West Africa Centre for Crop Improvement
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Item Breeding For Drought Tolerance And High Grain Yield Of Sorghum (Sorghum Bicolor [L.] Moench) In Tanzania(2020-12) Mwamahonje, A.S.ABSTRACT Sorghum is an important staple food crop for semi-arid areas in Tanzania. However, the productivity is very low due to several constraints, particularly drought. The present study was conducted to develop sorghum genotypes with improved drought tolerance and grain yield. The specific objectives were to: i) identify farmers‘ production constraints and traits preferences of sorghum in central Tanzania. ii) Introgress drought tolerant quantitative trait loci (QTL) from donor parents into farmers preferred sorghum varieties and iii) identify traits contributing to drought tolerance of sorghum genotypes. A participatory rural appraisal (PRA) was conducted at Kongwa district in Dodoma region and Ikungi and Iramba district in Singida region to identify constraints facing sorghum production, farmers‘ trait preferences and coping strategies to address drought. Two donor parents B35 and S35 with stay green (STG) QTL 1, 2 and 3 were introgressed to the farmers preferred sorghum varieties to develop F1, BC1F1 and BC2F1 populations. Five BC2F1 (NA307, W82, NA316, NA241 and SE438) populations and their parents were genotyped using 30 Single Nucleotide Polymorphism (SNP) markers. Results of the PRA showed that bird damage, poor soil fertility, drought stress, pests and diseases and lack of improved varieties were the major constraints of sorghum production. Early maturity, drought tolerance, high yield were ranked the highest preference when selecting new sorghum varieties. The coping strategies to address drought stress in sorghum involved early planting and use of drought tolerant varieties. Three (W82, NA241 and NA307) genotypes with heterozygous alleles and two genotypes (NA316 and SE438) with homozygous alleles were selected for selfing to generate BC2F3 populations. Moreover, plants with favourable alleles for either STG 1, 2, or 3 and good agronomic performance in field condition were selected. Eight genotypes namely NA241A, NA241B, NA307, NA316A, NA316B, NA316C, SE408 and SE438 from BC2F3 populations alongside with three parents and one check were selected after phenotyping BC2F2 population. The genotypes were planted in a split plot design under well watered and water stressed environments to determine the performance, correlation, heritability and genotypes by environments interaction. The results from the genotyping study revealed that, 7 out of 30 markers were for STG 1, 2 and 3 after genotyping of BC2F1 population; the remaining 23 markers were for traits contributing to STG in plants such as heat shock domain, programmed cell death triggering, aspartic proteases and chloroplast precursor. Genotyping of BC2F3 population indicated that, 7 SNP markers out of 10 had favourable alleles for STG in sorghum. Seventy one out of 728 BC2F1 samples genotyped were heterozygous. Of these, SNP markers snpSB00075, snSB00102 and snSB00103 were scored as heterozygous allele in seven samples of BC2F1 with B35*Wahi background. Markers snSB00049, snSB00077, snSB00102 and snSB00103 indicated heterozygous allele in 37 samples of BC2F1 with S35*Pato background. The rest (19) SNP markers showed homozygous alleles for BC2F1 population. Eighteen SNP markers indicated favourable alleles among 728 of BC2F1 samples genotyped including nsSB00049 and nsSB00054 for STG 1, snpSB00089 FOR STG 2 and nsSB00102 and nsSB00103 for STG 3. The rest of alleles were favourable for other roles related to STG in sorghum during post flowering drought condition. Similar trend were observed in the genotyping of BC2F3 population which seven SNP markers indicating favourable alleles for STG 1, STG 2 and STG 3. The SNP marker snpSB00089 indicated the highest (729) total number of favourable alleles for STG followed by snpSB00101 (728) and snpSB00102 with 727 after genotyping of BC2F3 population. However, the SNP marker snpSB00103 failed to identiy at least one favourable alleles for STG in this study.The genotype W82 was associated with snSB00102 marker, NA241 (snSB00102 and snSB00103) and NA307 was linked with snSB00101 and snSB00102 markers for STG 3 in BC2F1 population. Grain yield per hectare varied from 1770 kg/ha of donor parent B35 to 3415 kg/ha of BC2F3 genotype NA316C under well watered trial and from 1711 kg/ha of the donor parent B35 to 2652 kg/ha of genotype SE438 under water stressed trial. Significant differences were recorded in plant height, chlorophyll content, panicle length, panicle width, inflorescence exsertion, leaf rolling, grain weight per plant, panicle weight per plant and STG in both environments at P < 0.01. The mean performance of plant height was the highest (142.2 cm) in NA316C under water stressed condition and 143.3 cm under water irrigation. Interaction between genotypes by the environments were directed by majority of traits namely panicle length, panicle width, chlorophyll content, inflorescences exsertion, total number of leaves at physiological plant maturity, total number of green leaves at plant maturity, panicle weight, grain weight per panicle and root biomass. However, the interactions were not differed to plant height, leaf length and grain weight per plant. Panicle weight, panicle