Browsing by Author "Shanahan, Paul Edward."

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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 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 of sweet potato (Ipomoea batatas (L.) Lam.) for storage root yield and resistance to Alternaria leaf petiole and stem blight (Alternaria spp.) in Uganda.
(2013) Sseruwu, Godfrey.; Shanahan, Paul Edward.; Melis, Robertus Johannes Maria.
Alternaria leaf petiole and stem blight is an important disease of sweetpotato (Ipomoea batatas (L.) Lam.) causing yield losses in both landraces and improved cultivars. The most important species causing economic yield loss in Uganda are Alternaria bataticola and A. alternate with A. bataticola the most aggressive and widely distributed. The study was conducted to: i) establish farmer-preferred sweet potato attributes, production constraints and Alternaria leaf petiole and stem blight awareness; ii) evaluate Ugandan sweet potato germplasm for Alternaria leaf petiole and stem blight resistance; iii) determine the mode of inheritance of resistance to Alternaria leaf petiole and stem blight and storage root yield components of sweet potato through estimation of the general combining ability (GCA) of the parents and the specific combining ability (SCA) of the parents for each cross; and iv) determine the adaptability and farmer acceptability of selected F1 genotypes across environments. The participatory rural appraisal was conducted to establish farmer preferences and production constraints revealed that farmer preferred sweet-potato traits were high yield, sweetness (taste), early maturity, high dry mass, resistance to pests and diseases, and in-field root storability after maturity. A majority of the farmers considered Alternaria leaf petiole and stem blight a serious production constraint causing yield loss of over 50%. The main control measures against the disease were roguing of infected plants, spraying with fungicides, use of healthy planting materials and planting resistant genotypes. Thirty sweet potato land races and improved cultivars were evaluated for Alternaria blight severity; yield, dry mass, harvest index, sweetpotato weevil (Cylas spp.) damage and sweetpotato virus disease at two sites (Namulonge and Kachwekano) over three seasons (2010B, 2011A, 2011B) under Alternaria inoculum and fungicide spray treatments. Landrace Shock was more resistant to Alternaria blight than Tanzania, the resistant check. Genotypes NASPOT 1, NASPOT 7, New Kawogo and Dimbuka were the most susceptible. Thirty two F1 families were generated from 16 parents in two sets in a North Carolina II mating scheme. The families were evaluated at two sites using a 5 x 7 row-column design with two replications. There were significant (P<0.05) differences among the families in Alternaria blight severity. Both GCA and SCA mean squares (MS) for Alternaria blight were highly significant (P<0.001) but the predominance of GCA sum of squares (SS) for Alternaria blight at 67.4% of the treatment SS versus 32.6% for SCA SS indicated that additive effects were more important than the non-additive effects in controlling this trait. For the yield components, the GCA MS were significant (P<0.05) and accounted for more than 60% of the treatment SS except for percentage dry mass composition where SCA SS accounted for 53.0% of the treatment SS implying that non-additive genetic effects were slightly more important than additive for this trait. Some parents that had desirable high, negative GCA effects for Alternaria blight produced families with undesirable positive SCA effects and the reverse was also true. This implied that the best parents should not be chosen based on GCA effects alone but also on SCA effects of their best crosses. The promising F1 genotypes selected from previously evaluated crosses together with one Alternaria blight resistant check (Tanzania) and one susceptible check (NASPOT 1) were evaluated at three sites (Namulonge, Kachwekano and Serere) using a randomised complete block design with three replications. Scientists and farmers evaluated the agronomic performance and also quality traits of the genotypes before and at harvest. Genotypes G14, G16, G24, G29, G49, G59 and G69 were the most stable across the sites for low Alternaria blight severity and can, therefore, be recommended for further evaluation under both low and high disease pressure areas. Genotypes G67, G13, G14, G24, G29 and G53 were the most high yielding and stable across the sites and were therefore the most widely adapted. In the participatory selection, before harvest and at harvest, Spearman’s rank correlation of the scientists and farmers’ mean ranking of the genotypes at each site was positive and significant. This indicated that the scientists in the study were capable of selecting for farmer preferred traits.
Breeding, evaluation and selection of Cassava for high starch content and yield in Tanzania.
(2009) Mtunda, Kiddo J.; Shanahan, Paul Edward.; Melis, Robertus Johannes Maria.
High starch content is an important component of root quantity and quality for almost all uses of cassava (flour, chips, and industrial raw material). However, there is scanty information on genetic variability for dry matter and starch contents and relatively little attention has been paid to genetic improvement of root dry matter content and starch content in Tanzania. The major objective of this research was to develop improved cassava varieties that are high yielding, with high dry matter and starch content for Tanzania and specifically to: i) identify farmers’ preferences and selection criteria for cassava storage root quality characteristics and other traits of agronomic relevance for research intervention through a participatory rural appraisal; ii) determine the genotypic variability for starch quantity and dry matter content evaluated for three harvesting times in four sites; iii) determine the inheritance of dry matter and starch content in cassava genotypes; and iv) develop and evaluate clones for high storage root yield, high dry matter content and starch. Attributes desired by farmers were yield, earliness, tolerance to pests and diseases. The complementing attributes associated with culinary qualities were sweetness, good cookability, high dry matter content or mealyness and marketability. The preliminary study conducted to evaluate the variability in root dry matter content (RDMC) and starch quantity and yield of ten cassava cultivars indicated that RDMC ranged from 29 to 40% with the mean of 34.3%. The RDMC at 7 months after planting (MAP) was higher than at 11 and 14 MAP. Starch content (StC) ranged from 20.3% to 24.9% with the mean of 22.8%. The StC differed significantly between cultivars, harvesting time and sites. An increase in StC was observed between 0 and 7 MAP, followed by a decline between 7 and 11 MAP, and finally an increase again noted between 11 and 14 MAP. However, for most of the cultivars at Kibaha an increase in StC between 11 and 14 MAP could not surpass values recorded at 7 MAP. At Kizimbani, cultivar Kalolo and Vumbi could not increase in StC after 11 MAP. At Chambezi and Hombolo, a dramatic gain in StC was observed for most of the cultivars between 11 and 14 MAP. Starch yield ranged from 0.54 to 4.09 t ha-1. Both StC and fresh storage root yield are important traits when selecting for commercial cultivars for starch production. Generation of the F1 population was done using a 10 x 10 half diallel design, followed by evaluation of genotypes using a 4 x 10 á-lattice. Results from the diallel analysis indicated that significant differences in fresh storage root yield (FSRY), fresh biomass (FBM), storage root number (SRN), RDMC, starch content (StC), and starch yield (StY), and cassava brown streak disease root necrosis (CBSRN) were observed between families and progeny. The FSRY for the families ranged from 15.0 to 36.3 t ha-1; StC ranged from 23.0 to 29.9%; RDMC ranged from 31.4 to 40.1%; and StY ranged from 3.3 to 8.3 t ha-1. The cassava mosaic disease (CMD) severity ranged from 1.7 to 2.7, while cassava brown streak disease (CBSD) severity for above ground symptoms ranged from 1.0 to 1.9. Additive genetic effects were predominant over non-additive genetic effects for RDMC, StC, and CBSRN, while for FSRY, FBM, SRN, and StY non-additive genetic effects predominated. Negative and non-significant correlation between RDMC and FSRY was observed at the seedling stage (r=-0.018), while at clonal stage the correlation was positive but not significant (0.01). The RDMC and StC were positive and significantly correlated (r=0.55***) at clonal stage. However, the StC negatively and non-significantly correlated with FSRY (r=- 0.01). High, positive and significant correlation (r=0.94; p.0.001) was observed between the StY and FSRY at clonal stage. High, positive and significant correlations between the seedling and clonal stage in FSRM (r=0.50; p.0.01), RDMC (r=0.67; p.0.001), HI (r=0.69; p.0.001), and SRN (r=0.52; p.0.01) were observed, suggesting that indirect selection could start at seedling stage for FSRM, RDMC, HI, and SRN. The best overall genotype for StC was 6256 (40.9%) from family Kiroba x Namikonga followed by genotype 6731 (40.6%; Vumbi x Namikonga). Among the parents, Kiroba and Namikonga were identified as the best combiners in terms of GCA effects for StC. Genotype 6879 from family Vumbi x AR 42-3 had the highest StY value of 34.8 t ha-1 followed by genotype 6086 (30.4 t ha-1; Kalolo x AR 40-6). Among the parents, Kalolo and AR 42-3 were identified as good combiners for the trait. Mid-parent heterosis for StC ranged from 41.6 to 134.1%, while best parent heterosis ranged from 30.4 to 119.6%. Genotype KBH/08/6807 from family Vumbi x TMS 30001 had the highest mid-and best parent heterosis percentage for StC. For StY, mid-parent and best parent heterosis ranged from 168.0 to 1391.0%, and from 140.4 to 1079.0%, respectively, with the genotype 6879 (Vumbi x AR 42-3) exhibiting the highest mid- and best parent heterosis percentage for StY. Improvement for StC, RDMC, and CBSRN may be realized by selecting parents with the highest GCA effects for the traits and hybridize with those that combine well to maximize the positive SCA effects for the StC, RDMC and CBSRN. Selected genotypes from the clonal stage will be evaluated in preliminary yield trial and advanced further to multi-locational trials while implementing participatory approaches involving farmers and processors in selection. New promising lines should be tested at different sites and the best harvesting dates should be established.
Cassava breeding through complementary conventional and participatory approaches in western Kenya.
(2011) Were, Woyengo Vincent.; Melis, Robertus Johannes Maria.; Shanahan, Paul Edward.
Participation of farmers in plant breeding programmes has been reported to increase breeding efficiency. Farmers’ participation bridges the gap between variety development and dissemination and provides an opportunity for farmers to select varieties they prefer. The breeders on the others hand learn more about the farmers’ preferences and the environment in which the new varieties will be grown. However, the advantages of participatory breeding can best be realized when farmers’ indigenous technical knowledge (ITK) and experience complement the breeder’s scientific knowledge and skills. Cassava (Manihot esculenta Crantz) is a clonally propagated crop grown in diverse environments by small scale farmers for subsistence. Information on the roles of farmers and breeders at various stages of breeding and their ability to effectively participate in breeding programmes is limited. The objectives of this study were to determine: (1) cassava farmers’ preferences, production constraints and systems; (2) farmers’ selection criteria of cassava varieties; (3) genetic inheritance of farmer preferred traits; (4) how farmers and breeders complement each other at all stages and activities of cassava breeding. Participatory rural appraisal was conducted in three purposefully sampled districts of western Kenya based on ethnicity and agro-ecology. The results reveal that cassava is predominantly grown by small scale farmers with mean land size of 1.6 ha mainly under mixed cropping system for subsistence. The storage roots are eaten either after boiling or processing to flour. The majority of farmers (over 60%) are aware of the improved varieties but adoption rate is low (18% in some districts). The effects of pests and diseases, and the lack of high yielding varieties, capital, land, and disease free planting material are the most important constraints to cassava production. Farmers prefer tall, high yielding varieties that are resistant to diseases and pests, early maturing and long underground storability of harvestable storage roots. The districts surveyed significantly differed in popularity of utilization methods, traits preferences and relative ranking of the production constraints indicative of differences in ethnicity and agro-ecology. Three farmer groups from the three districts selected in western Kenya were used to study farmers’ variety selection criteria based on their own indigenous technical knowledge (ITK). The groups evaluated 15 (10 landraces and five improved) popular cassava varieties with concealed identities on their farms. The results revealed that farmers have effective methods of selecting varieties for most of their preferred traits. However, ITK alone cannot be used to evaluate all the important traits, such as cyanide content. The genetic inheritance of farmer preferred traits was determined through a genetic study. Six landraces and four improved varieties popular in western Kenya were crossed using the North Carolina mating design II to generate 24 full-sib families. The 24 families, represented by 40 siblings each, were evaluated at two sites, Kakamega and Alupe research station farms, in a 24 x 40 a-lattice design. General combining ability (GCA) and specific combining ability (SCA) mean squares were significant (P<0.05) for all traits evaluated except dry matter content and cyanide content. However, non-additive gene action predominated over additive gene for cassava mosaic disease (CMD) resistance, height to first branching, total number of storage roots per plant and fresh storage root yield in all environments. The best crosses were not necessarily obtained from parents with high general combining ability confirming the presence of non-additive gene action. The best performing parents per se did not necessarily have high GCA effects implying that selection based on the per se performance of parents may not always lead to development of superior hybrids. The clonal evaluation trial (CET) was established at Alupe research station and evaluated by the breeder and farmers from two districts independently. Three selection criteria were tested to determine the most appropriate approach to selection of varieties that meet both farmers’ and breeder’s preferences. The selection criteria were; farmers’ independent selection index (SI) derived from farmers’ selection criteria from each district, breeder’s negative selection and independent SI, and a participatory SI which combines farmers’ and breeder’s selection criteria. There was 14% overlap among the top 100 varieties selected by farmers from all districts and the breeder when independent SI were used. However, there was 49% overlap among the top 100 varieties selected by farmers using participatory SI and the breeder’s SI. The farmers and the breeder have a role to play in the variety development process. Varieties with traits preferred by both the farmers and the breeder are likely to enhance breeding efficiency and effectiveness.
Characterisation of Taro (Colocasia Esculenta (L) Scott) germplasm collections in South Africa : towards breeding an orphan crop.
(2017) Jansen van Rensburg, Willem Sternberg.; Modi, Albert Thembinkosi.; Shanahan, Paul Edward.; Bairu, Michael Wolday.; Shimelis, Hussein Ali.
Amadumbe (Colocasia esculenta), better known as taro, is a traditional root crop widely cultivated in the coastal areas of South Africa. Taro is showing potential for commercialisation. However, very little is known about the genetic diversity, potential and its introduction and movement in South Africa. This study was undertaken to (1) determine the genetic diversity in the ARC taro germplasm collection using agromorphological characteristics and microsatellite markers, (2) to determine if it is possible to breed with local taro germplasm and (3) to determine the effect of four different environments (Roodeplaat, Umbumbulu, Owen Sithole College of Agriculture and Nelspruit) on ten agro-morphological characteristics of 29 taro landraces Taro germplasm was collected in South Africa in order to build up a representative collection. Germplasm was also imported from Nigeria and Vanuatu. The South African taro germplasm, and selected introduced germplasm, were characterised using agromorphological descriptors and simple sequence repeat (SSR) markers. Limited variation was observed between the South African accessions when agro-morphological descriptors were used. Non-significant variations were observed for eight of the 30 agromorphological characteristics. The 86 accessions were grouped into three clusters each containing 39, 20 and 27 accessions, respectively. The tested SSR primers revealed polymorphisms for the South African germplasm collections. Primer Uq 84 was highly polymorphic. The SSR markers grouped the accessions into five clusters with 33, 6, 5, 41 and 7 accessions in each of the clusters. All the dasheen type taro accessions were clustered together. When grown under uniform conditions, a higher level of genetic diversity in the South African germplasm was observed when molecular (SSR) analysis was performed than with morphological characterisation. No correlation was detected between the different clusters and geographic distribution, since accessions from the same locality did not always cluster together. Conversely, accessions collected at different sites were grouped together. There was also no clear correlation between the clustering pattern based on agro-morphology and SSRs. Thus, in order to obtain a more complete characterisation, both molecular and morphological data should be used. Although the results indicated that there is more diversity present in the local germplasm than expected, the genetic base is still rather narrow, as reported in other African countries. Fourteen distinct taro genotypes were planted as breeding parents and grown in a glasshouse. Flowering were induced with gibberellic acid (GA3). Crosses were performed in various combinations; however, no offspring were obtained. This might be due to the triploid nature of the South African germplasm. It might be useful to pollinate diploid female parents with triploid male parents or use advanced breeding techniques, like embryo rescue or polyploidization, to obtain offspring with the South African triploid germplasm as one parent. The triploid male parents might produce balanced gametes at low percentages, which can fertilize the diploid female parents. Twenty-nine taro accessions were planted at three localities, representing different agroecological zones. These localities were Umbumbulu (South of Durban - KZN), Owen Sithole College of Agricultural (OSCA, Empangeni, KZN) and ARC - Vegetable and Ornamental Plants (Roodeplaat, Pretoria). Different growth and yield related parameters were measured. The data were subjected to analysis of variance (ANOVA) and additive main effects and multiplicative interaction (AMMI) analyses. Significant GxE was observed between locality and specific lines for mean leaf length, leaf width, leaf number, plant height, number of suckers per plant, number of cormels harvested per plant, total weight of the cormels harvested per plant and corm length. No significant interaction between the genotype and the environment was observed for the canopy diameter and corm breadth. From the AMMI model, it is clear that all the interactions are significant for leaf length, leaf width, number of leaves on a single plant, plant height, number of suckers, number of cormels harvested from a single plant and weight of cormels harvested from a single plant. The AMMI model indicated that the main effects were significant but not the interactions for canopy diameter. The AMMI model for the length and width of the corms showed that the effect of environment was highly significant. There is a strong positive correlation between the number of suckers and the number of leaves (0.908), number of cormels (0.809) and canopy diameter (0.863) as well as between the number of leaves and the canopy diameter (0.939) and between leaf width and plant height (0.816). There is not a single genotype that can be identified as “the best” genotype. This is due to the interaction between the environments and the genotypes. Amzam174 and Thandizwe43 seem to be genotypes that are often regarded as being in the top four. For the farmer, the total weight of the cormels harvested from a plant will be the most important. Thandizwe43, Mabhida and Amzam174 seem to be some of the better genotypes for the total weight and number of cormels harvested from a single plant and can be promoted under South African taro producers. The local accessions also perform better than introduced accessions. It is clear that some of the introduced accessions do have the potential to be commercialised in South Africa. The study indicate that there are genetic diversity that can be tapped into for breeding of taro in South Africa. However, hand pollination techniques should be optimized. Superior genotypes within each cluster in the dendrograms as well as Thandizwe43, Mabhida and Amzam174 (identified by the AMMI analysis as high yielding) can be identified and used as parents in a clonal selection and breeding programme. Additionally, more diploid germplasm can be imported to widen the genetic base. The choice of germplasm must be done with caution to obtain germplasm adapted to South African climate and for acceptable for the South African consumers.
