JA-Biological Sciences

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Open Access
Predicting the Longevity of Finger Millet and Vegetable Amaranth Seeds During Storage Under Controlled Temperature and Moisture Content Conditions
(Association of Official Seed Analysts and the Society of Commercial Seed Technologists, 2001-01-31) Mutegi, E.; Misra, A. K.; Kiambi, D.K.
Seeds of finger millet (Eleusine coracana (L.) Gaertn. var. KAT/FM-1) and those of Amaranth (Amaranthus hybridus (L.) ssp. cruentus (L.) Thell.) were stored in hermetically sealed, laminated aluminum foil packets, for up to 252 days at different constant conditions, which included combinations of temperatures ranging from 15° C to 40° C and moisture contents ranging from 5.3% to 17.3% (fresh weight basis). Seeds were sampled from storage for viability determination at different intervals depending on the storage regimens. Viability decline during storage was generally rapid at higher temperature and/or moisture content combinations. The effect of storage conditions on viability was quantified using viability equations. For each of the two species, the estimated periods for viability to fall to 50% (p50 value) decreased with an increase in the storage temperature and/or moisture content. Viability constants for each of the two species were obtained and used to predict longevity at various non-extreme hypothetical storage conditions. At comparative storage temperature and moisture content combinations, seeds of the two species differed considerably in longevity. The constants obtained in the present study could be applied in predicting storage life of seeds of the two species, especially under short to medium-term storage conditions.
Open Access
Plant Genetic Resources in Africa: Opportunities, Challenges and Priorities
(AGRA, 2010-07-19) Kiambi, D K; Attere, F.; Mgonja, M.
Africa’s strength lies in its natural resources, including the genetic resources that are the foundation for growth and stability in agriculture, forestry, adaptation to climate change and environmental conservation in its entirety. Africa’s economies, cultures and political systems are primarily dependent, albeit precariously, on how well plant genetic resources are conserved and utilized. In the light of this, the continent’s economic transformation and its ability to integrate itself into the evolving global system, to a large measure, depends on agricultural transformation that is based on plant genetic resources (PGR). Plant genetic resources are a key component of global biodiversity and it lends itself as a resource to be tapped as human needs and economic demands change. Humanity derives most of its food, many medicines and industrial products from both wild and domesticated components of plant genetic resources. However, the reduction of this biodiversity has been an inevitable consequence of human development as species-rich forests and wetlands are converted to relatively species-poor farmlands and plantations. It is now believed that 17 million hectares of tropical forests are being cleared annually and scientists estimate that at this rate roughly 5-10% of the tropical forest species may face extinction within the next 30 years (IUCN, 1990). Overall, scientists believe that about 60,000 of the world’s 240,000 plant species that have been described could be lost within the same time unless deforestation is slowed. This may lead to the loss of vital genetic resources especially wild relatives of crops and other economically important species. The many values of plant genetic resources and its importance for agricultural and economic development are sufficient incentives for development of articulate conservation measures. Their conservation entails a shift from protection to efforts that seek to meet people’s needs and economic development from biological resources while ensuring the long-term sustainability of this important biotic wealth and heritage. This involves not only the conservation of natural habitats and wild plants but also safeguarding the genetic diversity of economically important plants. Plant genetic resources are the biological basis of the world’s food security and directly or indirectly support the livelihoods of every person on earth. The International Treaty on Plant Genetic Resources (ITPGR) defines plant genetic resources as “any genetic material of plant origin that is of actual or potential economic value”. They consist of the diversity of genetic material contained in traditional varieties and modern cultivars grown by farmers as well as crop wild relatives and other wild plant species that can be used as food, medicines, essential oils, gums and resins, fodder and forages, fibres, shelter, wood, timber and fuel wood among others. The conservation and utilization of this vital component of biodiversity is therefore imperative for people’s sustainable livelihood, agricultural productivity and economic development. Today, access to food around the world is not secure Eight hundred million people are undernourished and 200 million children under five years of age are underweight. In the next 30 years, the world’s population is expected to grow by over 2,500 million to reach 8,500 million. Reliable and sustainable improvements in yield will be needed to meet the demands of this growing population. The conservation and sustainable utilization of plant genetic resources are the keys to improving agricultural productivity and sustainability, thereby contributing to national development, food security and the alleviation of poverty. As the worldwide loss of plant genetic resources accelerates, awareness has grown of the potentially disastrous consequences of this trend for the earth’s ecological functions and the fulfillment of basic human development needs. This trend is especially important in sub-Saharan Africa where people depend on plant genetic resources to a far greater extent than most other parts of the world. However, ways must be found to raise production and incomes while at the same time developing better biological resources management options.
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
Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region
(Wiley: Evolutionary Applications, 2016-06-23) Kiambi, Dan K ; Labeyrie, V; Deu, M.; Dussert, Y.; Rono, B.; Lamy, F.; Marangu, C.; Calatayud, C.; Robert, T.; Leclerc, C.
