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Maize lethal necrosis (MLN) is a new disease in Sub-Saharan Africa (SSA) caused by double infection by maize chlorotic mottle virus (MCMV) with any of the many viral agents in the Potyviridae family. It has become one of the key constraints to maize production in the region due to the significant crop losses caused since its emergence in 2011. Sustainable management of MLN is achievable through genetic improvement and replacement of old susceptible varieties with farmer-preferred varieties that combine MLN resistance with tolerance to other prevailing biotic and abiotic stresses. To effectively breed for MLN resistance, it is important to identify sources of resistance, determine the genetic nature of resistance and employ efficient breeding techniques that will result in high genetic gains from selection. This study aimed to dissect the genetic nature of MLN using elite and introduced inbred lines from tropical and temperate maize genetic pools, new biparental populations and potential hybrids. The genetic analysis was conducted in five studies representing the major stages of maize breeding, from pre-breeding to variety development. In the pre-breeding study, the breeding potential for MLN resistance among 18 tropical and temperate inbred and doubled haploid (DH) lines was conducted to identify the best parents for population development. The second study on the genetic potential and usefulness of new pedigree populations was conducted using nine segregating biparental populations derived by crossing susceptible elite and recycled DH lines to two introduced MLN resistant lines from the KS23 pool. The third study, using a section of these populations, selected three sizable populations, which were phenotyped, genotyped and used to validate quantitative trait loci (QTL) linked to MLN resistance in the KS23 genetic background. The fourth study, moving towards product development, entailed determining the potential of new lines and single crosses for use as MLN resist

In 2016 sub-Saharan Africa (SSA) was invaded by the transboundary maize-eating pest, fall armyworm [Spodoptera frugiperda (J.E. Smith); FAW]. The pest has threatened food security and livelihoods of the majority of smallholder farmers in the region. The main aim of this study was to investigate the potential of breeding maize with resistance to FAW in southern Africa. The first study aimed to assess the breeding potential of introduced exotic FAW resistant trait donor maize lines with southern Africa germplasm. Thirteen mid-altitude adapted inbred lines were crossed with seven FAW-resistant exotic donor lines, in a line x tester mating scheme that produced 84 F1s which were evaluated together with checks at four locations under natural FAW infestation. The best exotic donor lines with low and negative general combining ability (GCA) effects for foliar FAW damage (FFAWD) resistance scores and good grain yield (GYD) per se performance were CML139, CML67, CML121 and CML345. Local lines that showed similar good attributes were CimExp1, CimExp4, CimExp5, CimExp8 and CimExp10. The best crosses were CimExp1/CML331, CimExp1/CML345, CimExp10/CML331 CimExp5/CML331 and CimExp5/CML345. In the second study, two sets of germplasm (hybrids/OPVs and inbred lines) were evaluated for FAW resistance under managed and natural FAW infestation. The objective was to evaluate commercial and experimental maize hybrids and parental lines cultivated in southern Africa for resistance to FAW. Commercial cultivars were significantly more affected by FAW infestation than experimental hybrids. The introduced FAW-resistant donor lines (CML338, CML67, CML121 and CML334) showed better resistance to FAW damage, individually and in hybrid combinations. Local inbreds, SV1P, CML491 and CML539, also showed good FAW resistance. Husk cover, ear rot, anthesis date and plant height were correlated with FAW resistance. The third study aimed to investigate the stability of grain yield performance and resistance

The aim of this study was to identify farmers’ adoption challenges, perceptions and preferences of yellow-flesh cassava. Combining ability and stability of these genotypes were also determined. Total carotenoid content (TCC), proximate values and hydrogen cyanide (HCN) of the yellow-flesh cassava were measured and the retention of carotenoids in boiled biofortified cassava was determined. This information will help breeders to identify genotypes with the best nutritional quality across the tested locations for planting and promotion in Ghana also could provide a basis for implementing a recurrent selection scheme for developing cassava varieties with high levels of carotenoids and dry matter. In all the locations visited, farmers’ knowledge on the improved cassava varieties (white flesh) and the yellow-flesh cassava were generally poor among the men and women interviewed, due to their inability to access planting materials, which could be improved by strengthening the cassava seed system for awareness, and increased availability of the varieties to farmers. Very few men and women cultivated improved varieties and yellow-flesh cassava. The young adults, who are the future of the agricultural sector, lacked access to improved varieties and they must be given extra attention to understand the activities of cassava breeding programmes, to empower them to make use of these materials. The general combining ability (GCA) was larger than specific combining ability (SCA) for cassava mosaic disease (CMD), harvest index (HI) and TCC, with predictability ratios (0.98, 0.88 and 0.92 respectively) close to one. Hence, there is a possibility for improvement of the characteristics by selection. Positive significant correlation between pulp colour and TCC (r=0.59) and pulp colour and cortex colour (r=0.58) were observed. Negative significant correlation were seen between CGM and HI (r=-0.50), CMD and RTN (r=-0.45), and HI and RTN (r=-0.51). It implies that these key traits could be

Water-limited stress (WLS) is associated with adverse changes at morphological, physiological, biochemical and molecular levels among genotypes, which consequently affects crop growth and productivity. These changes are useful indicators in breeding of drought tolerant genotypes. This study was, therefore, carried out to identify genotypes that are good performing under WLS conditions and to determine traits’ response to WLS using a combination of morphological traits, physiological traits, water use efficiency and grain yield. In addition, interrelationships among morphological traits, physiological traits and water use efficiency were determined in order to identify traits that contribute to grain yield under WLS conditions. The study also elucidated the association between drought tolerance indices and grain yield under WLS conditions in separating tolerant genotypes from sensitive genotypes. It further looked at the impact of drought on grain yield of soybean with change in environment and season. The study also tried to understand the mode of gene action considering that the majority of the characteristics of importance in a crop are inherited quantitatively. Genotypes showed significant variability in tolerance levels to WLS. Genotypes with a high drought tolerance level generally exhibited a higher grain yield, 100-seed weight, plant height, number of pods per plant, minimal grain yield reduction, maintained a higher relative chlorophyll content, quantum yield of efficiency for photosystem II and water use efficiency under severe WLS compared to genotypes with a low drought tolerance level. Among the physiological traits, relative chlorophyll content was most significantly associated with genotype, while quantum yield of efficiency for photosystem II, photoprotective nonphotochemical quenching and non-photochemical quenching basal dissipation of light energy for other unregulated process were more frequently and significantly associated with WLS. Plant height