width and panicle length were significantly correlated with grain yield. STG and inflorescences exsertion were negatively correlated with grain yield. Chlorophyll content was correlated with total number of green leaves. A negative correlation was detected between traits STG and total number of green leaves. Above 50% heritability estimates were recorded in well watered and water stressed conditions. However, the interaction between genotypes by environments lowered the heritability of traits evaluated. Geometric mean productivity (GMP) and mean productivity (MP) were significantly correlated with yield under well watered environment (YP) and yield under water stressed environment (YS) and each other. There was low correlation between tolerance index and grain yield (0.12) in water stress environment. Stress sustainability index (SSI) showed low correlation with all indices compared thus; SSI is suggested as the best index for screening low yield under stressed environments. The genotypes NA307, NA316C and SE408 produced the highest grain yield per hectare across the environments. Therefore this study provided the bases of new genotypes which are promising for drought tolerance and yield. The genotypes should be advanced to lines and recommended for release after further evaluations in different geographical locations cultivating sorghum in Tanzania.Item Genetic Studies of Salinity Tolerance of Mangrove Rice Varieties in Sierra Leone(University Of Ghana, 2019-12) Vangahun, J.M.Rice is a major food crop in Sierra Leone with a high per capita consumption of 104 kg annually. Average yield (t/ha) is low, leading to a yield gap of 350,000 metric tons, which is met through import. A good number of rice farmers in Sierra Leone are cultivating on mangrove swamps, which are highly associated with salinity, resulting in the low average yield (tonnes per hectare). Salinity is a major abiotic stress devastating rice production in saline soils, including the mangrove ecology. Rice has been listed as the most salt sensitive cereal crop with a threshold of 3 dsm-1 beyond which yield begins to decline for most cultivated species. Understanding farmer’s knowledge on local rice varieties / land races and incorporation of molecular tools may enhance breeding for tolerance to salt stress in mangrove rice. The present study was undertaken to: (1) evaluate production constraints and varietal preferences of rice farmers in the mangrove ecology of Sierra Leone; (2) characterize the genetic diversity and population structure of mangrove rice landraces; (3) identify salinity tolerant QTL using DarT markers; and (4) estimate the relative efficiency of selection for tolerance to salinity in rice. A focus group discussion (FGD) and semi structured questionnaire were used in this study to sample responses from farmers. A total of 90 rice accessions collected from three districts (Kambia, Port Loko, and Moyamba) in Sierra Leone were evaluated in a completely randomised (CRD) design under screen house conditions in two replications. A cross between salt tolerance line (Nerica L9) and susceptible line (Sahel 317) was performed and a total of 462 F3:4 progenies were generated. The progenies, together with the two parents, were evaluated for tolerance to salinity in two replications under field conditions in Mbe, AfricaRice, Bouake. The 462 F3:4 progenies were genotyped for tolerance to Salinity using 13,432 SNP markers. Selection index and morphological characters were determined using BC1F3 populations. The present study identified major production constraints such as high cost of labour, salinity, lack of credit, lack of access to improved seeds and fertilizer, crab damage pest and diseases as most important. High yield, tall plant height, late maturity, good taste and high tillering ability were the top five traits farmers considered in selecting a variety. The cluster analysis found four distinct groups within the 90 germplasm which were also confirmed by the molecular analysis. The present study identified two major QTL (qDTF1.1 and qDTF1.2.) for time to 50% flowering on chromosome one, One major QTL (qDTF2) for the same trait on chromosome two. Two major QTL (qPH1.1 and qPH1.2) for plant height on chromosome one. Two QTL on chromosome 1 (qPN1) and chromosome two (qPN2). The study found that salt tolerance indices STI, DMP and TSI had discriminated among rice populations for yield under saline field conditions. Five agronomic traits including days to 50% flowering, plant height, number of tillers, number of panicle and filled-grain showed strong and positive correlations with grain weight hence are good selection indices under salt stress. The findings highlighted above could provide useful information for breeding for salt tolerance in mangrove rice in Sierra Leone.Item Genomic Study and Genetic Improvement of Sorghum (Sorghum Bicolor (L) Moench] for High Protein Digestibility(University of Ghana, 2018-12) Diatta, E.Sorghum is a staple crop and a major source of food and energy for the World’s developing countries. However, its utilization as human food is constrained by the low availability of its proteins after wet cooking which could lead to malnutrition, especially in sub-Saharan Africa. West Africa has a great diversity of sorghum yet, its study and use for improved protein digestibility remains unexplored. To provide