Development of cassava (Manihot esculenta Crantz) cultivars for resistance to cassava mosaic disease in Zambia.
(2011) Chikoti, Patrick Chiza.; Melis, Robertus Johannes Maria.; Shanahan, Paul Edward.; Chisi, M.
Despite the increasing number of farmers growing cassava in Zambia, yield per hectare has remained low at 5.8 t ha-1. The major constraints contributing to low yields are pests and diseases of which cassava mosaic disease (CMD) caused by East Africa cassava mosaic virus (EACMV), Africa cassava mosaic virus (ACMV) and South Africa mosaic virus (SACMV) is the most important. Breeding of cassava is restricted by limited information on viruses and associated satellites, and farmer preferences. Most of the farmers cannot manage to institute control strategies that require buying of chemicals. The most feasible option remains improving existing cultivars through resistance breeding. The study therefore was conducted to: i) establish farmers’ perception and knowledge of CMD; ii) to identify viruses of cassava occurring in Luapula province; iii) evaluate the performance of local and improved cultivars for agronomic traits; iv) evaluate the performance of F1 progenies for CMD resistance; and v) determine general combining ability and specific combining ability for CMD resistance. The studies were carried out between 2008 and 2011 at different locations in Zambia. The information generated was important in formulating a local breeding strategy for CMD resistance. A participatory rural appraisal and a structured survey was conducted in Mansa, Samfya and Mwense districts in Luapula province involving farmers to ascertain farmers’ perceptions of CMD. The results of the study showed that the majority of the respondents (97.6%) were not aware of CMD. Most of the farmers grew landraces on small pieces of land. Although, the cultivars (local and improved) were widely grown, they were susceptible to CMD. The farmers preferred cultivars with high yielding and early bulking characteristics among others. A CMD survey conducted between April and May 2009 in Samfya, Mansa, Mwense, Kawambwa and Nchelenge districts in Luapula province established East Africa cassava mosaic virus (EACMV), and Africa cassava mosaic virus (ACMV) as the most prominent viruses in the area. Symptoms of satellites were also observed in the farmers’ fields in most of the areas visited. Satellite II and III were detected in leaf samples. The CMD incidence (59.1%) and severity (2.4) was moderate across the districts surveyed. The CMD symptoms on the cassava plants were variable with plants showing mild and severe symptoms characterised with narrowing and reduced leaf blades. The transmission of CMD infections was mainly through cuttings rather than via whitefly infection which means that most of the planting materials used by the farmers were infected. Evaluation of cassava cultivars for CMD resistance was conducted in 2009/2010 and 2010/11 seasons at Mansa Research Station in Luapula province using a 4 x 4 α lattice design. Both introduced and locally grown cultivars had significant (P<0.001) differences in their reaction to CMD. Bangweulu, Namuyongo, Kalaba, Chikula, Mwakamoya, Chila7 and Chila11 were the most susceptible genotypes. Mweru, Tanganyika, and Nalumino were moderately tolerant to CMD. Eight hundred F1 genotypes developed using a North Carolina II mating design were evaluated in a 4 x 5 α lattice design in 2011 at Mansa Research Station, Luapula province to determine combining ability for reaction to CMD, yield and yield components. The plants were harvested 7 months after planting (MAP). Significant (P<0.001) general combining ability and specific general combining ability were recorded for CMD. The SCA effects were more important for CMD than GCA effects suggesting that non-additive gene action was more prominent than the additive gene action in determining CMD reaction. Parent lines with desired significant, negative GCA effects for reaction to CMD were Bangweulu, Kampolombo, Nalumino and TME2. In general, the survey and participatory rural appraisal established CMD as one of the constraints to cassava production and created a basis for the research study. The findings indicate opportunities that exist in creating genotypes with tolerance to CMD. The study identified cassava lines with resistance to CMD. The lines that expressed the above trait should be selected and tested further for release to the farmers in Zambia. Since the clonal evaluation trial was harvested at 7 MAP, there is need to investigate further for earliness trait in best performing lines in different locations.
Direct transformation of maize (Zea mays L.) tissue using electroporation and particle bombardment, and regeneration of plantlets.
(1996) Jenkins, Megan Joy.; Shanahan, Paul Edward.
Please open electronic version for Abstract.
Fluctuation of non-structural carbohydrates in the stem and ears of maize (Zea mays (L.)) during grain fill as influenced by water stress.
(1991) Shanahan, Paul Edward.; Greenfield, Peter L.
Stems of maize plants may serve as reservoirs for photosynthate produced in the leaves which may then be utilized for cell growth and maintenance requirements of the plants, and in particular for grain requirements during grain fill. Experiments were designed to ascertain the extent to which non-structural carbohydrates accumulate and are depleted in the stem and ears of locally cultivated maize hybrids during grain fill under conditions of water stress. Maize plants were grown: (i) under field conditions; (ii) under a rain-out shelter; and (iii) in pots placed inside a growth tunnel during grain fill. In the latter experiment whole maize plants were exposed to (14)C0(2) at selected intervals during grain fill. In the field trial large differences in the accumulation and depletion of total non-structural carbohydrates (TNC) were found between the six hybrids tested. The water stress conditions that prevailed from mid-grain fill (MGF) to physiological maturity (PM) resulted in TNC content levels being lower at PM than at anthesis in all hybrids except for SR 52. Total non-structural carbohydrate content in the whole stem of PNR 6427, CG 4602 and PNR 473 declined from anthesis to PM. In contrast TNC content in the whole stem of SA 60 and HL 1 declined from anthesis to MGF and then increased substantially in SA 60 and marginally in HL 1 from MGF to PM. In the rain-out shelter trial, water stress resulted in a 38 % reduction in final grain yield in SA 6 compared to 25 % in K78Y x I137TN. The greater tolerance to water stress of the more modern hybrid K78Y x I137TN compared to the obsolete hybrid SA 6 may be attributed to a number of factors, namely: (i) K78Y x I137TN recorded a higher leaf area index throughout grain fill under stress and non-stress conditions compared to SA 6; (ii) it did not partition as much non-structural carbohydrate to the stem during the first three weeks of grain fill as did SA 6 and did not markedly deplete stem non-structural carbohydrate pools to the same extent as did SA 6 under stress and non-stress conditions; and (iii) in the last week of grain fill as the leaf water potential of K78Y x I137TN increased sharply under stress conditions, it exhibited an ability to deplete stem non-structural carbohydrates to supplement the supply of current photosynthate to the grain. In the 14(C)-labelling pot trial, the maize single cross hybrid B254W X M162W generally depleted TNC in vegetative organs in the latter half of grain fill under stress conditions, while under non-stress conditions TNC continued to accumulate in vegetative organs until PM. Both stressed and non-stressed plants assimilated less 14(C) on consecutive labelling occasions during grain fill. The amount of 14(C) assimilated at six weeks after anthesis was only 12,1 and 16,3 % of that assimilated at anthesis in stressed and non-stressed plants, respectively. Stressed and non-stressed plants labelled at anthesis translocated a smaller proportion of assimilated 14(C) to the grain during grain fill than plants labelled later. Consequently, stressed and non-stressed plants labelled at anthesis recorded the highest proportion of whole plant 14(C) recovered in the whole shoot at PM compared to plants labelled on any of the other occasions. At anthesis the primary ear was not yet established as the major sink for photosynthate and much of the 14(C) assimilated at anthesis was utilized for final structural growth of the whole shoot including the cob and husks of the primary ear. Stressed and non-stressed plants assimilated similar amounts of 14(C) at anthesis and two weeks after anthesis, however, stressed plants assimilated less 14(C) than non-stressed plants at four and six weeks after anthesis. Forty-eight hours after each labelling occasion, the stressed plants had partitioned a higher proportion of assimilated 14(C) to the grain than the non-stressed plants. However, by PM the non-stressed plants had partitioned an equal or greater proportion of whole plant 14(C) recovered at PM to the grain compared to the stressed plants. Radioactivity associated with component non-structural carbohydrates, was determined using ion-exchange column chromatography and thin-layer chromatography. These procedures provided detailed data of the partitioning of 14(C) among glucose, fructose, sucrose and starch.
