar PAN 3161 has consistently displayed adult plant resistance (APR) to stem rust, prompting an investigation into the genetics thereof. An F2 population was developed from a cross between PAN 3161 and the susceptible parent Line 37 − 07 and tested against Pgt race PTKST in the field. F3 families were also assessed in the field to confirm the F2 segregation ratios. Molecular marker genotyping combined with bulk segregant analysis (BSA) on 128 F2 plants identified markers on the short arm of chromosome 4D to be linked to stem rust resistance. Simple sequence repeat (SSR) marker wmc720 flanked the APR gene, SrPan3161, distally at 1.8 cM. Five co-segregating SSR markers gpw7414, gpw8038, wmc52, psp3103 and cfd23 flanked SrPan3161 proximally at 1.8 cM. PAN 3161 tested negative for Lr67/Yr46/Sr55/Pm46/Ltn3, and linked (csSNP856) and diagnostic single nucleotide polymorphism (SNP) markers (SNP1-TM4 and SNP2-TM10). Quantitative trait loci (QTL) analysis was performed to confirm linkage mapping results and identified a single major QTL that explained 71.5% of the phenotypic variation for resistance to Pgt race PTKST. The closely linked SSR markers psp3103 and cfd23 were 100% predictive of SrPan3161 in a set of 55 wheat cultivars and breeding lines, thus validating chromosome 4D as the region carrying SrPan3161 and their potential effectiveness in marker-assisted selection. Results suggest that SrPan3161 was introduced into South African winter wheat through the cultivar Tugela (pedigree Kavkaz/Jaral), first released for production in 1985.

Bread wheat is a widely cultivated crop with production that is often negatively influenced by disease outbreaks. Biological constraints in production include the wheat rusts (leaf rust, stem rust and stripe rust) and Fusarium head blight (FHB). Different strategies are available in the control of these important fungal diseases. However, resistance breeding remains the preferred option of control as it lowers the risk of disease outbreaks and is a more cost effective and environmentally friendly approach. Many effective rust and FHB resistance genes have been discovered and successfully deployed through resistance breeding worldwide. However, some of these genes, when deployed singly, are vulnerable to evolving pathogens. In this study we aimed to develop wheat lines with the prospect of durable resistance against the rusts and FHB through combining eight resistance genes/quantitative trait loci; Lr19, Lr34/Yr18/Sr57/Pm38/Ltn1, Sr2/Yr30, Sr26, Sr39, Fhb1, Qfhs.ifa-5A-1 and Qfhs.ifa-5A-2 into a single wheat plant using marker-assisted selection. Cross and self-pollinated populations were developed to increase the frequency and homozygosity levels of resistance genes in progeny. Molecular markers were furthermore applied to determine the identity of the high molecular weight-glutenin subunits (HMW-GS) and to screen for the presence of the 1BL.1RS translocation in the final populations. We were successful in developing wheat plants containing complex sources of rust and FHB resistance and confirmed the presence of HMW-GS markers linked to strong dough strength and good bread making qualities in these genotypes.

Race 2SA55 of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici, was described for the first time during 2000 in South Africa. This race is of particular interest as it was the first local report of increased virulence towards barley cultivars by wheat stem rust. Using three original accessions of 2SA55 from the rust collection of the University of the Free State, nine single pustule isolates were established. Phenotyping of isolates to characterise 2SA55 according to the North American nomenclature system revealed variation in virulence for Sr9g on the tester lines Kubanka and Acme, which was not detected in the initial description of 2SA55. Seven isolates coded as BNGSC, which except for virulence on Sr9b resembled the initial avirulence/virulence description for 2SA55. The remaining two isolates with Sr9g virulence coded as BPGSC. The seedling infection types for the two 2SA55 derived races BNGSC and BPGSC on the Stakman differential set as well as on an extended set of Sr lines and 144 South African wheat cultivars and advanced breeding lines revealed no further distinction in reaction between them. Microsatellite analysis indicated that while race BN/PGSC shares phenotypic similarity with several of the South African non-Ug99 races, it was genetically distinct.