knowledge on the characterization of West African sorghum germplasm for its exploitation in breeding programmes, a collection of 385 West African sorghum lines was assessed for seed quality, protein digestibility and anti-nutritional factors. Only 21% of the accessions were tannin-free, 56% had coloured seeds and protein content ranged from 9 to 18 g/100 g of samples. The largest variability for protein digestibility was found in accessions from Niger (1-55%). However, none of the lines of the entire collection was found to have highly digestible proteins after wet cooking i.e. at least 60% digestibility hence the need to explore other sources for variability. Chemical mutagenesis, applied to seeds of BTx623, generated three ethyl methanesulfonate (EMS) mutants with 26 to 37% higher digestible proteins as well as 50 to 100% increase in lysine and 30 to 50% more tryptophan content than their wild type parent. Two of those mutants had invaginated protein body (PB) phenotype while the third mutant displayed a phenotype close to the wild type round PB. Further characterization of the two mutants displaying contrasting PB phenotypes revealed that SbEMS3324 had more digestible proteins than P721Q while SbEMS1613 had harder seed kernels than P721Q, the first highly digestible mutant generated in 1975. The increase in digestible proteins in the mutant with invaginated PBs was controlled by a single recessive allele and linked to a point mutation on a kafirin gene (Sobic.005G189000) in SbEMS3324. However, in the mutant with round PBs, SbEMS1613, a missense mutation on a 26S proteasome PMSD10 subunit complex (Sobic.005G083340) located on chromosome 5 was causing the change in phenotype. Two pairs of SNP markers (ProF and ProR, KafF and KafR) were developed in this study and successfully shown to be linked to the genes causing the phenotype in each mutant. These primers could play a key role in accelerating the introgression of the high protein digestibility gene into locally-adapted sorghum varieties. Furthermore, to contribute to lower the humongous cost of wheat importation in Senegal as well as the use of maize in formulation of infant food and for poultry feed, the Senegalese research institute developed white grained high yielding sorghum varieties well adapted to different environments in Senegal, nevertheless, these varieties lack the essential amino acid lysine and have poorly digested proteins. To increase their nutritional value, these varieties were crossed to a mutant with high digestible proteins, P721Q. One of the crosses, exploited in this study led to the development of 128 BC3F3 progenies generated from a cross between lowly digestible Faourou and P721Q that were evaluated at Bambey in Senegal during the rainy season in 2017 along with the two parents. Amongst the 128 progenies, only 18 had highly digestible proteins after wet cooking. Eight progenies outperformed the donor parent in terms of digestibility which could be explained by the combination of favourable alleles in those progenies known as transgressive segregation. The identified highly digestible progenies, once released, will be potential varieties which would impact the food and feed industry in Senegal. It is recommended that they are further advanced and tested for yield performance across environments for possible release in Senegal.Item Identification of Sources and Loci for Development of Soyabean (Glycine Max (L.) Merrill] Cultivars That Combine Bacterial Pustule and Seed Decay Resistance with High Pod Clearance(University of Ghana, 2018-12) Barnor, M.T.Globally, diseases constitute a major biotic constraint to soyabean production. Although, the list of diseases of soyabean in Ghana has been published, the incidence, severity, and distribution of listed diseases were not indicated. Secondly, the Savannah Agriculture Research Institute (SARI) has accumulated considerable number of soyabean genotypes most of which were sourced from the International Institute of Tropical Agriculture (IITA) and the United States Department of Agriculture (USDA). Efficient use of germplasm depends on knowledge of variation that exists among genotypes for traits of interest coupled with an understanding of genetic diversity. Therefore, it was imperative to morphologically and genetically characterise genotypes in SARI’s germplasm to guide breeding efforts. Lastly, it is important to consider the architecture of released varieties in relation to farming systems including commercial farming. Most of the released soyabean varieties in Ghana belong to the early and medium maturing groups with low pod clearance. Low pod clearance is not a problem with subsistence farming systems where harvesting is manually done, but in commercial farms that use combine harvesters, low pod clearance could be the source of considerable losses. Detailed assessment of soyabean disease situation at production centres and detailed characterisation of genotypes in SARI’s soyabean germplasm have been carried out to identify sources and loci of resistance to predominant diseases of soyabean in Ghana. The objective of this study were to: (1) carry out a survey of soyabean diseases across major production centres in Ghana and their incidence and severity, (2) evaluate SARI’s soyabean germplasm for resistance to bacterial leaf pustule, (3) evaluate SARI’s soyabean germplasm for