Introgression Of Stay-Green Trait Into a Kenyan Farmer Prefered Sorghum Variety

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 E36-1 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.L'am\ue9loration par croisement en retour permet les am\ue9lirateurs \ue0 transf\ue9rer le trait d\ue9sir\ue9 d'une vari\ue9t\ue9 de sorgho Kenyan g\ue9n\ue9tiquement am\ue9lior\ue9 pour parent donneur de r\ue9sistance \ue0 la s\ue9cheresse, en parent r\ue9current d'un pass\ue9 g\ue9n\ue9tiquement favori. Cette \ue9tude a utilis\ue9 le croisement en retour pour transf\ue9rer le trait quantitatif locus de la persistance chlorophyllienne (QTLs) d'une lign\ue9e de parent donneur E36-1 dans la vari\ue9t\ue9 Kenyan pr\ue9f\ue9r\ue9e par les fermiers, Ochuti comme lign\ue9e parentale r\ue9currente. La lign\ue9e parentale E36-1 a 3 QTL de persistence chlorophyllienne SBI-01, SBI-07 et SBI-10 localis\ue9s sur divers chromosomes. Le transfert de ces QTL \ue9tait confirm\ue9 avec l'aide des marqueurs mol\ue9culaires \ue0 r\ue9p\ue9tition simple de s\ue9quences (RSS). Cinq marqueurs rapproch\ue9s qui \ue9taient polymorphoques parmi les deux g\ue9notypes parentaux \ue9taient utilizes pour identifier les individus de g\ue9n\ue9ration F1 qui avaient le QTL de persistence chlorophyllienne transf\ue9r\ue9e dans Ochuti. Un maximum de deux QTLs appel\ue9s SBI-07 et SBI-10 \ue9taient identifi\ue9 comme ayant \ue9t\ue9 transf\ue9r\ue9s dans trois g\ue9notypes individuels. Deux autres g\ue9notypes F1 avaient un QTL (SBI-10) transf\ue9r\ue9 dans Ochuti. Les g\ue9notypes h\ue9terozygotes F1\ue9taient utilis\ue9s comme de parents femelles dans la g\ue9n\ue9ration de BC1F1. Environ 25 % de prog\ue9nies BC1F1 qui \ue9taient g\ue9notyp\ue9s avaient au moins un QTL introgress\ue9. Comme c'est le cas dans toute amelioration par croisement de retour avec marqueur assist\ue9, le taux de r\ue9ussite en introgressant le QTL du donneur aux lign\ue9es parantales r\ue9currentes d\ue9pend du nombre de plants test\ue9s

Contrasting genetic diversity among Oryza longistaminata (A. Chev et Roehr) populations from different geographic origins using AFLP

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 (

Linking transcript profiles to metabolites and metabolic pathways: a systems biology approach to transgene risk assessment

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

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

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, SBI-07 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

GEOGRAPHIC INFORMATION SYSTEMS FOR ASSESSMENT OF CLIMATE CHANGE EFFECTS ON TEFF IN ETHIOPIA

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\u2019s 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.On ne saurait trop insister sur la valeur des Syst\ue8mes d\u2019Information G\ue9ographiques (SIG) pour l\u2019\ue9valuation d\u2019impacts des changements climatiques sur les rendements des cultures. Cette \ue9tude a \ue9t\ue9 men\ue9e pour \ue9valuer en utilisant le SIG la production du teff (Eragrostis tef) en Ethiopie. L\u2019investigation a port\ue9 sur les implications spatiales du changement climatique sur les zones favorables \ue0 la culture du teff en Ethiopie et l\u2019estimation des effets des changements environementaux sur la productivit\ue9 du teff. L\u2019\ue9tude a r\ue9v\ue9l\ue9 une relation non lin\ue9aire entre les indices de convenance et les r\ue9sultats de l\u2019analyse spatiale et des rendements de la culture de teff dans diff\ue9rentes zones agro-\ue9cologiques. Ceci a servi de base \ue0 l\u2019analyse des rendements des cultures dans tout le pays pour le pr\ue9sent et les futurs scenarios de changement climatique. En compl\ue9ment \ue0 cet effort, une enqu\ueate socio\ue9conomique \ue9tait conduite pour comprendre le d\ue9roulement des activit\ue9s agricoles dans la zone d\u2019\ue9tude. Sous les conditions climatiques actuelles, 87.7% de l\u2019Ethiopie convient pour le teff. D\u2019autre part, il est pr\ue9dit qu\u2019environ 67.7% de l\u2019Ethiopie seront encore faborable \ue0 la culture du teff en 2050. L\u2019indice de convenance et les donn\ue9es de rendements actuels ont montr\ue9 une forte corr\ue9lation positive (r = 74%). Par ailleurs, une diminution sensible de rendement du teff (-0.46 t ha-1) a \ue9t\ue9 pr\ue9dite pour l\u2019an 2050. Sur base de la superficie actuelle sous culture de teff en Ethiopie, cette chute de rendement correspond \ue0 une r\ue9duction de la production nationale d\u2019environ 1.190.784,12 t \ue9quivalents \ue0 une perte de 651 millions de dollars pour les producteurs. Ces r\ue9sultats indiquent que les rendements des cultures ont vari\ue9 significativement en fonction de la variation climatique et que le mod\ue8le est applicable dans le cas de l\u2019\ue9valuation de l\u2019impact du changement climatique sur la productivit\ue9 des cultures \ue0 diff\ue9rents niveaux consid\ue9rant les variabilit\ue9s spatiales du climat

Impact of farmers’ practices and seed systems on the genetic structure of common sorghum varieties in Kenya and Sudan

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

First experiences with a novel farmer citizen science approach: crowdsourcing participatory variety selection through on-farm triadic comparisons of technologies (TRICOT)

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 wide scaling, 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

Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-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

Geographical patterns of phenotypic diversity and structure of Kenyan wild sorghum populations (Sorghum spp.) as an aid to germplasm collection and conservation strategy

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 (H') 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 H' 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

Marker-assisted introgression improves Striga resistance in an Eritrean Farmer-Preferred Sorghum Variety

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC3F2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC3F3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC3F3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement