Browsing by Subject "West Africa"

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Association analysis of genes controlling variation of flowering time in West and Central African sorghum
(2012) Bhosale, Sankalp; Melchinger, Albrecht E.
Sorghum is extremely important for the food security in the arid to semi-arid regions of West and Central Africa (WCA). A serious constraint to the sorghum production in WCA is the scattered beginning but relatively fixed end of the rainy season among years, forcing farmers to adjust their individual sowing dates according to the start of the rains. Owing to the delayed sowing and fixed end of the rainy season, farmers require varieties that flower at the end of the rainy season, regardless of the sowing date. Photoperiod sensitivity of sorghum accessions is an important adaptation trait that allows flowering or synchronized flowering of the accessions at the end of the rainy season. This is also particularly important in avoiding grain mold, insect and bird damages for early maturing varieties, and incomplete grain filling due to soil water shortage occurring at the end of the season in late maturing varieties. Cultivars with photoperiod sensitivity may have the potential to increase yield and yield stability. Unfortunately, in WCA most of the present day cultivars are photoperiod insensitive. Furthermore, unavailability of simple screening methods in selecting photoperiod sensitive cultivars complicates the situation. Breeding techniques such as marker assisted selection (MAS) by employment of molecular markers would greatly enhance the selection efficiency for this major adaptation trait. Candidate-gene (CG) based association studies can assist in investigating the effect of polymorphisms in flowering time genes on phenotypic variation. Allele-specific molecular markers can be developed after a significant marker-phenotype association is identified. These markers can effectively be used in MAS of photoperiod sensitive sorghum cultivars. In this study we carried out a CG based association analysis to investigate the association between variation for photoperiodic sensitivity of flowering time in sorghum and polymorphisms in six partially amplified genes putatively related to variation in flowering time. Five out of six CGs were known to be involved in photoperiod pathway of flowering time [CRYPTOCHROME 1 (CRY1-b1), CRYPTOCHROME 2 (CRY2), LATE ELONGATED HYPOCOTYL (LHY), GIGANTEA (GI), HEADING DATE 6 (HD6)], and the gene SbD8 was involved in the gibberellic acid (GA) pathway of flowering time. In the first part of the study we determined the presence, the expression and the molecular diversity of genes homologous to the important flowering time gene D8 in maize on a set of 26 sorghum and 20 pearl millet accessions. Homologs of D8 were successfully amplified and tested for their expression in sorghum (SbD8) and pearl millet (PgD8). Pearl millet, because of its autogamous nature, showed higher nucleotide diversity than sorghum, which is an allogamous species. In maize, a 6 bp deletion flanking the SH2-like domain of D8 was found to be significantly associated with flowering by Thornsberry et al. (2001). We found in the PgD8 gene a 3 bp insertion or deletion (Indel) flanking the SH2 domain in the region, which was only conserved between D8 and PgD8. Cluster analysis performed for the D8, SbD8, and PgD8 indicated that maize is more closely related to pearl millet than sorghum. These findings suggest that, similar to maize, the indel in PgD8 flanking the SH2 domain might play an important role in determination of flowering. It is advisable to carry out an association study to reveal the potential role of PgD8 in flowering time control in pearl millet. After successfully amplifying and confirming the expression of SbD8 and PgD8, we carried out the association analysis on the selected CGs. A panel of 219 mostly inbred accessions of sorghum from major sorghum growing areas in WCA was complied. In the second part of the study the association analysis panel of accessions was phenotyped for their flowering response in the field in 2007 in Mali. The entire panel was sown twice (June and July), photoperiod response index (PRI) was estimated as the difference between DFL50% of the two sowing dates of the accessions. The PRI of the accessions showed a wide range from close to zero (photoperiod-insensitive) up to values close to 30 or above (highly-photoperiod sensitive). This result confirmed that the range of response based on the choice of the accessions was appropriate for an association analysis. The plant height reduction observed in accessions sown in July compared to the once sown in June was in accordance with previous studies performed in West African sorghum varieties. The sorghum accessions were genotyped using 27 simple sequence repeat markers. Population structure analysis using software STRUCTURE was carried out to control the false positives in the association analysis. The results showed existence of two subgroups in our sorghum accessions. The first subgroup included mainly race guinea (83%) originating from western West African countries such as Mali and Bukina Faso and the second subgroup included accessions