resistance to soyabean seed decay, (4) assess diversity, population structure and identify lines with high pod clearance among genotypes in SARI’s germplasm, (5) identify Phomopsis seed decay (PSD) and bacterial leaf pustule (BLP) resistant loci through genome-wide association mapping, (6 ) identify loci associated with pod clearance. Results of the survey revealed that some of the important diseases of soyabean in Ghana included Cercospora leaf blight (Cercospora kikuuchi), frog eye leaf spot (Cercospora sojina); target spot Corynespora cassiicola), bacterial leaf pustule (Xanthomonas campestris pv. glycine), downy mildew (Peronospor manshurica), leaf blight (Rhizoctonia solani), brown spot (Septoria glycine), soyabean mosaic, alfafa mosaic, and soyabean seed decay due to Diaporthe sp. Bacterial pustule was the most wide spread with incidence ranging from 15.3% at Wenchi to 84.7% at Malzire in the Yendi municipality. Two viral diseases, soyabean mosaic virus and alfalfa mosaic virus were present at all 15 locations but mostly at very low incidence except for Ejura and Wenchi where incidence was very high. Cercospora leaf blight and Frog eye leaf spot both occurred at 13 of 15 locations surveyed. Generally, incidence and severity of identified diseases was higher at Malzire, Karaga and Gushegu than other locations with the exception of soyabean mosaic virus for which the highest incidence occurred at Ejura followed by Wenchi. Furthermore, this study identified soyabean seed decay disease, and molecularly identified the causal agent as Diaporthe phaeolorum var. sojae and tentatively designated the isolate as MTB-1. This is the first report of Diaporthe phaeolorum var. sojae occurrence on soyabean pods and seeds in Ghana. Twenty-eight lines were identified with immune response to Xanthomonas axonopodis pv. glycines which could be used to develop resistant varieties. Area under chlorophyll retention curve had a negative correlation with area under disease progress curve, which translates to a positive correlation with resistance to bacterial pustule. Area under chlorophyll retention curve could replace disease severity score in bacterial pustule screening trials. Though disease pressure was high, eleven lines, PI416806B, PI224271, PI417120 BRS 361, PI417013, TGX 1903-7F, PI594767B, PI423958, TGX 1485-1D, TGX 2006-3F and Liu Yuemang were highly resistant to PSD infection. Genotypes within SARI’s germplasm differed widely for growth and reproductive parameters including plant height, number of branches, pod clearance, flowering and maturity periods, all of which were highly heritable except for number of branches. Likewise, high variation among genotypes for yield components, most of which were under genetic control was recorded. Principal component analyses identified number of pods per plants, number of seeds per plant, days to flowering and days to maturity as the main drivers of variation in SARI’s germplasm. Genetic diversity analyses of a 96 representative panel showed high diversity among genotypes. Structure analyses revealed nine sub-populations within the panel. Genetic variation among sub-populations was high as indicated by high allele divergence frequency among sub-population. All genotypes in the 96 representative panel were distinct and most were almost fixed as reflected in high Fst values. Genome-wide association studies identified two SNP markers, S3_14585048 and S3_1991311 with large negative effect on pod clearance. SAUR like-auxin responsive protein known to positively regulate cell expansion to promote hypocotyl growth was identified at the physical position of the SNPs. Associations between genomic locations and resistance to bacterial leaf pustule were identified but the associations were not significant because of low statistical power due to small sample size. Nonetheless, three SNP markers, S16_34242886, S16_35202484 and S1_38672307 were found linked to three candidate genes, Glyma.01go93200, Glyma.g187500 and Glyma.g187400. All three candidate genes code for Leucine-rich repeat receptor like protein kinases known for eliciting immune response to pathogen infection. The SNP, S18_7792728 associated with PSD resistance occurred at a genomic region that harbours the candidate gene AT3G07040.1 (NBARC-domain-containing disease resistance protein) known to play critical roles in plants response to pathogens. This confirms the existence of resistant genes for PSD among the lines in the representative panel. The identified SNP could be validated to aid with marker-assisted selection. This study presents a series of useful information on SARI’s soyabean germplasm, prevailing diseases of soyabean and their distribution, sources of resistance and resistant loci, and the discovery of informative markers that can alter the architecture of future varieties.Item Genetic Studies of Pearl Millet [Pennisetum Glaucum (L.) R. Br.] for Resistance to Striga Hermonthica(University of Ghana, 2018-12) Dawud, M.A.Pearl millet is a major food crop in the northern part of Nigeria. However, its production has been constrained due to several factors, among them is Striga hermonthica. To understand pearl millet farmers’ varietal preference traits, production constraints and knowledge of Striga infestation, a participatory rural appraisal was conducted across six districts in three local government areas of Jigawa