Fusarium Head Blight is a major disease of wheat and an important contributor to the reduced cultivation of wheat in South Africa, where the crop often is grown under irrigation. We collected Fusarium isolates from 860 Fusarium Head Blight-infected wheat heads in seven irrigated wheat-growing areas of South Africa. Six Fusarium species, i.e., F. chlamydosporum, F. crookwellense, F. culmorum, F. equiseti, F. graminearum and F. semitectum were recovered, three of which, i.e., F. chlamydosporum, F. equiseti and F. semitectum, were not previously associated with Fusarium Head Blight in South Africa. Fusarium graminearum occurred at high frequencies at all seven locations. Based on polymerase chain reaction (PCR) assays of diagnostic sequences, more isolates were predicted to produce deoxynivalenol than nivalenol. Fusarium graminearum (sensu lato) appears to be the primary causal agent of Fusarium Head Blight in irrigated wheat in South Africa, which may not be the case for wheat cultivated under rain-fed conditions. Rotations of irrigated wheat with other graminaceous crops and maize could increase fungal inoculum and disease pressure. The establishment of Fusarium Head Blight in the irrigated wheat region of the country means that resistant lines and alternative agronomic practices are needed to limit disease severity, yield losses and mycotoxin contamination.

Global efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency, which is widespread among resource-poor farmers in the developing world. As a staple crop for more than 500 million people in sub-Saharan Africa, cassava (Manihot esculenta Crantz) enriched with provitamin A carotenoids could have immense nutritional impact. To this effort, a genome-wide association study (GWAS) was conducted with the aim of identifying genomic regions controlling variation for carotenoid concentration in cassava as a basis for undertaking systematic genetic improvement for carotenoid content. A high throughput genotyping-by-sequencing platform was used to genotype a diverse association panel of 591 genotypes and identified 179,310 single nucleotide polymorphisms (SNPs) distributed across the cassava genome. A genomic region stretching 1.37 Mb on chromosome 1 was identified with four SNPs significantly associated with carotenoid content in cassava. A survey of cassava genome sequence v6.1 positioned these SNPs in the vicinity of Manes.01G124200.1 locus, which is a known gene responsible for increase in accumulation of provitamin A carotenoids in cassava roots. This study provides one of the pioneer insights into the practical application of GWAS for dissecting the genetic basis of nutritional traits in cassava. Findings presented herein offer practical grounds for improving carotenoid content in cassava through marker-assisted breeding and genomic selection.

The migration of Ug99 variants of Puccinia graminis f. sp. tritici is of concern to global wheat production (1). Seven races have been characterized in the Ug99 lineage (3), three of which occur in South Africa (4). During surveys of wheat fields for Ug99 in Zimbabwe and Mozambique in August and September 2010, high stem rust severities were found at Chiredzi, Chisumbanje, and Birchenough in Zimbabwe and at Rotanda in Mozambique. Stem rust was widespread in the lowlands ( References: (1) D. Hodson. Euphytica 179:93, 2011. (2) Y. Jin et al. Plant Dis. 92:923, 2008. (3) R. F. Park et al. Euphytica 179:109, 2011. (4) B. Visser et al. Euphytica 179:119, 2011.

