JA-Biological Sciences

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Open Access
Assessing climate change vulnerability and its effects on food security: Testing a new toolkit in Tanzania
(CGIAR, 2015-06-19) Ulrichs, M.; Cannon, T.; Etten, Jacob van; Morimoto, Y.; Yumbya, J.; Kongola, E.; Said, S.; van de Gevel, J.; Newsham, A.; Marshall, M.; Kabululu, S.; Kiambi, D. K.; Nyamongo, D.; Fadda, C.
The working paper presents a new toolkit for the implementation of a participatory vulnerability assessment (PVA) in rural localities, by introducing the methodology, as well as the findings, from a pilot study in Sokoine (Zepisa, Hombolo Ward) in Tanzania. It is based on a participatory methodological approach and follows a multidimensional conceptualisation of social vulnerability to climate change. The methodology is designed to equip project implementers who have limited resources to assess the occurrence and consequences of climate impacts on local livelihood strategies and food systems. It will assist them in understanding local views on how climate change may affect them, what kind of coping strategies are already in place and how their adaptive capacity can be enhanced through measures that are tailored to the profiles of different local groups.
Open Access
Assessment of Genetic Diversity and Structure of Sudanese Sorghum Accessions using Simple Sequence Repeat (SSRs) Markers
(2017-01-24) Gamar, Yasir A.; Kiambi, Dan; Kairichi, Mercy; Kyallo, Martina; Elgada, Mohamed H.
95 sorghum accessions (1,425 individuals) sampled represented most of crop- cultivated areas in Sudan. The genetic diversity and population structure was assessed using a panel of 39 SSRs marker, which covered the sorghum genome. Genotypic data was generated using the ABI 3730 genetic analyzer. The alleles were called and sized using GeneMapper software version 3.7. The molecular data analysis software’s PowerMarker v3.25, DARwin 5, and GenAIEx 6.5x were used to calculate the different diversity indices within and between populations. A total of 332 alleles were detected, with an average of 8.5 per marker pair. The gene diversity averaged at 0.6671. The Polymorphism Information Content (PIC) values averaged of 0.68 showing the highly polymorphic and discriminatory nature of the selected markers. The accessions showed lower mean of observed heterozygosity (Ho = 0.187) than the expected heterozygosity (He = 0.547). AMOVA calculated low variants among populations (1%), and moderate variants within individuals (20%). However, variants among individuals were relatively high within population (79%). The fixation indexes showed little genetic differentiation among populations (FST = 0.008, P = 0.012). However, in the total population high level of inbreeding (FIS = 0.802, P = 0.001) was exhibited with deviation from Hardy-Weinberg proportions (FIT = 0.804, P = 0.001). Neighbor joining rooted phylogeny tree based on genetic similarity coefficient revealed three distinct groups independent of their geographic origins clustering close to each other; groups also have sub-groups. The study estimated genetic diversity and structure of Sudanese sorghum accessions.
Open Access
Collection of wild rice (Oryza L.) in east and southern Africa in response to genetic erosion
(PGR Newsletter, 2018) Kiambi, D.K.; Ford-Lloyd, B.V.; Jackson, M.T.; Guarino, L.; Maxted, N.; Newbury, H.J.
