Plant Breeding

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A study of bruchid resistance and its inheritance in Malawian dry bean germplasm.
(2007) Kananji, Geoffrey Acrey Duncan.; Melis, Robertus Johannes Maria.; Derera, John.; Laing, Mark Delmege.
Dry bean (Phaseolus vulgaris L.) is economically and nutritionally an important legume, not only in Malawi, but in many parts of Africa and Latin America. Unfortunately, two bruchid species (Acanthoscelides obtectus Say, and Zabrotes subfasciatus Boheman) are known to cause extensive damage in storage, reducing the economic importance, food value and planting value of the crop. The aim of this study was to: i) ascertain farmers’ perceptions of the importance of bruchids as storage pests, and to identify their preferred varietal traits in dry beans; ii) screen Malawian dry bean landraces for effective and adaptable sources of resistance to the two bruchid species; iii) determine the gene action and inheritance of bruchid resistance. Farmers’ perceptions on the importance of the two bruchid species to beans both in the field and in storage were established using a participatory rural appraisal (PRA) in three extension planning areas (EPAs) in Lilongwe agricultural development division (ADD). Results confirmed that the two bruchid species are important storage pests, causing serious storage losses among smallholder farmers. In the absence of any control measures, farmers indicated that more than 50% of their stored beans could be lost to bruchids. Indigenous bruchid control measures are not very effective, making it necessary to search for other control methods. It was also clear from the PRA results that breeders need to consider both agronomic and culinary traits in bean cultivar development. This would enhance uptake of newly developed varieties. To address the problem of bruchid damage experienced by smallholder farmers, a total of 135 dry bean genotypes, comprising 77 landraces and 58 improved varieties (obtained from collaborating partners) were tested under laboratory infestation (nochoice test methods) and field infestation (free-choice test methods). The objective of this study was to identify effective sources of resistance to the two bruchid species. Results of the study showed that there was a wide variation among the genotypes for resistance to the two bruchid species. Overall results showed that 88% of the genotypes ranged from susceptible to highly susceptible to Z. subfasciatus and only 12% of the genotypes were moderately resistant to resistant. Genotype screening for resistance to A. obtectus showed that only 12.5% were resistant, whereas 87.5% were moderately to highly susceptible. All of the improved genotypes were 100% susceptible to A. obtectus in storage. One landrace, KK35, consistently showed a high level of resistance to both bruchids under laboratory infestation, with results similar to the resistant checks (SMARC 2 and SMARC 4), while another landrace, KK90, displayed stable resistance under both laboratory and field infestation. However, performance of most genotypes was not consistent with field and laboratory screenings, suggesting that mechanisms of bruchid resistance in the field are different from that in the laboratory and field screening should always be used to validate laboratory screening. Resistance in the field was not influenced by morphological traits. The seed coat played a significant role in conferring resistance to both bruchid species in the laboratory, whereas arcelin did not play any significant role in conferring resistance in the landraces. The inheritance of resistance to A. obtectus was studied in a 6 x 6 complete diallel mating design, involving crosses of selected Malawian dry bean landraces. The F1 crosses, their reciprocals, and six parents were infested with seven F1 generation (1 to 3 d old) insects of A. obtectus in a laboratory, no-choice test. There were significant differences among genotypes for general combining ability (GCA) and specific combining ability (SCA). However, SCA accounted for 81% of the sum of squares for the crosses, indicating predominance of the non-additive gene action contributing to bruchid resistance. A chi-square test for a single gene model showed that 5 of the 13 F2 populations fitted the 1:2:1 segregation ratio of resistant, intermediate and susceptible classes, respectively indicating partial dominance. The eight F2 populations did not conform to the two gene model of 1:4:6:4:1 segregation ratio of resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible classes, respectively. Average degree of dominance was in the partial dominance range in five F3 populations, but in general resistance was controlled by over-dominance gene action in the F2 populations. The additive-dominance model was adequate to explain the variation among genotypes indicating that epistatic effects were not important in controlling the bruchid resistance. The frequency distribution of the 13 F3 populations for resistance to A. obtectus provided evidence for transgressive segregation, suggesting that resistance is conditioned by more than one gene. Reciprocal differences were not significant in the F2 generation seed; but were significant in four crosses in the F3 generation seed for adult bruchid emergence, suggesting that maternal effects or cytoplasmic gene effects also played a role in the inheritance of resistance to the common bean weevil. Through this study, important sources of bruchid resistance in dry bean have been identified in Malawian landraces (KK35, KK90 and KK73). These resistant sources will be used in a breeding programme to develop bruchid resistant bean cultivars, as well as improve resistance in susceptible commercial bean cultivars currently grown by farmers in Malawi.
Agronomic and quantitative trait loci analyses of yield and yield-related traits in pigeonpea.
(2017) Kaoneka, Seleman Rashid.; Shimelis, Hussein Ali.; Varshney, Rajeev Kumar.
Abstract available in PDF file.
Assessment of groundnut (Arachis hypogaea L.) for genetic diversity using agro-morphological traits and SSR markers.
(2019) Chipeta, Olivia.; Sibiya, Julia.
Groundnut (Arachis hypogaea L.) offers one of the cheapest sources of proteins and economic empowerment to smallholder farmers in Africa, contributing significantly to world production and trade. Thus, improved groundnut seed with high quality attributes is needed. Therefore, pre-breeding activities involving agro-morphological attributes such as yield, disease tolerance/resistance, plant architecture among others are important in order to develop superior genotypes with the needed quality attributes. This study focused on assessing the performance and level of phenotypic variability and genetic diversity of groundnut genotypes using agronomic and morphological attributes, and simple sequence repeat (SSR) markers. Twenty-seven groundnut genotypes collected from International Crops Research Institute for the Semi-Arid Tropics (ICRISAT-Malawi) and Chitedze Agricultural Research Station (Malawi) showed highly significant differences in relation to number of branches, days to flowering, leaf color, seed yield and shelling percentage except for aflatoxin content and groundnut rosette disease. Moderate to high broad-sense heritability (0.56-0.71) was observed for number of branches, days to flowering and leafspot disease. The genotypes grouped into three main distinct clusters with those bred for low aflatoxin accumulation falling in the same cluster. Principal component analysis (PCA) had two PCs explaining 57.7% of the total variation with number of branches, flowering and aflatoxin contributing the most to the first PCA. Five genotypes; MP-68, ICGV-94379, ICGV-93305, CDI-1314 and CDI-0009 were identified as high yielding with low aflatoxin concentration hence are recommended for further pre-breeding activities such as increasing yield and resistance to diseases and aflatoxin. Using 20 SSR markers, 39 groundnut genotypes of diverse origin maintained at Agricultural Research Council – Grain Crops Institute in South Africa (ARC-GCI were assessed for genetic diversity. Results showed polymorphic information content (PIC) averaging 0.71, indicating the markers were very informative. A wide genotypic diversity with highest dissimilarity index of 6.4 between genotype pair RG562 and RG288, and smallest dissimilarity index of 0.9 between RG512 and RG562 was observed. Allelic diversity analysis showed high diversity among genotypes from southern Africa and southern America as indicated by the Shannon information index, mean number of observed alleles (Na) and mean number of effective alleles (Ne) which were relatively higher than in other groups. Analysis of molecular variation (AMOVA) results indicated that variation between and within individuals was more significant than between populations. Discrimination of the genotypes was not dependant on the geographical origin as genotypes belonging to different origins clustered in the same groups. Thus, genotypes with wide diversity can be used in breeding programmes as parents.
Assessment of maize germplasm lines for genetic diversity, cultivar superiority and combining ability.
(2012) Khoza, Suzan.; Derera, John.; Laing, Mark Delmege.
Maize (Zea mays L.) is an important crop in the world; however, its yield is compromised by new production challenges leading to poor yield in sub-Saharan Africa. This calls for a need to enhance maize adaptation to changing climate and challenging environments. The new maize varieties should be richly endowed with high frequency of genes that confer high yield under stress and non-stress conditions. Currently, such maize is not available, prompting research into development of new germplasm lines for use in developing new hybrids. The objective of the study was to determine i) the level of genetic diversity using SSR molecular markers and phenotypic data in a set of 60 maize inbreds from the breeding program, ii) genotype by environment interaction in maize hybrids, iii) cultivar superiority, iv) combining ability effects, v) the relationship between yield and secondary traits and vi) the relevant genetic parameters that underpin genetic gains in a breeding program. To study genetic diversity present in the germplasm, phenotypic data and 30 SSR markers were used to estimate the genetic distance between the inbreds. The results indicated that inbred lines which were put in the same cluster were related by pedigree and origin. To assess the level of genotype by environment interaction (GXE) and cultivar superiority of the new germplasm lines, hybrids were planted in five environments with two replications. Data were analysed using the REML and AMMI tools in GenStat 14th edition. The results revealed significant differences between hybrids and environments for grain yield. However, GXE interaction was also significant indicating possible challenges which can be encountered in selecting new hybrids. To determine combining ability estimates two different testers were used. The REML tool from GENSTAT was used to perform the line X tester analysis. Results indicated that both additive and non-additive gene action were important for grain yield. The direct selection strategy for yield was recommended because heritability of grain yield was high. Overall, results suggested that the information on genetic diversity will assist in defining heterotic groups; which will enable effective and efficient management of the germplasm lines to produce new maize hybrids.
Assessment of sweet sorghum lines for genetic diversity using quantitative traits and SSR markers.