The development of high yielding and stable quality protein maize (QPM) hybrids is important for increasing grain yield output per unit area, to support the fight against hunger and malnutrition in sub-Saharan Africa (SSA), as well as for feed supplement formulation for the animal and poultry industries. Despite the development of QPM genotypes with increased lysine and tryptophan content, important information is lacking on the yield potential of QPM genotypes compared to non-QPM (normal) genotypes. The main objective of this study was to quantify grain yield reduction (if any) due to the QPM trait. The specific objectives were to: (i) compare QPM and non-QPM inbred lines for yield and yield related traits, as well as quality traits, and determine stability for grain yield, (ii) compare QPM and non-QPM hybrids for yield and yield stability, (iii) estimate the combining ability for grain yield and quality traits of QPM and non-QPM inbred lines (iv) estimate the heritability, variance components, principal components, correlation coefficients, and do path analysis of grain yield, and agronomic and quality traits. In this study, 130 single cross hybrids were developed from 33 QPM and non-QPM inbred lines and four testers (two QPM and two non-QPM). Five hybrid checks (two QPM and three non-QPM, all single cross hybrids) were included, obtained from the International Maize and Wheat Improvement Center, Zimbabwe. The 135 hybrids together with the 40 inbred lines were evaluated in South Africa and Zimbabwe during the 2017/2018 and 2018/2019 cropping seasons. The inbred lines were evaluated at seven locations using a 5 x 16 alpha lattice design, while the hybrids were evaluated at 13 locations using a 5 x 27 alpha lattice design with two replications. In the field experiments, two plants per plot were selfpollinated for the determination of zein, tryptophan, amylose and starch, protein, oil, moisture and fibre contents. In the inbred line trials, the top six performing lin

Nitrogen (N) is one of the most yield limiting nutrients in maize. However, farmers in sub-Saharan Africa (SSA) use very little N due to low income. Nitrogen Use Efficient (NUE) varieties can provide a partial solution to the problem through efficient N uptake and utilisation. Designing an effective breeding strategy for improving any trait of interest requires knowledge of quantitative genetic parameters, genomic regions associated with the traits and the use of efficient selection methods. The objectives of this study were to 1) assess the efficiency of indirect selection for grain yield under low N stress conditions through grain yield under optimum N conditions and through secondary traits under low N conditions, 2) identify single nucleotide polymorphism (SNP) marker loci significantly associated with grain yield and secondary traits under low N and optimumconditions, 3) map and characterize the quantitative trait loci (QTL) for grain yield and some secondary traits under optimum and low N stressed conditions, and 4) evaluate the accuracy of genomic selection for improvement of grain yield and other secondary traits under optimum and low N stressed environments. Results showed that genetic variance for grain yield was highly affected by low N stress, more than secondary traits, and low correlation was observed between optimum and low N environments for grain yield. This lead to low relative efficiency of indirect selection for grain yield under low N using grain yield under optimum conditions. The efficiency of indirect selection for grain yield under low N through secondary traits under low N conditions was also low. The efficiency of selection could be enhanced through identification of genomic regions and associated markers linked with grain yield under low N. A total of 158 putative protein coding genes associated with significant SNPs, of which seven linked with four known genes, were identified through a genome-wide association study. Markers associated w, Borlaug LEAP

English: Cassava (Manihot esculanta Crantz) is a perennial woody plant which is cultivated in Africa, Asia and Latin America. It is tolerant to drought and grows in poor soils. It is a source of carbohydrates, vitamins and small quantities of proteins. In Malawi, it is the most important root crop and it is grown across the country. It is consumed as a staple food by 30% of the people living along the central and northern part of Lake Malawi. Its production is constrained by among others, diseases CMD and CBSD. These two diseases are known to spread through white flies. The magnitude of attack by the two diseases depends on the genotype and the environment. No released genotypes in Malawi have ever been evaluated in seed transmission of viruses’ studies. The experiment on the quantification of F1 cassava progenies from open pollinated F1 progeny crosses revealed that genotypes which show high severity of CMD are likely to allow rapid multiplication of EACMMV and SACMV. However, it has been proven that this might not always be the case as some genotypes may have higher virus quantities while showing slightly less severe symptoms. Genotypes which succumb to high disease symptom severity are likely to have high incidence of the disease. CMD symptom severity and incidence were positively correlated. The experiment on determination of virus quantities in different tissues has provided information that virus quantities in particular tissues depend on the cultivar used. The viruses can spread to all the tissues analysed in this research. It was shown that root parenchyma and leaf tissues accommodated most of CBSV and UCBSV in the cultivars used. When there was co-infection, CBSV and UCBSV were positively correlated. EACMMV and SACMV quantity can vary in cassava tissues depending on the cultivar. Leaves have shown to contain a relatively high quantity of the viruses. CBSV, UCBSV, EACMMV and SACMV symptoms were not observed in seedlings grown from seeds which were obtained f, Afrikaans: Cassava (Manihot esculanta Crantz) is ‘n meerjarige houtagtige plant wat verbou word in Afrika, Asië en Latyns Amerika. Dit is droogte tolerant en kan groei in swak grond. Dit is ‘n bron van koolhidrate, vitamines en klein hoeveelhede proteïene. Dit is die belangrikste wortelgewas in Malawi, en dit groei oral in die land. Dit word as stapelvoedsel gebruik deur 30% van die mense wat woon langs die sentrale en noordelike dele van die Malawi meer. Cassava produksie word beperk deur, onder andere, die siektes CMD en CBSD. Hierdie twee siektes word versprei deur witvlieë. Die erns van die infeksie deur hierdie twee siektes hang af van die genotipe en die omgewing. Inligting oor die reaksie van verskillende Malawi genotipes en hulle nageslag aangaande akkumulasie van virusse, is baie beperk. Geen vrygestelde genotipes in Malawi is nog ooit geëvalueer vir saadoordrag van virusse nie. Die eksperiment oor die kwantifikasie van cassava F1 nageslag van oop en spesifieke kruisings het getoon dat genotipes met ‘n hoë vlak van CMD ‘n vinnige vermeerdering van SACMV toelaat. Dit is egter bewys dat dit nie altyd die geval is nie, omdat sekere genotipes groter hoeveelhede virus gehad het terwyl hulle steeds minder simptome getoon het; daar was dus geen korrelasie tussen min simptome van SACMV en CMD en virus insidensie nie. Genotipes wat baie siektesimptome gehad het egter hoë virus insidensie getoon; dus was die graad van die siekte met die insidensie gekorreleer. Die eksperiment vir die bepaling van virus hoeveelhede in verskillende weefseltipes het getoon dat virus hoeveelhede in spesifieke weefsel afhang van die cultivar wat gebruik is. Virusse het versprei na alle weefsel wat in die studie geanaliseer is. Wortel parenkiem weefsel het meeste van die CBSV en UCBSV in die cultivars gehuisves. Waar daar ko-infeksie was, was CBSV en UCBSV positief gekorreleer. SACMV hoeveelheid het gewissel tussen die wortel parenkiem, wortel korteks en stam korteks (5 cm van bo), afhange