A new race of Puccinia triticina was collected from common wheat (Triticum aestivum) in the Eastern and Western Cape provinces during the annual rust survey in 2009. Six single-pustule isolates from a field collection, which were shown to be a new race in preliminary analyses, were inoculated onto seedlings of 16 Thatcher (Tc) near-isogenic differential lines (1) and other tester lines with known Lr genes. Standard procedures for inoculation, incubation, and rust evaluation were followed (4) and all infection studies were repeated. The low infection type of Lr18 was confirmed at 18°C. All six isolates were avirulent (infection types [ITs] 0; to 2) to Lr1, 2a, 2c, 9, 11, 16, 18, and 24 and virulent (ITs 3 to 4) to Lr3, 3ka, 10, 14a, 17, 26, 30, B, and Tc (control). The new race, named 3SA145 according to the ARC-Small Grain Institute notation, corresponds to race CCPS in the North American system (1). On the basis of seedling ITs of the extended Lr gene set, 3SA145 was avirulent (ITs 0; to 22+) to Lr2b, 19, 21, 23, 25, 28, 29, 32, 36 (E84081), 38, 45, 47 (KS90H450), 50 (KS96WGRC36), 51 (R05), and 52 and virulent to Lr3bg, 15, 20 (Thew), 27+31 (Gatcher), and 33. Lines containing the adult plant resistance (APR) genes Lr12 (RL6011, IT 3++), Lr13 (CT263, IT 3), Lr22b (Tc, IT 4), and Lr37 (RL6081, IT 3) were susceptible in the adult stage to 3SA145, whereas lines with the APR genes Lr22a (RL6044, IT ;1), Lr34 (RL6058, IT Z1), and Lr35 (RL6082, IT ;1) were resistant in controlled infection studies in a greenhouse. A control, the common race (3SA133), was virulent only on Tc adult plants. In seedlings, 3SA133 was avirulent to Lr15, 17, 26, and 27+31, but unlike 3SA145, it was virulent to Lr1, 2c, 11, 18, 24, and 28. Races 3SA133 and 3SA145 did not differ in their virulence to the remaining seedling genes. Virulence to Lr37 has been reported in several countries, including Australia, Canada, Uruguay, and the United States (1,2). Prior to the detection of 3SA145, adult plants of RL6081 were resistant to all wheat leaf rust races in South Africa. In 2009, however, RL6081 showed severity levels of up to 30S at certain Western Cape trap plot sites. Of 124 South African bread wheat cultivars and advanced breeding lines tested at the seedling stage, 3SA145 was virulent to 48, whereas 3SA133 was virulent to 36 entries. A further six entries were heterogeneous in their reaction to 3SA145. In adult plant infection studies of 48 South African spring wheats in a greenhouse, 19 were susceptible (flag leaf IT ≥3) and 22 were resistant to 3SA145. Seven entries showed a Z3 flag leaf IT indicating adult plant resistance. According to a simple sequence repeat (SSR) study using 17 primer-pair combinations described by Szabo and Kolmer (3), 3SA145 showed 30% homology with the dominant South African races. Although virulence to Lr12 and Lr13 has been known in different leaf rust races in South Africa, to our knowledge, this is the first report of combined virulence to Lr12, 13, and 37. The SSR data and unique avirulence/virulence profile suggest that 3SA145 may be an exotic introduction to South Africa. References: (1) J. A. Kolmer et al. Plant Dis. 89:1201, 2005. (2) B. McCallum and P. Seto-Goh. Can. J. Plant Pathol. 31:80, 2009. (3) L. Szabo and J. Kolmer. Mol. Ecol. Notes 7:708, 2007. (4) T. Terefe et al. S. Afr. J. Plant Soil 26:51, 2009.

Seven races have been described in the Ug99 race group of Puccinia graminis f. sp. tritici (2). Ug99-related races previously recorded in South Africa are TTKSF, TTKSP, and PTKST (4). In December 2010, severe stem rust infection of the winter wheat cv. Matlabas was observed for the first time in South Africa. Race analysis using the 20 North American (NA) stem rust differential lines and letter code system classified the race as TTKSF. In comparative infection studies in a greenhouse, cv. Matlabas seedlings were susceptible (infection type [IT] 4) to isolate UVPgt61/1 (TTKSF+) collected from Afrikaskop in the eastern Free State, whereas the cultivar was resistant (IT 1 to 2) to stem rust isolates 2013 (TTKSF), UVPgt55 (TTKSF), UVPgt59 (TTKSP), and UVPgt60 (PTKST). Isolate 2013 represents the original collection of race TTKSF in South Africa (1). In addition to the NA differentials, no variation in the IT range of seedlings of lines with Sr7a, 8b, 12, 13, 14, 16, 18, 19, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 39, 41, 42, 43, 44, Em, R, Tt2, and Satu was observed between UVPgt61/1 and UVPgt55. With the exception of cv. Matlabas, ITs of 106 South African cultivars likewise did not differentiate UVPgt61/1 and UVPgt55. Seedling IT studies were conducted at least twice. Microsatellite analysis (4) showed that all single pustule isolates established from the original Matlabas isolate formed part of the Ug99 group. When characterized with selected single nucleotide polymorphisms (SNPs), all single pustule isolates shared an identical genotype that differed from UVPgt55 (TTKSF), a foreign introduction into South Africa (1,3). SNP genotype analysis suggests that UVPgt61/1 is genetically dissimilar to UVPgt55, as is Zim1009, another TTKSF+ isolate that was collected from Birchenough in Zimbabwe. Studies are underway to determine the identity of the defeated Sr gene in Matlabas and the cultivar has been added to the South African stem rust differential set. TTKSF+ is the eighth race detected in the Ug99 group. Since no other cultivars or advanced lines were found to carry the Matlabas gene, it is unlikely that race TTKSF+ will threaten wheat production in South Africa. However, the occurrence of a new Ug99-related race emphasizes the variability within this internationally important group. References: (1) W. H. P. Boshoff et al. Plant Dis. 86:922, 2002. (2) R. F. Park et al. Euphytica 179:109, 2011. (3) B. Visser et al. Mol. Plant Pathol. 10:213, 2009. (4) B. Visser et al. Euphytica 179:119, 2011.