Genetic gain, advanced cycle pedigree breeding and correlated response to selection under varying moisture conditions in sunflower.
(2013) Chigeza, Godfree.; Shanahan, Paul Edward.
Sunflower (Helianthus annuus L.) is one of the most important oil crops in South Africa and genetic improvement for grain yield and oil-content was initiated in the country in the early 1970s. Commercial production of sunflower in South Africa is done under natural rainfall conditions in areas where frequencies of drought are high hence the requirement for drought tolerant cultivars. An assessment of the genetic gains in seed and oil yield achieved since 1970, the effects of re-cycling inbred lines and strategies for developing drought tolerant sunflower cultivars has not been done for South African sunflower breeding programmes. Two data-sets were used for the genetic gain studies: side-by-side evaluation of historical and current sets of popular cultivars in the same environment under one set of trial management practices; and yield trends in commercial farmers’ fields based on annual production estimates. The estimated relative genetic gain for seed yield based on side-by-side trials was 1.5% year−1 and the relative gain in seed yield per year under commercial production was 1.9% year−1. The contribution of new cultivars to total seed yield progress in sunflower were 56.3% for the period 1970 to 1989; 23.9% from 1990 to 2009 and the mean over the four decades under consideration from 1970 to 2009 was 41.6%. Quantifying the usefulness of inbred lines in advanced cycle plant breeding was done using four base breeding populations based on: phenotypic or genetic variability; heterosis; and combining ability. Significant genetic variation was evident for seed yield and oil yield while genetic variability for oil content was low. Genetic advance (GA%), with a 10% selection intensity, was high for seed yield and oil yield for each of the four populations ranging from 36-42% and 38-43%, respectively. The GA% for oil content was low ranging from 1.3% to 5.1% indicating the need to introgress high oil content germplasm in the present breeding populations in advanced cycle pedigree breeding. Founder parent heterosis (FPH), mid-standard heterosis (MSH) and high standard heterosis (HSH) indicated that some new testcross hybrids from the advanced cycle pedigree breeding populations were performing better than their founder parents in hybrid combination as well as the standard commercial hybrid checks. From variance component analysis, general combining ability (GCA) was predominant over specific combining ability (SCA) for seed and oil yields indicating that superior hybrids can be identified based on positive and significant GCA effects of the female lines. For oil content, SCA was predominant over GCA indicating that it would be best to select for specific hybrids combinations with high oil content rather than selecting female lines with high GCA effects. Variable moisture conditions characterise the sunflower production environments in South Africa. Breeding for such environmental conditions requires a combination of strategies including use of secondary traits and developing appropriate test environments. Three secondary traits, head diameter, stem diameter and stay green canopy which are easy to measure in the field were evaluated for their appropriateness for selecting for drought tolerance under three moisture conditions: random stress environments (RSE), managed drought stress environments (MSE) and well watered nonstress environments (NSE). Type A genetic correlations indicated that stay green canopy (SG) had the potential to be used as secondary trait to indirectly improve oil yield under the three moisture conditions. The indirect selection efficiency (ISE) for SG using genetic correlations based on H2 were 0.79, 0.82 and 0.78 in the RSE, MSE and NSE, respectively, while that using genetic correlation based on h2 were 0.67, 0.98, and 0.93 in the RSE, MSE and NSE, respectively. In both cases selection in the MSE had the highest efficiency using genetic correlations based on either H2 or h2. Estimates of indirect selection based on type B genetic correlations indicated that indirect selection for oil yield (OY) in the MSE and NSE for the target RSE was as effective as direct selection of OY in the RSE based on additive genetic correlations of 0.96 obtained in both selection environments. Overall, the results from the exploratory drought tolerance study should inform the development of breeding strategies to improve drought tolerance and associated yield stability of sunflower cultivars grown in South Africa and associated environments.
An investigation into the heritability of commercially important traits in a sugarcane population under dryland conditions.
(1995) O'Reilly, Kerry.; Shanahan, Paul Edward.; Hohls, Trevor.
Inheritance studies have previously been undertaken at the South African Sugar Association Experiment Station (SASEX) under irrigated conditions. Since most sugarcane is grown in South Africa under dryland (raingrown) conditions, heritability estimates were calculated under these conditions in this study and compared to those previously obtained under irrigated conditions. A sugarcane population consisting of 12 crosses, 32 offspring in each cross, and their parents were planted in the first two selection stages of the SASEX selection programme to ascertain which stage provided the most useful information when selecting parent cultivars. Data collected from Stage 2 was more reliable than data collected from Stage 1. Variance components, narrow and broad sense heritabilities, correlations among traits, and clonal repeatabilities between seasons were determined for 11 sugarcane traits at Stages 1 and 2. These traits studied included: stalk population; stalk diameter; stalk height; cane mass; dry matter % cane; fibre % cane; brix % cane; brix % dry matter; purity; pol % cane; and ers % cane. Narrow sense heritabilities of the sugarcane traits were estimated by mid-parent offspring regression . Alternative heritability estimates were obtained through restricted maximum likelihood (REML) analysis of the unbalanced North Carolina design II at Stage 2. Although narrow sense heritabilities determined by mid-parent-offspring regression were comparable with those previously determined at SASEX and by other workers, REML was more efficient than regression. Use of REML enabled additive and non-additive genetic variance components to be estimated by allocating degrees of freedom to treatments and the interactions between the different treatments. Heritability estimates varied for different traits and compared favourably with those obtained under irrigated conditions and by other workers. Additive genetic variance was more important than non-additive genetic variance for some characters, but not for stalk population, cane mass, and dry matter % cane, for which both variances were important. Selection of parent cultivars for all sucrose-related traits, fibre % cane, and stalk diameter should be as successful under raingrown as under irrigated conditions, provided that the environmental variation is determined efficiently under raingrown conditions. Environmental correlations were observed between some traits, particularly between the yield related traits, and may have influenced heritability estimates for those traits determined by mid-parent offspring regression. Stalk diameter, fibre % cane, and brix % dry matter were the most repeatable traits between seasons. Cane mass was the least repeatable trait between Stages 1 and 2 but was highly repeatable between plant (-P) and ratoon (-R) crops of Stage 2. Stalk diameter was positively correlated with brix % dry matter (0.457-P and 0.623-R) and strongly negatively correlated with stalk population (-0.790-P and -0.711-R) and fibre % cane (-0.628-P and -0.651-R). Cane mass was strongly positively correlated with brix % dry matter (0.638-P and 0.679-R). By selecting for brix % dry matter and stalk diameter, indirect selection for cane mass would be possible. Brix % dry matter was determined as the most reliable trait on which to base parental and commercial cultivar selection because it was highly heritable, highly repeatable and highly positively correlated with stalk diameter and cane mass.
An investigative study of the drought tolerance of F1 maize (Zea mays L.) single crosses derived from PANNAR and CIMMYT inbred lines.
(2015) Muyambo, Caiphas.; Shanahan, Paul Edward.