English: In Malawi maize is grown even in marginal lands, on steep slopes, wet lands, rocky areas and low pH soils due to the high human population which excert pressure on the land. The objectives of this study were to investigate genetically diverse maize genotypes for tolerance to low pH soil conditions. In the hydroponic experiment genotypes IWDC3SYNF2-B, VPO52, and LPHpop 4 had relatively higher nett seminal root length and were considered tolerant, and DT-YSTR SYNTHETIC-B, TZE-WPOPDTC2STR-B, TZE-YDTSTRC4-B, LPHpop3, LPHpop13, and LPHpop14 were sensitive or susceptible to Al toxicity. Under field conditions, genotypes LPHpop16, LPHpop3, VPO739, VPO5173 and LOW N POOL C3-B were identified to be relatively tolerant to low pH soil conditions. SYNDTE–STY-W-B ranked first in terms of root tolerant index (RTi) with a good NSRL in the glasshouse hydroponic experiment and this was followed by VPO717 which also had a relatively a better root tolerance index and nett seminal root length. Phenotypic traits associated with grain yield, such as plant vigour, seed size (100 seed weight), shelling percentage, number of ears per plant, ear height and plant height can be used alongside grain yield when selecting germplasm for tolerance to low pH stress. In general, the effects of low pH soil conditions contributed to reduction in grain yields and yield components. The combined mean yield reduction due to low pH soil in this study was 69.9%. From AMMI and GGE analysis, genotypes LPHpop21, VPO52, VPO72, VPO744 and VPO96 were identified as the most stable. VPO097 was identified as an unstable genotype. Chitala low-land optimal site was identified as the most discriminating environment in terms of genotypes while Chitedze mid-altitude optimal environment was identified as a stable environment. The diallel study revealed that additive and non-additive gene actions were at play in the expression of some of the traits like grain yield, number ears per plant, shelling percentage, 100 s, Afrikaans: In Malawi word mielies selfs in marginale grond, op steil hellings, vleilande, klipperige gebiede en in lae pH grond verbou, weens die hoë bevolking wat druk op die land plaas. Die doelwitte van hierdie studie was om geneties diverse mielie genotipes vir verdraagsaamheid vir lae pH grondtoestande te ondersoek. In die hidroponiese eksperiment het genotipes IWDC3SYNF2-B, VPO52 en LPHpop4 relatiewe hoër netto seminale wortel lengtes gehad en word as verdraagsaam beskou en DT-YSTR SYNTHETIC-B, TZEWPOPDTC2STR-B, TZE-YDTSTRC4-B, LPHpop 3, LPHpop13, en LPHpop14 was sensitief of vatbaar vir Al toksisiteit. Onder veldtoestande, is genotipes LPHpop16, LPHpop3, VPO739, VPO5173 en LOW N POOL C3-B as relatief verdraagsaam vir lae pH grondtoestande geïdentifiseer. In die glashuis hidroponiese eksperiment was SYNDTESTY-W-B eerste in terme van wortel tolerante indeks met 'n netto seminale wortel lengte van 2.5 cm en is gevolg deur VPO717 met ʼn wortel tolerante indeks van 1.0 en netto seminale wortel lengte van 1.7 cm. Fenotipiese eienskappe wat geassosieer word met graanopbrengs, soos groeikrag, saadgrootte (100 saad gewig), saad persentasie, die aantal koppe per plant, kop hoogte en plant hoogte kan gebruik word saam met graanopbrengs wanneer kiemplasma geselekteer word vir verdraagsaamheid vir lae pH stres. In die algemeen dra die effek van lae pH grondtoestande by tot die verlaging in graanopbrengste en opbrengs komponente. Die gekombineerde gemiddelde opbrengs verlaging as gevolg van lae pH grond in hierdie studie was 69.9%. Deur die AMMI en GGE analise is LPHpop21, VPO52, VPO72 is VPO744 en VPO96 geïdentifiseer as die mees stabiele genotipes. VPO097 is geïdentifiseer as 'n onstabiele genotipe. Chitala lae-ligging optimale omgewing is geïdentifiseer as die mees onstabiele omgewing in terme van genotipes terwyl Chitedze middel-ligging optimale omgewing geïdentifiseer is as 'n stabiele omgewing. Die dialleel studie het getoon dat beide additiewe en nie-additiewe geenak, Ministry of Agriculture