mainly from Nigeria and Niger and also accessions originating from other countries and other major races. The race guinea could clearly be distinguished from the other races. Fisher's exact test for the presence of earliness among subgroups showed that there are significantly (p = 0.06) more early maturing accessions in subgroup one than subgroup two. But there was an absence of a clear structuring pattern. The study suggests that the race, the geographical origin, and maturity of the accessions are the most likely forces behind the observed structuring pattern of the accessions. We found a high level of genetic diversity among the sorghum accessions. Race guinea was found to be the most diverse and race kaura was the least diverse. In general, the estimates of the gene diversity were comparable to previous studies. The results showed that clustering of early-intermediate maturing guinea varieties may have increased the linkage disequilibrium (LD) in subgroup one compared to subgroup two. The differences in the extent of LD between our study and those in the previous studies can be due to the differences in the molecular markers used as well as differences in the racial composition of the accessions studied. In the final part of the study the association analysis was carried out using a mixed-model method. This method takes both population structure and kinship information into account. The candidate genes polymorphism data were obtained by amplifying and sequencing of the chosen genes. The association analysis for the polymorphism found within the CGs was carried out using values of PRI for each accession. From the six genes studied, genes CRY1-b1 and GI had several polymorphic sites which were significantly (p < 0.005) associated with PRI variation in the sorghum panel. The most important polymorphism in the gene CRY1-b1 showed an effect on PRI value of up to -4.2 days. This single nucleotide polymorphism (SNP) at position 722 in CRY1-b1 was located in the flavin adenine dinucleotide binding domain (N-terminal domain) of SbCRY1; hence, this domain appears to be important in photomorphogenesis in sorghum. In the case of the GI gene homolog, SNP888 had the largest effect on PRI of about +8 days. Similar to the studies in rice, the GI gene delayed flowering under June sowing (long-day conditons) and shortened the time to flower in sorghum under July sowing (short-day conditons). Therefore, the action of the GI gene homolog in sorghum might be revealed by a detailed investigation of GI by comparison of sorghum accessions grown under short-day and long-day conditions. In the case of gene SbD8, no significant association with PRI could be found; hence, the potential involvement of this gene in flowering time control of sorghum was not confirmed. Negative Tajima?s D values, of CGs indicated that the genes may have been subjected to adaptive selection as variation in flowering time may confer adaptive advantages in sorghum. The results showed that CG-based association analysis using a mixed model approach can be successfully applied to unravel the genetic variation related to phenotypic variation in flowering time. The polymorphisms significantly associated with PRI can be used to develop cleaved amplified polymorphic sequence markers. Functional markers could also be created directly from the significant SNPs. These molecular markers can serve as powerful tools in MAS for sorghum to identify cultivars sensitive to photoperiod.
Mikrofinanzierung, Armutsbekämpfung und ländliche Entwicklung in Westafrika : Wirkungsanalysen in Côte d'Ivoire und Niger
(2008) Schäfer, Birgit; Heidhues, Franz
The aim of the study was to take a critical look at the impact of microfinance as a free market development instrument in terms of sustainable poverty reduction at the target-group level in rural areas of West Africa. On the basis of empirical surveys carried out in two microfinance projects supported by the GTZ, the ?Associations Féminines d?Epargne et de Crédit? (AFECs) in Côte d'Ivoire and the ?Mutuelles d?Epargne et Crédit? (MUTECs) in Niger, the strengths and limitations of microfinance in terms of structural poverty reduction were assessed and recommendations for action were drawn up for implementing the concept in the development cooperation context. The understanding of poverty is based on the idea of human capabilities put forward by Armatya Sen in conjunction with the concept of social vulnerability and the life dimensions approach of the UNDP. Sustainable poverty reduction means extending the scope of action and freedom of poor people to use and transform the set of material and immaterial resources available to them so as to increase their productive capacity and enhance their choices, with a view to improving their well-being as they see it. This study is intended to provide a conceptual framework enabling researchers, practitioners and politicians to carry out structured impact assessment of microfinance projects. By enabling more realistic estimation of the effectiveness of microfinance for poor target groups in rural regions in the countries of sub-Saharan Africa, it is also intended to provide a decision-making aid for planning and designing microfinance projects.