(2016) Chinyama, Sombo.; Sibiya, Julia.; Odindo, Alfred Oduor.
The increase in energy demand, volatile oil prices and climate change has led South Africa to reduce its dependency on fossil fuels and promote biofuels. Sweet sorghum [Sorghum bicolor (L.) Moench] has been considered as one of the promising crops due to its sugar-rich stalk to supplement sugarcane which is the major feedstock for bioethanol. Establishing genotypic variability for biomass yield and sugar-related traits in sweet sorghum is therefore essential for developing superior cultivars. The objectives of the study were: (i) to assess sweet sorghum lines for agronomic performance and genetic diversity using quantitative morphological traits and (ii) to assess sweet sorghum lines for genetic diversity and interrelationships using simple sequence repeat (SSR) markers. Twenty-five sweet sorghum lines collected from International Crops Research Institute for the Semi-Arid Tropics (ICRISAT-Kenya) and the African Centre for Crop Improvement (ACCI-South Africa) were evaluated during the 2015/2016 season in KwaZulu-Natal (KZN) province at Ukulinga Research Farm in Pietermaritzburg and Makhathini Research Station in Jozini. Seven agronomic traits; fresh biomass yield, fresh stalk yield, grain yield, plant height, stalk diameter, panicle length and days to 50% flowering, and six quality traits; fibre, dry matter, °brix, °total brix, total fermentable sugars and ethanol were recorded. The sweet sorghum lines revealed highly significant variations for the 13 quantitative characters assessed in this study. The extent of variation was highly influenced by environment and genotype by environment interaction. Genotypes designated as IS 2331, IESV 92008 DL, ICSV 700, AS 244, URJA and SS 27 were identified as suitable genotypes with high plant height, dry matter, fibre, °brix, °total brix, total fermentable sugars and ethanol. The specified genotypes also exhibited medium to late maturity with relatively high fresh biomass and fresh stalk yield. Genotype 91018 LT showed the highest fresh biomass yield, fresh stalk yield, stalk diameter and relatively high grain yield. High levels of trait heritability were observed for fresh stalk yield (98%), stalk diameter (93%), fresh biomass yield (81%), panicle length (76%), fibre (73%) and plant height (66%). Heritability estimates were influenced by the environment and genotype by environment interaction. Principal component analysis resulted in the first three principal components showing 83% of the total variability among the genotypes. Ethanol, total fermentable sugars, °total brix, fresh stalk yield and °brix contributed mainly to PC 1, whereas fresh biomass yield and stalk diameter contributed mainly to PC 2. The dendrogram generated from cluster analysis divided the genotypes into two main clusters and three singletons (ICSB 324, ICSB 654 and ICSV 700). Cluster I comprised 54% of the total germplasm and included only one ACCI genotype (SS 27), while cluster II comprised of 33% of the total variation. The morphological variability analysis of the genotypes was also complimented with the use of molecular markers. The 24 sweet sorghum lines were genotyped with 10 simple sequence repeat (SSR) markers and distance-based method was used to analyze the data. Variation was observed for all the markers with allelic size ranging from 1 to 36 bp. A total of 61 alleles were generated with an average of 6.1 alleles per locus. The polymorphism information content (PIC) values ranged from 0.32 to 0.86 with an overall mean value of 0.62, showing a high discriminating ability of the markers used. The largest genetic distance was observed for AS 244 (GD = 1.9), while IESV 92001 DL and IESV 92008 had the smallest genetic distance (GD = 0.50). The dendrogram generated from cluster analysis using SSR markers classified the 24 sweet sorghum lines into two major clusters. Cluster I comprised of 12.5% of the total genotypes which included URJA, SS 27 and ICSB 654. It was observed that all ACCI genotypes apart from AS 244 were grouped in Cluster I, with URJA and SS 27 being very closely related. Cluster II was observed to be the largest (87.5%) with 21 genotypes, which further formed 3 sub-clusters (A, B and C) and a singleton (AS 244). The results from molecular marker characterization were similar to those obtained using PCA analysis of morphological traits which grouped genotypes into four clusters, with the same type of genotypes in each group. The information obtained in this study coupled with phenotypic characterization can be used by plant breeders to select parents or pure lines that can be used in developing improved cultivars. This will therefore contribute to the production of sweet sorghum and promotion of its use for bioethanol in South Africa.
Breeding and evaluation of cassava for high storage root yield and early bulking in Uganda.
(2013) Tumuhimbise, Robooni.; Melis, Robertus Johannes Maria.; Shanahan, Paul Edward.
Cassava (Manihot esculenta Crantz), is the world’s most widely grown starch storage root crop. It is a principal food staple in sub-Saharan Africa where it accounts for approximately one-third of the total production of staple food crops. It plays a key role as a food security and an income-generating crop for millions of smallholder farmers. In Uganda, cassava ranks second to bananas (Musa spp.) in terms of area occupied, total production and per capita consumption; however, nearly 5% of the total population experiences hunger with the prevalence of food energy deficiency at the country level standing at 48%. Cassava is a crop with high potential to alleviate food shortages and energy deficiencies, owing to its unique advantages of producing acceptable yields and starch on infertile soils amidst erratic rainfall, when most other crops would fail. Hoewever, its yield potential has not been fully realised since most of the cassava cultivars grown are susceptible to pests and diseases, low yielding and late bulking. The main objective of the research was to develop high yielding, early bulking cassava genotypes that combine resistance to cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) with farmer preferred traits for cultivation in Uganda. The specific objectives were to: (i) evaluate farmers’ attitudes to and/or perceptions of cassava early bulking, production constraints and cultivar preferences; (ii) determine the extent of genetic variability in storage root bulking and other important traits of selected cassava genotypes; (iii) assess the effects of genotype x environment interaction on early bulking and related traits of selected cassava genotypes; (iv) develop and evaluate cassava F1 families for early bulking in terms of the attainment of early, high fresh storage root yield (FSRY) and resistance to CBSD and CMD; and (v) determine the combining ability and gene action controlling early bulking and yield-related traits, as well as resistance to CBSD and CMD. Through the farmer participatory survey, a number of cassava production constraints were identified, key of which were: diseases, especially CBSD and CMD; lack of early bulking cultivars; rodents and insect pests. Farmers rated early bulking as the second most important preferred trait after FSRY, but suggested that early bulking should be complemented with high dry mass content (DMC), sweetness, high FSRY and resistance to pests and diseases. The analysis of variance of 12 cassava genotypes selected for evaluation in three diverse locations and at five different harvest times indicated significant variation among genotypes, harvest times, locations and their interactions for FSRY and most of the other traits evaluated. Fresh storage root yield and the other traits evaluated were predominantly under the control of genetic variation, indicating that genetic advance would be achieved through hybridisation of the test genotypes. Additive main effects and multiplicative interaction (AMMI) analysis of the data collected at nine months after planting (MAP) indicated a non-significant GEI for early FSRY, but significant GEI for other traits assessed. Eight of the 12 genotypes analysed had relatively low interaction with locations for early FSRY, signifying that these genotypes were relatively stable for early FSRY. Thirty-six F1 families were generated from a 9 x 9 diallel and exhibited a high degree of variation between and within families for all the traits assessed at the seedling evaluation stage. Diallel analysis at the seedling evaluation stage at 10 MAP indicated that additive gene effects were predominant in the expression of early FSRY and most of the other traits analysed. At the clonal evaluation stage, the 36 families were assessed for early FSRY at 8 MAP and this trait together with most of the other traits assessed were found to be predominantly under the control of non-additive gene effects. High mid- and better-parent heterosis for early FSRY was recorded in most families at the clonal evaluation stage with NASE3 x Nyara, Nyara x B11 and NASE3 x B11 recording the highest. Selection from the 36 families at the clonal evaluation stage based on farmers’ top two preferred traits, viz. early bulking for FSRY and DMC, plus resistance to CBSD and CMD identified 50 genotypes that had early FSRY of ≥25 t ha-1 at 8 MAP compared to the best parent, CT1 that had 15.9 t ha-1 at 8 MAP. The selected genotypes also had high DMC and dual resistance to CMD and CBSD. Advancement of the selected genotypes should go a long way towards increasing cassava yield per unit time, reducing food shortages and increasing the income of smallholder farmers in Uganda.
Breeding bambara groundnut (vigna subterranea (L.) verdc) for enhanced yield and nutritional quality in South Africa.
(2023) Majola, Nomathemba Gloria.; Shimelis, Hussein.; Gerrano, Abe Shegro.
