Josphert N. Kimatu

DNA cytosine methylation in plant development

Cytosine bases of the nuclear genome in higher plants are often extensively methylated. Cytosine methylation has been implicated in the silencing of both transposable elements (TEs) and endogenous genes, and loss of methylation may have severe functional consequences. The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity. In addition, the fresh studies also revealed the more dynamic nature of this epigenetic modification across plant development than previously believed. Cytosine methylation of gene promoter regions usually inhibits transcription, but methylation in coding regions (gene-body methylation) does not generally affect gene expression. Active demethylation (though probably act synergistically with passive loss of methylation) of promoters by the 5-methyl cytosine DNA glycosylase or DEMETER (DME) is required for the uni-parental expression of imprinting genes in endosperm, which is essential for seed viability. The opinion that cytosine methylation is indispensible for normal plant development has been reinforced by using single or combinations of diverse loss-of-function mutants for DNA methyltransferases, DNA glycosylases, components involved in siRNA biogenesis and chromatin remodeling factors. Patterns of cytosine methylation in plants are usually faithfully maintained across organismal generations by the concerted action of epigenetic inheritance and progressive correction of strayed patterns. However, some variant methylation patterns may escape from being corrected and hence produce novel epialleles in the affected somatic cells. This, coupled with the unique property of plants to produce germline cells late during development, may enable the newly acquired epialleles to be inherited to future generations, which if visible to selection may contribute to adaptation and evolution.

Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement

A polyploid organism by possessing more than two sets of chromosomes from one species (autopolyploidy) or two or more species (allopolyploidy) is known to have evolutionary advantages. However, by what means a polyploid accommodates increased genetic dosage or divergent genomes (allopolyploidy) in one cell nucleus and cytoplasm constitutes an enormous challenge. Recent years have witnessed efforts and progress in exploring the possible mechanisms by which these seemingly intangible hurdles of polyploidy may be ameliorated or eventually overcome. In particular, the documentation of rapid and extensive non-Mendelian genetic and epigenetic changes that often accompany nascent polyploidy is revealing: the resulting non-additive and novel gene expression at global, regional and local levels, and timely restoration of meiotic chromosomal behavior towards bivalent pairing and disomic inheritance may ensure rapid establishment and stabilization as well as its long-term evolutionary success. Further elucidation on these novel mechanisms underpinning polyploidy will promote our understanding on fundamental issues in evolutionary biology and in our manipulation capacities in future genetic improvement of important crops that are currently polyploids in genomic constitution. This review is intended to provide an updated discussion on these interesting and important issues within the scope of a specific yet one of the most important plant groups-polyploid wheat and its related species.

Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress

Cytosine-5 hypomethylation or hypermethylation have been shown to regulate plant development and abiotic stress-responsive genes expression. However, some combinatory stresses in plants like saline and alkaline could have varied responses that could contribute to their adaptive evolution trends. We evaluated root and leaf DNA methylation patterns of cotton in salt (S, 9:1 molar ratio of NaCl to Na 2 SO 4 , pH 6.96) and alkali (A, 9:1 molar ratio of NaHCO 3 to Na 2 CO 3 , with higher pH 9.21) stresses using methylation sensitive amplified polymorphism (MSAP) method and found out that in general, demethylation events occurred more than methylation events in both leaves and roots samples. In addition, the total methylation variation frequency was only 1.38% in leaves and 2.2% in roots under salt stress. However, the alkali stress triggered more alterations and decreased the DNA methylation level significantly (P<0.05) compared to salt stress. This was up to 2.59% and 12.44% in the scored CCGG sites in leaves and roots, respectively. These results suggest that more adaptive and possibly complex gene expression alterations could be occurring in the tolerance of the cotton root in response to salt and alkali stresses coupled with DNA methylation alterations, although exclusion physiological mechanisms cannot be ruled out. Key words : Salt stress, alkali stress, Gossypium hirsutum L., DNA methylation, methylation sensitive amplified polymorphism (MSAP).