Drought is the most devastating abiotic stress limiting the production of maize (Zea mays L.) worldwide. The effect of drought stress is greatest in sub-Saharan Africa (SSA) where most small scale farmers rely on open pollinated varieties (OPVs); rather than certified hybrid seed grown under dryland1 conditions. Small scale farmers perceive OPVs to be drought tolerant and yet the yields are as low as 1-2 t ha-1 . In many parts of SSA, therefore, hybrid adoption rate is still below 20%. With the projected population growth in SSA, food insecurity is likely to worsen. However, the development of drought tolerant maize hybrids to help address declining food security is a relevant strategy in SSA. This is so because, drought tolerant hybrids will out yield OPVs. The main objective of this study was to investigate the drought tolerance of F1 single cross maize hybrids developed from CIMMYT drought tolerant donor inbred lines and PANNAR elite inbred lines. The hybrids were tested under random and managed drought stress environments. The first set of F1 hybrids was produced using a 12x12 North Carolina factorial mating design during winter (April-August 2012) and the second set of hybrids was produced in summer (November 2012-March 2013). Seventy F1 hybrids were tested during the summer season (November 2012- April 2013) under random drought stress (RDS) environments in South Africa and Zimbabwe. One hundred hybrids were tested during the winter season (April – September 2013) in Zimbabwe at CIMMYT experimental stations in Save Valley and Chisumbanje under managed drought stress (MDS). The main traits measured included grain yield (GY), ear plant-1 (EPP), anthesis-silking interval (ASI) and days to anthesis (DTA). Statistical analysis of collected data was conducted using GenStat 16th edition. Significant differences between hybrids and environments for grain yield and secondary traits were obtained. The genotype x environment (GxE) interactions was significant under both RDS and MDS environments indicating the differential performance of hybrids across environments. Using stability indices, the relatively stable hybrids were identified. General and specific Combining ability (GCA and SCA) analysis revealed lines that could be used as potential parents in development of hybrids. However, the presence of GCAxE and SCAxE interactions indicated that selection of inbred lines and their hybrid crosses should be done at target environments. Under RDS and MDS, EH79 and EH24 appeared to be the best performing hybrids, respectively, whereas inbred lines DT2, DT7 and UT8 had the best GCA and SCA under both RDS and MDS. Further efforts are required to develop potential drought tolerant hybrids and test for adaption in target environments.
Manipulating morphological traits of cassava to enhance host plant resistance and biological control of cassava green mite in Zambia.
(2013) Chalwe, Able.; Melis, Robertus Johannes Maria.; Shanahan, Paul Edward.
Understanding direct and indirect defense mechanisms that enhance host plant resistance (HPR) and biological control is critical for successful development of an integrated pest management (IPM) approach. Cassava green mite (CGM) (Mononychellus tanajoa Bondar (Acari: Tetranychidae)) is a major arthropod pest of cassava (Manihot esculenta Crantz) in Africa. Strategies to control CGM include HPR and biological control by use of exotic natural enemies particularly the predatory mite Typhlodromalus aripo DeLeon (Acari: Phytoseiidae). The success of the latter depends on continuous survival of the natural enemy which requires suitable host plants and weather conditions. Various plant morphological traits have been recognized as indirect defense mechanisms that enhance HPR to CGM, and/or attract T. aripo in cassava. It was envisaged that integration of HPR and classical biological control approaches through manipulation of such indirect defense traits would lead to a more sustainable management of CGM in view of anticipated climate change. Lack of information on farmers’ perception of CGM and preferred varietal attributes, and gene action controlling the inheritance of CGM resistance also limits success of resistance breeding and adoption of varieties. This research was undertaken to gather information on farmers’ perceptions of cassava varietal attributes and cultural practices in relation to CGM resistance, identify suitable sources of resistance and environments for future breeding; and to determine the nature of gene action controlling CGM resistance and the inheritance of plant morphological traits that enhance the ability of cassava to host and support continuous survival of natural enemies. High fresh storage root yield (FSRY), high storage root dry mass percentage (SRDM%), earliness combined with extended underground storability, and resistance to foliar pests and diseases are the major factors that influence adoption and retention of genotypes by farmers. Moles, termites and CGM are the most widespread and most damaging pests. However, due to the non-conspicuous nature of CGM, its effects are under-estimated and are given limited attention by farmers. The majority of the farmers are familiar with CGM leaf damage symptoms but they cannot associate them with the actual pest. Participation of farmers in field training and field research activities helps them to know CGM. Crop rotation, intercropping, removal of shoot tips, selective pruning of infested shoots, and burning of cassava fields are some of the ways used by farmers to manage CGM. Farmers associate hairy broad-leaved, tall cassava genotypes and pink leaf pigmentation (anthocyanin) with low CGM damage. There is substantial genetic variability in the Zambian cassava germplasm for CGM resistance and associated plant morphological traits such as leaf pubescence (Pbs), leaf retention (LR), stay green (SG), tip size (TS), tip compactness, and plant height (PH), stem diameter (StD), SRDM% and FSRY. Genotypes with wide or specific adaptability for these traits have been identified, and should be recommended for general or localized production and for use as sources of desired genes in crop improvement. Genotypes L9.304/147, 92/000, TME2, 4(2)1425, I60/42 and L9.304/175 combine wide adaptability with high levels of resistance to CGM. Genotypes Kapeza, L9.304/147 and 4(2)1425 are able to produce 13-15 t ha ¯¹ at 9 months after planting suggesting their potential for early bulking. This study has shown that both additive and non-additive gene effects play a role in the expression of CGM resistance and associated plant morphological traits. The best combinations of parents for resistance against CGM were 4(2)1425 x L9.304/147 and Mweru x L9.304/147, while L9.304/147 x I92/000 displayed combined resistance to CGM and cassava mosaic disease (CMD). The resistance of cassava to CGM is positively correlated with Pbs, LR, and TS, SG, PH, StD. Overall, the study has shown that there is wide diversity in the expression of valuable indirect defense traits among genotypes, indicating that there is scope for integration of biological control and host plant resistance for CGM in Zambia. The release of genotypes that exhibit high level of intra-season and inter-season stability for enhanced expression of LR, SG, and Pbs will minimize the impact of CGM on FSRY and SRDM% that results from seasonal effects. Such genotypes should also provide habitat for and thus help to ensure the survival of T. aripo in cassava fields. The study has contributed to the promotion of food security through identification of early-bulking genotypes which also have good potential for extended underground storability of roots. Early-bulking, high FSRY and SRDM% and SRR resistance are farmer-preferred traits. Therefore, enhancement of such traits through plant breeding is likely to increase the adoption of new genotypes by farmers.
Morphological and cytological diversity of some yams (Dioscorea spp.) in Sierra Leone.
(2010) Norman, Prince Emmanuel.; Tongoona, Pangirayi.; Shanahan, Paul Edward.
Yam (Dioscorea spp.) is a major source of income and a food security crop for many households in Sierra Leone. Despite the economic importance of the yam crop its improvement has suffered from the lack of knowledge of existing germplasm and the genetic potential within the yam gene-pool. As a consequence, many species of yam are being lost to changing tastes, industrialization and urbanization. All these lead to habitat destruction. This study assessed the extent of diversity in some yam germplasm from Sierra Leone using morphological and cytological descriptors, and ascertained the interrelationship between these two data sets. To this end, 52 genotypes comprising of forty three D. alata, two D. bulbifera, and seven D. rotundata sampled from the Sierra Leone germplasm were grown in a three replicate, in a randomized complete block design (RCBD) during 2010 planting season at the University of KwaZulu-Natal, Pietermaritzburg, South Africa. Principal component analysis (PCA) of 28 morphological characters indicated that the first 10 principal components (PCs) with eigen-values greater than 0.6 explained 86.61% of the total variation. The PCs that largely contributed to the variability included number of days to shoot emergence, leaf position, leaf shape, leaf size, density of leaf, leaf vein colour; colour of leaf, petiole, petiole wing and stem, shoot growth rate, tuber shape and flesh colour of central cross section of tuber. The two-dimensional plot of the first two PCs grouped the accessions according to their species, but did not separate them into the tuber shape groups of irregular, oblong, oval-oblong, round and cylindrical. Factor analysis (FA) grouped the morphological traits into six factors, which together explained 75% of the total phenotypic variation in the dependence structure. Factor 1 was strongly associated with absence or presence of wings, distance between lobes, leaf apex shape, leaf colour, leaf margin colour, leaf measurement length-2, leaf vein colour of upper surface, number of branches, number of stems, stem colour and tip length of mature leaf; factor 2 with leaf density, leaf measurement length-1, leaf vein colour of lower surface, petiole wing colour, tip colour, wing colour and flesh colour of central cross section of tuber; factor 3 with leaf measurement width-1; factor 4 with leaf measurement width-2; factor 5 with stem colour; and factor 6 with number of days to emergence. The dendrogram of the cluster analysis produced six major groups supporting the PCA and FA groupings. Clusters A, B, C, D, E and F were formed at the dissimilarity distance = 0.90; and they consisted of two, thirty eight, one, seven, two and two genotypes respectively. Genotypes of cluster A belong to D. bulbifera, while genotypes of clusters B, C, E and F belong to D. alata, and genotypes of cluster D belong to D. rotundata. The ploidy levels of the 52 genotypes were determined by flow cytometry. The various ploidy levels obtained included diploid (2x), triploid (3x), tetraploid (4x), pentaploid (5x) and hexaploid (6x). The estimated nuclear DNA content ranged from 1.634 pg for G1 nuclei of diploid Dioscorea alata to 2.118 pg for G1 nuclei of hexaploid Dioscorea rotundata. Genotypes NR 07/045 (4x) and NR 07/040 (5x), which belong to D. bulbifera had nuclear DNA content of 1.905 and 2.017 pg respectively. The nuclear DNA content per genome was higher in diploids compared to polyploids. The variations within the 4x accessions (p<0.005) and among the three species (p<0.037) were significant. Root tips of six genotypes were prepared for chromosome counting using the acetocarmine staining technique. Genotype ER 07/030 had 20 chromosomes, four genotypes including ER 07/036, NR 07/060, NR 07/071 and SR 07/072 had 40 chromosomes, and TDr 95/18544 had 60 chromosomes. The findings agree with the hypothesis that studied germplasm from Sierra Leone were morphologically different expressing inter- and intra-group variability. Duplicate accessions were observed supporting the hypothesis that some genotypes had different names in diverse cultural setting. Flow cytometric measurements and conventional chromosome counting showed the existence of inter- and intra-group diversity in ploidy level and nuclear DNA content. A correlation was established between agro-morphological and cytological traits used in the study. This study contributes to an understanding of yam diversity in Sierra Leone which will facilitate yam genetic resource management, conservation and utilization.
Near infrared analysis of sugarcane (Saccharum spp hybrid) bud scales to predict resistance to Eldana stalk borer (Eldana saccharina Walker).
(2003) Coetzee, N. A.; Shanahan, Paul Edward.; Greenfield, Peter L.
The eldana stalk borer (Eldana saccharina Walker) is the most serious pest of the Southern African sugarcane industry, and it is imperative that effective control measures are available to minimize economic damage. Because conventional control methods have had limited success, cultivar resistance is seen as the most viable method of controlling infestation. However, due to the space- and time-consuming nature of the present screening methods, only small numbers of cultivars can be tested relatively late in the Plant Breeding selection programme. Increased resistance in breeding and selection populations is therefore slow. Buds are a preferred entry point of eldana larvae as they are softer than the rind that is present on the rest of the stalk surface. Preliminary results by other workers suggested that near infrared spectroscopy (NIRS) could provide a rapid screening method for the chemical profile in bud scales, the outer coating of buds and therefore the first contact point of an invading larva. If feasible, analysis of samples using this method could be done in the South African Sugar Experiment Station's (SASEX) stage two selection trials, providing an early indication of eldana resistance on large numbers of cultivars, without the necessity of separate trials. However, knowledge of how environments, position of bud scales on the stalk and age affect NIRS is required in order to determine the feasibility of the method. Planting of a trial with an identical set of genotypes across a range of environments, sampled at a number of ages, would provide the necessary information on environmental effects, whilst simultaneously providing the necessary range of samples to develop a calibration between bud scale chemical profiles and eldana resistance ratings. Inheritance patterns of the characteristics being measured is also required if they are to be used in a breeding programme. The original work by Rutherford (1993) was carried out on only five calibration sets (a set of standard clones with relatively well-known eldana resistance ratings), and different sets were not comparable due to what was assumed to be environmental differences between calibration sets. One aspect of the current experiment was to examine more closely the effect of genotype x environment interaction (G x E) on the performance of the NIRS technique under a range of conditions. Two sites were chosen to represent the conditions encountered in trials carried out by SASEX. The crops were sampled at three ages, representing the range of ages at which sugarcane is harvested in South Africa. Two locations on the stalk were also examined, top and bottom, for removal of bud scales, based on the assumption that aging of bud scales may affect chemical composition. A new NIRSystems 6500 instrument was acquired during the course of this study. Data from the new instrument indicated that there were no longer differences between the different calibration sets, and therefore no longer differences between environments. Spectra for different samples were very close, the differences being of the same scale as those recorded with repeated measures of the same samples, or between the readings for the standard solvent solution. This led to the conclusion that the differences observed on the original NIRSystems 5000 instrument were due to instrument error, not environmental differences. More importantly, the different calibration sets were not comparable despite being similar to each other. Prediction from one calibration set to another was low. These observations led to the conclusion that NIRS was not a suitable method for determining chemical compounds associated with tolerance of sugarcane genotypes to eldana borer. The original NIRS instrument was subject to error, and the small number of calibration sets included in the study led to the erroneous conclusion that NIRS was suitable for the prediction of varietal tolerance to eldana. With the acquisition of the new instrument, the errors generated by the old instrument became apparent. With the increase in number of calibration sets included in the study, it also became apparent that a global calibration covering all environments was not possible. An analysis of the heritability of the chemical compounds associated with eldana resistance was also included in this study. A biparental progeny design of 24 crosses with 33 unselected offspring per cross was used. This trial would have been analysed once the calibration had been developed using the environmental trial, and it would have provided knowledge of the breeding behaviour of the chemical compounds associated with tolerance to eldana. Because the NIRS technique proved to be unsuitable for detection of chemical compounds associated with eldana resistance, the heritability of these chemical compounds could not be studied. As the NIRS study did not produce data, the G x E interaction analysis and determination of heritability was applied to the bud scale mass data set. This study showed a relatively low positive correlation between bud scale mass and resistance to eldana. The broad sense heritability estimate for bud scale mass from the G x E interaction analysis was 0.45, and the narrow sense heritability estimate from parent-offspring regression analysis was approximately 0.27, suggesting a low degree of genetic determination in bud scale mass. The G x E interaction analyses gave varying results depending on the method used. The ANOVA analysis suggested that ages, sites and years had an effect on bud scale mass, while deviation from maximum plot showed no significance for G x E interactions. The number and choice of genotypes selected as unstable also varied with the method used to determine the stability of individual genotypes. Regression analysis and rank order analysis revealed a number of unstable genotypes, whilst stability variance and ecovalence, which produced similar results, detected only two unstable genotypes. In the rank order analysis correction of data to remove genotype effect, reduced the number of unstable genotypes, suggesting that the G x E interaction effect was partially confounded with the bud scale mass of the genotypes. This was a more reliable method than the uncorrected rank order analysis, and would be the preferred analysis type of all those tried.
Optimisation of the randomly amplified polymorphic DNA (RAPD) technique for the characterisation of selected South African maize (Zea mays L.) breeding material.
(2000) Edwards, Nicola Rachel.; Shanahan, Paul Edward.
Maize (Zea mays L.) is an important agronomic crop with the maize industry forming an important component of the South African economy. Considerable effort has been directed towards the genetic improvement of maize through both conventional breeding and biotechnology. Genotype identification by DNA fingerprinting is becoming an important activity in plant breeding. A widely used molecular based and relatively inexpensive method for DNA fingerprinting is the randomly amplified polymorphic DNA (RAPD) technique. The RAPD technique was tested in this study for its potential use in maize breeding programmes. Initial results using the technique showed a low degree of reproducibility, therefore both the DNA isolation and RAPD protocols were extensively optimised. DNA quality and quantity, and choice of Taq polymerase buffer were three of the variables found to be influential in ensuring reproducibility. The ability of the RAPD technique to characterise seven maize genotypes was evaluated. Sixty random oligonucleotide primers were screened. Forty two primers scored a total of 233 fragments (an average of 5.5 per primer), but not all primers gave reproducible profiles. Eighteen primers scored a total of 110 loci for the presence (1) and absence (0) of DNA fragments. RAPD markers were able to distinguish between all seven genotypes with five primers producing specific fragments for four genotypes. Genetic similarity matrices were calculated using two software programmes i.e. Genstat 5™ release 4.1 (1993) and PAUP (Phylogenetic Analysis Using Parsimony) 4.0 beta version (Swafford, 1998). Cluster analysis was used to generate dendrograms to visualise the genetic relationships of the seven maize genotypes (only minor differences were observed between the Genstat or PAUP method of analysis). Genetic diversity ranged from 0.62 to 0.96. The estimation of genetic relationship was in accordance with the presumed pedigree of the genotypes showing that the RAPD technique demonstrates potential for genome analysis of maize. The applicability of the technique for marker assisted selection was also evaluated. Near-isogenic lines (NILs) for leaf blight (Helminthosporium spp.) were screened for polymorphisms using a total of 120 primers. Ten primers identified polymorphisms between the NILs. Four primers produced five polymorphic fragments present in the resistant inbred K0315Y and absent in the susceptible inbred D0940Y. A small F2 population of 14 individuals was produced by selfing the F1 of a cross between K0315Y and D0940Y. To speed up the generation time, the F1 and F2 plants were cultured by embryo rescue from 18d old harvested seed. One fragment of 627 base pairs produced by primer OPB-01 (5' GTTTCGCTCC 3') showed a 3: 1 segregation in the small F2 population and was considered putatively linked to the HtN gene for leaf blight resistance. This study shows that the RAPD technique does have application in maize breeding programmes.
Participatory-based development of early bulking cassava varieties for the semi-arid areas of Eastern Kenya.
(2006) Kamau, Joseph Wainaina.; Melis, Robertus Johannes Maria.; Laing, Mark Delmege.; Shanahan, Paul Edward.
Cassava (Manihot esculenta Crantz) is an important food security crop in the semi-arid areas of Eastern Kenya. It provides food for more days in a calendar year than any other crop grown. Kenya has relied on varieties bred in other countries and because of this, local breeding methodologies and expertise are lacking. Access to appropriate varieties and adequate planting materials are major limiting factors to cassava production. Farmers grow late bulking landraces that take up to 18 mo to harvest. Efforts to introduce early bulking genotypes from IITA failed because of poor end-use quality. Local cassava breeding is necessary to alleviate the production constraints. Before a local breeding program can be established, farmers' preferences and production constraints must be identified and methodology appropriate to the Kenyan environment must be developed. The aims of this study were to identify farmer production constraints and preferences, to develop methods appropriate for cassava breeding in the semi-arid areas of Kenya, develop a population segregating for bulking period to estimate genetic variances that would explain the gene effects controlling yield components, and through participatory selection identify varieties that combine early bulking and preferred end-user traits. PRA tools, focus groups and individual interviews were used to identify production constraints and farmer preferences for cassava varieties. The PRA found that farmers grow 13 landraces in the area and 11 production constraints were identified and prioritised. The four most limiting in the order of importance were drought, lack of planting material, pests and diseases. Crosses between cassava varieties often do not produce much seed and the seed produced does not germinate well. Germination studies were done with open pollinated seeds to identify conditions favourable for seed germination in Kenya. The highest germination of the seeds was at 36°C. The control seeds had a higher germination percent (77%) compared to the seeds which were pre-heated at 36°C (57%). Crosses were made between selected IITA and local Kenyan genotypes following the NC 11 mating design to develop new genotypes which combine early bulking along with other farmer/end-user preferred characteristics. The hybrid progenies were evaluated in a seedling trial and clone genotypes advanced to a clonal trial and performance trial. The clonal trial was destroyed by red spider mites and cassava green mites, and only the tolerant 225 genotypes were planted in a performance trial that was harvested at 6, 7 and 8 mo after planting. The SCA effects were estimated to be 57% to 75% for most of the traits, except root number, which was mainly controlled by GCA effects (55%). Participatory selection of genotypes that combined early bulking and end-user qualities at the 7 and 8 mo after planting was done by farmers. Thirty genotypes that combined early bulking and end-user qualities were identified and ranked according to their performance in both agronomic and end-use traits using a selection index. A number of selected genotypes yielded more than three times the yield of the best parents, showing strong progress in breeding. Combining the farmers' preference aggregate score and the selection index based on the agronomic data, assisted in the final identification of the best genotypes developed in the breeding process. These results clearly demonstrated that it is possible to breed early bulking varieties with good end-use quality in the semiarid areas.
Screening sweetpotato (Ipomoea batatas L.) for drought tolerance and high β-carotene content in Mozambique.
(2011) Ricardo, José.; Shanahan, Paul Edward.
Sweetpotato (Ipomoea batatas, L.) is one of the important sources of carbohydrates and economic income in Mozambique. As with most of the food crops in Mozambique, it is usually produced by small-scale farmers under dryland conditions. Despite the importance of the crop, the storage root yields are still low and it is difficult to keep planting material (vines) for the next planting season. One of the major challenges to production is drought stress. Drought stress affects sweetpotato by retarding aboveground growth, reducing total root yield, percentage of dry mass, and reducing the quality of the roots as a result of the increase in damage caused by the sweetpotato weevil (Cylas formicarius). The objective of this study was to identify sweetpotato genotypes tolerant to drought particularly amongst the orange fleshed types which can be used in breeding programmes to improve the drought tolerance of genotypes grown in Mozambique. To this end, 48 genotypes were evaluated in both field and greenhouse studies conducted at Umbeluzi Research Station (26º 03’ S, 32ºC 23’ E; 12 masl) located about 30 km from Maputo city. The field trial was a three replicate, α-design with split-plots. Genotypes were the wholeplot treatment factor and irrigation levels were the sub-plot treatment factor. The three irrigation levels imposed were: nonstressed plants irrigated from planting to 120 DAP; moderately stressed, plants irrigated until 60 DAP; and severely stressed, plants irrigated until 30 DAP. In the greenhouse trial the 48 genotypes were grown in wooden boxes arranged in a two replicate, randomized complete block design. The plants were exposed to water stress from 10 DAP to the end of experiment at 60 DAP. Genotypes were significantly different for all traits, namely: survival %, vine vigour, aboveground biomass, total and commercial root yield, total fresh biomass, harvest index, β-carotene content, % dry mass, dry mass yield, incidence of sweetpotato virus disease, and incidence of weevil damage. Irrigation levels were significant for the traits: survival %, vine vigour, aboveground biomass, total and commercial root yield, total fresh biomass, harvest index, β-carotene content, % dry mass, and dry mass yield. Irrigation levels were not significant for incidence of sweetpotato virus disease and incidence of weevil damage. The genotypes x irrigation levels interaction was significant for: total and commercial root yield, and incidence of weevil damage; and not significant for: survival %, vine vigour, aboveground biomass, total fresh biomass, harvest index, β-carotene content, % dry mass composition, dry mass yield and incidence of sweetpotato virus disease. The mean dry mass yields across irrigation levels of the national breeding lines and introduced genotypes were higher than the landrace genotypes. Most of the national breeding lines had higher β-carotene content than the introduced and landrace genotypes. The landrace genotypes had relatively higher % dry mass composition compared to the national breeding lines. The stress tolerance index (STI) separated the 48 sweetpotato genotypes evaluated in the field trial into three groups: drought tolerant (high STI); moderate drought tolerant (intermediate STI); and drought sensitive (low STI). Under moderate stress, yield potential (Yp) and yield in a stress environment (Ys) were highly significant, positively correlated with Mean productivity (MP), Geometric mean productivity (GMP), Stress tolerance index (STI) and Tolerance index (TOL). Under severe stress the same correlations were reported. Under moderate and severe stress, the correlation between stress tolerance index (STI) and Stress susceptibility index (SSI) was significant and negative. In the greenhouse trial, differences between genotypes in vine length increment, vine diameter increment, leaf width increment and number of nodes vine-1 were significant (P<0.05). Vine length, vine diameter, leaf width and length increments either increased or were reduced due to water stress. Less than 10% increment in vine length (between 25 and 50 DAP) was recorded in MGCl01, Atacama, Cordner, Beauregard, and CN1448-49. Higher than 40% vine length increment was recorded in Jonathan and UNK-Malawi, Naspot, MUSG0614-24, Resisto, K566632, Tainung64, Ejumula and MUSG0623-09. Vine diameter decreased in Manhissane and MUSG0616-18. No change in leaf length in Tacna and Jonathan and in leaf width in Xihetamakote and Resisto-Nairobi was recorded. The longest petiole length at 30 DAP was recorded by Tacna and the shortest by Nhacutse4. The longest internode length was recorded in 199062.1. Similar to petiole length, Nhacuste4 reported the shortest internode length. The highest number of primary vines was recorded by MUSG0608-61 and lowest by Beauregard. Of the 48 genotypes exposed to water stress, 18 survived until the end of the greenhouse experiment at 60 DAP and were therefore considered to be drought tolerant.
A study of the diversity, adaptation and gene effects for blast resistance and yield traits in East African finger millet (Eleusine coracana (L.) Gaertn) landraces.