State in Nigeria. Data were sourced using a semi-structured questionnaire among 143 farmers that involved focus group discussion sessions were used to verify information gathered from the questionnaires. Results showed that resistance to Striga infestation, resistance to downy mildew, tolerance to shattering, lodging tolerance and good quality local beverage were the most preferred traits by farmers. Major production constraints identified by farmers across the study areas were poor soil fertility, Striga infestation, downy mildew, and high cost of labour. Farmers were well informed about Striga as a menace and emphasized that it is likely to become worse unless controlled. A germplasm collection composed of 240 accessions of pearl millet were screened under natural Striga hermonthica infestation in the field. The results showed significant variation in the resistance of pearl millet genotypes to Striga. Fifteen genotypes identified as the most resistant were free of emerged Striga shoots, 10 genotypes supported 1-4 Striga shoots but with appreciable yield and 15 genotypes with 1-4 Striga shoots and low grain yield. Principal Component and cluster analyses grouped these genotypes into three main clusters as medium yielding tolerant to Striga, low yielding susceptible to Striga and medium to high yielding resistant to Striga. The high level of resistance observed in some breeding lines enabled the selection of suitable parents for population development. Two resistant and two susceptible to Striga genotypes selected from the field screening were used to study the gene effects controlling resistance to Striga in pearl millet. Six basic generations each were developed for the two sets of crosses and evaluated for resistance to Striga in the field. Results showed significant variation for resistance to Striga among genotypes and genotype by environments interactions. Additive and non-additive of gene actions were responsible for three indices of Striga resistance assessed; area under Striga number progress curve, Striga damage rating and the number of tillers and these varied from cross to cross and from environment to environment. In addition, a genome-wide association study (GWAS) aimed at identifying genomic loci and SNP markers associated with Striga resistance was performed using 188 pearl millet lines and 4802 SNP markers. Genotyping was achieved using the Diversity Array Technology (DArT) high-throughput genotyping-by-sequencing (GBS). Results revealed the presence of two sub-groups and a third mixed group were identified among the lines tested. Sixteen significant SNP markers associated with area under Striga number progress curve (ASNPC) were identified on five chromosomes; 2, 3, 4, 5 and 7 across all the three locations. The QTLs on chromosome 5, 2 and 3 accounted for 11 to 13% phenotypic variation. Six significant SNPs were detected for tiller number and two of these SNPs located on chromosome 1 and 5 were consistent across two locations. New SNPs were identified for Striga resistance and number of tillers (NTL). These need to be validated and fine-mapped for their use in marker-assisted selection for Striga resistance in pearl millet. The study further investigated genetic variation in production of strigolactone and tillering ability in ten pearl millet lines selected from the mapping population used for GWAS. Two major strigolactones; orobanchol and 5-deoxystrigol were identified and characterized. Five pearl millet lines; 16_R, 153_R, 96_R, 172_S and 140_S produced the highest level of orobanchol. All the test lines produced significantly lower 5-deoxystrigol than IBL (susceptible control) except 158_R. The susceptible lines 172_S and140_S induced highest Striga germination. The lines 153_R and 196_R that produced high orobanchol had the highest number of tillers. There is a positive correlation between orobanchol production and tillers production for 153_R and 96_R and a negative correlation between orobanchol and 5-deoxystrigol. A weak positive correlation was observed between Striga germination and orobanchol. These results demonstrated that genetic variability in the number of tillers is related to genetic variation in Strigolactone production and could be used as a morphological marker to select lines with low susceptibility to Striga infestation.Item Genetic Studies and QTL Mapping of Drought Related Traits in a Sweetpotato (Ipomea Batatas(L.) Bi-Parental Mapping Population(University of Ghana, 2018-12) Utoblo, O.G.The study was carried out to understand the genetic basis for yield under drought environments, and to map quantitative trait loci associated with yield and yield related components under drought stress in sweetpotato. The sweetpotato BxT mapping population, generated from a cross between sweetpotato varieties Beauregard and Tanzania was used for this study. Genotypes were evaluated in irrigated and drought environments to evaluate the effect of drought on yield and yield related parameters as well as genetic variability under drought conditions. Drought affected root yield, foliage yield, biomass and harvest index at varying degrees, with highest relative yield reduction in root yield. Drought tolerance indices were estimated based on root yield under drought and irrigated conditions. Suitable drought tolerance indices identified were geometric mean productivity, mean