Since the first appearance of wheat stripe rust in 1996 in South Africa, four Puccinia striiformis races have been described. The first detected race, 6E16A−, was proposed to be a foreign introduction from Central or Western Asia that subsequently gained additional virulence through step-wise mutations. Simple sequence repeat markers were used to determine the genetic relationships between the four races, as well as a P. striiformis isolate collected from wild rye and two Kenyan isolates. A single isolate of P. striiformoides collected from Dactylis glomerata was included as an out-group. While the genetic similarity between P. striiformoides and the two Kenyan P. striiformis isolates was low, both shared only 48% genetic similarity with the South African isolates. In contrast, the South African P. striiformis isolates shared at least 74% genetic similarity with each other, with 6E16A−, 6E22A− and 7E22A− being the most similar. A minimum spanning network analysis confirmed this close relationship with sev...

Efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency (VAD), which has afflicted the health of resource-poor people in the developing world. As a staple crop for more than 500 million people in sub-Saharan Africa, cassava enriched with provitamin A carotenoids could have a widespread nutritional impact. To this effect, 13 provitamin A clones were evaluated in a randomized complete block design in six environments to assess genotype by environment interaction (GEI) effects for total carotenoid (TCC) and dry matter content (DMC) in roots. Additive main effect and multiplicative interaction analysis showed significant variation among genotypes for TCC, DMC, fresh root weight and harvest index. Environmental effects were non-significant for TCC, but GEI effects were significantly large for all traits measured. There were significant temporal increments for all traits measured within 12 months after planting. TCC correlated negatively with DMC, illustrating an important challenge to overcome when developing provitamin A cassava varieties without compromising DMC, which is a major farmer-preference trait. Nonetheless, best performing genotypes were identified for TCC, DMC and FRW, and these could constitute genetic resources for advancement or developing breeding populations through hybridization.

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.

To identify races of Puccinia triticina in southern Africa, samples of infected wheat leaves obtained from Zimbabwe, Zambia and Malawi were analysed at the University of the Free State, Bloemfontein and the Agricultural Research Council-Small Grain Institute, Bethlehem, South Africa (SA). Four races were identified from 63 isolates obtained during 2011–2013. Using the North American notation, these races coded to MCDS (74.6 %), TCPS (12.7 %), FBPT (6.3 %) and SCDS (6.3 %). MCDS and TCPS occurred in both Zimbabwe and Zambia whereas FBPT and SCDS were only detected in Zimbabwe and Malawi, respectively. Three of these races (MCDS, FPBT and SCDS) are also known in SA. SSR analysis of races detected in southern Africa suggested that MCDS and FPBT are more closely related to CCPS (3SA45), a race identified in SA in 2009. Occurrence of similar races across southern Africa indicates migration of inoculum between countries, and highlights the need for each country to monitor and share information on virulence changes in the region. In seedling tests, over 72 % of Zimbabwean commercial cultivars were susceptible to race TCPS which occurred in both Zimbabwe and Zambia. To predict occurrence of adult plant resistance (APR) in these cultivars, they were tested for the presence of gene Lr34 which confers durable resistance to multiple fungal pathogens. Only three cultivars were positive for this gene suggesting that most of the current Zimbabwean commercial cultivars may be susceptible to leaf rust both as seedlings and adult plants, assuming the absence of other APR genes. Three cultivars and 15 breeding lines, all highly resistant as seedlings across races, carried Lr19. One line contained Lr19 and Lr34. It is suggested that sources of race non-specific resistance genes be included in wheat breeding programs in Zimbabwe.

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selection-enhanced breeding of this important crop.