English: Rice is an important food crop with two domesticated species namely Oryza glaberrima Steud. also known as African rice and O. sativa L. also known as Asian rice. Rice is a self-pollinating plant that shows some level of outcrossing under field conditions. Understanding the levels of gene flow is important for managing the conservation and maintenance of germplasm for gene banks and plant breeding programmes. It is equally important for the production of quality rice seed. There is also the concern of gene flow between genetically modified rice and other rice species; wild relatives and weedy (red) rice. This study used agro-morphological and microsatellite markers to evaluate the diversity in a collection of 36 accessions consisting of intraspecific (O. sativa and O. glaberrima) and interspecific (O. sativa x O. glaberrima) hybrid genotypes. The Shannon-Weaver diversity index was low measured by agro-morphological markers. The highest level of diversity was detected in the Indica accessions and the lowest diversity in the O. glaberrima accessions. Japonica accessions had brown or green apiculus and were awnless. O. glaberrima and landrace accessions had purple apiculus and some were awned. The Japonica group comprised mostly of improved varieties with a white pericarp whilst O. glaberrima accessions and landraces had a red pericarp. Selected interspecific hybrids combined traits of O. sativa and O. glaberrima to varying degrees. Microsatellite markers showed a total of 321 alleles with an average of 11.9 alleles per locus and an average major allele frequency of 0.29 per locus. The average gene diversity value was 0.81 and polymorphism information content was 0.80 per locus. Diversity indices for interspecific hybrids were intermediate between O. sativa and O. glaberrima, but closer to the O. sativa Japonica group. Two populations were revealed which corresponded to the O. sativa Indica group and O. sativa Japonica group. Interspecific hybrid accessions wer, Afrikaans: Rys is ‘n belangrike voedselgewas met twee aangeplante spesies naamlik Oryza glaberrima Steud., ook bekend as Afrika rys en O. sativa L., ook bekend as Asiese rys. Rys is ‘n selfbestuiwende gewas met ‘n persentasie kruisbestuiwing onder veldtoestande. ‘n Begrip van die hoeveelheid geenvloei is belangrik vir die bestuur en onderhoud van kiemplasma vir geenbanke en planteteelt programme. Dit is net so belangrik vir die produksie van kwaliteit ryssaad. Daar is ook kommer oor geenvloei tussen GM rys en ander rys spesies; wilde verwantes en onkruidagtige (rooi) rys. Hierdie studie het agro-morfologiese en mikrosatelliet merkers gebruik om diversiteit in ‘n versameling van 36 inskrywings bestaande uit intraspesifieke (O. sativa L. en O. glaberrima Steud.) en interspesifieke (O. sativa x O. glaberrima) rys genotipes te bepaal. Resultate van kwalitatiewe en kwantitatiewe eienskappe het verskille in diversiteit tussen die inskrywings getoon. Die waargenome diversiteit in O. glaberrima was laer as in O. sativa. Interspesifieke rys het intermediêre vlakke van diversiteit getoon. Die Shannon-Weaver diversiteitsindeks was laag gemeet aan agro-morfologiese merkers. Die hoogste diversiteitsvlak is gesien in die Indica inskrywings en die laagste diversiteit in die O. glaberrima inskrywings. Japonica inskrywings het bruin of groen aarpunte gehad en was baardloos. O. glaberrima en landrasinskrywings het pers aarpunte gehad, en sommige het baarde gehad. Die Japonica groep het meestal bestaan uit verbeterde variëteite met ‘n wit perikarp terwyl O. glaberrima inskrywings en landrasse ‘n rooi perikarp gehad het. Die interspesifieke basters het eienskappe van O. sativa en O. glaberrima gekombineer in verskillende grade. Mikrosatelliet merkers het ‘n total van 321 allele getoon met ‘n gemiddeld van 11.9 allele per lokus en ‘n gemiddelde major alleel frekwensie van 0.29 per lokus. Die gemiddelde geendiversiteitswaarde was 0.81 en die polimorfisme informasie inhoud was 0.80 per lo, Africa Rice Center (AfricaRice)