productivity and drought tolerance index. Genotypes were grouped as drought tolerant and high yielding (DTHY), drought tolerant and low yielding (DTLY), drought susceptible and high yielding (DSHY) and drought susceptible and low yielding (DSLY) based on their root yield means. Drought also reduced chlorophyll content, leaf area, normalized difference vegetation index (NDVI), photosynthetically active radiation, and increased canopy temperature. Observed low heritability and non-significant variation among genotypes for physiological traits indicates inefficiency of these traits for selection of drought tolerant genotypes in the BxT mapping population. However, morphological traits had significant variability among genotypes, high to moderate heritability under drought stress indicating they could be considered as potential secondary traits for selection of drought tolerant genotypes. To understand the genetic basis of drought tolerance in sweetpotato, QTLs associated with yield and yield related components under irrigated, drought and rainfed conditions were mapped using the genotype by sequencing method, GBSpoly. The occurrence of four QTLs on linkage group 9 in single environments and on linkage groups 11 and 6 for combined environments under only drought stressed conditions is indicative of drought specific QTLs. With further studies, confirmation and validation of these QTLs may be useful for drought tolerance-oriented breeding programmes in sweetpotatoItem Genetic and Genomic Resources to Improve Resilience to Striga [Striga Gesnerioides (Wild.) Vatke] and Drought in Cowpea(University of Ghana, 2018-12) Diangar, M.M.Cowpea (Vigna unguiculatan (L.) Walp.) is a grain legume cultivated worldwide in over 14 million ha but its productivity in Senegal is seriously affected by the infestation of Striga gesnerioides (Wild.) Vatke, a parasitic weed. Striga resistance is an important trait that is missing to most cultivated varieties in Senegal. Its negative effect on cowpea is exacerbated by drought which is a threat to agriculture. The present dissertation describes various options taken on the improvement of cowpea for Striga resistance and drought tolerance using microsatellite markers and drought tolerance indices and cultivar superiority coefficients. The first breeding activity describes methods and results obtained in identifying farmer concerns and interest on profile of their desired ideotype in Louga, Kebemer and Tivavouane involving 109 farmers. The second breeding activity was conducted in response to Participatory Rural Appraisal (PRA) indication on major constraints to anticipate on pre-breeding in order to identify drought tolerant lines that can be used as parental lines in developing new varieties. This study used phenotypic data recorded from well-watered and water-stressed experimental fields in Bambey (ISRA, CNRA de Bambey) and involved 112 accessions from the Senegalese cowpea breeding programme. The third breeding activity focused on cowpea resistance to Striga gesnerioides using Marker-assisted selection (MAS). The different options deployed involved in MAS were the creation of bi-parental lines of hybrids, RIL populations and advanced backcross populations using Marker-assisted backcrossing (MABC), the validation of resistance of the developed backcross lines in field in natural infestation and the identification of loci associated to Striga resistance in cowpea using Genome-Wide Association Analysis (GWAS) on a wide population composed of 367 unrelated accessions from diverse origins in the word. PRA revealed that drought was the major constraint to cowpea production and farmers were interested in large and brown seeded cowpea grain type in Senegal. Striga was important only in some divisions. Preliminary field and pot screening identified several lines more tolerant to drought compared to best tolerant check Mouride, reliability of markers used in MABC were weak, resistant BC4 lines performed unexpectedly in field in regards to SNP screening predictions. Significant markers were identified in 2 environments out of 4. Six candidate genes were identified in regions neighbouring identified markers and annotated. SNPs identified were not reported before in any article to best of our knowledge. The identified genetic and genomic resources could be used in population development for drought tolerance and S. gesnerioides resistance in cowpea.Item Breeding Sorghum [Sorghum Bicolor (L.) Moench] for High Quality Stover for Niger(University of Ghana, 2018-12) Diakite, O.S.Pasture shortage during March to July is the main constraint in cattle productivity in Niger. To alleviate this pasture shortage, farmers use dual purpose sorghum varieties where the grain is used as food and the nutritionally low quality stover as feed for their cattle during dry season. Consequently, cattle productivity is reduced. One sustainable means is to pave the way for better stover quality availability through incorporation of the brown midrib trait, which is known to improve quality of stover, into sorghum varieties. The main objective of this study was to develop dual purpose sorghum lines with high quality stover for sustained livestock productivity. The specific objectives were to (1) identify farmers’ and stover traders’ preferences on sorghum stover varieties; (2) introgress brown midrib6 and brown midrib12 