Sorghum breeding strategies for phosphorus-limited environments in Western Africa : from field to genome level
(2014) Leiser, Willmar Lukas; Haussmann, Bettina
A growing world population juxtaposed with dwindling phosphorus (P) resources present new challenges to current and future global agricultural production. The burden of depleting phosphorus resources is particularly felt in sub-Saharan Africa (SSA). The expected doubling of its population by 2050 and the widespread poor soil fertility will pose an enormous task to future food security in SSA. Plant breeding can be considered as one major factor to improve agricultural production under these harsh low-input conditions. Nevertheless, until recently there have been no thorough breeding efforts to enhance crop production for low-P soil conditions in SSA. Sorghum (Sorghum bicolor L. Moench) is the world’s fifth and Africa’s second most grown cereal crop. Sorghum is a staple crop of SSA and is mostly grown in resource poor regions under low-input cropping conditions, with the largest share in West Africa (WA). Its good adaptation to harsh environmental conditions makes it an important crop for the arid and semi-arid regions, hence a crop vital for food security and increasingly farm income in WA. Breeding sorghum specifically targeting P-limited soils is considered as one of the major challenges for future food production and can serve millions of smallholder farmers in WA. Nevertheless, plant breeders are mostly reluctant to conduct breeding experiments under low-input conditions due to a higher spatial variability of soil properties leading to a lower response to selection. In an unprecedented large scale multi-environment experiment from 2006-2012 in three WA countries, namely Mali, Senegal and Niger, 187 WA sorghum genotypes were evaluated for their performance under P-sufficient and P-deficient conditions. The main goal of this study was to establish a breeding strategy for sorghum targeting P-limited environments. In order to establish such a strategy, the following objectives were defined: (I) to evaluate the impact of spatial models on genotypic selection in low-input field trials, (II) to develop a selection strategy for sorghum targeting P-limited environments, based on quantitative genetic parameters and (III) to identify genomic regions influencing sorghum performance in P-limited environments using modern genomic tools. The major findings of this study can be summarized as follows: Spatial models can increase the precision and efficiency especially of low-input field trials and may lead to different genotype rankings. Hence spatial models and/or adequate field designs are necessary tools for efficient genotype selection under low-input conditions and must be considered in a breeding program targeting P-limited conditions. Sorghum performance is severely impeded by low-P soil conditions and shows large grain yield and plant height reductions and delayed flowering. Nevertheless, WA sorghum is generally well adapted to low-P soil conditions and shows a large exploitable genetic variation for P efficiency. Direct selection under low-P conditions is feasible, necessary and more efficient than indirect selection under high-P conditions and should be pursued in a breeding program targeting P-limited environments. Landrace genotypes are more specifically adapted to low-P conditions and show a higher P acquisition capacity, Durra and Guinea race sorghums show a similar specific low-P adaptation, hence these genotype groups are very promising source germplasm for further breeding efforts. Photoperiod sensitive genotypes show less delay in heading, a higher P acquisition rate and a specific low-P adaptation, hence should be considered for climate and low-P resilience breeding. Selection for low P concentration of grain can be used to enhance internal P use efficiency, therefore decreasing further soil P mining. WA sorghum shows a large genetic diversity, hence providing a valuable source for genetic studies examining the underlying genetics of low-P adaptation. There are many genomic regions involved in sorghum adaptation to low-P soil conditions. Nevertheless, some regions could be identified as major contributors, showing large effects on and strong associations to genotypic performance. Molecular markers in sorghum homologs of the major P efficiency gene PSTOL1 from rice stably enhanced P uptake and crop performance through an increased root growth of sorghum under low-P soil conditions and can be used in marker assisted selection for grain yield production under P-limited conditions. Furthermore, it was observed that grain yield production under P-limited conditions and Al-tolerance are pleiotropically regulated by the same genomic region and most probably the same gene SbMATE. Molecular markers of this region and within the gene SbMATE should be used for marker assisted selection to simultaneously enhance the tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. WA Guinea race sorghums are an excellent source not only for low-P specific alleles, but also for Al-tolerance and represent therefore an excellent source germplasm for allele mining and marker assisted selection. Genomic selection appears to be a very promising approach to further increase the response to selection. But methods giving more weight to single molecular markers linked to Al-tolerance should be considered. The laid out results show that breeding sorghum specifically targeting P-limited conditions is necessary and feasible using advanced statistical models and modern genetic tools, and should be pursued as a major selection criterion in WA sorghum breeding programs. Nevertheless, only by combining agronomic and socio-economic measures with plant breeding efforts, millions of WA smallholder farmers can be reached and major yield increases can be expected in the near future.