Samples of wheat and triticale infected with leaf rust were collected from 2008 to 2010 in South Africa to identify Puccinia triticina races. Races were identified based on their virulence profile on standard differential lines. Eight races were identified from 362 isolates. The dominant races were 3SA133 (syn. PDRS) in 2008 (78 %) and 2009 (34 %), and 3SA145 (47 %) in 2010. Race 3SA145 (CCPS) identified in 2009 was a new race in South Africa with virulence for the adult plant resistance gene Lr37. Another new race, 3SA146 (MCDS), was identified in 2010. Race 3SA146 is also virulent for Lr37 but unlike 3SA145, it is virulent for Lr1 and Lr23 and avirulent for Lr3ka and Lr30. Microsatellite analysis showed that 3SA145 and 3SA146 shared 70 % genetic similarity with each other, but only 30 % similarity with other races in South Africa, suggesting that both represent foreign introductions. In seedling tests of 98 South African winter and spring cultivars and advanced breeding lines, 27 % were susceptible to 3SA145 and 3SA146 but resistant to 3SA133. In greenhouse studies of 59 spring wheat adult plants, 19 % of breeding lines and 46 % of cultivars were susceptible to 3SA145, whereas 29 % of the lines and 53 % of cultivars were susceptible to 3SA146. The cssfr6 gene-specific DNA marker confirmed the presence of Lr34 gene for leaf rust resistance in a homozygous condition in 28 wheat entries. Five entries were heterogeneous for Lr34. Several entries which were susceptible as seedlings to the new races carried Lr34. These lines are expected to show lower levels of leaf rust as adult plants. Results of these studies indicate a continued vulnerability of South African wheat cultivars to new races and emphasise the importance of regular rust monitoring and the need to incorporate genes for durable resistance.

Seed oil content and composition are important considerations in sunflower breeding programmes because these traits are related to oil quality. They are complex traits that are determined by genotypic factors and environmental conditions. The objective of this study was to estimate the interaction between genotype and environment for oil content and major fatty contents in traditional, high and mid-oleic sunflower genotypes and to identify stable genotypes. Combined analyses of variance of oil, oleic and linoleic acid content of 16 genotypes tested over six locations showed highly significant mean squares for genotype, environment and the interaction between them. On average the mid-oleic and standard genotypes had similar oil contents, but the high oleic genotypes had lower oil contents than the standard genotypes. Stability analyses indicated that one standard, one high oleic and one mid-oleic genotype were relatively stable with average to above average oil content. One high oleic genotype was stable across locations with an oleic acid content of above 80 %. The unstable high oleic acid genotypes that showed variation for oleic acid content across locations may be a consequence of location, temperature and rainfall effects. With adequate location and planting dates, high and mid-oleic hybrids could be produced with oil that meets the oil quality standards.

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

High temperature stress is a major environmental factor influencing processes such as growth, yield and quality of crops. The objective of this study was to assess the effect of heat stress, applied during grain-filling, on seed yield- and oil quality components in high- and mid-oleic sunflower hybrids. Genotypes were exposed to a temperature range of 24/36 °C (night/day) for 10 consecutive days starting at 15 days after flowering. Heat treatment altered all measured traits; however, genotypes differed in their sensitivity to temperature. Head diameter and the sterile area of the head increased, but number of filled seeds per head and seed weight were reduced. HO 4 showed an increase in grain yield, but showed the largest decrease in oil content. The average oil concentration was significantly reduced by 6%. Concentrations of palmitic, stearic and oleic acids were increased, whereas linoleic acid was reduced. Stable genotypes, that were least responsive to heat stress, were identified for seed yield (MO genotypes 6, 8 and 12), oil concentration (MO genotypes 8 and 10), and oleic and linoleic acid concentration (HO genotype 4 and MO genotype 11). No single genotype was stable for all traits.Keywords: grain-filling, oil quality, sunflower, temperature, yield components

Cassava brown streak disease (CBSD) is an economically important virus disease causing significant losses to cassava root yield and quality in east, central and southern Africa. Breeding for resistance in cassava requires an understanding of the underlying genetic control of CBSD resistance. Sources of CBSD resistance are available but little is known on the value of those varieties as parents for CBSD resistance breeding. Two resistant and two susceptible varieties were crossed in a half diallel design and 35 F1 progeny from each of the six families, plus parents, were screened at two locations in a randomised complete block design with four replications in warm sub-humid environments of coastal Tanzania in 2008. Screening for CBSD field resistance was done using disease severity scoring on a scale of 1–5. Significant variations in disease severity were observed for crosses, general combining ability (GCA) and specific combining ability (SCA) at both locations. The CBSD shoot symptom severity scores ranged from 1 to 4.4 while root necrosis ranged from 1.3 to 4.5. The contribution of GCA to the total sum of squares of crosses for disease scores ranged from 86.9 to 95.2 % compared to SCA that ranged from 4.8 to 14.2 %. Additive gene effects were more important than non-additive effects indicating that CBSD resistance is genetically determined and that selection should be successful to improve resistance. Selection of parents with good GCA effects will be important for success in CBSD resistance breeding.