Bambara groundnut (Vigna subterranea (L.) Verdc.; 2n= 2x = 22) is a nutrient-dense grain legume cultivated in sub-Saharan Africa (SSA) and Asia. The current food systems in tropical and subtropical regions depend on the cultivation and use of a few commodity crop species. This causes most indigenous crop species, such as Bambara groundnut, to remain neglected by researchers and underutilised in the value chains. Underutilised crop species have received limited research and development attention from researchers and policymakers, and hence, their economic value, production methods, seed enterprises, product development and commercialisation are not yet fully explored. Due to a lack of systematic genetic improvement, the yield of most underutilised crops is low (<0.85 ton ha-1) and stagnant. Unlocking Bambara groundnut’s economic and value-adding potential as an essential multipurpose food and cash crop will enhance food and nutritional security in developing countries. Research on Bambara groundnut in South Africa is relatively peripheral and there are no known improved varieties of this crop with high yield and nutritional quality. Therefore, specific objectives of this study were: (1) to document the progress made on Bambara groundnut production, utilisation and genetic improvement in SSA to discern the key production constraints, genetic resources and analysis, breeding methods and gains on yield and nutrition to guide breeding; (2) to assess them genotype-by-environment interaction (GEI) effect on grain yield and to select best adapted Bambara groundnut genotypes in South African target production areas for breeding; (3) to determine the compositions of phytochemicals and mineral elements present in Bambara groundnut genetic pool to identify superior and contrasting genotypes to guide product development and breeding; (4) to determine the magnitude of the genetic diversity and population structure of Bambara groundnut collections of South Africa using high throughput single nucleotide polymorphisms (SNP) markers to complement phenotypic and nutrition profile data for genotype selection and breeding; and (5) to determine the combining ability effects and gene action conditioning yield and related traits in Bambara groundnut genotypes to identify the best combiner donor parents and progenies for genetic advancement, cultivar development and release. The first part of the study reviewed progress on Bambara groundnut production, utilisation and genetic improvement in SSA. The study presented key production constraints, genetic resources and analysis, breeding methods and genetic gains on yield and nutritional quality. Modern crop management, production technologies, and value chains are yet to be developed in Africa to achieve economic gains from Bambara groundnut production and marketing. Improved crop management and post-harvest handling technologies, modern varieties with high yield and nutritional quality, value addition and market access are among the key considerations in current and future Bambara groundnut research and development programs. Information presented will guide sustainable production and effective crop breeding to pursue food and nutrition security and improved livelihoods through Bambara groundnut enterprises. In the second chapter of the study, 75 Bambara groundnut genotypes were evaluated across seven selected environments using a 5 x 15 alpha lattice design with three replications. The study revealed significant (p<0.05) differences among genotypes (G), environments (E) and GEI effects on grain yield. A high proportion of the observed variation was due to GEI (36.62%), followed by environment (35.63%) and genotype (24.16%) effects. Grain yield across environments ranged from 1.4 ton ha-1 for ARC Bamb-68 to 0.10 ton ha-1 for ARC Bamb-74. Genotype ARC Bamb-68 (0.96 ton ha-1), ARC Bamb-9 (0.88 ton ha-1) and ARC Bamb-54 (0.84 ton ha-1) attained the highest grain yield across locations, while ARC Bamb-74 exhibited the lowest grain yield of 0.16 ton ha-1. The genotype and genotype-by-environment biplot identified ARC Bamb-17, ARC Bamb-14, ARC Bamb-20, ARC Bamb-18, ARC Bamb-14, and ARC Bamb-26 as the most stable genotypes across locations, while ARC Bamb-18 and ARC Bamb-54 were specifically adapted to Loskop and Brits. The Mafikeng site was ideal for Bambara groundnut evaluation, genotype differentiation, and large-scale seed production. The selected genotypes with high grain yields and stability are valuable genetic resources as breeding parents for Bambara groundnut improvement in South Africa. In the third chapter of the study, 75 genetically diverse Bambara groundnut genotypes were field evaluated across four environments using a 15 x 5 alpha lattice design with three replications during the 2020-2021 cropping season. Genotypes were profiled for fat, phenolic and flavonoids contents at the Agricultural Research Council (ARC) analytical laboratory in South Africa. Further, the genotypes were assessed for the contents of the following minerals: calcium (Ca), iron (Fe), potassium (K), phosphorus (P), zinc (Zn) and nitrogen (N). The nutritional content of the test genotypes varied significantly (P<0.05), which were affected by the genotype and environment interactions. The Ca, Fe, K and Zn content varied from 150.70 to 216.53, 4.30 to 16.77, 771.99 to 1155.89 and 5.50 to 7.17 mg.100 g−1 dry seed sample, respectively. Genotypes, including ARC Bamb-2, ARC Bamb-19, ARC Bamb-73, ARC Bamb-56, ARC Bamb-37, ARC Bamb-3 and ARC Bamb-69 exhibited the highest fat content (>6.00 %). ARC Bamb-40 and ARC Bamb-59 recorded a higher mean Fe content of 16.00 mg.100 g−1. ARC Bamb-2 was the top-performing genotype with high fat content (6%), Ca (211.93 mg.100 g−1), and Zn (7.17 mg.100 g−1 ). Ca, K, and N contents displayed strong correlations (r>0.60, P<0.05). Phosphorus and Zn contents exhibited moderate correlations with Ca. Overall, the study selected genotypes ARC Bamb-73, ARC Bamb-19, ARC Bamb-9 and ARC Bamb-2 with high compositions of essential nutrients for product development or breeding. The selected genetic resources are valuable for trait integration and developing new breeding populations with enhanced nutrient compositions and agronomic and market-preferred traits. In the fourth part of the study, the magnitude of the genetic diversity and population structure of South Africa Bambara groundnut collections was determined using high throughput single nucleotide polymorphisms (SNP) markers. Ninety-three genotypes were genotyped with 2286 SNP markers and phenotyped with some unique complementary morpho-agronomic traits of the crop. The mean genetic diversity value was 0.32, revealing moderate genetic differences among the assessed genotypes. Cluster and structure analyses grouped the tested genotypes into two distinct categories. Further, the analysis of molecular variance partitioned the total genetic variation into among genotypes (90%), within genotypes (8%) and among populations (2%). The results revealed two heterotic groups for hybridisation and selection programs. The following unique genotypes were selected: ARC Bamb-37 (with spreading growth type), ARC Bamb-49 (bunch type), ARC Bamb-61 (semi-bunch) and ARC Bamb-83 (spreading) using the SNP markers and desirable agronomic traits. The study provided new insight on Bambara groundnut genetic profiles of South African collections, which will assist in conservation strategy and management of the crop for effective breeding. The final part of the study assessed combining ability effects and gene action conditioning yield and related traits in Bambara groundnut genotypes to identify the best combiner donor parents and progenies for genetic advancement and breeding. Ten contrasting parents were selected and crossedusing a 10 × 10 half-diallel mating design, and 45 progenies developed. The progenies and their parents were field evaluated using a 5 × 11 alpha lattice design with two replications in two contrasting locations in South Africa. Data was collected on agronomic traits and subjected to statistical analyses to compute genetic parameters. Genotype × location interaction effect was significant (P < 0.05) for the studied agronomic traits. General combining ability (GCA) and specific combining ability (SCA) effects were significant in most assessed agronomic traits, including yield per plant. The GCA × location and SCA × location interaction effects were significant for most traits. A Baker’s ratio of < 1 were recorded for most assessed traits, indicating the preponderance of non-additive gene effects conditioning the traits. The parental lines such as ARC Bamb-25, ARC Bamb-8 and ARC Bamb-55 recorded positive and desirable GCA effects for yield per plant. The progenies ARC25×ARC8, ARC44×ARC9 and ARC6×ARC9 had desirable SCA effects for yield per plant, ARC44×ARC8, ARC44×ARC68, ARC42×ARC8 for higher number of secondary branches per stem, ARC25 ×ARC8 for early maturity, ARC42×ARC55 for higher number of pods per plant and ARC42 ×ARC57 for increased seed width. The new families selected in the current study are useful breeding populations and will be subjected to selection and multilocation evaluation to release the best-performing varieties. Overall, the present study appraised the present production constraints, genetic resources and analysis, breeding methods and genetic gains on yield and nutritional quality to guide future breeding. Moreover, new Bambara groundnut breeding populations were developed with enhanced yield and nutritional compositions for genetic advancement and multilocation selection for variety release and adoption in South Africa.
Breeding bread wheat (Triticum aestivum L.) for drought- tolerance in Ethiopia.
Belete, Yared Semahegn.; Shimelis, Hussein.; Laing, Mark Delmege.