Stirring up sorghum hybrid breeding targeting West African smallholder farmers low input environments
(2019) Kante, Papa Ndiaga Moctar; Haussmann, Bettina
Food supply and income in rural areas of West Africa (WA) depend strongly on the local production, and mostly on farmers’ field production of root and tuber crops, and cereals. To feed an ever-increasing population in a context of climate-change and low-input cultural conditions, breeding for resilient crops can guarantee smallholder farmers food security and cash income for a sustainable rural development. Sorghum hybrids for WA were first explored in the early 1970s and hybrid crosses of Malian landraces with introduced Caudatum-race seed parents were evaluated in the early 80s. Although those hybrids exhibited good heterosis for grain yield, their lack of grain quality made them commercially unsustainable. Efforts by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and its partners resulted in the first series of Guinea-race based hybrids. The short statured hybrids were evaluated in several on-farm farmer-managed yield trials, and showed satisfactory grain yield and quality under farmers’ cultivation conditions. Although taller- relative to shorter- height sorghum can help reduce risks of panicle loss by grazing transhumant cattle, no indication on the yield potential of the tall statured hybrids is available. The advances achieved by ICRISAT and its partners in hybrid development justified establishing a long-term hybrid breeding program to provide farmers with hybrids with sufficient grain yield and good grain quality under low input conditions. However, the lack of quantitative genetic information about the genetic value of new experimental hybrids and their parents (Guinea-Caudatum to complete Guinea background, from different WA origins), or about the efficiency of alternative selection methods for targeting yield performance in the predominantly low-input and phosphorous-deficient sorghum production conditions hinders sorghum hybrid development for this region. Sorghum hybrid breeding was commercially feasible only after the identification of a heritable and stable cytoplasmic male sterility (CMS) mechanism. Hybrid breeding in WA can benefit from molecular marker, especially for the fertility restoration/sterility maintenance of the predominant A1-type of CMS. The major outcomes of this thesis are presented as follow: Mean yields of tall hybrids were 3 to 17% (ranging from 6 to 28 g m−2) higher than that of the local check across all 37 on-farm farmer-managed environments and were highest (14–47%) averaged across the seven trials with the lowest mean yields. The yields of the new set of experimental hybrids were substantially superior to farmers’ local Guinea-race varieties, with 20 to 80% higher means over all hybrids in both low phosphorus (LP) and high phosphorus (HP) environments. Average mid-parent and better-parent heterosis estimates were respectively 78 and 48% under HP, and 75 and 42% under LP. Direct selection under LP was predicted to be 20 to 60% more effective than indirect selection under HP conditions, for hybrid performance under LP. The combining ability estimates provide initial insights into the potential benefit of germplasm from further east in West and Central Africa for developing a male parental pool that is distinct and complimentary to the Malian female pool. On chromosome SBI-05, we found a major A1 CMS fertility restorer locus (Rf5) explaining 19 and 14% of the phenotypic variation in either population. Minor quantitative trait loci (QTL) were detected in these two populations on chromosomes SBI-02, SBI-03, SBI-04 and SBI-10. In the third population, we identified one major A1 CMS fertility restorer locus on chromosome SBI-02, Rf2, explaining 31% of the phenotypic variation in the F2 mapping population. Pentatricopeptide repeat genes in the Rf2 QTL region were sequenced, and we detected in Sobic.002G057050 a missense mutation in the first exon, explaining 81% of the phenotypic variation in an F2:3 validation population and clearly separating B- from R-lines. The Guinea-race hybrids’ substantial yield superiorities over well adapted local Guinea-race varieties suggests that a strategy of breeding hybrids based on Guinea-germplasm can contribute to improving the livelihood of many smallholder farmers in WA. Although the usefulness of direct selection under LP for hybrid performance in the predominantly P-limited target environments was proven, companion evaluations of hybrids under HP would be desirable to identify also new hybrids that can respond to improved fertility conditions for sustainable intensification. The developed KASP marker stands as a promising tool for routine use in WA breeding programs.
