Santie de Villiers

Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers’ knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.

Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system

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 outcrossing 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.

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity.

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.

Investigation of pollen competition between wild and cultivated sorghums (Sorghum bicolor (L.) Moench) using simple sequence repeats markers

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 two 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 that the 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.

Enhanced Utilization of Biotechnology Research and Development Innovations in Eastern and Central Africa for Agro-ecological Intensification

The Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA) through its Agrobiodiversity and Biotechnology Programme is enhancing the utilization of biotechnology research and development innovations in Eastern and Central Africa (ECA). We present successes in the application of biotechnology to enhance the productivity of cassava, sweet potato, banana, maize and sorghum in ECA. These products—drought tolerant maize, sorghum resistant to striga, as well as the technology for producing and distributing disease free planting materials of cassava, sweet potato and banana to farmers—are central for the agro-ecological intensification of farming systems in the central African highlands.

Morphological Variation in the Wild-Weedy Complex of Sorghum bicolor In Situ in Western Kenya: Preliminary Evidence of Crop-to-Wild Gene Flow?

Crop wild relatives are important components of agroecosystems and have over the years been exploited in breeding programs as sources of genes for novel traits. Information on the extent and patterns of variability is important in formulating effective conservation and utilization strategies for existing crop wild relative populations. We conducted surveys and collections of wild and weedy accessions of Sorghum bicolor (L.) Moench in Lambwe Valley in western Kenya in order to investigate occurrence, distribution, and morphological variability in the wild-weedy complex of S. bicolor under local agroecological conditions. We also attempted to understand the role, if any, of crop-to-wild gene flow in structuring variability within and among populations. The morphological data presented here showed wide variability within wild-weedy sorghum populations with respect to habitats and morphotypes. True wild sorghum populations in national parks and the sugarcane belt were clearly distinguishable from the putative hybrids or intermediate forms found in sorghum fields, in sorghum field margins, and, to some extent, by the roadside near sorghum fields. The existence of these intermediate forms is empirical evidence of introgression between cultivated sorghum and its wild-weedy relatives. Extensive introgression, especially within in situ conservation areas and/or in areas of high diversity, would lead to genetic erosion and possible depletion of these important wild sorghum genetic resources.