genes in two Nigerien elite sorghum lines; (3) determine the agronomic and nutritive potential of new brown midrib (bmr) derived lines and (4) identify Single Nucleotide Polymorphism (SNP) mutations in Ethly methanesulfonate (EMS) sorghum mutants used in the national sorghum improvement programme. A Participatory Rural Appraisal (PRA) consisting of focus group discussions followed by semi-structured interviews, was conducted in three agro-ecological areas in Niger. Two bmr genes (bmr6 and bmr12) from three donor parents were introgressed into two Nigerien recurrent parents using hand emasculation in Sotuba, Mali. Ninety-four (94) derived BC1F3 families plus 6 checks were phenotyped using alpha lattice design in two sites (Tillabery and Konni) in Niger in 2017 rainy season. Selected derived families’ chemical compositions were analyzed at Sotuba Animal Nutrition Laboratory (LNA) in 2018 in Mali. Ten (10) EMS mutated accessions out of 554 phenotyped in Niger, were sequenced for candidate SNP discovery in Purdue University in 2018. PRA results revealed that farmers cultivated sorghum for dual purpose (grain and stover) with high preference for sorghum stover compared to pearl millet for cattle feeding. Farmers complained of feed shortage during dry season coupled with poor quality of their millet and sorghum stovers. Stover trading was a growing business despite the traditional poor management practices. Main criteria for forage quality traits were higher biomass, juiciness, stay-green for both farmers and traders. There were significant to highly significant differences among bmr derived families for grain and dry matter yield potential within and across sites. Grain yield ranged from 3271.2 kg/ha to 1205.4 kg/ha while dry matter yield varied from 6909.8 kg/ha to 2867.0 kg/ha. Significant variations were observed for the dry matter, Neutral Detergent Fiber (NDF), Acid Detergent Fiber (ADF) and Acid Detergent Lignin (ADL) contents between parental and derived lines. Results from 10 EMS lines revealed bmr2, bmr6, bmr12 and stacked bmr2/bmr6 genotypes. No candidate SNP was found for 2 EMS mutants for the known bmr genes suggesting that these could represent new mutations. Further investigations may identify the nature of their candidate mutations. Deeper phenotyping on field and nutritional values are essential to detect higher yielding lines to confirm the already interesting data collected during the course of this study for improved cattle production in Niger.Item Genetic Studies of Pearl Millet [Pennisetum Glaucum (L.) R. Br.] For Resistance to Striga Hermonthica(University of Ghana, 2018-12) Dawud, M.A.Pearl millet is a major food crop in the northern part of Nigeria. However, its production has been constrained due to several factors, among them is Striga hermonthica. To understand pearl millet farmers’ varietal preference traits, production constraints and knowledge of Striga infestation, a participatory rural appraisal was conducted across six districts in three local government areas of Jigawa State in Nigeria. Data were sourced using a semi-structured questionnaire among 143 farmers that involved focus group discussion sessions were used to verify information gathered from the questionnaires. Results showed that resistance to Striga infestation, resistance to downy mildew, tolerance to shattering, lodging tolerance and good quality local beverage were the most preferred traits by farmers. Major production constraints identified by farmers across the study areas were poor soil fertility, Striga infestation, downy mildew, and high cost of labour. Farmers were well informed about Striga as a menace and emphasized that it is likely to become worse unless controlled. A germplasm collection composed of 240 accessions of pearl millet were screened under natural Striga hermonthica infestation in the field. The results showed significant variation in the resistance of pearl millet genotypes to Striga. Fifteen genotypes identified as the most resistant were free of emerged Striga shoots, 10 genotypes supported 1-4 Striga shoots but with appreciable yield and 15 genotypes with 1-4 Striga shoots and low grain yield. Principal Component and cluster analyses grouped these genotypes into three main clusters as medium yielding tolerant to Striga, low yielding susceptible to Striga and medium to high yielding resistant to Striga. The high level of resistance observed in some breeding lines enabled the selection of suitable parents for population development. Two resistant and two susceptible to Striga genotypes selected from the field screening were used to study the gene effects controlling resistance to Striga in pearl millet. Six basic generations each were developed for the two sets of crosses and evaluated for resistance to Striga in the field. Results showed significant variation for resistance to Striga among genotypes and genotype by environments interactions. Additive and non-additive of gene actions were responsible for three indices of Striga resistance assessed; area under Striga number progress curve, Striga damage rating and the number of tillers and these varied from cross to cross and from environment to environment. In addition, a genome-wide association study (GWAS) aimed at identifying genomic loci and SNP markers associated with Striga resistance was performed using 188 pearl millet lines and 