Towards understanding the genetics of tolerance to low soil phosphorus conditions in West African pearl millet
(2015) Gemenet, Dorcus Chepkesis; Haussmann, Bettina
About two hundred and twenty three million people are undernourished in Sub-Saharan Africa (SSA) with 11 million people being food insecure in the Sahel region of West Africa (WA). A growing global population and climate change are expected to exacerbate this situation and present new challenges on global food production. Phosphate rock, a non-renewable resource is expected to be depleted in about 40-400 years depending on the source of information but a phosphorus (P) peak (where P demand exceeds P supply) is likely to occur before 2040. The effects of limited global P supply are expected to be felt more by resource poor smallholder farmers in SSA. This is also the region already with the lowest inorganic fertilizer use and highly weathered P deficient soils. Given these factors, breeding for low-P tolerance in crop plants offers the main environmental friendly and economically feasible strategy for improving crop productivity under low-P soils for smallholder farmers in WA conditions. This will not only contribute towards food security in the short term but also in the long term by contributing towards the efficient use of a scarce resource. In the Sahel region of WA where pearl millet is the staple cereal, it contributes to food security by providing calories as well as contributing towards nutritional security by providing higher iron and zinc levels than most staple cereals. Despite this fact, the available pearl millet germplasm had never been evaluated for grain yield performance under low-P conditions within this region prior to this study and the magnitude of the genetic component of variation had not been tested from a breeding perspective. To fill in this knowledge gap, three genotype groups: open-pollinated varieties, inbred lines and their testcrosses were evaluated in large-scale multi-environment trials in four countries under two P-levels between 2010 and 2012. In addition, the open-pollinated varieties and inbred lines were evaluated for P-efficiency related traits at early growth stage in pot conditions and at mature plant stage under field conditions (inbred lines only). The main aim of these evaluations was to explore the prospects of plant breeding for improving pearl millet grain yield under low-P conditions in WA. We sought to achieve the following specific objectives: (i) to estimate quantitative-genetic parameters for grain yield in order to establish a selection strategy for pearl millet targeting P-limited environments in WA; (ii) to determine the relationship between P-efficiency related traits and grain yield in order to make inferences on which target traits should be considered in adapting pearl millet to low-P conditions in WA; and (iii) to identify genetic regions underlying quantitative traits which are related to P-efficiency based on diversity array technology (DArT) markers. There is significant genetic variation for pearl millet performance in low-P soils; hence genetic improvement for low-P conditions should be possible. Both wide and specific adaptation can be followed in breeding pearl millet varieties for low-P conditions in WA. Direct selection of pearl millet under low-P conditions is more efficient and should be carried out in breeding activities targeting low-P environments. Pearl millet in WA exhibits a wide genetic variation for P-uptake and internal use efficiency. P-uptake efficiency is more correlated to grain yield in pearl millet than P-utilization efficiency, and given the interactions among P, drought and other soil characteristics evident within the region, P-uptake efficiency under these conditions should be selected for. However, given the already low P content of the soils in the region and the low input conditions, genotypes selected for low-P environments should combine both P-uptake efficiency and internal P-utilization efficiency to avoid further depletion of the soils. Nine markers were associated with different P-efficiency-related traits such as P concentration in stover, P concentration in grain, P uptake and P utilization efficiency. Nine markers and thirteen markers were found to be associated with flowering time and grain yield respectively. Each of these markers individually explained between 5.5 to 15.9 % of the observed variations indicating the polygenic nature of low P tolerance in pearl millet. The results presented in the current study indicate potential of improving pearl millet grain yield under P-limited conditions through breeding both conventionally and through molecular technologies. Given the global P crisis, other agronomic, socio-economic and policy approaches need to be effected alongside breeding activities if the pearl millet production system should be made sustainable to ensure food security for current and future generations.