Wheat (Triticum aestivum L.; 2n=6x=42; AABBDD) is one of the major staple cereal crops in the world. The demand for wheat has rapidly increased in sub-Saharan Africa including Ethiopia because of the growing population, changing food preferences and socio-economic change associated with urbanization. However, production and productivity of wheat in the region is affected by various biotic, abiotic and socio-economic factors. Drought is one of the major abiotic constraints limiting wheat productivity in Ethiopia. Adoption of new improved varieties by farmers is relatively low in marginal, drought-prone areas of the country because of a lack of improved varieties with desirable agronomic and drought-adaptive traits. Developing wheat cultivars, which are drought-tolerant, high and stable yielding with farmers’ preferred traits, is a sustainable strategy to ensure food security and to improve livelihoods of farmers in marginal areas. Therefore, the objectives of this study were: i) to assess farmers’ production practices, perceived production constraints and preferred traits of bread wheat varieties as a guide to variety development and deployment in drought-prone areas of Ethiopia; ii) to screen bread wheat genotypes for drought-tolerance using phenotypic analysis to select promising lines for use in breeding for drought-tolerance; iii) to estimate the genetic parameters and association of yield and yield components and thus determine the selection criteria to increase genetic gains under drought stress conditions; iv) to assess the genetic diversity and relationships among the selected wheat genotypes using simple sequence repeat (SSR) markers in order to complement the phenotypic data in identifying complementary parents for further breeding for drought-tolerance; and v) to determine combining ability effects of the selected wheat genotypes, thereby deducing gene action controlling traits of interest and identifying promising families for drought-stress conditions, and to advance these families through the single seed descent selection method. Separate but complementary research activities were conducted to attain the aforementioned objectives. A participatory rural appraisal (PRA) study was conducted involving 170 randomly selected wheat producing farmers in selected districts of Arsi zone in the Oromia Regional State of Ethiopia during 2018. Moisture-stress, disease (wheat rusts) and the high cost of fertilizers were the first, second and third ranked production constraints in the study areas. Varietal attributes such as early maturity (p<0.01) and tall plant height (p<0.05) had positive and significant effects on the adoption of new, improved varieties, while poor adaptation and poor baking quality had negative and significant (p<0.05) influences. High grain yield was the most preferred trait as perceived by the farmers in the study areas, followed by stress adaptation (drought and heat stresses-tolerance), disease-resistance and early maturity. In the second part of the study, 120 genotypes were evaluated at five test sites in the 2018/19 cropping season using a 10 x 12 alpha lattice design with two replicates. The level of drought-stress was imposed using different sowing dates (early planting resulted in non-stressed plants, while late planting created drought-stressed conditions) following the onset of the main seasonal rain at each site. Grain yield and yield components were recorded, and drought indices were calculated for each genotype. Genotypes such as ‘YS-39’, ‘YS-119’ and ‘YS-109’ were the earliest to mature and can be used in droughttolerance breeding. Among the drought-tolerance indices, Geometric Mean Productivity (GMP), Mean Productivity (MP), Harmonic Mean (HM), Stress Tolerance Index (STI) and Yield Index (YI) were found to be the most suitable for predicting drought-tolerance because they had significant and positive correlations with yield under drought-stressed and non-stressed conditions. Genotypes ‘YS-41’, ‘YS- 92’, ‘YS-115’, ‘YS-34’ and ‘YS-93’ were found to be drought-tolerant, and exhibited dynamic stability, with relatively high yield under both drought-stressed and non-stressed conditions. ‘YS-90’, ‘YS-106’, ‘YS-96’, ‘YS-102’ and ‘YS-101’ were susceptible to drought-stress, while ‘YS-32’, ‘YS-29’, ‘YS-14’, ‘YS-53’ and ‘YS-11’ were relatively drought-tolerant, but exhibited static stability under non-stressed conditions. In the third part of the study, the extent of the genetic parameters and associations of yield and yield components were determined among the aforementioned 120 genotypes in order to design appropriate breeding strategies for yield improvement in wheat. The highest estimates for genetic variance were obtained for days to heading (DH; 54.0%), followed by Spike length (SL; 38.3%). The high heritability estimated for DH (94.4%), SL (90.2%) and spikeletes per spike (SS; 85.2%), coupled with a high rate of genetic advance, suggest that direct selection for these traits would be effective. Grain yield (GY) exhibited low genetic advancement (9%) and heritability (41.5%) estimates, which were concomitant with its polygenic and complex inheritance pattern. Correlation and path analyses revealed that plant height (PH) and 1000-kernel weight (TKW) were the most important contributing traits for improving grain yield under drought-stress conditions. In the fourth part of the study, 52 selected bread wheat genotypes were assessed using 20 SSR markers. SSR analysis identified a total of 181 alleles, with a mean of 10.1 alleles per locus. Population structure analysis grouped the test genotypes into three main populations. Analysis of molecular variance revealed that 85% of the variance emanated from intra-population differences. Cluster analysis also grouped the test genotypes into three major groups. In the fifth part of the study, eight parental lines and 28 crosses obtained from a half-diallel mating design were evaluated at two sites representing drought-stressed and non-stressed conditions. The genotypic effects were significant for all traits studied except grain-filling period (GFP) across the test environments. The parental line ‘YS-32’ was the best general combiner for DH, days to maturity (DM), GFP and TKW, enabling direct selection for improved grain yield under drought-stress conditions. Parent ‘YS-85’ can also be used for improving grain yield under drought-stress conditions due to its positive and significant GCA effect on GY. The highest specific combining ability (SCA) effects under drought-stressed for improving GY were obtained in families ‘YS-32’ x ‘YS-85’, ‘YS-102’ x ‘YS-82’ and ‘YS-102’ x ‘YS-92’. Overall, the present study revealed drought-stress was the major bread wheat production constraint in drought-prone agro-ecologies of Ethiopia. And, farmers had varying varietal preferences for adopting newly improved varieties. The tested genotypes proved to be valuable genetic resources to enhancing drought-tolerance and improving farmers’ preferred traits. In future, these genetic resources will be used either for developing mapping populations for quantitative trait loci (QTL) analysis underlying traits of interest under drought-stress conditions to serve as long-term breeding materials or release directly as cultivars incorporating farmers’ preferred traits.
Breeding cowpea (Vigna unguiculata (L.) walp.) for improved drought tolerance in Mozambique
(2010) Chiulele, Rogério Marcos.; Mwangi, Githiri.; Tongoona, Pangirayi.
Cowpea yields in Mozambique can be increased through breeding farmers’ accepted cultivars with drought tolerance and stability across environments. A study was conducted in the southern region of Mozambique to: (1) determine farmers perceptions on major constraints limiting cowpea production and identify preferences regarding cultivars and traits, (2) determine the variability of selected cowpea germplasm for drought tolerance, (3) determine the gene action controlling drought tolerance, yield and yield components in cowpea, and (4) assess the genotype × environment interaction and yield stability of cowpea genotypes under drought-stressed and non-stressed conditions. The study on farmers’ perceptions about the major constraints limiting cowpea production and preferences regarding cowpea cultivars and traits established that cowpea was an important crop, cultivated for its grain, leaves and fresh pods for household consumption and the market. The study revealed that cowpea grain and leaves were equally important across the three districts in the study. Differences in accessibility to markets between districts influenced the ranking of grain and leaves among districts. Grain was more important in Bilene and Chibuto districts which are situated far from the major urban centre, Maputo, while leaves were more important in Boane district which is near the major market of Maputo. Fresh pods were important in Bilene district which is situated along the major highway connecting Maputo and other provinces. Drought was the most important production constraint followed by aphids, bruchids and viral diseases. The criteria used by farmers to select cowpea varieties included high grain and leaf yield, large seed size, earliness, smoothness of the testa and potential marketability of the variety. The implication of this study is that different types of varieties need to be developed for different areas. Dual-purpose or grain-type varieties need to be developed for areas situated far away from the major markets while varieties for leaf production need to be bred for areas near major markets. During the breeding process, a selection index needs to be adopted whereby drought tolerance, high grain and leaf yield, large seed size, smooth testa, earliness, aphids and bruchids resistance should be integrated as components of the index. High grain yield should receive high weight for varieties developed for areas located far from major markets while high leaf yield would receive high weight for varieties developed for areas located near major markets. The study on variability of cowpea germplasm collections for drought tolerance revealed wide genotypic variability among the tested germplasm. Biplot displays indicated that the genotypes could be grouped into four categories according to their drought tolerance and yielding ability as indicated below: high yielding-drought tolerant (group A), high yielding-drought susceptible (group B), low yielding-drought tolerant (group C), and low yielding-drought susceptible (group D). Examples of high yielding-drought tolerant genotypes were Sh-50, UC-524B, INIA-24, INIA-120, IT96D-610 and Tete-2. Stress tolerance index was the best criterion for assessing genotypes for variability in drought tolerance because it enabled the identification of high yielding and drought tolerant genotypes (group A). The assessment on gene action controlling drought tolerance (stay-green), yield and components indicated that both additive and non-additive effects were involved in controlling all of these traits. Additive gene action was more important than non-additive gene affects in controlling stay-green, days to flowering, number of pods per plant, number of seeds per pod and hundred seed weight. Under no-stress conditions, additive gene action was more important than non-additive gene action while under drought-stressed conditions, non-additive gene effects were more important than additive gene effects. Stay-green can easily be assessed visually in early segregating populations while yield and yield related traits cannot. Hence, selection for drought tolerance using the stay-green trait would be effective in early segregating generations while selection for yield and number of pods per plant would be effective in late segregating generations. Selection for yield could be conducted directly under no-stress conditions and indirectly using the number of pods per plant under drought stress conditions. Genotype INIA-41 would be the most desirable to use as a parent for drought tolerance and IT93K-503-1 would be the most desirable to use as a parent for drought tolerance and yield. The assessment on genotype × environment interaction and cowpea grain yield stability for forty-eight (48) cowpea genotypes grown under drought-stressed and non-stressed conditions indicated that cross-over genotype × environment interactions were present for yield indicating that genotypes responded differently to varying environmental conditions. Genotypes adapted to specific environmental conditions could be identified. Genotypes IT-18, INIA-51, INIA-51A and Nhavanca were adapted to non-stressed environments that were either drought stressed or non-stressed while VAR-11D was adapted to low yielding, stressful environments. Genotypes INIA-23A, INIA-81D, INIA-24, INIA-25, INIA-16 and INIA-76 were high yielding and stable while genotypes IT-18, INIA-51, INIA-51A, Nhavanca and VAR-11D were high yielding and unstable. Genotypes Bambey-21, INIA-36, INIA-12 and Monteiro were consistently low yielding and stable except INIA-12 that was consistently unstable. Chókwè was a high yielding environment and suitable for identifying high yielding genotypes but not ideal for selection because it was not representative of an average environment while Umbeluzi was low yielding and not ideal for selection. Overall, the study revealed that genetic improvement of drought tolerance and yield would be feasible. Potential parents for genetic improvement for yield and drought tolerance were identified. However, further studies for assessing yield stability of cowpea genotypes are necessary and could be achieved by including more seasons and sites to get a better understanding of the genotype × environment interaction and yield stability of cowpea in Mozambique.