4802 SNP markers. Genotyping was achieved using the Diversity Array Technology (DArT) high-throughput genotyping-by-sequencing (GBS). Results revealed the presence of two sub-groups and a third mixed group were identified among the lines tested. Sixteen significant SNP markers associated with area under Striga number progress curve (ASNPC) were identified on five chromosomes; 2, 3, 4, 5 and 7 across all the three locations. The QTLs on chromosome 5, 2 and 3 accounted for 11 to 13% phenotypic variation. Six significant SNPs were detected for tiller number and two of these SNPs located on chromosome 1 and 5 were consistent across two locations. New SNPs were identified for Striga resistance and number of tillers (NTL). These need to be validated and fine-mapped for their use in marker-assisted selection for Striga resistance in pearl millet. The study further investigated genetic variation in production of strigolactone and tillering ability in ten pearl millet lines selected from the mapping population used for GWAS. Two major strigolactones; orobanchol and 5-deoxystrigol were identified and characterized. Five pearl millet lines; 16_R, 153_R, 96_R, 172_S and 140_S produced the highest level of orobanchol. All the test lines produced significantly lower 5-deoxystrigol than IBL (susceptible control) except 158_R. The susceptible lines 172_S and140_S induced highest Striga germination. The lines 153_R and 196_R that produced high orobanchol had the highest number of tillers. There is a positive correlation between orobanchol production and tillers production for 153_R and 96_R and a negative correlation between orobanchol and 5-deoxystrigol. A weak positive correlation was observed between Striga germination and orobanchol. These results demonstrated that genetic variability in the number of tillers is related to genetic variation in Strigolactone production and could be used as a morphological marker to select lines with low susceptibility to Striga infestation.Item Genetic Studies of Rice (Oryza Sativa) for Improvement of Yield and Aroma in Togo(University of Ghana, 2018-12) Dewa, K.M.K.In Togo, the quantity of rice produced is very low compared to the needs of the country. Farmers and consumers prefer aromatic rice. The main objective of this research was to increase the local production and supply farmers with aromatic and higher yielding varieties. It was conducted to lay the foundation of a rice breeding programme in Togo. Therefore, the research investigated farmers’ preferences and production constraints, established a germplasm collection and studied its genetic diversity, characterized the germplasm for yield and aroma, developed aromatic and high yielding F1 hybrids and estimated genetic parameters. The methods used to achieve the set goals consisted of focus group discussions and questionnaire survey to record information from farmers, collection of accessions around the country through prospecting survey, genetic diversity studies (notably principal components and cluster analyses), phenotypic and genotypic characterization of the germplasm for aroma and yield, as well as crosses of the parents identified (using the North Carolina Design II) and genetic analysis [notably Genotype by Environment (GxE) interactions, combining ability and genetic variance components] of yield and its component traits at four locations. From the participatory rural appraisal, absence of aroma in the new varieties introduced was the main reason for which farmers failed to adopt them. Their major preferences were presence of aroma, yield and earliness. Birds, insects and iron toxicity were their major production constraints. Collected germplasm comprising of 50 accessions were grouped, after diversity study using 30 agro-morphological traits and 5,736 informative Single Nucleotide Polymorphism (SNP) markers, in four and five clusters respectively, with 13 distinct samples of IR 841, the most widely cultivated aromatic rice variety in the country. Three aromatic (IR 841_Sot, Orylux 5 and Chapeau vert) and six high yielding (Chinoivi, Sipi, Berice 21, Gambiaca_Dan, Londo londo and Wita 4) parents were selected from the characterization, and used respectively as male and female parents to develop 18 F1 progeny families. The evaluation of the 18 F1s and their nine parents in the four agro-ecological zones of the country showed large phenotypic variability in the performance of the 27 genotypes for yield and its component traits. The hybrid N3A1 had the highest yield across the sites: 13 t/ha. Significant GxE interactions were detected for the four traits: grain yield, number of panicles per plant, number of grains per panicles, and 100-grain weight. The site Adéta produced more stable yield and number of panicles per plant but had the lowest performance for all the traits. All the traits were highly heritable (> 0.85) except for yield. The parent N5 had a significant general combining ability (GCA) for number of grains per panicle, and the hybrids N1A1 and N6A3 had significant specific combining ability (SCA) for 100-grain weight. No parent nor hybrid had significant GCA nor SCA for yield, showing the challenges to develop F1 hybrid rice varieties for farmers with these nine parents used. However, the progeny families from the parent N5 viz N5A1, N5A2 and N5A3 will be advanced using single seed descent selection method.