Collecting germplasm is the first step in ex situ conservation and clearly an important prerequisite for the use of the material by breeders. The reasons for collecting germplasm include danger of genetic erosion or extinction, users at national and international level have expressed a clear need for the germplasm, the genetic diversity is missing or insufficiently represented in existing ex situ germplasm conservation, and that more needs to be known about it (Engels et al. 1995). Floristic studies, plant inventories and herbarium specimens indicate that the east and southern Africa region is home to five wild species of Oryza. These are Oryza barthii, O. brachyantha, O. eichingeri, O. longistaminata and O. punctata (Fernandes et al. 1971; FAO 1987; Vaughan 1989, 1994; Leistner 1990). Clayton (1968, 1970) clarified the species names for the African wild relatives of cultivated rice by distinguishing O. barthii as the annual relative of O. glaberrima and O. longistaminata as the rhizomatous perennial relative. Studies on the origin and evolution of twin microsatellites in the genus Oryza have now clearly revealed that O. barthii is the ancestor of the cultivated African rice, O. glaberrima (Akagi et al. 1998), primarily found in west Africa but has now spread to parts of east Africa, Zanzibar in particular (Vaughan 1994; WARDA 1997). Geographically, the species are widely distributed in different countries of this region. The highest inter-specific diversity is found in Zambia and Tanzania, in each of which at least four out of the five species occur (Clayton 1968, 1970; Fernandes et al. 1971; FAO 1987; Leistner 1990; Vaughan 1994; Phillips 1995). The wild relatives of rice are an important source of agronomically useful traits that have been extensively used in rice improvement programmes (IRRI 1970; Khush 1977; Lin and Yuan, 1980; Agueirro et al. 1984; Heinrichs et al. 1985; Jena and Khush 1990; Khush et al. 1990; Brar et al. 1991; Amante et al. 1992; Ishii et al. 1994; Multani et al. 1994; Brar and Khush 1995). In particular, there are reports of the invaluable contribution that the germplasm of the wild relatives of cultivated rice found in east and southern Africa has made in rice breeding programmes. For example, O. long staminate A. Chev. et Roehr. has been reported to have genes for bacterial blight resistance, high pollen production, long stigmas and drought tolerance (Second et al. 1977; Taillebois 1983; Khush et al. 1990; WARDA 1997). Resistance to Meloidogyne graminicola, the nematode species causing significant damage to rice in west Africa, was found in an O. long staminate accession originating from Botswana (Jones et al. 1996). Genes forresistance to brown plant hopper and bacterial blight have been transferred from O. brachyantha A. Chev. et Roehr. to O. sativa L. (Khush et al. 1990). Oryza brachyantha also has traits for adaptation to lateritic soils, and resistance to yellow stemborer, leaf folder and whorl maggot (Khush 1977; Heinrichs et al. 1985; IRRI 1990; Brar and Khush 1995). Oryza barthii A. Chev. has resistance to green leaf hopper, sheath blight and bacterial blight, and shows characteristics for drought resistance (Henrichs et al. 1985; Amante et al. 1990). Ou (1985) has reported that genes for tolerance to yellow mottle occur in O. eichingeri A. Peter, while salt tolerance was found in O. punctata Kotschy ex Steud. by Farooq et al. (1994). The tetraploid race of this last species, reported in Tanzania, was found to have resistance to zigzag leaf hopper (Heinrichs et al. 1985). Marshall and Brown (1975) and Brown and Marshall (1995) suggested that the objective of any germplasm sampling strategy is to include in the sample at least one copy of 95% of the alleles that occur in the target population at frequencies greater than 0.05, i.e. the so-called ‘common’ alleles. However, Allard (1970) recognized that collectors might have little time and resources at their disposal. Therefore, the problem is to define a sampling procedure that yields the maximum amount of useful genetic variation within a specified and limited number of samples (Marshall and Brown 1983). The diversity of the wild rice species is gradually being eroded for a multiplicity of reasons. These include destruction of natural wild rice habitats to pave the way for expanding agricultural activities resulting from increasing population pressure, overgrazing and changes in land use (Reid et al. 1988; NWCMP 1996; Emerton and Muramira 1999). The need to assess the socio-economic activities that are causing genetic erosion, as well as collect and conserve this diversity, is therefore high. In the past there have been some collecting missions in Kenya, Tanzania, Madagascar and Zambia by D. Vaughan of the International Rice Research Institute (IRRI) and others, as reported in Bezançon and Second (1979), Miezan and Second (1979) and Katayama (1987, 1990). However both the species’ and geographical coverage were narrow. Consequently, the wild rice gene pool of the region was poorly represented in gene bank collections. According to Vaughan et al. (1991) and Vaughan (1994), prior to the collection missions reported in this paper, only 52 accessions of the wild rice relatives from the region were conserved in the International Rice Genebank at IRRI. This represented only 2.75% of the total world wild rice collection and 21% of the total wild rice accessions from Africa, despite their widespread distribution and occurrence in the continent. Moreover, before the collection missions reported in this paper, there were no wild rice germplasm collections conserved in the National Plant Genetic Resources Centres of the countries that participated in the work because, at the time of earlier collections, these countries didn’t have appropriate conservation facilities. This made