South Africa hosts the largest cactus pear germplasm bank in Africa. However, since cactus pear undergoes significant genotype × environment (G × E) interaction, characterisation based on agronomic and morphological traits in a country such as South Africa is complicated by its wide agro-ecological regions. However, the effects of G × E interaction on characterisation can be circumvented by the use of molecular markers. Therefore, AFLP markers were used to estimate the genetic diversity among 38 cactus pear cultivars from the South African genebank. The number of polymorphic fragments between different accessions varied with the use of different AFLP-primer combinations, suggesting that sufficient detectable genetic differences exist within the germplasm for the use of AFLP markers for genetic diversity assessment, cultivar identification and parental selection. A large number of markers had polymorphic information content (PIC) values between 0.3–0.5, indicative of good discriminatory ability. The majority of the cultivars grouped into two main clusters. The commonly grown cultivars were dispersed amongst the different clusters, with the greatest percentage falling in clusters i and sub-cluster iib. Culitvars that originated from Botswana (R1251, R1259, and R1260) clustered together, whilst those from Israel (‘Sharsheret’, ‘Ofer’, and ‘Messina’) were dispersed within cluster ii. Ten genotype specific fragments (GSF) were generated from six primer combinations (E-AGG M-CAT, E-ACT MCAG, E-ACT M-CAT, E-ACA M-CAT, E-ACA M-CTT, and E-ACA M-CAG). These GSF should be tested further, since they will allow varietal identification if proven to be repeatable. The genetic similarity values indicated in this study will provide breeders with information useful for selecting diverse parents with desired traits for their crosses.

Microsatellite analysis of ten South African races of Puccinia triticina, the causal organism of leaf rust of wheat (Triticum aestivum), divided the population into two groups sharing 32% genetic similarity. In the first group, race 3SA145 (Agricultural Research Council notation) clustered with 3SA122 and 3SA125, two races that have not been detected recently. This grouping was supported by avirulence for Lr1 in all three races. The second group included the current dominant race 3SA133, that shared 42% genetic homology with the remaining six races. Five of these, including 3SA144, formed a sub-group with 96% genetic homology amongst them. It was concluded that 3SA144, detected on triticale in 2005 and virulent for Lr32, probably represents a mutation from an existing race, whereas 3SA145 most likely was an exotic introduction. Race 3SA145 was first detected in 2009 and differed from known races in terms of combined virulence for the adult-plant resistance genes Lr12, Lr13 and Lr37. Microsatellite analysis complemented traditional phenotypic characterization of P. triticina and provided insight on genetic relationships amongst older and more recently detected races in South Africa.

The appearance and spread of races of Puccinia graminis f. sp. tritici with virulence for the Sr31 resistance gene has renewed interest in breeding for durable resistance to stem rust of wheat. Since the occurrence of stem rust has been low in South Africa until the detection of race TTKSF in 2000, breeding for resistance to this disease has not been a primary objective. The aim of this study was to test bread wheat cultivars and lines at the seedling stage for their infection response to stem rust, thus determining their level of resistance or vulnerability. A collection of 65 bread wheat entries was tested with one USA race, two Eastern African races, and three South African races of P. graminis f. sp. tritici. The Eastern African and South African races all belong to the Ug99 lineage. The cultivars Duzi, Caledon, Elands, PAN 3364, PAN 3191, SST 047, SST 399, and Steenbras produced resistant infection types (IT < 3) to all races. The molecular marker Sr24#50 indicated the presence of Sr24 in 12 entries. In cultivars resistant to TTTTF, TTKSF, and TTKSP but susceptible to TTKSK and PTKST, the iag95 DNA marker indicated the presence of Sr31 in five wheat lines. Using the cleaved amplified polymorphic sequence marker csSr2, Sr2 was detected in PAN 3377, Inia, and Steenbras. Few South African wheat cultivars appear to have a broad-based resistance to stem rust, as 88% of the entries were susceptible as seedlings to at least one of the races tested. Diversification of resistance sources and more directed breeding for stem rust resistance are needed in South Africa.