Breeding cowpea (Vigna unguiculata [L.] Walp) for improved yield and related traits using gamma irradiation.
(2016) Horn, Lydia Ndinelao.; Shimelis, Hussein Ali.
Cowpea is an important grain legume widely grown in sub-Saharan Africa for food and feed. In Namibia cowpea productivity is considerably low due to a wide array of abiotic and biotic stresses and socio-economic constrains. The overall objective of this study was to develop farmers’ preferred cowpea varieties with enhanced grain yield and agronomic traits through mutation breeding. The specific objectives of the study were to: (1) assess farmers’- perceived production constraints, preferred traits and the farming system of cowpea, and its implication for breeding in northern Namibia, (2) determine an ideal dose of gamma radiation to induce genetic variation in selected cowpea genotypes, (3) identify desirable cowpea genotypes after gamma irradiation of three IITA acquired cowpea varieties widely grown in Namibia including Nakare (IT81D-985), Shindimba (IT89KD-245-1) and Bira (IT87D-453-2) through continuous selections from M2 through M6 generations, (4) determine G x E interaction and yield stability of elite mutant cowpea selections and to identify promising genotypes and representative test and production environments, and (5) select elite cowpea varieties that meet farmers’ needs and preferences through farmers’ participation and indigenous knowledge. Participatory rural appraisal (PRA) study was conducted across four selected regions of northern Namibia including Kavango East, Kavango West, Oshikoto and Omusati where cowpea is predominantly cultivated involving 171 households. The majority of respondent farmers (70.2%) grow local unimproved cowpea varieties. About 62.6% of interviewed farmers reported low yields of cowpea varying from 100-599 kg/ha, while 6% of respondents achieved good grain harvests of 1500-1999 kg/ha. Farmers who grow local unimproved avarieties also indicated that the local varieties were not readly available and most have lost them to prolonged droughts and poor rainfall. Most farmers (59.1%) produced cowpea for home consumption, while 23.4% indicated its food and market value. Field pests such as aphids (reported by 77.8% respondents), leaf beetles (53.2%) and pod borers (60%) and bruchids (100%) were the major constraints. Striga gesnerioides and Alectra Vogelii (Benth) were the principal parasitic weeds reported by 79.5% respondent farmers. Soil fertility levels were reported to be very low across regions and all farmers did not apply any fertilizers on cowpea. Farmers-preferred traits of cowpea included a straight pod shape (reported by 61.4% respondents), a long pod size bearing at least 10 seeds (68.4%), white grain colour (22.2%) and high above ground biomass (42.1%). Inter-cropping of cowpea with sorghum or pearl millet was the dominant cowpea farming system in northern Namibia. About 68.4% of farmers used a relatively smaller proportion of their land (<1 ha) for cowpea production, while only 9.9% allocated more than 5 ha-1. Before a large scale mutagenesis an appropriate dose of radiation should be established on target genotypes. Therefore, seeds of the following three cowpea genotypes widely grown in Namibia: Nakare (IT81D-985), Shindimba (IT89KD-245-1) and Bira (IT87D-453) were gamma irradiated using seven doses (0, 100, 200, 300, 400, 500 and 600 Gy) at the International Atomic Energy Agency, Austria. The optimum doses at LD50 for the genotypes Nakare and Shindimba were 150 and 200 Gy, respectively while genotype Bira tolerated high dose of 600 Gy. Using linear regression model, the LD50 for genotypes Nakare, Shindimba and Bira were established to be 165.24, 198.69 and 689 Gy, respectively. Large scale mutagenesis were undertaken through gamma irradiation using seeds of the three varieties (Nakare, Shindimba and Bira). Field experiments were conducted in order to identify agronomically desirable cowpea genotypes. Substantial genetic variability was detected among cowpea genotypes after mutagenesis across generations including flowering ability, maturity, flower and seed colours and grain yields. Overall 34 elite cowpea mutants were selected from 37 genotypes including 3 parental lines showing phenotypic and agronomic stability. The selected 34 promising mutant lines along with the 3 parents were recommended for adaptability and stability tests across representative agro-ecologies for large-scale production or breeding in Namibia. The lines were subjected to G x E study conducted at three selected sites (Bagani, Mannheim and Omahenene) and two cropping seasons (2014/2015 and 2015/2016) providing six environments. The following four promising mutant genotypes: G9 (ShL3P74), G10 (ShR3P4), G12 (ShR9P5) and G4 (ShL2P4) were identified with better grain yields of 2.83, 2.06, 1.99 and 1.95, t.ha-1, in that order. The parental lines designated as G14 (Shindimba), G26 (Nakare) and G37 (Bira) provided mean grain yields of 1.87, 1.48 and 1.30 t.ha-1, respectively. The best environments in discriminating the test genotypes were Bagani during 2014/15 and Omahenene during 2014/15. Participatory cowpea varietal selection was undertaken in the northern Namibia using a set of newly developed 34 elite cowpea varieties. Genotypes were evaluated along with the three parents. Field evaluations were conducted across three selected villages in Omusati Region of northern Namibia where the crop is predominantly cultivated. Test varieties were independently assessed and scored using nine agronomic traits involving 114 participating farmers. Overall, the following 10 farmers-preferred cowpea varieties were selected: R9P5 (Sh200), R3P4 (Sh100), R4P1 (Sh100), L3P74 (Sh100), R1P12 (Nk100), R8P9 (Nk150), R5P1 (Nk150), R2P9 (Nk150), R10P5 (Nk150) and R11P2 (Bi600) for their larger seed size, white grain colour, high pod setting ability, insect pest tolerance, early maturity, longer pod size, drought tolerance, high biomass and pod yields. Generally, the study identified valuable cowpea mutants derived from three local varieties Shindimba, Bira and Nakare using gamma irradiation. The identified genotypes are phenotypically and agronomically stable and recommended to distinct, uniformity and stability (DUS) trials for varietal registration and release in northern Namibia.
Breeding dual-purpose Sweetpotato [Ipomoea batatas (L.) Lam.] varieties in Rwanda.
(2017) Shumbusha, Damien.; Shimelis, Hussein Ali.; Laing, Mark Delmege.
Sweetpotato [Ipomoea batatas (L.) Lam] is a multi-purpose crop where the fresh roots are used for human food and aboveground biomass for animal feed. In Rwanda, sweetpotato plays a key role in the mixed crop-livestock farming systems providing economic opportunities from livestock and crop production enterprises. However, dual-purpose sweetpotato varieties (DPSVs) with farmer-preferred traits and enhanced yields are yet to be developed and deployed in sub-Saharan Africa including in Rwanda. Therefore, the objectives of this study were: (i) to assess the role of sweetpotato in the crop-livestock farming system practised in Rwanda, to identify farmer-preferred traits and to establish farmer-led priorities in breeding dual-purpose sweetpotato varieties, (ii) to assess the level of phenotypic diversity present among sweetpotato varieties grown in Rwanda, and to select suitable parents for breeding DPSVs, (iii) to characterize diverse sweetpotato germplasm using simple sequence (SSR) markers to identify potential parents for breeding DPSVs, and (iv) to determine gene action and heritability of storage root and aboveground biomass yields, and yield components, in sweetpotato varieties, and to undertake early clonal selections for future release of DPSVs. In the first study, a participatory rural appraisal (PRA) was undertaken in the following three selected districts of Rwanda: Bugesera, Huye and Nyagatare. Data were collected through semi-structured interviews, focus group discussions and a transect walk. All respondents wanted to grow new sweetpotato varieties with improved storage root production combined with high aboveground biomass. About 87.7, 66.6 and 51.1% of the respondents indicated that root-related traits of the crop such as high dry matter content, red skin colour and yellow flesh colour were additional preferred traits, respectively. Secondly, fifty one diverse sweetpotato genotypes were evaluated in field trials conducted at the Rubona and Karama experimental stations of the Rwanda Agriculture Board (RAB) using a 6 x 9 unbalanced alpha lattice design with three replications. The top two genotypes selected for their high yields of storage roots were RW11-4923 and RW11-2419, with yields of 20.91 t.ha-1 and 20.18 t.ha-1, respectively. The genotypes RW11-4923 and Wagambolige were the best performers for aboveground yields, producing 23.67 t.ha-1 and 23.45 t.ha-1 of vines, respectively. The genotype Ukerewe performed well for its dry root yield (7.09 t.ha-1), while RW11-4923 had the highest mean dry vine yield (5.17 t.ha-1). The genotypes RW11-2910 and 8-1038 had root-to-vine ratios of 2.0 and 1.5, respectively. Two main phenotypic groups with 10 sub-groups were detected through cluster analysis and 24 sweetpotato clones were selected for their combination of high storage root yields, heavy vine production and prolific flowering ability. Thirdly, the above 24 selected sweetpotato genotypes were genotyped with nine highly polymorphic SSRs. Cluster analysis allocated the test genotypes into three distinct genetic groups: I, II and III, with 6, 5 and 13 genotypes, respectively. Eight genetically diverse clones were selected, namely SPK004 and K5132/61 (from Group I), 4-160, Ukerewe, RW11-2910 (Group II), RW11-1860, Wagabolige, 2005-179 (Group III), with key agronomic traits for breeding DPSVs. Finally, a half-diallel mating design was used and crosses were performed involving eight parents selected for their complementary traits including storage root and aboveground biomass production, dry matter content and farmer-preferred traits. A total of 28 families and 8 parents were field evaluated at Rubona, Karama and Ngoma research stations of RAB. Families had highly significant (P < 0.001) differences for fresh root yield (FRY), root dry matter content (RDMC), dry root yield (DRY), fresh vine yield (FVY), vine dry matter content (VDMC), dry vine yield (DVY), total biomass on dry weight basis (TBDW), root-to-vine ratio (R:V) and harvest index (HI). The general combining ability (GCA) and specific combining ability (SCA) effects were significant for FRY, RDMC, DRY, R:V, HI and VDMC. The GCA/SCA ratios were 0.75, 0.81 and 0.88 for DRY, RDMC and FRY, respectively, suggesting that additive gene action was more important than non-additive gene action in the expression of these parameters. Conversely, the GCA/SCA ratio was relatively lower, ranging between 0.09 and 0.28 for vine and root-vine combined parameters, suggesting that the non-additive component of the genetic variance, either dominance or epistasis, was more influential in controlling the traits. This implies that parental performance cannot necessarily be the basis of progeny performance prediction for these traits. The broad-sense heritability (H2) values were above 0.5 for all assessed traits, with FRY, HI and RDMC having higher estimates of 0.80, 0.81 and 0.92, in that order. RDMC had a high narrow-sense coefficient of genetic determination (NSCGD) of 0.80, while this parameter varied between 0.09 and 0.49 for the rest of the tested traits. The parent K5132/61 was the best combiner for FRY and HI, while the parents RW11-1860, RW11-2910, SPK004 and Ukerewe were best general combiners for RDMC. The parent Wagabolige was the best general combiner for FRY, DRY and R:V. Based on desirable SCA effects for FVY, DVY, TBDW, RDMC, R:V and FRY, the most promising families selected in this study were K5132/61 x Wagabolige, 4-160 x 2005-179, K5132/61 x RW11-1860 and RW11-2910 x 2005-179. Overall, the study developed promising families with high storage root and aboveground biomass yields. From these families, novel progenies were selected and are recommended for advanced clonal selection across multiple sites to release DPSVs in Rwanda or similar agro-ecologies in SSA.