collection and conservation of the germplasm urgent in order to expediently respond to the erosion pressures facing the wild rice species. This paper reports some of the indicators of genetic erosion of wild rice diversity, and the systematic collection and conservation of this germplasm in nine countries of the east and southern Africa region. The collecting missions were undertaken under the auspices of acollaborative programme involving the national PGR programmes of the region, the IRRI, SADC Plant Genetic Resources Centre (SPGRC), and the International Plant Genetic Resources Centre (IPGRI). The collaborators from the national programmes were: Joseph Kemei (Kenya National Gene Bank); Charles Mhazo and A. Mafa (Department of Research and Seed Services, Zimbabwe); Paulino Munisse ( Instituto du Investigacao Agraria, Mozambique); John Wasswa ( National Agricultural Research Organization of Uganda; Edwin Chiwona(Chitedze Agricultural Research Station, Malawi); M. Nawa (National Plant Genetic Resources Centre, Zambia); Herta Kolberg (National Biodiversity Institute, Namibia) and Margaret Nkya (Tanzania NPGRC). The objective was to sample the diversity of wild rice species in all the geographic and ecological areas where they have been recorded. The target taxa were O. barthii, O. brachyantha, O. eichingeri, O. longistaminata and O. punctata. The species are all inbreeding, with the exception of O. longistaminata, which is outcrossing. This paper also reports the field observations and the overall results of collecting missions coordinated by the first author and highlights observations made in Kenya, Uganda, Zimbabwe, Mozambique and Malawi where the author participated in the collecting mission
Open Access
Contrasting genetic diversity among Oryza longistaminata (A. Chev et Roehr) populations from different geographic origins using AFLP
(2017-01-19) Kiambi, D. K.; Newbury, H. J.; Ford-Lloyd, B. V.; Dawson, I.
Molecular markers have been used extensively in studying genetic diversity, genetic relationships and germplasm management. However, the understanding of between and within population genetic variation and how it is partitioned on the basis of geographic origin is crucial as this helps to improve sampling efficiency. The objective of this study was therefore to assess the intra-specific diversity in Oryza longistaminata and how the variation is partitioned within and between different geographic locations, using molecular markers. AFLP analysis generated 176 bands that revealed high levels of polymorphism (95.6%) and diversity within and between populations. The mean Nei’s genetic diversity for all the 176 loci in the 48 populations was 0.302 and diversity for populations within countries ranged from 0.1161 to 0.2126. Partitioning of between and within population diversity revealed that the mean allelic diversity at each polymorphic locus was HT = 0.3445. The within population diversity was (HS = 0.1755) and the between population diversity was (DST = 0.1688). Results of AMOVA revealed significant differences (p<0.05) in genetic variation among populations within different countries of the region. Genetic parameters estimated from AFLP data indicated that there are high levels of genetic diversity in the wild populations of O. longistaminata studied and that this diversity is higher within than between populations. Hierarchical partitioning also revealed that most of this diversity is found between populations within countries than among countries. Regional collection and conservation strategies therefore need to consider country differences while national strategies should consider population differences within countries.
Open Access
Ecogeographic genetic erosion, seed systems and conservation of plant genetic resources in Kabale highlands, Uganda
(2017-01-24) Mbabwine, Y.; Sabiiti, E.N.; Kiambi, D.; Mulumba, J.W.
lying causes of genetic erosion, identified farmers’ seed sources and exchange systems and documented conservation practices in the Kabale highlands of south-western Uganda. Data were collected using pre-tested structured questionnaires from a random sample of 120 farmers from six parishes. The analysis revealed substantial loss of traditional varieties of sweet potatoes (Ipomea batatas), potatoes (Solanum tuberosum), beans (Phaseolus vulgaris) and peas (Pisum sativum). More than 18, 7, 9, and 3 varieties, respectively were reported to have been lost completely. The most frequently mentioned underlying cause of genetic erosion (cited by 93.7% of the farmers) was introduction of new varieties. Other causes were lack of market (68.8%), diseases (45.6%), shortage of land (41.9%), pests (33.4%), shortage of labour (23.5%), change in weather (19.6%) and loss of soil fertility (15.8%). Farmers relied mainly on their own seed for traditiona varieties (81.5% of farmers), while nearly half of farmers obtained seed of new or modern varieties by cash purchase from the market. The exchange of seeds of modern varieties between the farmers was common practice. This has resulted in rapid and wide spread of modern varieties and has contributed to the abandonment of the traditional cultivars. Farmers maintained field stocks of vegetatively propagated crop species. For seed-propagated crops farmers mainly stored dried seeds in gunny sacks in their houses. Very few farmers employed traditional seed storage methods. The loss of landraces is a threat to national food security. Without adequate reservoirs of diverse genetic resources, future genetic improvement programmes will be jeopardized. There is therefore an urgent need to collect, document, conserve and utilize the traditional varieties and formulate policies that will protect them from further genetic erosion. Farmers and policy-makers should be sensitized on the value of maintaining crop genetic diversity.
Open Access
Experimentalstudiesonpollen-mediatedgeneﬂowin Sorghum bicolor(L.)Moench using male-sterile bait plants
(2017-01-24) Rabbi, I. Y.; Parzies, H. K.; Kiambi, D.; Haussmann, B. I. G.; Folkertsma, R.; Geiger, H. H.
Information on the potential of pollen mediated gene ﬂow (PMGF) in sorghum is required for ensuring varietal purity and to mitigate risk transgenic gene ﬂow. Replicated trials were conducted in Kenya using a local landrace, Ochuti as pollen donor surrounded by male-sterile pollen baits. Frequency of PMGF decreased with the increase of distance from pollen sources and was signiﬁcantly inﬂuenced by wind direction and speed. Anther dehiscence correlated with increase in vapour pressure deﬁcit in the morning. A negative exponential regression model with logarithmic transformation of PMGF and square-root transformation of distance from source ﬁeld best ﬁtted the data. Up to 50% of female ﬂorets on a male sterile (MS) plant were pollinated at 1m from pollen source and declined to 14% at 10 m.The maximum distance of PMGF using the PMGF model, based on a threshold of one seed per MS plant, was 203 m when data above the 95th percentile is considered. However, in the presence of self produced pollen of male-fertile target plants, the possibility of long distance cross-pollination may be very low.
Open Access
FIRST EXPERIENCES WITH A NOVEL FARMER CITIZEN SCIENCE APPROACH: CROWDSOURCING PARTICIPATORY VARIETY SELECTION THROUGH ON-FARM TRIADIC COMPARISONS OF TECHNOLOGIES (TRICOT)
(2017-01-24) Van Etten, Jacob; BEZA, ESKENDER; CALDERER, LLUÍS; Van Duijvendijk, Kees; Fadda, Carlo; Fantahun, Basazen; KIDANE, YOSEF GEBREHAWARYAT; VAN DE GEVEL, JESKE; GUPTA, ARNAB; MENGISTU, DEJENE KASSAHUN; Kiambi, Dan; MATHUR, PREM NARAIN; MERCADO, LEIDA; MITTRA, SARIKA; MOLLEL, MARGARET J.; ROSAS, JUAN CARLOS; STEINKE, JONATHAN; SUCHINI, JOSE GABRIEL; ZIMMERER, KARL S.
Rapid climatic and socio-economic changes challenge current agricultural R&D capacity. The necessary quantum leap in knowledge generation should build on the innovation capacity of farmers themselves. A novel citizen science methodology, triadic comparisons of technologies or tricot, was implemented in pilot studies in India, East Africa, and Central America. The methodology involves distributing a pool of agricultural technologies in different combinations of three to individual farmers who observe these technologies under farm conditions and compare their performance. Since the combinations of three technologies overlap, statistical methods can piece together the overall performance ranking of the complete pool of technologies.The tricot approach affords widescaling, as the distribution of trial packages and instruction sessions is relatively easy to execute, farmers do not need to be organized in collaborative groups, and feedback is easy to collect, even by phone. The tricot approach provides interpretable, meaningful results and was widely accepted by farmers. The methodology underwent improvement in data input formats. A number of methodological issues remain: integrating environmental analysis, capturing gender-speciﬁc differences, stimulating farmers’ motivation, and supporting implementation with an integrated digital platform. Future studies should apply the tricot approach to a wider range of technologies, quantify its potential contribution to climate adaptation, and embed the approach in appropriate institutions and business models, empowering participants and democratizing science.
