Biology subjects

Wilkin, P.

Publications and source records attributed to Wilkin, P..

9 recordsLinked to original sources

bioRxiv2025

Recurrent evolution of cryptic triploids in cultivated enset increases yield

The high incidence of polyploidy in crops could be explained if domestication involved the selection of polyploids (cytotypes with more than two sets of chromosomes). Ancestral horticulture could have targeted desirable traits including yield, robustness to stress and to disease, rather than requiring knowledge of polyploidy itself. We find evidence for this process underway in enset (Ensete ventricosum, Musaceae) - a highly resilient crop constituting the main staple for over 20 million people in Ethiopia, which is clonally propagated and cultivated for its starch-rich corm and pseudostem. Prior to this study, enset was thought to be exclusively diploid (2n = 2x = 18). Using a newly-assembled chromosome-scale reference genome, and sequence data from 723 wild and domesticated enset individuals from southwestern Ethiopia, we demonstrate that around 20% of cultivated enset clones are triploid. We show that triploidy has arisen multiple times independently, that the triploid lineages have been given distinct landrace names, and planted disproportionately frequently. As well as providing evidence for enduring selection on triploids, our results reveal valuable genetic diversity captured by these triploid lines. They represent key resources for scientifically directed breeding of this major crop in the Ethiopian agrosystem, and could improve food security in sub-saharan Africa. Author SummaryDuplication of a species entire genome (polyploidization) plays an important part in evolution. Domestication may have favoured polyploid crops including wheat, coffee, potato, cotton, strawberry, and banana. It has been proposed that this trend is explained by the selection of advantageous traits exhibited by polyploids compared to their relatives with unduplicated genomes. These desirable traits include bigger fruits, seeds or other edible organs, and better tolerance to stress and disease. We unexpectedly find that a large proportion of cultivated enset lines have three copies of their genome (triploidy) instead of two (diploid). Enset is a highly resilient crop in the banana family; its stem and leaves are processed to provide one of the main food sources for over 20 million people in Ethiopia. Prior to our study, enset was thought to be exclusively diploid. Farmers use landrace names that distinguish diploids from triploids without having this new genetic information, showing the differences between them are recognised and given importance. Triploids were planted disproportionately and appear to grow faster, suggesting they are being selected for their higher productivity. These triploid ensets are an important genetic resource for scientifically directed breeding of new varieties, which could improve food security in sub-saharan Africa.

evolutionary biology↗

bioRxiv2023

Wild edible yams from Madagascar: New insights into nutritional composition support their use for food security and conservation

Yams (Dioscorea species) are an important food resource in Madagascar, where both cultivated winged yam (D. alata) and wild edible yams are consumed. However, there is limited knowledge on the nutrient composition of wild edible yams in Madagascar, and on how they compare with the cultivated winged yam. Therefore, in this study, nine wild edible yam species, one with two subspecies from Madagascar (D. bako, D. buckleyana, D. irodensis, D. maciba, D. orangeana, D. pteropoda, D. sambiranensis subsp. bardotiae and subsp. sambiranensis, D. seriflora and Dioscorea species Ovy valiha), were analysed for their nutrient composition, compared with cultivated D. alata. They include 6/6 of the most favoured wild edible yam species in Madagascar. We present new nutrient composition data (protein, carbohydrate/starch, energy, lipid, {beta}-carotene, minerals) for these nine wild edible yam species and show that they contain comparable levels of lipids and starch to D. alata, but none are better sources of protein than D. alata. We show that D. irodensis contains a significantly higher {beta}-carotene content when compared to all other edible yams analysed, and that D. buckleyana, D. irodensis and D. sambiranensis subsp. bardotiae have a higher calcium content than cultivated D. alata, while all nine wild edible yam species analysed contain a higher iron content, compared to cultivated D. alata. The nutrient composition data presented could provide new incentives to conserve wild edible yams and inform on strategies to select Disocorea species for sustainable cultivation and use, providing opportunities to enhance future food security in Madagascar.