English: Eastern Africa, where sorghum is a significant arable crop, is arid and areas are at risk of desertification. Consequently, many valuable landraces of sorghum are at risk for genetic erosion. Genetic diversity plays a vital role in the success of any breeding programme. This study aimed to investigate the genetic diversity and genetic relationships in germplasm accessions among east African countries using morpho-agronomical and simple sequence repeat (SSR) markers in order to (i) understand the extent of genetic variation in different countries, and (ii) quantify the genetic structure and how the diversity is distributed among and within countries. The extent of regional patterns of phenotypic diversity was assessed in 1013 accessions using 13 qualitative and five quantitative traits. A total of 1108 sorghum accessions from Sudan, Kenya, Uganda, Ethiopia, Eritrea, Rwanda, and Burundi were assessed using 39 SSR markers. Results on qualitative and quantitative traits data showed that there was a high level of morpho-agronomical diversity among accessions studied. Analysis of variance revealed highly significant differences between accessions pooled over countries and between countries. Based on SSR data, Sudan had the highest genetic diversity and Rwanda the lowest. Levels of genetic diversity differed significantly, with most of the diversity being partitioned more within than between countries. Results suggested that despite sorghum‟s predominantly autogamous mating system, countries clustered totally separately with almost no integration and therefore emphasized the role of farmers‟ practices in the preservation of landrace identity and the favouring of genetic diversity. The morpho-agronomical and molecular marker data showed a high level of variation among accessions, and indicated that sorghum populations studied were a mixture of a large number of different genotypes. Therefore, future germplasm collection should take all levels of variation into cons, Afrikaans: Oostelike Afrika, waar sorghum „n belangrike verboude gewas is, is waterarm en gebiede is in gevaar om woestynagtig te word. Die gevolg is dat waardevolle sorghum landrasse deur genetiese erosie bedreig word. Genetiese diversiteit speel „n belangrike rol in die sukses van enige teelprogram. Die doel van hierdie studie was om die genetiese diversiteit en genetiese verwantskappe in kiemplasma genotipes uit oos Afrika lande te ondersoek deur van morfo-agronomiese en eenvoudig herhalende volgorde (SSR) merkers gebruik te maak ten einde (i) die omvang van genetiese variasie in verskillende lande te ondersoek en (ii) die genetiese struktuur te kwantifiseer en te bepaal hoe die diversiteit tussen en binne lande versprei is. Die fenotipiese diversiteitspatrone van verskillende streke is ondersoek deur van 13 kwalitatiewe en vyf kwantitatiewe eienskappe gebruik te maak. „n Totaal van 1108 sorghum genotipes van Sudan, Kenia, Uganda, Etiopië, Eritrea, Rwanda and Burundi is ondersoek deur van 39 SSR merkers gebruik te maak. Resultate gebaseer op kwalitatiewe and kwantitatiewe eienskapdata het aangetoon dat daar „n hoë vlak van morfo-agronomiese diversiteit tussen die bestudeerde genotipes was. Analise van variasie het hoogs betekenisvolle verskille tussen genotipes, gekombineer oor lande asook tussen lande, aangetoon. Gebaseer op SSR data het Sudan die hoogste en Rwanda die laagste genetiese diversiteit getoon. Vlakke van genetiese diversiteit het betekenisvol verskil en meeste van die variasie was meer binne as tussen lande verdeel. Resultate het getoon dat ten spyte van sorghum se hoofsaaklik outogame voortplantingsisteem, lande totaal apart gegroepeer het met amper geen integrasie nie. Dit het die rol van boere se praktyke in die bewaring van die identiteit van landrasse en die bevordering van genetiese diversiteit uitgewys. Die morfo-agronomiese en molekulêre merker data het „n hoë vlak van variasie tussen genotipes aangedui en aangetoon dat die bestudeerde sorgh

English: The aim of this study was to assess genetic diversity, combining ability, heterosis, heritability of traits, stability and farmer preference of cassava germplasm in Ghana in order to structure an effective breeding programme. The assessment of genetic diversity in a collection of local cassava genotypes using 33 SSR markers revealed a high overall heterozygosity. The SSR markers identified 63 duplicates in the collection. The heterotic pools were distinct for the savannah and the forest ecological zones and this was the basis for the selection of progenitors for the rest of the study. Seven and five cassava progenitors were crossed in a diallel design without reciprocals in the forest and savannah ecologies respectively. The progenitors and progenies were evaluated for CMD, CBB, yield and its components in two seasons in the forest and one season in the savannah zone. The GCA:SCA ratio indicated that the GCA was larger than SCA for average root number, indicating additive gene effects and a possibility for improvement by selection. SCA was larger than GCA for harvest index and fresh root yield, indicating environmental effects on the trait and confirms the non-additive effects mainly determining expression of root yield. The parental genotypes were selected from a particular region where CMD is the main economic constraint. Debor had the best GCA effect for cassava mosaic severity reaction; while Tuaka had the best GCA effect for fresh root weight. Debor x Kwasea was the best combination for CMD resistance. Debor and Kwasea were the best parents for resistance breeding to CMD. The predictability ratio varied between 0.58 and 0.84. CMD and root number had a ratio close to one for the savannah and forest zones, showing that these traits were highly heritable and influenced by additive gene action. Marker assisted selection was used to search for new sources of CMD resistance in the progenies and progenitors. Crosses among CIAT elite genotypes and landraces re, Afrikaans: Die doel van hierdie studie was om genetiese divers iteit, kombineervermoë, heterose, oorerflikheid van eienskappe, stabiliteit en die bo ere se voorkeur vir cassava kiemplasma in Ghana te evalueer sodat ‘n effektiewe teelprogram g estruktureer kan word. Die evaluasie vir genetiese diversiteit met 33 SSR merkers in ‘n vers ameling van plaaslike cassava genotipes het baie heterosigose getoon. Die SSR merkers het 63 du plikate in die versameling uitgewys. Die heterotiese groepe was duidelik verskillend vir die savannah en die woud ekologiese sones en dit was die basis van seleksie van ouers in hierdie stu die. Sewe en vyf cassava ouers onderskeidelik is gekruis in ‘n dialleel ontwerp sonder resiproke, in die woud en savannah ekologiese sones. Die ouers en die nageslag is geëvalueer vir CMD, CBB, o pbrengs en die opbrengs komponente in twee seisoene in die woud en een seisoen in die sav annah sone. Die GCA:SCA verhouding het gewys dat die GCA groter was as SCA vir die aantal wortels, wat additiewe geenaksie wys, dus is verbetering moontlik met seleksie. SCA waardes w as hoër as GCA vir oesindeks en vir vars wortel opbrengs wat wys dat daar groot omgewingseff ekte op opbrengs is en dat nie-additiewe geeneffekte ‘n groot rol speel. Die ouers is gesele kteer uit ‘n spesifieke gebied waar CMD die grootste ekonomiese beperking is. Debor het die bes te GCA effekte vir CMD reaksie gehad; terwyl Tuaka die beste GCA effekte vir vars wortel opbrengs gehad het. Debor x Kwasea was die beste kombinasie vir CMD weerstand. Debor en Kw asea was die beste ouers vir CMD weerstandsteling. Die voorspelbaarheidsverhouding h et gevarieer tussen 0.58 en 0.84. CMD en aantal wortels het ‘n verhouding van na aan een geh ad vir die woud en savannah sones, wat getoon het dat hierdie eienskappe hoogs oorerflik i s, en deur additiewe geenaksie bepaal word. Merker ondersteunde teling en soeke na nuwe bronne van CMD weerstand in die ouers en nageslag is gedoen in kruisings tussen CIAT elit, IPICS