Open Access
Genetic diversity among Ethiopian sorghum [Sorghum bicolor (L.) Moench] gene bank accessions as revealed by SSR markers
(African Journal of Biotechnology, 2020-02-01) Tirfessa, A.; Tesso, T.; Adugna, Asfaw; Mohammed, H.; Kiambi, D.
The presence of genetic variation in plant populations is useful for conservation and use in breeding programs. This study was conducted to estimate the extent and patterns of genetic diversity among 200 sorghum accessions collected from different parts of Ethiopia and preserved in a gene bank. Using 39 polymorphic simple sequence repeat (SSR) markers, which were previously mapped, 261 alleles were produced with mean 6.7 alleles per SSR. Polymorphism Information Content (PIC) and Dice’s similarity coefficient values ranged from 0.06 to 0.81 and from 0.062 to 0.96, respectively. Hierarchical clustering using UPGMA analysis revealed three major clusters with no clear distinction among geographical origins. Moreover, analysis of molecular variance (AMOVA) indicated that the majority of the variation (99.62%) observed was attributed to differences among accessions and only a small fraction of the total variation (0.38%) was related to regions of original collection, which may indicate that geographical origin is not a useful guide to follow for germplasm collection. Rather, agro-ecological classifications may be better for collection mission. Furthermore, crossing of accessions from the three distant clusters could result in promising genotypes for use as varieties or parents for the future breeding programs.
Open Access
Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya
(2017-01-24) Muraya, Moses M.; de Villiers, Santie; Parzies, Heiko K.; Mutegi, Evans; Sagnard, Fabrice; Kanyenji, Ben M.; Kiambi, Dan; Geiger, Hartwig H.
Wild sorghums are extremely diverse phenotypically, genetically and geographically. However,thereis an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various geographical regions.This is a major obstacle to both their effective conservation and potential use in breeding programs.The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene ﬂow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reﬂecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene ﬂow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene ﬂow, suggests a potential crop-to-wild gene ﬂow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.
Open Access
Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers
(2017-01-24) Mutegi, E.; Sagnard, F.; Semagn, K.; Deu, M.; Muraya, M.; Kanyenji, B.; de Villiers, S.; Kiambi, D.; Herselman, L.; Labuschagne, M.
Understanding the extent and partitioning of diversity within and among crop landraces and their wild/ weedy relatives constitutes the ﬁrst step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored signiﬁcantly more genetic diversity than its domesticated counterpart, a reﬂection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene ﬂow between the two congeners, with differences in farmers’ practices explaining inter-regional gene ﬂow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agroclimatic level. This indicated that gene ﬂow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.
Open Access
GEOGRAPHIC INFORMATION SYSTEMS FOR ASSESSMENT OF CLIMATE CHANGE EFFECTS ON TEFF IN ETHIOPIA
(2017-01-24) de Vaate, M.D BIJ; Kiambi, D.; Rao, K.P.C
The value of Geographic Information Systems (GIS) for assessing climate change impacts on crop productivity cannot be over-emphasised. This study evaluated a GIS based methodology for teff (Eragrostis tef) production in Ethiopia. We examined the spatial implications of climate change on areas suitable for teff, and estimated the effects of altered environments on teff’s productivity. There was a non-linear relationship between suitability indices, the output of spatial analysis and teff yield data collected from diverse ecological zones. This served as the basis for country-wide crop yield analysis for both current and future climate scenarios. To complement this effort, a socio-economic survey was carried with a thrust of understanding the agricultural activities in the study area. With the current climatic conditions, 87.7% of Ethiopia is suitable for teff. On the other hand, approximately 67.7% of Ethiopia is expected to be suitable for teff production by 2050. Suitability index (SI) and the actual crop yield data showed a strong positive correlation (r = 74%). There is a predicted severe drop in teff yield (-0.46 t ha-1) by the year 2050. Based on the current area under teff in Ethiopia, this equals an overall reduction in national production of about 1,190,784.12 t, equivalent to a loss of US$ 651 million to farmers. The results indicate that crop yield varied significantly as a function of climatic variation and that the model is applicable in assessing the impact of climate change on crop productivity at various levels taking into consideration spatial variability of climate.