Breeding for ascochyta blight [Phoma exigua var. diversispora (Bubak) Boerema] resistance of the common bean (Phaseolus vulgaris L.) in Rwanda.
(2017) Urinzwenimana, Clement.; Melis, Robertus Johannes Maria.; Sibiya, Julia.
Abstract available in PDF file.
Breeding for Cassava brown streak resistance in coastal Kenya.
(2008) Munga, Theresia Luvuno.; Melis, Robertus Johannes Maria.; Shanahan, Paul Edward.; Laing, Mark Delmege.
Cassava (Manihot esculenta Crantz ssp. esculenta) is the second most important food crop and a main source of income for the rural communities with potential for industrial use in the coastal region of Kenya. However, its productivity of 5 to 9 t ha-1 is low due to the low yield potential of the local cassava landraces caused by cassava brown streak disease (CBSD) among other biotic and abiotic constraints. Breeding for CBSD resistant varieties with farmer desired characteristics is hampered by limited information on the current status of the disease and farmers’ preferred characteristics of new CBSD resistant genotypes. In addition, there is a lack of an effective inoculation technique for cassava brown streak virus (CBSV) for screening genotypes for CBSD resistance. Information about the general combining ability (GCA) and specific combining ability (SCA) for CBSD above and below ground symptoms, fresh biomass yield (FBY) and fresh storage root yield (FSRY) (kg plant-1), harvest index (HI), dry matter % (DM %) and picrate score (PS) is limited and conflicting especially for the cassava germplasm in Kenya. These studies were carried out to update information on the status of CBSD, farmer’s preferences for cassava genotypes, and identify the most effective CBSV inoculation technique. In addition, the studies aimed to: determine the GCA and SCA for, and gene action controlling, the incidence and severity of above ground CBSD, root necrosis, FBY, FSRY, HI, DM %, and PS; and identify CBSD resistant progeny with farmers’ desired characteristics. A survey carried out in three major cassava-growing divisions in Kilifi, Kwale and Malindi Districts indicated that there was potential to increase production and productivity by increasing the area under cassava production and developing CBSD resistant genotypes that are early maturing, high yielding and sweet. In addition, CBSD was widely distributed, being present in 98.0% of the farms surveyed at a mean incidence of 61.2%. However, 99.0% of farmers interviewed lacked awareness and correct information about the disease. The genetic variability of cassava within the farms was low as the majority of farmers grew one or two landraces. Highly significant differences (P < 0.01) were observed among inoculation techniques for CBSV for which the highest infection rate of up to 92.0% was observed in plants inoculated by wedge grafting infected scion. Highly significant differences (P < 0.01) were observed among genotypes, between sites and their interaction for incidence of CBSD and root necrosis, while the differences among genotypes and the interaction between genotypes and the period of ratings were highly significant (P < 0.01) for the severity of CBSD and root necrosis. Above ground CBSD symptoms were not always associated with below ground CBSD symptoms and below ground CBSD symptoms were more severe at 12 months after planting (MAP) than at 6 MAP. Therefore, selecting cassava genotypes with resistance to below ground CBSD is more important than selection based on resistance to above ground CBSD and should be done after 12 months. Genotypes 5318/3 (exotic) followed by Msa140 and Plot4 (both local) had high resistance and can be used as new sources of resistance to root necrosis. Both GCA and SCA effects were highly significant with GCA sums of squares (SS) predominant over the SCA SS for most traits evaluated except for DM % at the clonal stage. These results indicate that although additive and non-additive genetic effects are involved in the inheritance of these traits, the additive genetic effects are more important except for DM %. Therefore breeding for CBSD-resistant genotypes that have characteristics desired by farmers in the coastal region of Kenya can be achieved through recurrent selection and gene pyramiding followed by participatory selection or use of a selection index that incorporates characteristics considered important by farmers.
Breeding for common bacterial blight resistance in common bean (Phaseolus vulgaris L.) in Ethiopia.
(2021) Hurisa, Kidane Tumsa.; Shimelis, Hussein.; Laing, Mark Delmege.; Mukankusi, Clare.
Abstract available in PDF.
Breeding for durable resistance to angular leaf spot (Pseudocercospora griseola) in common bean (Phaseolus vulgaris) in Kenya.
(2014) Njoki, Ng'ayu-Wanjau Beatrice.; Melis, Robertus Johannes Maria.; Mwangi, Githiri.; Sibiya, Julia.
Common bean (Phaseolus vulgaris L.) is an important legume crop in Kenya and is a cheap source of proteins. The small scale farmers in Kenya produce common bean under low agricultural input systems and this predisposes the crop to pests and diseases. Among the diseases, angular leaf spot (ALS) is a major constraint to common bean production and contributes to yield losses as high as 80%. The causative pathogen Pseudocercospora griseola (Sacc.) Crous & Braun is highly variable and several races have been reported. There are few common bean genotypes with resistance to this disease. Therefore breeding for resistance to ALS is important for the country. This study was carried out to; i) evaluate the common bean production systems, constraints and farmer varietal preferences in Kenya, ii) evaluate local landraces and selected introductions of common bean for yield performance and reaction to ALS, iii) study the genetics of resistance to ALS in common bean and iv) develop a breeding method for durable resistance to ALS in common bean. To determine the common bean production systems, farmers’ preferred traits and their knowledge on common bean constraints including ALS, a survey was conducted in Kiambu county using a semi-structured questionnaire, interviews, and focus group discussions. The study revealed that farmers cultivate common beans during the short and long rain seasons. However, they experience better yields in the short rains due to reduced disease incidence. The majority of the farmers (71%) intercrop common bean and this ensures maximum utilisation of space. A high percentage (70%) of the farmers utilise their retained seed for production. The farmers identified ALS as one of the most important constraints to production. The only preventative measure they undertake to control the disease is weeding. The farmers reported that they would prefer improved varieties that were resistant to ALS. Farmers have a preference for particular common bean traits that include high yield (80%), resistance to insect-pests and diseases (72%), type I growth habit (52%), early maturity (68%), seed size and colour (21%) and cooking time (20%). These should be incorporated in breeding programmes. Two hundred common bean landraces and market class varieties were evaluated for ALS resistance in a nethouse at University of Nairobi, Kabete Field Station and for ALS resistance and yield in the field in KARI-Tigoni. The results showed that disease severity scores for the genotypes were similar in the two locations, with the top three resistant genotypes being Minoire, GBK 028123 and Murangazi with disease severity scores of 2.9, 2.9 and 3.2 in Kabete and 2.6, 2.8, and 2.9 in Thika respectively. These resistant genotypes can be used as sources of resistance in a breeding programme or they can be used as resistant varieties. All the market class varieties were susceptible to ALS (disease severity score 6.7-8.0). There was a non-significant correlation between disease and yield most likely because most of the resistant genotypes were exotic and hence not adapted to the local conditions. There was also a non-significant correlation between disease and seed size. The two hundred common bean genotypes were evaluated for yield at University of Nairobi, Kabete Field Station and KARI-Thika. The results indicated that the 2011 and 2012 seasons had similar mean yields and that yields at Kabete were higher than at KARI-Thika. The highest yielding genotypes across the two locations were; GLP 2 (766 kg ha-1), Nyirakanyobure (660 kg ha-1), GBK 028110 (654 kg ha-1), GLP 585 (630 kg ha-1) and Mukwararaye (630 kg ha-1). There was a significant genotype x environment interaction and hence it is important for breeders to carry out stability analysis, so as to recommend varieties for a wide range of environments. To study the genetics of ALS resistance in common bean, three inter-gene pool crosses: Super-rosecoco x Mexico 54, Wairimu x G10909 and Wairimu x Mexico 54 were made. The resistant genotypes were Mexico 54 and G10909, while Super-rosecoco and Wairimu were susceptible. The generations F1, F2, BC1P1 and BC1P2 for each of the crosses were developed. The parents P1, P2 and the five generations of each cross were evaluated for resistance to ALS in Kabete Field Station. Results showed that both dominance and additive gene action were important in the expression of resistance to ALS. However, additive gene action was predominant over dominance gene action. There was a moderately high narrow sense heritability estimate (52.9-71.7%). The minimum number of genes controlling resistance to ALS was between 2 and 3. The predominance of additive gene effects and the moderately high narrow sense heritability estimates recorded imply that progress in resistance to ALS could be made through selection in the early segregating generations. A double cross followed by selection against resistant genotypes was used to develop a method to breed for durable resistance to ALS in common bean. The method was used to accumulate minor genes of ALS resistance into single genotypes. Four intermediate resistant landraces were used to develop a double cross population that was screened using a mixture of ALS races. Selection in F1 and F2 population was done on the basis of intermediate resistance (disease severity score 4.0-6.0), while selection from F3 population was based on resistance (disease severity score 1.0-3.0). Ten advanced F4 lines along with their parents were evaluated for ALS resistance. The F4 advanced lines had a significantly improved resistance to ALS compared to their parents. Hence the method was successful in accumulating minor genes for resistance thus showing significant breeding progress in breeding for durable resistance.