plant biology↗

bioRxiv2022

Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity

O_LICrop diversity plays a major role in underpinning food security. It is especially important to smallholder and subsistence farmers, who often rely on crop diversity for stable and resilient production. Despite this, global expansion of a small pool of major crops and the associated homogenisation of global agricultural systems may decrease on-farm crop diversity. C_LIO_LIWe surveyed 1,369 subsistence farms stratified across climate gradients in the Ethiopian Highlands, to characterise the richness and cultivated area of the 83 edible crops they contained. We further categorise these crops by their period of introduction to Ethiopia. We apply non-metric multidimensional scaling and mixed effects modelling to characterise agrisystem composition and test the impact of crop introductions. C_LIO_LIWe find a significant positive relationship between introduced and indigenous crop richness, suggesting that crop introductions have tended to supplement rather than replace or reduce indigenous crop diversity. Geographically matched farms with higher proportions of introduced crops, had significantly higher overall crop richness. Analysis of socio-economic drivers indicates that both poverty and low accessibility are associated with reduced cultivation of modern introductions. C_LIO_LIWe conclude that global patterns of major crop expansion do not necessarily result in agrobiodiversity loss for subsistence farmers, in our Ethiopian case study. Importantly, socioeconomic factors may strongly influence the farmers propensity to adopt novel species, suggesting targets for agricultural extension policies. Given the rapid climatic, economic and demographic changes impacting global food systems and the threats to food security these entail, robust indigenous agricultural systems supplemented with diverse introduced crops may enhance resilience. C_LI

ecology↗

bioRxiv2021

Distinct within-host bacterial populations ensure function, colonization and transmission in leaf symbiosis

Hereditary symbioses have the potential to drive transgenerational effects, yet the mechanisms responsible for transmission of heritable plant symbionts are still poorly understood. The leaf symbiosis between Dioscorea sansibarensis and the bacterium Orrella dioscoreae offers an appealing model system to study how heritable bacteria are transmitted to the next generation. Here, we demonstrate that inoculation of apical buds with a bacterial suspension is sufficient to colonize newly-formed leaves and propagules, and to ensure transmission to the next plant generation. Flagellar motility is not required for movement inside the plant, but is important for the colonization of new hosts. Further, stringent tissue-specific regulation of putative symbiotic functions highlight the presence of two distinct subpopulations of bacteria in the leaf gland and at the shoot meristem. We propose that bacteria in the leaf gland dedicate resources to symbiotic functions, while dividing bacteria in the shoot tip ensure successful colonization of meristematic tissue, glands and propagules. Compartmentalization of intra-host populations, together with tissue-specific regulation may serve as a robust mechanism for the maintenance of mutualism in leaf symbiosis. ImportanceSeveral plant species form associations with bacteria in their leaves, called leaf symbiosis. These associations are highly specific, but the mechanisms responsible for symbiont transmission are poorly understood. Using the association between the yam species Dioscorea sansibarensis and Orrella dioscoreae as a model leaf symbiosis, we provide experimental evidence that bacteria are transmitted vertically and distributed to specific leaf structures via association with shoot meristems. Flagellar motility is required for initial infection, but does not contribute to spread within host tissue. We also provide evidence that bacterial subpopulations at the meristem or in the symbiotic leaf gland differentially express key symbiotic genes. We argue that this separation of functional symbiont populations, coupled to tight control over bacterial infection and transmission, explain the evolutionary robustness of leaf symbiosis. These findings may provide insights into how plants may recruit and maintain beneficial symbionts at the leaf surface.

microbiology↗

bioRxiv2021

Modelling potential range expansion of an underutilised food security crop in Sub-Saharan Africa

Despite substantial growth in global agricultural production, food and nutritional insecurity is rising in Sub-Saharan Africa. Identification of underutilised indigenous crops with useful food security traits may provide part of the solution. Enset (Ensete ventricosum) is a perennial banana relative with cultivation restricted to southwestern Ethiopia, where high productivity and harvest flexibility enables it to provide a starch staple for ~20 million people. An extensive wild distribution suggests that a much larger region may be climatically suitable for cultivation. Here we use ensemble ecological niche modelling to predict the potential range for enset cultivation within southern and eastern Africa. We find contemporary bioclimatic suitability for a 12-fold range expansion, equating to 21.9% of crop land and 28.4% of the population in the region. Integration of crop wild relative diversity, which has broader climate tolerance, could enable a 19-fold expansion, particularly to dryer and warmer regions. Whilst climate change may cause a 37% - 52% reduction in potential range by 2070, large centres of suitability remain in the Ethiopian Highlands, Lake Victoria region and the Drakensberg Range. We combine our bioclimatic assessment with socioeconomic data to identify priority areas with high population density, seasonal food deficits and predominantly small-scale subsistence agriculture, where integrating enset may be particularly feasible and deliver climate resilience. When incorporating the genetic potential of wild populations, enset cultivation might prove feasible for an additional 87.2 - 111.5 million people, 27.7 - 33 million of which are in Ethiopia outside of ensets current cultivation range. Finally, we consider explanations why enset cultivation has not expanded historically, and ethical implications of expanding previously underutilised species.