Open Access
Geographical patterns of phenotypic diversity and structure of Kenyan wild sorghum populations (Sorghum spp.) as an aid to germplasm collection and conservation strategy
(2017-01-24) Muraya, Moses M.; Geiger, Hartwig H.; Mutegi, Evans; Kanyenji, Ben M.; Sagnard, Fabrice; de Villiers, Santie M.; Kiambi, Dan; Parzies, Heiko K.
Kenya lies within sorghum centre of diversity. However, information on the relative extent of diversity patterns within and among genetically deﬁned groups of distinct ecosystems is lacking. The objective was to assess the structure and phenotypic diversity of wild sorghum populations across a range of geographical and ecological conditions in the country. Sixty-two wild sorghum populations (30 individuals per population) sampled from four distinct sorghum growing regions of Kenya and covering different agroecologies were characterized for ten qualitative traits. Plant height, number of tillers, panicle sizes and ﬂag leaf dimensions were also recorded. Frequencies of the phenotypic classes of each character were calculated. The Shannon diversity index (H0) was used to estimate the magnitude of diversity. Principal component analysis was used to differentiate populations within and between regions. Wild sorghum is widely distributed in Kenya, occurring in sympatric ranges with cultivated sorghum, and both have overlapping ﬂowering windows. All characters considered displayed great phenotypic diversity. Pooled over characters within regions, the mean H0 ranged between 0.60 and 0.93 in Western and Coast regions, respectively. Wild sorghum was found to show a weak regional differentiation, probably reﬂecting the importance of seed-mediated gene ﬂow in shaping the wild sorghum population structure. Trait distribution was variable among regions, but there was no conspicuous distribution of the traits studied in any given region. Spontaneous hybridization and introgression of genes from cultivated to wild sorghum seems to be likely, and may already have occurred for a long time, although undocumented. Implications for in situ and ex situ genetic resources conservation are discussed.
Open Access
How to collect, handle and store seeds
(Kengo Publications, 2020) Mbonye, A.; Kiambi, D. K.
Seed is very delicate and therefore has to be handled with great care to prevent loss of viability. There are some important procedures that have to be carefully followed to ensure effective germination of the seed. These procedures include harvesting from a good mother tree, proper seed collection techniques, careful handling and extraction, good packaging and proper storage facilities. Effective pre-sowing treatment methods and good soil are also important for seed to germinate.
Open Access
Impact of farmers’ practices and seed systems on the genetic structure of common sorghum varieties in Kenya and Sudan
(2017-01-24) Rabbi, Ismail Y.; Geiger, Hartwig H.; Haussmann, Bettina I. G.; Kiambi, Dan; Folkertsma, Rolf; Parzies, Heiko K.
To understand the effect of different farming systems on the dynamics of diversity of sorghum (Sorghum bicolor (L.) Moench) crop, genetic structure of widely used landraces and modern varieties collected from two contrasting agroecosystems, in eastern Sudan and western Kenya, were analysed with 16 polymorphic microsatellite markers. A total of 1104 accessions, grouped into 46 samples from individual farmers, were genotyped. Cluster analysis of the samples from the two countries displayed contrasting patterns. Most strikingly, differently named landraces from western Kenya formed widely overlapping clusters, indicating weak genetic differentiation, while those from eastern Sudan formed clearly distinguishable groups. Similarly, samples of the modern variety from Sudan displayed high homogeneity, whereas the most common modern variety from western Kenya was very heterogeneous. The high degree of fragmentation of farmlands of western Kenya, coupled with planting of different sorghum varieties in the same ﬁelds, increases the likelihood of inter-variety gene ﬂow. This may explain the low genetic differentiation between the differently named landraces and heterogeneity of the modern variety from western Kenya. This study highlights the important role of farmers in shaping the genetic variation of their crops and provides population parameter estimates allowing forecasting of the fate of ‘modern’ germplasm (conventional or genetically modiﬁed) when introduced into subsistence farming systems.
Open Access
Improving Drought Tolerance in Sorghum bicolor L. Moench: Marker-Assisted Transfer of the Stay-Green Quantitative Trait Loci (QTL) from a Characterized Donor Source into a Local Farmer Variety
(2017-01-24) Ngugi, Kahiu; Kimani, Wilson; Kiambi, Dan; Mutitu, Eunice W.