Crop populations in smallholder farming systems are shaped by the interaction of biological, ecological, and social processes, occurring on diﬀerent spatio temporal scales. Understanding these dynamics is fundamental for the conservation of crop genetic resources. In this study, we investigated the processes involved in sorghum and pearl millet diversity dynamics on Mount Kenya. Surveys were conducted in ten sites distributed along two elevation transects and occupied by six ethno linguistic groups. Varieties of both species grown in each site were inventoried and characterized using SSR markers. Genetic diversity was analyzed using both individual- and population based approaches. Surveys of seed lot sources allowed characterizing seed-mediated gene ﬂow. Past sorghum diﬀusion dynamics were explored by comparing Mount Kenya sorghum diversity with that of the African continent. The absence of structure in pearl millet genetic diversity indicated common ancestry and/or important pollen and seed-mediated gene ﬂow. On the contrary, sorghum varietal and genetic diversity showed geographic patterns, pointing to diﬀerent ancestry of varieties, limited pollen mediated gene ﬂow, and geographic patterns in seed-mediated gene ﬂow. Social and ecological processes involved in shaping seed-mediated gene ﬂow are further discussed.
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
Molecular genetic variation in the African wild rice Oryza longistaminata A. Chev. et Roehr. and its association with environmental variables
(2017-01-19) Kiambi, D. K.; Newbury, H. J.; Maxted, N.; Ford-Lloyd, B. V.
Molecular markers, complemented by appropriate Geographical Information System (GIS) software packages are powerful tools in mapping the geographical distribution of genetic variation and assessing its relationship with environmental variables. The objective of the study was therefore to investigate the relationship between genetic diversity and eco-geographic variables using Oryza longistaminata as a case study. The methodology used was a novel technique that combined hierarchical cluster analysis of both molecular diversity generated using Amplified Fragment Length Polymorphism (AFLP) and climate data available in a GIS software. The study clearly established that there is a close relationship between genetic diversity and eco-geographic variables. The study also revealed that genetic diversity is a function of annual rainfall, and peak diversity occurs in intermediate rainfall areas reflecting the ‘curvilinear theory’ of clinal relationship between the level of genetic diversity and rainfall. The clear association of genetic diversity with rainfall allows the extrapolation of the potential impacts of global warming on diversity when empirical data on predicted climate models, particularly rainfall, are available. This knowledge would therefore be useful in the development of conservation measures to mitigate the effects of genetic erosion through climate change.
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
Molecular genetic variation in the African wild rice Oryza longistaminata A. Chev. et Roehr. and its association with environmental variables
(2017-01-24) Kiambi, D. K.; Newbury, H.J.; Maxted, N.; Ford-Lloyd, B. V.
Molecular markers, complemented by appropriate Geographical Information System (GIS) software packages are powerful tools in mapping the geographical distribution of genetic variation and assessing its relationship with environmental variables. The objective of the study was therefore to investigate the relationship between genetic diversity and eco-geographic variables using Oryza longistaminata as a case study. The methodology used was a novel technique that combined hierarchical cluster analysis of both molecular diversity generated using Amplified Fragment Length Polymorphism (AFLP) and climate data available in a GIS software. The study clearly established that there is a close relationship between genetic diversity and eco-geographic variables. The study also revealed that genetic diversity is a function of annual rainfall, and peak diversity occurs in intermediate rainfall areas reflecting the ‘curvilinear theory’ of clinal relationship between the level of genetic diversity and rainfall. The clear association of genetic diversity with rainfall allows the extrapolation of the potential impacts of global warming on diversity when empirical data on predicted climate models, particularly rainfall, are available. This knowledge would therefore be useful in the development of conservation measures to mitigate the effects of genetic erosion through climate change.
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
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
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
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
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
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
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
Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system
(2017-01-24) Mutegi, Evans; Muraya, Moses; Geiger, Hartwig H.; de Villiers, Santie M.; Sagnard, Fabrice; Kanyenji, Ben M.; Kiambi, Dan; Parzies, Heiko K.
Knowledge of mating systems is required in order to understand the genetic composition and evolutionary potential of plant populations. Outcrossing in a population may co-vary with the ecological and historical factors inﬂuencing it. However, literature on the outcrossing rate is limited in terms of wild sorghum species coverage and eco-geographic reference. This study investigated the outcrossing rates in wild sorghum populations from different ecological conditions of Kenya. Twelve wild sorghum populations were collected in four sorghum growing regions. Twenty-four individuals per population were genotyped using six polymorphic simple sequence repeat (SSR) markers to compute their indirect equilibrium estimates of out crossing rate as well as population structure. In addition, the 12 populations were planted in a ﬁeld in a randomised block design with ﬁve replications. Their progeny (250 individuals per population) were genotyped with the six SSR markers to estimate multi-locus outcrossing rates. Equilibrium estimates of outcrossing rates ranged from 7.0 to 75.0%, while multi-locus outcrossing rates (tm) ranged from 8.9 to 70.0% with a mean of 49.7%, indicating that wild sorghum exhibits a mixed mating system. The wide range of estimated outcrossing rates in wild sorghum populations indicate that environmental conditions may exist under which ﬁtness is favoured by outcrossing and others under which selﬁng is more advantageous. The genetic structure of the populations studied is concordant with that expected for a species displaying mixed mating system.
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
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
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
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.

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