Breeding for durable resistance to Cercospora Leaf Spot diseases in groundnuts (Arachis hypogaea L.) in Tanzania.
(2018) Kongola, Eliud Francis.; Sibiya, Julia.; Melis, Robertus Johannes Maria.
Lack of high yielding groundnut cultivars tolerant to Cercospora leaf spot disease (CLD) and stable across different environments is one of the challenges to groundnut production by smallholder farmers in Tanzania. This makes selection of adaptable high yielding stable varieties under the different agro-ecological zones before release a very important part of the breeding program as this has an impact on the adoption and productivity of the cultivar. The objectives of this study were to evaluate and select genotypes that are tolerant to CLD, high yielding and identify environments that can be used for selection. A total of 24 groundnut genotypes comprising of six double cross population, twelve single cross parents and six checks from the three botanical groups (Valencia, Virginia and Spanish) were evaluated over six environments (viz Tumbi in Tabora region, Mlali, Ilindi and Hombolo in Dodoma region, Njoro in Manyara region and Ikhanoda in Singida region in Tanzania in the 2016/17 cropping season. The experiment was laid out in a 6x4 alpha lattice design replicated twice. Additive main effect and multiplicative interaction (AMMI) model was used in analysis. The study result revealed that, Tumbi (E1) was the most discriminating environment followed by Ilindi (E3), Mlali (E2), Hombolo (E4), Njoro (E5) and Ikhanoda (E6) respectively. The Hombolo (E4), Njoro (E5) and Ikhanoda (E6) environments showed a high correlation, therefore, indirect selection can be applied across the environments. The existence of such unique correlation among test environments has the advantage of reducing the number of sites used for evaluation and thus reducing cost of evaluating the genotypes. Using the first and second interaction principal component axis (IPCA1 and IPCA 2) genotype G2, G5, G11, G7, G3 and G8 was identified as the best performing genotypes however, G7 had relative stability and adaptability across the testing environments. These crosses will be advanced through selfing and selection of CLD tolerant progenies that are yielding high. Key words: AMMI, Cercospora leaf spot disease, Environments, Groundnuts, IPCA1, IPCA2, Stability, Adaptability.
Breeding for high leaf yield and minerals content in Gynandropsis gynandra (L.) Briq.
(2022) Houdegbe, Aristide Carlos.; Sibiya, Julia.; Achigan-Dako, Enoch Gbenato.
Gynandropsis gynandra (Spider plant) is an African leafy vegetable rich in minerals, vitamins, and health-promoting compounds with great potential in addressing malnutrition. The species is used as food and medicine and provides substantial incomes for smallholder’s farmers with an increasing interest for its cultivation in Africa. Spider plant is also an important resource for pharmaceutical industries. However, its production is still hampered by low leaf yield, early flowering, pests and disease and poor seed germination, resulting from the lack of improved cultivars. Our study intended to develop high yielding and nutrient-dense cultivars for farmers through merging modern molecular and classical plant breeding tools to increase income generation and improve nutrition and health. Specifically, the study: i) assessed the phenotypic variability among advanced lines of spider plant using biomass and related traits; ii) profiled the leaf mineral content among advanced lines of G. gynandra; iii) determined the combining ability, gene action and heterosis of mineral content in spider plant; iv) identified the genetics of the inheritance of biomass and related traits in spider plant; and v) deciphered genomic regions associated with combining ability and heterosis of biomass and related traits in G. gynandra. The evaluation of 71 advanced lines of spider plant derived from accessions originating from Asia, East, Southern and West Africa using biomass and related traits revealed significant difference among lines and principal component analysis grouped them into three clusters: Asia (Cluster 1), West Africa (Cluster 2), and East/Southern Africa (Cluster 3). The West and East/Southern African groups were comparable in biomass productivity and superior to the Asian group. Specifically, the West African group had high dry matter content and flowered early while the East/Southern African group was characterized by broad leaves and late flowering. The maintenance of lines’ membership to their group of origin strengthens the hypothesis of geographical signature in cleome diversity as genetic driver of the observed variation. The leaf mineral profile of 70 advanced lines of spider plant derived from accessions originating from Asia, East, Southern and West Africa revealed significant variation among lines and zinc, calcium, phosphorus, copper, magnesium, and manganese as landmark elements in the genotypes. East and Southern African genotypes were clustered together in group 1 with higher phosphorus, copper and zinc contents than Asian and West African lines, which clustered in group 2 and were characterized by higher calcium, magnesium and manganese contents. An additional outstanding group 3 of six genotypes (three, two, and one from Asia, Southern Africa and Eastern Africa, respectively) was identified with high iron, zinc, magnesium, manganese and calcium contents and potential candidates for cultivar release. Significant differences (P < 0.001) were observed among and between experimental hybrids and parents for the levels of all mineral contents. Significant general and specific combining ability effects together with variance components analysis revealed that both additive and nonadditive gene action controlled mineral content with a predominance of nonadditive gene action. Mid- and best-parent heterosis ranged from -84.98 and 404.79% for minerals. Parents with good general combining ability were identified, as well as crosses with high specific combining ability and heterosis. There were significant and moderate to strong correlations between mean hybrid performance, specific combining ability effects and heterosis levels and low to moderate correlations between general combining ability and mean parents’ performance. Similar to leaf mineral content, significant differences (P < 0.001) were observed among and between hybrids and parents for fourteen agronomic traits. Hybrids outperformed their parents with more than 50% for total and edible fresh biomass, showing the existence of hybrid vigour. Mid- and best-parent heterosis varied between -51.89% and 192.10% with only positive heterosis effects for leaf area and total fresh biomass, characterized by an average mid-parent heterosis greater than 50%. Significant general and specific combining ability (GCA and SCA) effects together with variance component analysis revealed that both additive and nonadditive gene action, controlled biomass and related traits in the species with the predominance of additive gene action. Moderate to high broad- and narrow-sense heritability was observed for most agronomic traits, except for dry matter content. The environment significantly interacted with genotype, GCA and SCA. Parents with good GCA and crosses with high SCA and heterosis were identified. There were significant changes from parents to hybrids in the association of harvest index and time to 50% flowering with biomass per plant and leaf traits on the one hand and between harvest index and dry matter content on the other hand. A core set of 594 diversity array technology sequencing (DArt-seq) markers were identified and differentiated the 38 parental lines into three clusters linked with the provenance of the original accession. Using this set of markers, a genome-wide association analysis revealed two markers linked to heterosis level for flowering time, a single marker for edible biomass, one marker for total fresh biomass and one marker for the number of primary branches. Specifically, the marker MABiomLa1 was a pleiotropic marker and was associated with heterosis level for biomass and leaf area. In contrast, no consistent markers associated with combining ability were observed for general combining ability and might be due to the low number of parents and the density of markers used. The study thus revealed that reciprocal recurrent selection would be a sound breeding strategy for G. gynandra improvement with the development of hybrid cultivars to exploit heterosis. These findings showed that G. gynandra could be used as a model plant to study the genetic mechanism underlying heterosis in orphan leafy vegetables. The identified markers open room for implementing marker-assisted selection in the species for better exploitation of heterosis.
Breeding for resistance against angular leaf spot disease of common bean in the Southern Highlands of Tanzania.
(2016) Mongi, Rose John.; Tongoona, Pangirayi.; Shimelis, Hussein Ali.; Sibiya, Julia.
Abstract available in PDF file.
Breeding for resistance to rice yellow mottle virus and improved yield in rice (oryza sativa L.) in Tanzania.
(2020) Suvi, William Titus.; Shimelis, Hussein.; Laing, Mark Delmege.