Real-world complexity of food security and biodiversity conservation

Abstract Feeding the booming human population and at the same time conserving biodiversity is a global challenge. Yet, it is particularly acute in developing countries where biodiversity is high and food-security low. There is an ongoing debate whether land for nature and for agriculture should be segregated (land sparing) or integrated (land sharing). While these strategies still need unambiguous empirical validation, we here illustrate the real-word complexity of this issue by focusing on the case of Kenya, hosting one of the fastest growing populations in the world. We discuss historical effects and those arising from recent demographic pressure, and integrate these with biotic and abiotic constraints (soil fertility and climate) that additionally challenge land sparing and sharing strategies for biodiversity conservation. Generically, our contribution stresses the importance of recognising the specific context in which land-use strategies are to be applied, and underline the need of a deeper understanding of local conditions. This work goes beyond the current theoretical and highly abstract land-use debate that has been published in high impact journals but which may be less efficient on solving local conflicts.

Morphological and cytosine DNA methylation changes induced by a combined effect of boron (B) and salt toxicity in Sorghum bicolor inbred line

Boron (B) toxicity is one of the abiotic stresses limiting plant growth in arid and semi arid regions globally. Although studies have been conducted on the combined effect of B and sodium chloride (NaCl) toxicity on overall plant growth revealing an antagonistic relationship, the morphology and epigenetic interactions have not fully been explained. Germinating seeds of an inbred line of Sorghum bicolor (YN267) were subjected to various concentrations of B (10, 50, 100, 200, 300 and 400 mM) in a constant concentration of high NaCl (100 mM). Methylation-sensitive amplification polymorphism (MSAP) was used in the assessment of changes in the methylation levels and patterns. Morphological results show that plants at the B concentration range of 10 to 200 mM were adversely affected by the combined stress application than at 300 and 400 mM. In addition, the cytosine methylation status at 300 mM showed an increased overall hypermethylation, while hypomethylation was induced at 400 mM. These results show that not only did the combined treatment induced cytosine DNA methylation changes which was reflected in the plant morphology, but the alleviating effects of the combination at toxic levels are suggested to be due to the epigenetic alterations and expression/repression of stress responsive genes. Keywords: Cytosine DNA methylation, Sorghum bicolor L, boron and sodium chloride toxicity, methylation-sensitive amplification polymorphism (MSAP)

Genome-wide analysis of cytosine DNA methylation revealed salicylic acid promotes defense pathways over seedling development in pearl millet

ABSTRACT Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were performed in 4 pearl millet (Pennisetum glaucum) varieties. Seedlings of 4 early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA. Root growth was used as a parameter to evaluate the effects of SA at early stage development. DNA from these seedlings was extracted and Methylation-Sensitive Amplified Polymorphism (MSAP) was measured to assess the effects of SA on methylome. The methylation analysis revealed that SA treatment decreased the methylation, while inhibiting the root growth for all varieties tested, except in PMG at 0.5 mM, indicating a dose and a genotype response-dependence. The methylation level was positively correlated with the root growth. This suggests that SA influences both the methylome by demethylation activities and the root growth by interfering with the root development-responsive genes. The demethylation process, induced by the REPRESSOR OF SILCENCING 1 (ROS1) may activate R genes, or GH3.5 and downregulate the hormonal pathway under root development. These findings showed the pearl millet metabolism prioritized and promoted the defense pathways over vegetative development during stress.

Genetic Diversity, Habitat Fragmentation and Epigenetic Variations

There is an increase in the levels in which tropical rainforest and temperate grasslands have become anthropogenically fragmented in recent years. However, an understanding of the genetic and epigenetic mechanisms coupled with conservation biology and biodiversity studies is crucial in explaining habitat fragmentation implications in stable ecosystems (Fahrig, 2003; Henle et al., 2004). The utilization of genetic variability and adaptability can be used as a stepping stone in identifying germplasms that can be used in the search of new ecotypes with novel genes which can be incorporated in crop, fodder and cover tree improvement programs in other similar reclaimable ecological zones. Studies have shown that there is a considerable genetic variability within or between natural populations. This variability provides a genomic flexibility that can be used as a raw material for plant adaptation as pioneer species. There is need to seek for higher genetic variability so as to increase the capacity of an organism to adapt to the ever changing environmental conditions (Ellstrand and Elam, 1993). Low genetic variability has been associated with the inability to cope with abiotic and biotic stresses (Valen, 1965). It is now possible to compare and analyze the pattern and spectrum of genetic variations within or between using molecular genetic tools (Zhang et al., 2009, Madan et al., 2002; Reisch et al., 2005). The amplified fragment length polymorphism (AFLP) is one of the most precise, cost effective polymerase chain reaction (PCR) based ecological tool that has been used for molecular analysis of such population genetic diversity analysis (Vos et al., 1995; Bensch, and Akesson, 2005). It has been shown to be comparatively highly informative, reliable and efficient tool in other grass investigations (Fjellheim and Rognli, 2005). Such tools can be used to determine the correlation between the genetic differentiation and geographic distance among different populations. However, the level of genetic differentiation can be affected by more than one ecological factor in a geographical region, especially environmental heterogeneity (Liu et al., 2004). Other factors could be natural mutation, artificial selection, and combined ecological factors which are instrumental in the differentiation into ecotypes (Liu et al., 2002). Therefore, variations in gene expressions which are caused by abiotic and biotic stresses in the environment trigger epigenetic mechanisms like cytosine DNA methylation which have