An improved understanding of phenotypic variation within cassava germplasm in southern, eastern and central Africa will help to formulate knowledge-based breeding strategies. Thus, the overall objective of this study was to examine the phenotypic variation in cassava germplasm available within six breeding programmes in Africa, namely Uganda, Kenya, Tanzania, Rwanda, Democratic Republic of Congo and Madagascar. In each country, single-row plots were used for assessment of 29 qualitative traits and evaluation of four quantitative traits: root dry matter content (DMC), harvest index (HI), leaf retention (LR) and root cortex thickness. Qualitative traits provided limited discrimination of cassava germplasm. However, differences in DMC, HI, LR and root cortex thickness were observed among the germplasm indicating scope for genetic improvement. Highest average DMC was registered in Uganda (39.3%) and lowest in Tanzania (30.1%), with the elite genotypes having a relatively higher DMC than local genotypes. Highest average HI was observed in Uganda (0.60) and lowest in Kenya (0.32). Cassava genotypes displayed varied root peel thickness (0.34–4.89 mm). This study highlights variation in agronomic traits that could be exploited to increase cassava productivity.

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.

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.

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.

To monitor genetic diversity in the field it is important that it is measured accurately. Here, we elucidate the potential of single nucleotide polymorphisms (SNPs) for measuring genetic diversity in cassava. The nature and frequency of SNPs was characterised and their utility in genetic diversity assessment compared to that of simple sequence repeats (SSRs). This was achieved by direct sequencing of amplicons in diverse cassava varieties. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP every 121 nucleotides. Nucleotide diversity ranged from 7.8 × 10−4 to 5.6 × 10−3. Average haplotype-based polymorphic information content (PIC = 0.414) was higher than for individual SNPs (PIC = 0.228). The Mantel test indicated interdependence (r = 0.219; P < 0.001) between SNP and SSR genotypic data. Individual SNPs had lower PIC values than SSRs. For this reason larger numbers of SNPs may be necessary to achieve the same level of discrimination among genotypes provided by SSRs.

Knowledge of genetic diversity within and among genotypes of any crop is fundamental for estimation of the potential genetic gain in a breeding programme and effective conservation of available genetic resources. Currently, different molecular marker techniques are being developed for measuring genetic diversity. Comparison among molecular marker techniques is important for effective marker selection. However such types of efforts are rare for arabica coffee. This study was conducted to compare the efficiency of simple sequence repeat (SSR) analysis for determining genetic relationships of 28 Coffea arabica L. genotypes collected from different parts of Ethiopia with work previously done using amplified fragment length polymorphism (AFLP) analysis. A total of 22 SSR fragments were amplified and compared with 712 previously amplified AFLP fragments. AFLP and SSR markers were positively and significantly correlated (0.217) in estimating genetic similarity among genotypes. The average genetic similarity coefficient calculated using SSR markers was much lower (0.560 with a range of 0.286-1.000) compared to AFLP markers (0.915 with a range of 0.860-0.982) indicating the higher information content of SSR markers. AFLP markers distinguished all genotypes, while SSR markers distinguished 64.3% of the genotypes. Results indicated that AFLP markers were more efficient compared to SSR markers for characterization of the evaluated coffee genotypes.

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 cannabinusc andH. cannabinusa) clustered separately from the commercial and Russian accessions. One of the wild types,H. cannabinusb 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.

BACKGROUND: Although people began to consume coffee for its stimulating effect, the demand for decaffeinated coffee is increasing and now accounts for 10% of the total amount of coffee consumed in the world. Forty-two arabica coffee genotypes originating from Ethiopia were tested to assess caffeine content variability among them, and the correlation of caffeine content with cup quality and green bean physical characteristics. RESULTS: Green bean caffeine content was measured using high-performance liquid chromatography, while cup quality was determined by professional coffee tasters. Caffeine content ranged from 9.1 to 13.2 g kg −1 on dry mass basis (d.m.b.). Six genotypes – AD0291, AD0591, AD2491, AD2691, AD2791 and AD2891 – had a caffeine content of less than 10.0 g kg −1 . Caffeine content showed negative and statistically significant correlations with cup quality attributes. Correlations between caffeine content and green bean physical characteristics were non-significant. CONCLUSIONS: Simultaneous selection for low caffeine content and good cup quality is possible. Some accessions had low caffeine content, and may serve as a source of desirable genes for variety development of types with relatively low caffeine content.  2008 Society of Chemical Industry

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.

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.

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.