Rice [Oryza sativa (L.), 2n = 2x = 24] is the second most important staple food crop after wheat (Triticum aestivum L.) serving more than half of the world’s population. In Tanzania, rice is the second most important cereal crop after maize (Zea mays L.). However, rice production and productivity in the country is hindered by several factors. One of the leading biotic constraints is the rice yellow mottle virus (RYMV) disease which is devastating the existing rice varieties, and causes severe yield losses of 20 to 100 % under field conditions. Both landraces and introduced varieties that are grown by farmers succumb to RYMV. Several control strategies have been recommended to reduce RYMV infection: however, the development and deployment of RYMV resistant varieties is the most effective, economical and environmentally friendly approach for subsistence farmers. Breeding for resistance to RYMV and improved yields are the main goals for rice breeders aiming to develop and release improved rice cultivars that meet the preferences of the farmers and their markets. Therefore, the objectives of this study were to: (i) assess farmers’ perceptions, production constraints and variety preferences of rice in Tanzania to guide breeding; (ii) determine variation among Tanzanian rice germplasm collections based on agronomic traits and resistance to RYMV to select unique parents for breeding; (iii) assess the genetic diversity and population structure of rice genotypes using simple sequence repeat (SSR) markers to complement phenotypic profile and select parents; and (iv) determine the combining ability and gene action for resistance to RYMV disease and for key agronomic traits in rice, and thereby to develop new populations of parental germplasm for future breeding. A participatory rural appraisal study was conducted involving 180 participants, using a structured questionnaire and focused group discussions with 90 farmers in the Mvomero, Kilombero and Kyela districts of Tanzania. The results indicated that rice was the most important food and cash crop, followed by maize, cassava (Mannihot esculenta Crantz), sweetpotato (Ipomoea batatas [L..] Lam.), sugarcane (Saccharum officinarum L.), pigeonpea (Cajanus cajan L.), cowpea (Vigna unguiculata [L.] Walp.), sesame (Sesamum indicum L.), common bean (Phaseolus vulgaris L.), cocoa (Theobroma cacao L.), banana (Musa acuminate L.), groundnut (Arachis hypogaea L.), and oil palm (Elaeis guineensis Jacq.). The majority of the respondents (67.2%) used farm saved seed from the previous rice harvest. The major constraints limiting rice production and productivity in all studied areas were diseases, insect pests, frequent droughts, the non-availability and high cost of fertilizers, a limited number of improved cultivars, poor soil fertility and bird damage. The farmers preferred rice varieties with high yield, disease resistance, drought tolerance, high market value, early maturity, attractive aroma, and local adaptation. A systematic rice-breeding program aimed at improving RYMV resistance and incorporating farmers’ preferred traits should be designed and implemented as a means to increase the productivity and adoption of new cultivars by the farmers across the rice-growing areas of Tanzania. Fifty-four rice genotypes were field evaluated at two important rice production sites (Ifakara and Mkindo), which are recognized as RYMV hotspots in Tanzania, using a 6 × 9 alpha lattice design with two replications. There were significant (p<0.05) genotypic variations for agronomic traits and RYMV susceptibility in the tested germplasm. Seven genotypes with moderate to high RYMV resistance identified, namely Salama M-57, SSD1, IRAT 256, Salama M-55, Mwangaza, Lunyuki, and Salama M-19 were identified as new sources of resistance genes. Positive and significant correlations were detected between grain yield and number of panicles per plant (NPP), panicle length (PL), number of grains per panicle (NGP), percentage-filled grains (PFG), and thousand-grain weight (TGW), which are useful traits for simultaneous selection for rice yield improvement. A principal component analysis resulted in five principal components accounting for 79.88% of the total variation present in the assessed germplasm collection. Traits that contributed most to the total genotypic variability included NPP, number of tillers per plant (NT), PL, grain yield (GY), and days to 50% flowering (DFL). Genotypes, Rangimbili, Gigante, and SARO have complementary agronomic traits and RYMV resistance, and can be recommended for further evaluation, genetic analysis and breeding. The genetic relationship and divergence of the 54 rice selected genotypes mentioned above were examined using 14 polymorphic simple sequence repeats (SSR) markers to select unique parents for breeding. Data analysis was based on marker and population genetic parameters. The mean polymorphic information content (PIC) was 0.61, suggesting a high level of polymorphism for the selected SSR markers among the rice accessions. The population structure revealed a narrow genetic base, with only two major sub-populations. Analysis of molecular variance revealed that only 30% of the variation was attributed to population differences, while 47% and 23% were due to variation among individuals within populations and within individual variation, respectively. The genetic distance and identity among genotypes varied from 0.083 to 1.834 and 0.159 to 0.921, respectively. A dendrogram grouped the genotypes into three clusters with wide variation. The selected genetic resources, namely IR56, Mwanza, Salama M-55, Sindano nyeupe, SARO, Gigante, Lunyuki, Rangimbili, IRAT 256, Zambia and Salama M-19, will be useful resources for rice breeding in Tanzania and other African countries because they are genetically diverse. The final study involved combining ability analysis of the above selected genotypes and derived families to assess gene action conditioning RYMV resistance and agronomic traits. Ten parental lines and their 45 F2 progenies were field evaluated at three selected locations using a 5 × 11 alpha lattice design with two replications. The genotype × site interaction effects were significant (p<0.05) for the NT, NPP, NGP, percentage of filled grains (PFG), TGW, rice yellow mottle virus disease (RYMVD) resistance and GY. The variance due to the general combining ability (GCA) and the specific combining ability (SCA) effects were both significant for all assessed traits, indicating that both additive and non-additive gene actions were involved in governing trait inheritance. The high GCA to SCA ratios calculated for all the studied traits indicate that additive genetic effect was predominant. Parental lines, Mwangaza, Lunyuki, Salama M-57, Salama M-19, IRAT 256 and Salama M-55, which had negative GCA effects for RYMVD, and families such as SARO × Salama M-55, IRAT 245 × Rangimbili, Rangimbili × Gigante and Rangimbili × Mwangaza, which had negative SCA effects for RYMVD were selected for RYMV resistance breeding. The crosses such as Rangimbili × Gigante, Gigante × Salama M-19 and Rangimbili × Salama M-55 were selected due to their desirable SCA effects for GY. The predominance of additive gene effects for agronomic traits and RYMVD resistance in the present breeding populations suggest that rice improvement could be achieved through gene introgression using a recurrent selection method. Overall, the present study resulted in selection of agronomically superior and RYMV resistant breeding parents and new rice families for further evaluation and variety release in Tanzania.
Breeding gains diversity analysis and inheritance studies on soybean (Glycine max (L.) Merrill) germplasm in Zimbabwe.
(2013) Mushoriwa, Hapson.; Derera, John.; Tongoona, Pangirayi.
The soybean programme in Zimbabwe is over seventy years old. However, there is lack of information on breeding gains, genetic diversity, heritability, genetic advance, combining ability, gene action and relationships between grain yield and secondary traits available for breeding. Therefore, the aim of the present study was to characterise the genetic diversity of the available germplasm, determine gene action conditioning grain yield and estimate the breeding gains that have been realised since the inception of the breeding programme. Evaluation of 42 soybean genotypes for genetic diversity conducted during 2010/11 and 2011/12 cropping seasons, using phenotypic and molecular characterisation approaches, revealed evidence of wide diversity among the genotypes. The phenotypic traits and SSR markers assigned the soybean genotypes to 8 and 15 clusters respectively. The SSR marker technique was more polymorphic, informative and highly discriminatory. The clustering pattern and relatedness from SSR data was in agreement with the pedigree data while the phenotypic clustering was divorced from pedigree data. Genotypes, G41 and G7; G41 and G1; G41 and G42 were the most divergent; therefore, they could be utilized as source germplasm in cultivar development and commercial cultivars. Investigations on breeding gains involving 42 cultivars (representing a collection of all the varieties that were released in Zimbabwe from 1940 to 2013) showed that improvement in grain yield was slowing down. However, annual genetic gain was estimated to be 47 kg ha-1 year-1 representing an annual gain of 1.67%. Furthermore, grain yield ranged from 2785 to 5020 kg ha-1. Genotypes, G16, G15, G17, G1 and G42 exhibited superior performance in grain yield and other agronomic traits and are therefore, recommended for utilisation in the hybridisation programme. Seed protein concentration decreased by 0.02 year-1 while oil increased by 0.02, 100 seed weight increased by 0.21 g year-1 over time. In addition, number of days to 95% pod maturity and pod shattering increased by 0.35 and 0.38 days year-1 respectively while lodging declined by 0.31%. Results indicated that emphasis should be refocused on grain yield to restore the original linear increase. Assessment of the magnitude of GEI and stability of 42 released cultivars was done over 13 environments and two seasons using additive main effects and multiplicative interaction, cultivar superiority and rank analyses. Results showed that environment and GEI captured larger portion of the total sum of squares, which reveals the influence of the two factors on grain yield, hence, the need for evaluating soybean genotypes in multi-environment trials and over years. Further, the data revealed that GEI was of a crossover type because of differential yield ranking of genotypes. The three stability parameters selected two genotypes, G1 and G15, as the most productive, consistent and stable, thus they could be produced in diverse environments while G2, G4, G5, G7, G16, G40, G17, G18 and G31 were identified as unstable and suitable for specific adaptation. Correlation and path analyses showed that grain yield was positively and significantly correlated with number of branches per plant, number of nodes per plant, shelling percentage, and number of days from 95% pod maturity to first pod shattering, implying that breeding and selection for these traits probably improved grain yield. Number of nodes per plant, plant height and 100 seed weight exhibited highest direct effects on grain yield while, number of nodes per plant and plant height presented the highest indirect effects on grain yield. These results demonstrated that number of nodes per plant and plant height could be recommended as reliable selection traits for developing high yielding genotypes of soybean.

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