Methylation analysis revealed salicylic acid affects pearl millet defense through external cytosine DNA demethylation

ABSTRACT The cytosine DNA methylation and demethylation have a role in regulating plant responses to the environment by affecting the promoter regions of most plant defense-related genes through the CpG islands or the CCGG motifs. Salicylic acid, a defense and signaling plant hormone, is seen playing crucial role in the variation of the methylome. In this study, the effects of salicylic acid and feeding of the millet headminer (Heliocheilus albipunctella de Joannis) on pearl millet DNA methylome changes were evaluated through MSAP epigenotyping during panicle development. The results showed that millet headminer feeding increased the level of genomic methylation while application of salicylic acid caused DNA demethylation occurring mostly at external cytosine and accompanied by a decrease of the number of larvae per panicle. This suggests that hemimethylation (external cytosine methylation) has key role in regulating defense responses and conferring tolerance to pearl millet through salicylic acid application.

Effects of agro ecosystem land use types on the diversity, abundance and ecosystem functions of insect pollinators

Land degradation in agricultural farms is mainly manifested through loss of ecosystem services such as pollination. In Kenya, farmers knowledge of pollination is limited, many farmers lump pollinators together with insect pests and do not explicitly manage to conserve them, although pollinators may contribute substantially to yields at no cost to the farmer. Insect pollinators of crops and wild plants are threatened worldwide by pesticide use and the spread of disease and parasites. This research is multidisciplinary in approach, in this research niche theory and ecosystem functions concepts to determine the status of insect pollinators in agro-ecosystems of Mua Hills location were used. The aim of this research was to determine the diversity and abundance of pollinator insects for their role in ecosystem function (pollination) and increase of passion fruit yield. The diversity and abundance of insect pollinators was found to be least in horticultural land use type and this was attributed to the use of agro-chemicals. This research is an issue of environmental management because it focuses on natural patch land use type for sustainable use of agro-ecosystems to avoid decline of pollinators. It advocates for conservation of the environment and management of carpenter bee (Xylocopa spp) because it is an efficient pollinator of passion fruit thus makes farming more profitable through higher yield of the crop. The findings from this research are aimed to help the subsistence farmers achieve good produce in passion fruit farming. The study promotes the conservation of insect biodiversity within the existing land use types to improve pollination of horticultural crops.

Introducing Efficient Low Cost Smoked Pots for Water Purification for Developing Countries

Ceramic materials are easy to make using most African soils. They have been used for a long time mainly for cooking and water storage. However, in other low income economies these clay ceramic filters have been shown to have the potential of being improved by being embedded with carbonaceous materials for water purification. In this research we have produced efficient physiological and biological gravity operated smoked pots for water purification. We used well calculated volume ratios of black clay, red and sand soils (B:R:S) and soil balls; All these were baked at different smoke infusing kiln temperatures for efficient water purification. We analyzed water purification efficiencies of the pot ceramics and the trickling rates at different conditions. We isolated the best B:R:S to be the 40:40:20. We found significant reductions in turbidity (99.95%), salinity (21.42%), microbial populations, total dissolved solutes (TDS) (17.19%), pH (1.39%) and electrical conductivity (EC) (16.92%). These ceramics can be crucial for common or nomadic communities in sub-Saharan rural areas and in times of disaster to guarantee a cheap continued supply of clean potable water for better health amongst the low income earning societies.