In Tanzania, cotton is of great economical importance, representing a large percentage of agricultural exports, but yield and lint quality is still relatively poor. The aim of this study was to identify parents to improve boll and lint yield and quality. Parents and F1 progeny of a 7 × 7 diallel were evaluated in four different environments. Results indicated significant variation for especially yield components, yield, ginning outturn and fibre quality. Parents with high and positive GCA like NTA 93-21, Delcot 344, Auburn 56 and MZ561 and combinations with high and positive SCA for the characteristics were identified. Additive genetic effects were seen for most of the characteristics, except for fibre strength at one locality. Parents with high GCA effects for certain characteristics produced combinations with high SCA effects for the same characteristics. This study indicated that there is enough genetic variability for boll and lint yield and quality for effective selection, and good parents that can be included in the breeding programme.

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 Jaccard's 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.

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.

Knowledge of genetic diversity is vital for genetic improvement and germplasm conservation. The genetic relationship of 28 Coffea arabica genotypes from Ethiopia was assessed using 10 AmplifiedFragment Length Polymorphism (AFLP) primer combinations. The level of polymorphism was 30.9% and 18 markers were unique to 10 genotypes. Pair-wise genetic similarity coefficients ranged from 0.851 to 0.982, AD1491 being the most divergent and AD5091 the most closely related to all genotypes. All genotypes were independently distinguished and did not cluster according to collection region, demonstrating the presence of coffee genetic resource diversity within each region. Results of this study will be utilised for germplasm collection, conservation as well as in variety development efforts.

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers’ practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.

Eleven isolates of Puccinia triticina Erikss. collected from bread wheat (Triticum aestivum L.) in the Western Cape during the 2010 annual rust survey were pathotyped to a race not previously recorded in South Africa. Replicated race analysis on seedlings of 16 Thatcher (Tc) near-isogenic differential lines at two rust laboratories confirmed avirulence (infection types [ITs] 0; to 2+) for lines with Lr1, Lr2a, Lr9, Lr11, Lr16, Lr24, and Lr26 and virulence (ITs 3 to 4) for lines with Lr2c, Lr3, Lr3ka, Lr10, Lr14a, Lr17, Lr18, Lr30, and LrB. Thatcher lines with LrB, Lr10, Lr14a, and Lr18 were added as the fourth set to the 12 original differential lines (1,2). This profile codes to race FBPT according to the North American system, and, based on these differentials, resembles a P. triticina isolate from Gwebi, Zimbabwe, in 2012 (Z. A. Pretorius, unpublished data). When additional single gene lines were tested with FBPT (race 3SA147 according to the ARC-Small Grain Institute rust notation procedure), lines with Lr2b, Lr15, Lr19, Lr20, Lr21, Lr25, Lr27+31, Lr28, Lr29, Lr32, Lr36, Lr38, Lr45, Lr47, Lr50, Lr51, and Lr52 were effective, whereas lines with Lr3bg, Lr23, Lr28, and Lr33 were ineffective. In adult plant tests in a greenhouse, Thatcher lines containing Lr12 (IT ;1c), Lr13 (IT ;1c), Lr22a (IT 1), Lr35 (IT ;1+), and Lr37 (IT ;1) were resistant, whereas Thatcher (Lr22b) was susceptible. Of 146 South African cultivars and lines infected as seedlings with 3SA147 (FBPT), 83% were resistant (IT ≤ 2) and 5% showed within-line variation. Entries showing compatible ITs with 3SA147 (FBPT) were also susceptible to either or both of 3SA133 (PDRS) and 3SA146 (MCDS). In addition, the new race was genotyped using 16 simple sequence repeat (SSR) primer-combinations (3). Three single pustule isolates of 3SA147 (FBPT) were identical and showed 82% and 76% similarity with the recently described races 3SA146 (MCDS) and 3SA145 (CCPS), respectively (4). Minimum spanning network analysis confirmed this close genetic relationship among the three races. However, since their virulence phenotypes differ, it is proposed that 3SA147 (FBPT) is not a stepwise mutation from either 3SA145 (CCPS) or 3SA146 (MCDS), but rather a foreign introduction into South Africa. As most current breeding lines and wheat cultivars are resistant, it is unlikely that race FBPT will threaten wheat production in South Africa, but its detection underlines the fact that new P. triticina variants have been occurring at regular intervals in the region. References: (1) J. A. Kolmer et al. Austr. J. Agric. Res. 58:631, 2007. (2) D. L. Long and J. A. Kolmer. Plant Dis. 79:525, 1989. (3) L. J. Szabo and J. A. Kolmer. Mol. Ecol. Notes 7:708, 2007. (4) T. Terefe et al. Plant Dis. 95:611, 2011.