Drought stress is a major constraint to sorghum production in Kenya, especially during flowering stage. This study aimed at developing drought tolerant sorghum varieties by transferring the stay green trait that confers drought tolerance in sorghum from a mapped and characterized donor source into an adapted farmer preferred variety. The drought tolerance donor source, E36-1 originally from Ethiopia was backcrossed into a Kenyan farmer-preferred variety, Ochuti until BC2F1 generation and the stay-green Quantitative Trait Loci (QTL) were transferred through Marker Assisted Breeding (MAB) strategy. Five polymorphic Simple Sequence Repeat (SSR) markers were used to select the 3 stay green QTL of E36-1 found in SBI-01, SBI07 and SBI-10 linkage groups. In the F1 generation, two of these QTL, were transferred into three genotypes. In the BC1F1 generation, 32 genotypes had at least one QTL incorporated. From a population of 157 BC2F1 progenies, 45 genotypes had incorporated either one or two of the stay-green QTL. Despite a few number of genotypes obtained through the backcrosses, the results showed that stay-green QTL and consequently drought tolerance can be transferred successfully into farmer preferred sorghum varieties through MAB
Open Access
Introgressing Striga Resistance from a Mapped Donor Source into a Rwandan Adapted Sorghum Variety
(2017-01-24) Niyibigira, Theogene; Ngugi, Kahiu; de Villiers, Santie; Kiambi, Dan; Mutitu, Eunice; Osama, Sarah; Ngugi, Abigail J.; Abdalla, Mohamed; Ali, Rasha; Mugoya, Charles; Masiga, Clet; Gahakwa, Daphrose
Sorghum is the world’s fifth most important cereal, in terms of both production and area planted. Striga hermonthica is one of the major constraints of sorghum production globally and particularly so in Eastern Africa. This study aimed at transferring five Striga resistances Quantitative Trait Loci (QTL) located on linkage groups SBI-01, SBI-02, SBI-05 and SBI-06 from a genetically mapped donor source line N13 into a locally adapted farmer preferred variety, IS8193 using Simple Sequence Repeats (SSRs). Nine polymorphic SSR markers were used to identify F1 generations and the subsequent BC1F1 progenies carrying Striga resistance QTL. Sixteen F1 progenies and twelve BC1F1 were found to have incorporated one to three Striga resistances QTL. The twelve BC1F1 lines with Striga resistance QTL were subsequently backcrossed to IS8193 to produce BC2F1 generation for further fore-ground and back-ground selection in the future. This work was conducted during March 2010 to August 2011 at University of Nairobi and at Biosciences eastern and central Africa (BecA)-Nairobi Kenya.
Open Access
INTROGRESSION OF STAY-GREEN TRAIT INTO A KENYAN FARMER PREFERED SORGHUM VARIETY
(2017-01-24) Ngugi, K.; Kimani, W.; Kiambi, D.
Backcross breeding enables breeders to transfer a desired trait from a Genetic Improvement of Kenyan sorghum variety for drought resistance donor parent, into the favoured genetic background of a recurrent parent. This study utilised back-cross breeding to transfer stay green quantitative trait locus (QTLs) from the donor parental line E361 into a Kenyan farmer-preferred variety, Ochuti as the recurrent parental line. The parental lines E36-1 has 3 stay green QTLs, SBI-01, SBI-07 and SBI-10 located at various chromosomes. The transfer of these QTLs was confirmed with the help of Simple Sequence Repeats (SSRs) molecular markers. Five foreground markers that were polymorphic among the two parental genotypes were used to identify individuals of F1 generation that had stay green QTLs transferred into Ochuti. A maximum of two QTLs, namely, SBI-07 and SBI-10 were identified as having been transferred into three individual genotypes. Two other F1 genotypes had only one QTL (SBI-10) transferred into Ochuti. The heterozygous F1 genotypes were used as the female parents in the generation of BC1F1. About 25% of the BC1F1 progenies that were genotyped had at least One QTL introgressed. As is the case in all marker-assisted back-cross breeding, the rate of success in introgressing QTL from donor to recurrent parental lines depends on the number of plants screened.