ecology↗

bioRxiv2020

The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces

BackgroundEnset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed and fiber. It contributes to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. Socio-economic changes and the loss of indigenous knowledge might lead to the decline of important medicinal landraces and their associated genetic diversity. However, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity ResultsWe evaluated the genetic diversity of 51 enset landraces of which 38 have reported medicinal value. A total of 38 alleles were detected across the 15 SSR loci. AMOVA revealed that 97.6% of the total genetic variation is among individual with an FST of 0.024 between medicinal and non-medicinal landraces. A neighbor-joining tree showed four separate clusters with no correlation to the use values of the landraces. Principal coordinate analysis also confirmed the absence of distinct clustering between the groups, showing low differentiation among landraces used in traditional medicine and those having other use values. ConclusionWe found that enset landraces were clustered irrespective of their use value, showing no evidence for genetic differentiation between enset grown for medicinal uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, a product of interaction with the environment or management practice, or partly misreported. The study provide baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces

genetics↗

bioRxiv2020

The Distribution of Enset Pests and Pathogens and a Genomic Survey of Enset Xanthomonas Wilt

Mapping the distribution of crop pests and pathogens is essential to safeguard food security and sustainable livelihoods. However, these data are unavailable for many neglected and underutilised crops, particularly in developing countries. In Ethiopia, the worlds largest historic recipient of food aid, the indigenous banana relative enset (Ensete ventricosum) is threatened by multiple pests and pathogens whilst providing the staple starch source for 20 million people. Foremost among these is Xanthomonas Wilt of enset (EXW), caused by Xanthomonas vasicola pv. musacearum (Xvm), a globally important disease of bananas (Musa sp.) that likely originated in enset. Here we collate 1069 farm surveys to map the distribution and relative prevalence of enset pests and pathogens across the entire enset growing region. We find that EXW is the most frequently encountered pathogen, and that farmers consistently ranked EXW as the most significant constraint on enset agriculture. Our surveys also showed that corm rot, and the pests root mealybug, mole rat and porcupine are all virtually ubiquitous. Finally, we apply genotyping-by-sequencing to the detection of Xvm and demonstrate that it is present even in asymptomatic domesticated and wild enset samples, suggesting that management of plants displaying symptoms alone may not be sufficient to reduce disease transmission. Holistic understanding of pests and pathogen distributions in enset may have significant benefits for both food security in Ethiopia, and preventing proliferation in related crops such as banana across central and east Africa.

ecology↗

bioRxiv2020

Germination ecology of wild and domesticated Ensete ventricosum: Evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop

O_LILoss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop. C_LIO_LIWe examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterise optimum germination requirements. C_LIO_LIWe report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution. C_LIO_LIOur findings provide evidence that sexual reproductive capacity has been maintained despite long-term near-exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology, may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding. C_LI

ecology↗

bioRxiv2019

Micronutrient composition and microbial community analysis across diverse landraces of the Ethiopian orphan crop enset

Enset (Ensete ventricosum) is a major starch staple and food security crop for 20 million people. Despite substantial diversity in morphology, genetics, agronomy and utilization across its range, nutritional characteristics have only been reported in relatively few landraces. Here, we survey nutritional composition in 22 landraces from three enset growing regions. We present mineral characterization of enset corm tissue, free amino acid characterization of raw and processed (fermented) tissues and genomic analysis of the microbial community associated with fermentation. We show that compared to regionally important tubers and cereals, enset is high in calcium, iron, potassium and zinc and low in sodium. We report changes in free amino acid composition due to processing, and establish that the bacteria genera Acetobacter, Lactobacillus and Bifidobacterium, predominate during fermentation. Nutritional and microbial variation presents opportunities to select for improved composition, quality or safety with potentially significant impacts in food security and public health.

plant biology↗