Cassava provides more dietary energy per unit area than any staple crop but native cassava starch has limited food and industrial applications. Different transgenic biotechnology approaches and ex situ physical and chemical starch modifications have been used to obtain desirable traits suitable for various food applications. But consumers are skeptical about the safety of the genetically modified foods and chemical residues. To meet the demand, gamma irradiation (this is energetic electromagnetic wave) which does not leave any residue, was used as a tool to induce in planta variation in amylose production. The four highest amylose producing plants N441P54 (32.7%), N223P12 (31.1%), N373P2 (27.2%), N329P11 (26.8%) and four lowest amylose producing plants N96P16 (14.0%), N353P6 (13.9%), N166P2 (13.2%), N476 P22 (11.7%) observed in the M1V2 generation were found to be significantly different from any one of the four controls HO008 (19.7%), HO001 (22.0%), UCC090 (22.6 %) and UCC026 (20.9%). Mutation is uncontrollable and could also lead to unexpected useful mutants. From this study four unexpected putative free-sugar mutants were identified, which could be used for bioethanol and glucose syrups production; two exceptional deep fissured and flaky mutants for the food industry; seven mutants with transition from A- to C-types of X-ray diffraction patterns with very high levels of crystallinity indexes suitable for replacing acid modified starches in pressing tablets in the pharmaceutical industries were discovered. Based on DSC classification, three gelatinization categories were observed. These were plants without gelatinization transition, plants with gelatinization transition and plants with merged gelatinization and melting transitions, occurring within gelatinization zone during calorimetric scanning from 25 – 110°C. The first and third categories included most of the putative mutants described in the research chapters and they were suitable for shortening the starch

Cassava brown streak disease (CBSD) is an important biotic constraint to cassava production in cassava growing areas of east, central and southern Africa. A study was initiated to study the genetics of CBSD resistance and search for molecular markers associated with disease resistance. Two resistant and two susceptible cassava parents were selected based on their flowering ability, genetic distance and phenotypic reaction to CBSD. They were crossed in a half diallel to produce six families and F1 progeny plus parents were screened for their reaction to CBSD and evaluated for yield traits at two locations. Results indicated that general combining ability (GCA) was higher than specific combining ability (SCA) for CBSD root necrosis, CBSD severity in the shoot at three, six and nine months after planting (MAP), cassava mosaic disease (CMD) severity at three, six and nine MAP and harvest index indicating the importance of additive gene action in controlling CBSD resistance. Results indicated that CBSD resistance was quantitatively controlled by polygenic genes. Higher SCA than GCA was detected for number of roots per plant, fresh root weight per plant and fresh shoot weight per plant indicating the importance of non-additive gene effects in controlling yield traits. The Namikonga x Albert cross was used to generate a segregating mapping population comprising of 190 F1‟s which was planted and screened for CBSD reaction at two locations and genotyped using 605 SSR markers. A total of 220 polymorphic SSR markers, tested on 60 F1 and 51 S1, were finally used for linkage analysis and four genetic linkage maps were produced. The maps produced included integrated (male and female), Namikonga (female), Albert (male) and Namikonga-S1maps which spanned a distance of 995.46cM, 779.48 cM, 854.26 cM and 524.58 cM consisting of 174, 131,123 and 124 mapped SSR markers respectively. Mean map distance between markers ranged from 4.23 cM in Namikonga-S1 to 6.94 cM in Albert map while ave, Rockefeller Foundation, AGRA

English: Cocoyam (C. esculenta (L.) Schott and X. sagittifolium (L.) Schott) belongs to the family Araceae. Cocoyam has the potential to contribute significantly to world agriculture in terms of food, nutrition and crop diversification. Despite this the crop remains neglected in terms of research focus. Limited or no information exists on the prevalence, preference and utilisation as well as the pattern and level of diversity that exists in cocoyam germplasm found in Malawi. This study determined the level and pattern of genetic diversity of cocoyam from Malawi using ethno-botany, morphological characters and AFLP markers. Mineral composition of selected genotypes was also determined. The ethno-botanical survey showed that farmers in Malawi maintain a large amount of cocoyam germplasm. These farmers have rich ethno-botanical and ecological knowledge of the cocoyam cultivars they conserve. Farmer’s preferences regarding cocoyam cultivars included uses of plant parts, adaptation and eating quality. Morphological characters showed high levels of variation among accessions. Two main species of cocoyam, Colocasia and Xanthosoma were identified based on leaf base shapes (petiole attachment). AFLP markers showed low levels of genetic diversity between accessions as opposed to the high morphological diversity. A combined (morphological characters and AFLP data) analysis using UPGMA clustering, PCA and AMOVA further alluded to the presence of the two cocoyam species within the germplasm. High levels of variation were detected between the two species and low levels of variation were observed within each of the two species (Colocasia and Xanthosoma). The PCA exhibited a better representation of the genetic diversity pattern than the hierarchical clustering. Accessions showed high levels of mineral composition. Potassium was identified as the major mineral component. Accessions also exhibited high levels of essential minerals (Ca, Fe and Zn). Incorporating cocoyam into the diet, Afrikaans: Amadumbie (C. esculenta (L.) Schott en X. sagittifolium (L.) Schott) behoort aan die Araceae familie. Amadumbie het die potensiaal om betekenisvol tot wêreldlandbou in terme van voedsel, voedingswaarde en gewasdiversifikasie by te dra. Ten spyte hiervan word die gewas nog steeds in terme van navorsing afgeskeep. Beperkte of geen inligting is oor die voorkoms, voorkeure en gebruik van die gewas sowel as die patroon en vlak van diversiteit wat voorkom in kiemplasma van Malawi beskikbaar. In hierdie studie is die patroon en vlak van genetiese diversiteit in amadumbie kiemplasma van Malawi met behulp van etnobotanie, morfologiese eienskappe en AFLP merkers bepaal. Minerale inhoud van geselekteerde genotipes is ook bepaal. Die etno-botaniese opname het getoon dat boere in Malawi ‘n groot hoeveelheid genotipes onderhou. Die boere wat die kiemplasma aanplant het ‘n ryk etno-botaniese en ekologiese kennis van die genotipes wat hulle bewaar. Die boere se voorkeur in terme van amadumbie cultivars sluit in die potensiële gebruik van plantdele, aanpassing en eetbaarheid. Morfologiese eienskappe het hoë vlakke van variasie tussen genotipes getoon. Die twee hoof spesies van amadumbie, Colocasia en Xanthosoma, is op grond van blaarbasis vorms (petiool aanhegting) geïdentifiseer. AFLP merkers het lae vlakke van diversiteit tussen genotipes getoon, wat teenstrydig was met die hoë morfologiese diversiteit. Gekombineerde analises (morfologiese eienskappe en AFLP data) met UPGMA groepering, PCA en AMOVA het die teenwoordigheid van twee amadumbie spesies in die kiemplasma bevestig. Hoë vlakke van variasie tussen die spesies en lae vlakke binne die twee spesies (Colocasia en Xanthosoma) is waargeneem. Die PCA het ‘n beter verteenwoordiging van die genetiese diversiteitspatrone as hierargale groepering gegee. Genotipes het hoë mineraalinhoudvlakke getoon. Kalium was die belangrikste minerale komponent. Genotipes het ook hoë vlakke van noodsaaklike minerale (Ca, Fe en Zn) gehad.

