Evans Mutegi

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.

Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers

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 agro-climatic 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.

Species-specific SSR alleles for studies of hybrid cattails (Typha latifolia × T. angustifolia; Typhaceae) in North America

UNLABELLED PREMISE Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effects of hybridization. Hybridization between Typha angustifolia and T. latifolia produce long-lived clones, known as Typha ×glauca, which are considered to be invasive. Although morphological variation in cattails makes it difficult to recognize early- and later-generation hybrids, several dominant, species-specific RAPD markers are available. Our goal was to find codominant, species-specific markers with greater polymorphism than RAPDs, to identify later-generation hybrids more efficiently. • METHODS We screened nine SSR (simple sequence repeat) loci that were described from populations in Ukraine, and we surveyed 31 cattail populations from the upper Midwest and eastern USA. • KEY RESULTS Seven SSR loci distinguished the parent taxa and were consistent with known species-specific RAPD markers, allowing easier detection of backcrossing. We used linear discriminant analysis to show that F(1) hybrid phenotypes were intermediate between the parent taxa, while those of backcrossed plants overlapped with the hybrids and their parents. Log(leaf length/leaf width), spike gap length, spike length, and stem diameter explained much of the variation among groups. • CONCLUSIONS We provide the first documentation of backcrossed plants in hybridizing cattail populations in Michigan. The diagnostic SSR loci we identified should be extremely useful for examining the evolutionary and ecology interactions of hybridizing cattails in North America.

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.

The potential for crop to wild hybridization in eggplant (Solanum melongena; Solanaceae) in southern India.

UNLABELLED • PREMISE OF THE STUDY In India and elsewhere, transgenic Bt eggplant (Solanum melongena) has been developed to reduce insect herbivore damage, but published studies of the potential for pollen-mediated, crop- to- wild gene flow are scant. This information is useful for risk assessments as well as in situ conservation strategies for wild germplasm.• METHODS In 2010-2014, we surveyed 23 populations of wild/weedy eggplant (Solanum insanum; known as wild brinjal), carried out hand-pollination experiments, and observed pollinators to assess the potential for crop- to- wild gene flow in southern India.• KEY RESULTS Wild brinjal is a spiny, low-growing perennial commonly found in disturbed sites such as roadsides, wastelands, and sparsely vegetated areas near villages and agricultural fields. Fourteen of the 23 wild populations in our study occurred within 0.5 km of cultivated brinjal and at least nine flowered in synchrony with the crop. Hand crosses between wild and cultivated brinjal resulted in seed set and viable F1 progeny. Wild brinjal flowers that were bagged to exclude pollinators did not set fruit, and fruit set from manual self-pollination was low. The exserted stigmas of wild brinjal are likely to promote outcrossing. The most effective pollinators appeared to be bees (Amegilla, Xylocopa, Nomia, and Heterotrigona spp.), which also were observed foraging for pollen on crop brinjal.• CONCLUSION Our findings suggest that hybridization is possible between cultivated and wild brinjal in southern India. Thus, as part of the risk assessment process, we assume that transgenes from the crop could spread to wild brinjal populations that occur nearby.

Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: Implications for conservation

UNLABELLED • PREMISE OF THE STUDY Crop wild relatives represent important genetic resources for crop improvement and the preservation of native biodiversity. Eggplant (Solanum melongena), known as brinjal in India, ranks high among crops whose wild gene pools are underrepresented in ex situ collections and warrant urgent conservation. Knowledge of outcrossing rates and patterns of genetic variation among wild populations can aid in designing strategies for both in situ and ex situ preservation.• METHODS We used 14 microsatellite (simple sequence repeat) markers to examine genetic diversity, population structure, and outcrossing in 10 natural populations of wild/weedy eggplant (S. insanum = S. melongena var. insanum) and three cultivated populations in southern India.• KEY RESULTS Multilocus FST analyses revealed strong differentiation among populations and significant isolation by distance. Bayesian model-based clustering, principal coordinate analysis, and hierarchical cluster analysis grouped the wild/weedy populations into three major clusters, largely according to their geographic origin. The three crop populations were similar to each other and grouped with two wild/weedy populations that occurred nearby. Outcrossing rates among the wild/weedy populations ranged from 5-33%, indicating a variable mixed-mating system.• CONCLUSION Geographic isolation has played a significant role in shaping the contemporary patterns of genetic differentiation among these populations, many of which represent excellent candidates for in situ conservation. In two cases, close genetic affinity between cultivars and nearby wild/weedy populations suggests that gene flow has occurred between them. To our knowledge, this is the first study investigating population-level patterns of genetic diversity in wild relatives of eggplant.

Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.

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.

Population Genetics and Seed Set in Feral, Ornamental Miscanthus sacchariflorus

Ornamental grasses may become invasive weeds depending on their ability to naturalize and outcompete other species. Miscanthus sacchariflorus (Maxim) Franch. (Amur silvergrass) is a tall, self-incompatible, nonnative grass that has become naturalized in eastern North America, forming monospecific stands and raising concerns about its potential invasiveness. To understand the extent of clonal and sexual reproduction in feral populations, we examined their population genetic structure, seed production, and ploidy. We surveyed 21 populations in Iowa and Minnesota using eight polymorphic microsatellite markers. Only 34 multilocus genotypes (MLGs) were detected from a total of 390 samples. All of the study populations had more than one MLG, thereby allowing cross-pollination with near neighbors, but most were dominated by one or a few MLGs. Low genetic divergence suggests that all populations may have originated from similar cultivars. Cluster analysis showed that the six populations from Minnesota were extremely similar to each other, whereas the 15 populations from Iowa were somewhat more diverse. Seed production was quantified for 20 populations and ploidy for 11 populations. Average seed production was very low (< 0.30 seeds per panicle), although most populations did produce seeds. Because the populations were diploid (2x), they also may have the potential to hybridize with ornamental varieties of Miscanthus sinensis (Chinese silvergrass; eulaliagrass), a diploid close relative. Clonal growth, self-incompatibility, and spatial isolation of compatible clones may contribute to pollen-limited seed set in these populations. Low seed set may affect the rate of spread of feral M. sacchariflorus, which appears to disperse vegetatively as well as by seed. Although this species is not widely viewed as invasive, it is worth monitoring as a species that may become more widespread in the future. Nomenclature: Amur silvergrass, silver banner grass, Miscanthus sacchariflorus (Maxim.) Franch.; Chinese silvergrass, Miscanthus sinensis Anderss. Management Implications: Ornamental perennial grasses may have the potential to become invasive in areas where they can easily naturalize and disperse. In the nonnative genus Miscanthus, unwanted establishment of feral populations of ornamental M. sinensis (Chinese silvergrass) already has occurred in parklands and other areas, primarily in the eastern and southeastern United States. Its close relative, M. sacchariflorus (Amur silvergrass), also establishes feral populations, typically in more northern regions, but these stands are not as widespread as M. sinensis, nor do they produce abundant seeds. Low seed production could be a factor that limits population growth rates in feral M. sacchariflorus. The co-occurrence of genetically distinct individuals is a requirement for cross-pollination and seed set in this clonally reproducing, self-incompatible species. If several cross-compatible individuals occur in close proximity, this might lead to more abundant seed production and subsequent dispersal to other sites. In the current study, we found that feral populations of M. sacchariflorus in Iowa and Minnesota are genetically similar and highly clonal, but more than one genetic individual was present at each of our study sites. At present, we do not know whether M. sacchariflorus is in a temporary “lag phase” that precedes greater invasiveness. In any case, this tall, vigorously clonal perennial is able to establish extensive monospecific stands that crowd out other species, which is why managers of natural areas typically try to eradicate newly established populations. Ornamental plantings of M. sacchariflorus continue to be popular in northern areas of the United States and in southern Canada; this species is more cold tolerant than M. sinensis. The silvery inflorescences of M. sacchariflorus are attractive for landscaping, and the plant is easy to cultivate, but it has the potential to become a nuisance. Therefore, it is prudent to monitor the surrounding area for feral volunteers, which are much easier to eradicate at an early stage compared with after they have propagated clonally to form large stands along ditches, roadsides, wet meadows, and other areas.

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.