(2013) Manyasa, Eric Okuku.; Tongoona, Pangirayi.; Shanahan, Paul Edward.; Mwangi, Githiri.
Finger millet (Eleusine coracana) productivity in East Africa has remained low in all production agro-ecologies for decades owing to the low yielding potential of existing that are susceptible to the blast disease caused by the fungus Magnaporthe grisea (Hebert) Barr. and the limited research on the crop. The region holds large finger millet germpasm collections whose value is not yet been fully exploited. However, with the ongoing breeding efforts through hybridization, there is a need to comprehensively characterize the germplasm to identify valuable traits to address biotic and abiotic stresses that affect finger millet productivity. Studies on gene action and inheritance of key traits that contribute to yield improvement are also required to help formulate an effective breeding strategy for finger millet improvement. The objectives of this study were to (i) determine the genetic diversity in a set of germplasm from East Africa (ii) determine association between grain yield and its component traits (iii) identify genotypes for target production agro-ecologies (iv) identify blast resistant finger millet genotypes for use in breeding and production and (v) generate information on the inheritance of blast, grain yield and yield components for the development of an effective breeding strategy. A total of 340 finger millet accessions were collected from three countries in East Africa: Kenya, Tanzania and Uganda and 80 global minicore accessions sourced from ICRISAT-India. High phenotypic variability in the germplasm was recorded for 23 quantitative traits, blast reaction and five qualitative traits. Both morphological and molecular characterization (using SSR markers) of the 340 accessions revealed higher diversity within than among the countries Kenya, Tanzania and Uganda. Seven morphological clusters and three major genetic clusters were detected. Morphological diversity delineation was largely influenced by leaf sheath length, plant height, peduncle length, panicle exertion and grain yield. The mean polymorphic information content (PIC) of 19 polymorphic markers was 0.606 with mean alleles of 195 with sizes that ranged from 148-474 base pairs. The Kenyan and Tanzanian accessions had higher diversity than the Ugandan with the Kenyan and Ugandan, and the Kenyan and Tanzanian accessions being closely related than the Tanzanian and Ugandan. The low diversity in the Ugandan accessions could be attributed to higher research intervention in the country leading to the promotion and use of improved cultivars. Efforts have to be directed towards collection and conservation of valuable diversity before it is lost. The diversity in plant height, maturity, yield and blast reaction and the cluster groups detected in the germplasm should provide a basis for finger millet improvement through hybridization and selection. Higher genotypic than phenotypic correlations were recorded for most of the traits studied with grain yield having high positive correlations with finger width, grains per spikelet, threshing percent, peduncle length and panicle exertion. Both grain yield and days to flowering had negative correlations with all three blast types (leaf, neck and finger). Path coefficient analysis revealed that productive tillers per plant, 1000 grain mass, grains per spikelet and threshing percent had positive direct genetic effects on grain yield with strong indirect effects from several of the other traits which necessitates simultaneous selection for those traits with strong direct effects and those with strong indirect effects for grain yield improvement. High broad sense heritability estimates and high genetic advance as percent of mean were recorded in fingers per panicle, flag leaf sheath length, 1000 grain mass, finger length, peduncle length, panicle exertion, number of leaves per plant and leaf sheath length probably indicating the predominance of additive gene effects in controlling these traits hence the potential for improvement through selection. Adaptation and stability analysis using the GGE biplot model identified Lanet 2012 long rains, Serere 2012 long rains and Miwaleni 2012 long rains as the most discriminating environments for the low temperature, sub-humid mid altitude and dry lowland areas, respectively. Alupe 2012 long rains was the ideal environment for genotype discrimination for blast while Lanet 2012 long rains was best for grain yield. Genotypes G3, G5, G17, G25, G28, G36 and G71 were identified as being stable across environments and G1, G18, G19, G37, G54, G61, G74, G75, and G77 were found ideal for specific adaptation. Disease severity scores were highly negatively (P<0.01) correlated with days to flowering and grain yield suggesting that early lines suffered more disease damage leading to reduced yield. Resistant genotypes were slow blasting (probably associated with horizontal resistance) which may enable them to withstand blast pathogen variability for longer periods. Nine genotypes were identified with high resistance to blast and will be useful for breeding as blast resistance sources. Resistant genotypes had low AUDPC values and disease severity rating for the three blast types and vice-versa for susceptible genotypes. Further investigations need to be carried out to determine the possibility of the three blast types being controlled by the same genes. Early maturing blast susceptible genotypes with good yield potential could be utilized in areas with low blast prevalence. To understand the gene action for inheritance of the various traits 16 F2 families plus their four female and four male parents were evaluated at Alupe and Kakamega western Kenya under artificial blast inoculation. Significant additive genetic effects were recorded for all traits (except for finger width and grains per spikelet) meaning that improvement for these traits would be possible through the common selection methods for self pollinating crops. Parent lines KNE 392, and KNE 744 and IE 11 were found to be suitable for blast resistance breeding while Okhale 1 was found to be suitable for high grain yield and blast resistance improvement due to their high desirable GCA effects. Most of the F2 families showed transgressive segregation for the three blast types in either direction which gives hope for the development new pure lines with better blast resistance than the parents. Crosses IE 3104 x KNE 796, KAT FM 1 x Okhale 1, IE 11 x Okhale, IE 11 x P 224 and KNE 744 x KNE 392 have potential to generate lines with blast resistance due to their high desirable SCA effects. The F2 segregation distributions for blast indicated quantitative inheritance. However the one to four minimum number of genes (effective factors) detected for resistance control in all the three blast types was not in sync with the segregation patterns in the F2 families and further investigations are required. There were differences in segregation patterns between crosses which may suggest the presence of different resistance genes in the different parents used. This would call for gene pyramiding for durable resistance. These results confirm the potential of sourcing valuable parental stocks in the local germplasm for the development of genotypes to improve finger millet productivity in East Africa. Already some of the high yielding and blast resistant genotypes identified here have been incorporated in the regional cultivar trials. The diversity information generated will facilitate effective conservation and utilization of this germplasm. Results of gene action for inheritance of the various traits from this study will enable breeders to develop sound breeding strategies for finger millet improvement in the region.
Towards enhancement of B-carotene content of high dry mass sweetpotato genotypes in Zambia.
(2009) Chiona, Martin.; Shanahan, Paul Edward.; Melis, Robertus Johannes Maria.; Laing, Mark Delmege.
The enrichment of B-carotene, a precursor to vitamin A, in the local sweetpotato (Ipomoea batatas L.) cultivars is an attractive option in order to improve vitamin A intake in Zambia. The study was conducted to: 1) identify sweetpotato genotypes high in B-carotene content and high root dry mass (RDM) and to determine their combining ability, as measured through their progeny performance; and 2) screen progeny for root characteristics, yield, B-carotene content, and RDM. Firstly, a participatory rural appraisal (PRA) was conducted to determine the consumer preferences for sweetpotato. These preferences would form the basis for selecting desirable genotypes. Secondly, five selected parents were crossed in a full diallel for genetic variance studies. A selected subset of the diallel progeny were evaluated in three environments. Thirdly, 15 polycross progeny were evaluated for stability in five environments using additive main effect and multiplicative interaction (AMMI). The PRA revealed that consumers preferred high RDM combined with high fresh root yield. The diallel crosses recorded significant general combining ability (GCA) and specific combining ability (SCA) effects for B-carotene, RDM, harvest index (HI) and root fresh yield (RFY). The ratios of GCA to SCA variances were large (0.68-0.92). Two high B-carotene parents exhibited positive high GCA effects, indicating that additive gene effects were predominant in the inheritance of B-carotene. Reciprocal mean squares were not significant for RDM but they were significant (p=0.01) for B-carotene content. The estimate of narrow sense heritability of RDM (76.3%) was high; but heritability of B-carotene (20.9%), HI (29.1%) and RFY (34.9%) were much lower. These results suggest that rapid genetic gains should be possible with mass selection breeding techniques based on the phenotype of the parent for RDM but progress will be slow for B-carotene content HI, and RFY. The AMMI analysis identified progeny G2 (B-carotene content = 5.0 mg 100 g-1 and RDM = 37%), G6 (B-carotene content = 4.7 mg 100 g-1 and RDM = 37%), and G8 (B-carotene content = 4.7 mg 100 g-1, RDM = 35%) from the polycross as stable across environments for both B-carotene content and RDM. Genotype G3 was best suited to one of the test environments and had the highest B-carotene content (9.421 mg 100 g-1) and a high RDM (35.47%).