English: Science-driven interventions aimed at increasing cassava’s (Manihot esculenta Crantz), productivity will positively impart on communities that primarily depend on it. Data presented in this thesis contributed towards this goal. Specifically, this thesis examined phenotypic variation in cassava germplasm available within selected national breeding programmes, analysed patterns of allele frequency distribution in the cassava germplasm, characterised single nucleotide polymorphisms (SNPs) in the cassava genome and examined variation for two agronomic [root dry matter content (DMC) and harvest index (HI)] and one quality trait (amylose content) in S1 cassava inbreds. The 29 qualitantive traits provided limited discrimination of cassava germplasm from Uganda, Kenya, Tanzania, Rwanda, Democratic Republic of Congo and Madagascar. However, significant differences in root DMC, HI, leaf retention (LR) and root cortex thickess were observed in this germplasm. Highest average DMC was registered in Uganda (37.7%) and lowest in Tanzania (30.1%), with the elite genotypes having a relatively higher DMC than local genotypes. Similary, highest average HI was observed in Uganda (0.60) and lowest in Kenya (0.32). This germplasm (1401 local and elite cassava genotypes) were furthermore genotyped using simple sequence repeat (SSR) markers. Genotypes were assigned to three distinct populations, with no appreciable gene differentiation (FST = 0.089) observed. Most genetic variation (> 89%) was detected within individuals. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP for every 121 nucleotides. Nucleotide diversity ranged from 7.8 x 10-4 to 5.63 x 10-3. Average haplotype-based polymorphism information content (PIC = 0.414) was higher than for individual SNP (PIC = 0.228). HI and DMC varied both within and between the cassava S1 families. The highest reduction in HI was observed in S1 progeny from Bamunanika (83.3%), Afrikaans: Wetenskaplik-gedrewe intervensies wat ten doel het om cassava (Manihot esculenta Crantz) se produktiwiteit te verbeter, sal ‘n positiewe impak maak op gemeenskappe wat primêr daarop staatmaak. Data wat in hierdie tesis voorgehou is, het tot hierdie doel bygedra. Hierdie tesis het spesifiek die fenotipiese variasie in cassava kiemplasma beskikbaar binne geselekteerde nasionale teelprogramme ondersoek, patrone van alleel frekwensie verspreiding binne die cassava kiemplasma geanaliseer, enkel nukleotied polimorfismes (ENP) in die cassava genoom gekarakteriseer en die variasie vir twee agronomiese [wortel droë materiaal opbrengs (DMO) en oesindeks (OI)] en een kwaliteitseienskap (amilose inhoud) in S1 cassava ingeteelde lyne ondersoek. Die 29 kwalitatiewe eienskappe het tot beperkte diskriminasie van die cassava kiemplasma van Uganda, Kenia, Tanzanië, Rwanda, Demokratiese Republiek van die Kongo en Madagaskar gelei. Betekenisvolle verskille in wortel DMO, OI, blaarretensie (BR) en wortel korteksdikte is egter in hierdie kiemplasma waargeneem. Die hoogste gemiddelde DMO is in Uganda (37.7%) en die laagste in Tanzanië (30.1%) waargeneem, met die elite genotipes wat ‘n relatiewe hoër DMO as die plaaslike genotipes gehad het. Net so is die hoogste gemiddelde OI in Uganda (0.60) en die laagste in Kenia (0.32) waargeneem. Hierdie kiemplasma (1401 plaaslike en elite cassava genotipes) is verder genotipies getipeer deur van eenvoudige volgorde herhalende (EVH) merkers gebruik te maak. Genotipes is in drie duidelike populasies gegroepeer, sonder enige beduidende geen differensiasie (FST = 0.089). Die grootste gedeelte van die genetiese variasie (> 89%) is tussen individue waargeneem. ‘n Totaal van 26 ENPs is van kwaliteitsvolgordes van nege gene geïdentifiseer, wat ‘n geraamde frekwensie van een ENP vir elke 121 nukleotide gee. Nukleotied diversiteit het van 7.8 x 10-4 tot 5.63 x 10-3 gevarieer. Gemiddelde haplotied-gebaseerde polimorfiese informasie inhoud (PII = 0.4