Open Access
Investigation of pollen competition between wild and cultivated sorghums (Sorghum bicolor (L.) Moench) using simple sequence repeats markers
(2017-01-24) Muraya, Moses M.; Geiger, Hartwig H.; de Villiers, Santie; Sagnard, Fabrice; Kanyenji, Ben M.; Kiambi, Dan; Parzies, Heiko K.
In self-compatible plant species stigmata receive a mixture of self and outcrossed pollen and competition between them is expected to play a major role in determining the pollen-mediated gene ﬂow. The use of male sterile bait plants in ﬁeld trials to demonstrate the rate of gene ﬂow is questionable due to lack of pollination competition. However, little direct evidence has been published. A ﬁeld experiment of male sterile and male fertile sorghum pollen recipient bait plants was conducted to evaluate pollen competition between wild and cultivated sorghums and the effects of pollen competition on gene ﬂow assessment. Pollen competition between wild and cultivated sorghums was estimated from two-component pollen mixtures of wild and cultivated sorghum (1:1 ratio) applied to wild, cultivated and male-sterile maternal bait plants. Paternity was determined in the progeny using the diagnostic. Simple Sequence Repeat markers. The study found that self pollen has higher seed-siring success. Maternal genotype inﬂuences the siring ability of the pollen donor components which signiﬁcantly deviated from the 1:1 pollen loads. The study showed that published estimates of gene ﬂow derived from studies using male-sterile bait plants seriously overestimate gene ﬂow and that pollen competition may be a signiﬁcant factor inﬂuencing outcrossing rates.The results suggest tha tthe predominant direction of gene ﬂow is from cultivated to wild sorghum, potentially leading to introgression of crop genes into wild sorghum. Pollen competition should be taken into account in gene ﬂow estimation, since presence of self-pollen can account for over half of seed produced irrespective of maternal genotype.
Open Access
Linking transcript profiles to metabolites and metabolic pathways: A systems biology approach to transgene risk assessment
(2017-01-24) Kiambi, D. K.; Fortin, K.; Stromvick, M.
In recent years, questions related to molecular composition and its implications for nutrition and health have been raised as advances in technology speed up the introduction of new diversity into breeding programs, either via transgenic technology or by using molecular markers in combination with wide crosses. Metabolite profiling offers great opportunities for characterization of this diversity phenotypically with respect to its metabolite composition. It provides a powerful resource to guide breeding programs and to alert researchers to positive or detrimental traits at an early stage. The power of this approach will be vastly increased by combining it with transcript profiling and a systematic survey of the metabolite composition of the plant products that are already on the market. This integrated approach and holistic profiling within a systems biology approach enables the careful tracking of the response of the organism to conditional perturbations at different molecular and genetic levels using available databases. This approach to profiling will not only provide a baseline for comparison of plants with novel traits (PNTs) with traditional comparators that are ‘generally recognized as safe’, but also provide a rational framework for risk assessment via 'substantial equivalence'. It also provides important inputs into nutritional research and contributes to the public debate about the acceptability of changes in food-production chains and development of science based regulation of plants with novel traits.
Open Access
Local scale patterns of gene ﬂow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural ﬁeld conditions in Kenya
(2017-01-24) Mutegi, E.; Sagnard, F.; Labuschagne, M.; Herselman, L.; Semagn, K.; Deu, M.; de Villiers, S.; Kanyenji, B. M.; Mwongera, C.N.; Traore, P.C.S.
Little information is available on the extent and patterns of gene ﬂow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa.As well as expanding knowledge on the evolutionary and domestication processes for sorghum,such information also has importance in biosafety, conservation and breeding programmes. Here,we examined the magnitude and dynamics of crop–wild gene ﬂow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum,and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis,population assignment,and analyses of spatial genetic structure to assess the extent and patterns of geneﬂow and diversity between cultivated and wild sorghum. Our results indicate that geneﬂow is asymmetric with higher rates from crop to wild forms than viceversa. Surprisingly,our data suggests that the two congeners have retained substantial genetic distinctness in the face of geneﬂow. Nevertheless,we found no signiﬁcant differences in genetic diversity measures between them. Our study also did not ﬁnd evidence of isolation by distance in cultivated or wild sorghum,which suggests that gene dispersal in the two con speciﬁcs is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop– wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.