English: Diallel crosses were evaluated in three agro-ecologies in Colombia and parents and families selected for conventional and molecular breeding trials conducted during the study. At the same time an inter-specific cross was evaluated for the effective introduction of higher DMC from wild cassava relatives. High positive and negative GCA and SCA values were estimated for the agronomic yield traits. Harvest index and DMC were under the influence of additive gene action, while ComRt, FRY and DRY were more influenced by non-additive effects. Moderate to high heritability estimates were obtained for the different agronomic traits. High heritability values were estimated for DRY, FRY, DMC, HI, RtPlt and moderate for RtWt. AMMI analysis ranked FRY, DRY, HI and RtPlt as stable, DMC relatively stable and RtWt as unstable across environments. In the seedling stage DRY, FRY, RtWt, and ComRt ranked parents in the same direction. Dry matter content and HI ranked parents similar but in the opposite direction for other yield characteristics. Overall rating ranked MPER 183 and CM 4574-7 as best parents followed by SM 1565-15 and SM 1665-2. Seedling nursery and the diallel analysis identified SM 1741-1 and MPER 183 as good parents for a number of traits. Replication and blocking during clonal evaluation greatly reduced the non-genetic factors resulting in high correlation among traits evaluated. Fresh root yield, DMC, HI, RtWt and RtPlt were found to be important in determining DRY. Root weight was found to be the most important indicator of DRY. Crossing of the elite cultivar MTAI-8 to the wild relative M. tristis resulted in high DMC values ranging from 34.39% to 42.73%. Bulk segregant analysis showed that parent SM 1741-1 was associated with favourable QTLs for DMC. Markers SSRY 150 (R2=18.1%) and SSRY 160 (R2=28.9%) in the diallel cross, SSRY 99 (R2=22.68), SSRY 141 (R235.89) and NS 169 (R2=20.01) in the wild cross and SSRY 11 (R2=34.57), SSRY 62 (R2=50.21) and NS 644 (R2=, Afrikaans: Dialleel kruisings is in drie agro-ekologiese areas in Kolombië geëvalueer en ouers en families is vir konvensionele en molekulêre telingseksperimente geselekteer vir hierdie studie. Terselfdertyd is ‘n inter-spesifieke kruising vir die effektiewe oordrag van droë materiaal opbrengs gene geëvalueer. Hoë positiewe en negatiewe algemene en spesifieke kombineervermoë waardes is vir agronomiese opbrengs eienskappe gevind. Oesindeks (OI) en droë materiaal opbrengs (DMO) was onder invloed van additiewe geenaksie, terwyl kommersiële wortels, vars en droë wortelopbrengs meer deur nie-additiewe geeneffekte beheer is. Gemiddeld tot hoë ooreflikheidswaardes is vir die verskillende agronomiese eienskappe gevind. Hoë oorerflikheid is vir droë en vars wortelmassa, DMO, OI en wortels per plant en gemiddelde oorerflikheid vir wortelmassa gevind. AMMI analise het vars en droë wortelopbrengs, OI en wortels per plant as stabiel geklassifiseer, DMO relatief stabiel en wortelgewig as onstabiel oor omgewings. In die saailingfase was ouers vir droë en vars wortelopbrengs, wortelmassa en kommersiële wortels ongeveer in dieselfde rangorde. Vir DMO en OI was ouers se rangordes weer ongeveer dieselfde, maar in die teenoorgestelde rigting as vir die ander opbrengseienskappe. In die geheel was MPER 183 en CM 4574-7 die beste ouers, gevolg deur SM 1565-15 en SM 1665-2. Die saailingkwekery en dialleel analise het SM 1741-1 en MPER 183 as goeie ouers vir ‘n aantal eienskappe geïdentifiseer. Herhaling en blokke tydens klonale evaluasie het die effek van nie-genetiese faktore grootliks verminder wat tot hoë korrelasies tussen die eienskappe wat geëvalueer is gelei het. Vars wortelopbrengs, DMO, OI, wortelmassa en wortels per plant was belangrik in die bepaling van droë wortel opbrengs. Wortelmassa was die belangrikste faktor in bepaling van droë wortel opbrengs. 190 Die kruising van die elite cultivar MTAI-8 met die wilde tipe M. tristis het tot hoë DMC waardes gelei wat tussen 34.39% en, Rockefeller foundation

English: Cassava has been neglected and considered as a primitive crop, food for the poor and a crop with poor nutritional value for a long time. Cassava provides more dietary energy per unit area than any staple crop. Population increase, multiplicity of cassava uses, unusual climatic variations and prospects of global warming highlight advantages of possible uses of this hardy drought tolerant crop. Policy makers realised the importance of cassava and are encouraging its promotion through research, production and utilisation. Since the crop has lagged behind for a long time, there exist knowledge gaps in many areas. Commercialisation of cassava, and biotic and abiotic factors encourage genetic erosion. Management and use of germplasm in production and breeding programmes need knowledge of genetic diversity. Hence, there existed a need to collect, characterise, evaluate, conserve and use Malawian cassava germplasm. Indigenous knowledge revealed wide genetic diversity because farmers reported a wide range of quantitative and quality attributes, which they preferred or disliked in existing Malawian cassava germplasm. Morphological markers failed to uniquely distinguish all analysed accessions. Manyokola5 and Mbundumali1, Gomani1 and 2, and Matuvi and Depwete were morphologically identical. However, morphological markers revealed high levels of genetic diversity with Dice genetic similarity (GS) ranging between 0.083-1.000. The most distant accessions were Beatrice (local cultivar) and Yizaso (CH92/112; locally screened). AFLP characterisation using cluster analysis indicated narrow genetic diversity with a GS range between 0.778-0.946 and uniquely differentiated all analysed accessions. The closest accessions were Mabundumali1 and Manyokola5 (GS=0.946), and Gomani1 and 2 (GS=0.938). PCA analysis for AFLP markers revealed that PCA axis 1 displayed narrow genetic diversity but PCA axes 2 and 3 displayed wide genetic diversity. AFLP analysis of cassava germplasm grouped, International Programme in the Chemical Sciences (IPICS)