Biology subjects

Runo, S.

Publications and source records attributed to Runo, S..

7 recordsLinked to original sources

bioRxiv2026

Expanding the repertoire of suicidal germination stimulants for control of parasitic weeds

Witchweeds (Striga spp.) are parasitic plants that severely constrain cereal production across sub-Saharan Africa, threatening food security for millions of people (Runo and Kuria, 2018). Striga infection begins when dormant seeds germinate in response to host-derived biomolecules, primarily strigolactones which plants emit to regulate shoot branching and to communicate with beneficial microbes. This obligate dependence on host signals can be exploited for Striga control through suicidal germination, whereby strigolactone-like compounds induce parasite germination in the absence of a host. Although this strategy proved highly effective during Striga eradication efforts in the United States using ethylene gas as a Striga germination inducer (Eplee, 1975; Iverson et al., 2011), its deployment in Africa has been limited by capacity to synthesize cost-effective strigolactone-like Striga germination inducers. Here, we show that structure-guided in silico screening of chemical libraries using AlphaFold2-modeled receptor-ligand interactions improve the efficiency and likelihood of identifying previously unknown strigolactone analogs. Using this approach, we identify a structurally simple synthetic lactone scaffold that induces Striga germination at nanomolar concentrations. These results present new avenues for the development of strigolactone analogs and support revisiting suicidal germination as a practical Striga control strategy in Africa.

plant biology↗

bioRxiv2025

Strigolactone effects on Sorghum bicolor ecophysiology and symbioses

Strigolactones are ecologically, developmentally, and physiologically important hormones, but much remains unknown about their evolution and role in non-model species. Sorghum is a globally important C4 cereal and exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to parasitic plants, but with evidence for potential trade-offs. We studied sorghum mutants of loci in the strigolactone biosynthetic pathway, CAROTENOID CLEAVAGE DIOXYGENASE 8 (SbCCD8b) and LOW GERMINATION STIMULANT 1 (LGS1), previously shown to be Striga resistant by stimulating little germination of the parasite. SbCCD8b CRISPR-Cas9 deletions changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and diminished the establishment and benefit of mycorrhizal symbionts. For Striga-resistant LGS1 CRISPR-Cas9 deletions, differentially expressed genes were enriched with promoter motifs for stress response and growth pathways, net carbon assimilation rate was reduced, and the colonization of mycorrhizal symbionts was delayed. We additionally restored functional LGS1 into the RTx430 genetic background, which normally has the lgs1-2 natural deletion allele. While root exudates from LGS1 insertion mutants rescued Striga susceptibility, we did not see consistent rescue of other traits impacted in LGS1 loss-of-function mutants. We hypothesize that epistasis with a neighboring strigolactone synthesis gene, which is rarely lost without concomitant loss of LGS1, may alter the phenotypic effects of LGS1 variation. Our study gives context to potential trade-offs associated with host resistance to parasitic plants and, more broadly, builds on the contribution of strigolactones in shaping sorghum physiological processes, growth, and development.

plant biology↗

bioRxiv2025

Delivering trait-enhanced varieties to African smallholders through a pangenomic breeding network

Pangenomics has been promoted to accelerate breeding of orphan crops, but smallholder farmers in developing nations have seen little benefit so far. To address this gap, we built a global pangenomic breeding network, integrating African breeding programs, U.S. land grant universities, and international nonprofit research organizations. Here we demonstrate that pangenomics, when integrated with local crop improvement knowledge and global scientific partnerships, can facilitate breeding of drought and pest resilient varieties for smallholders. To breed trait-enhanced sorghum varieties with lgs1-1 resistance to witchweed (Striga hermonthica) for smallholders in Niger, one of the worlds least developed nations, we used population genomics across local and global scales to develop lgs1-1 Striga resistance markers, and deployed them for rapid introgression of resistance into locally-preferred varieties. Genomic characterization, along with controlled experiments in laboratory, pot, field stations, and smallholder farms, confirmed lgs1-1 resistance was introgressed without loss of essential local-preference traits. New pangenomic resources, including global resequencing and graph pangenomes, further accelerated design of broadly-applicable markers. Unlocking the potential of pangenomics for stress-resilience breeding depended on stakeholder input, strong inference, South-led decision support software, and a dense collaborative network. The experience of the network provides a scalable roadmap for collaborative pangenomic breeding of trait-enhanced varieties for the worlds lowest-resourced farmers.

genomics↗

bioRxiv2025

Genomics of Root System Architecture Adaptation in Sorghum under Nitrogen and Phosphorus Deficiency

Plant root systems play a crucial role in water and nutrient uptake so understanding the genetic mechanisms underlying root architecture adaptation to the environment is key, particularly in non-model crops. Here, we investigate the diversity of root system architecture (RSA) in Sorghum bicolor under nitrogen (N) and phosphorus (P) deficiency. We used a globally diverse sorghum panel to identify single nucleotide polymorphisms (SNPs) associated RSA responses under N and P deficiency through a genome-wide association study (GWAS). RSA adaptation under P deficiency involved development of fine exploratory roots marked by increased total root length and fine root classes (root length diameter ranges 1 and2), coupled with reduced radial expansion. Under N deficiency, adaptation also involved suppression of root radial growth but without elongation. In both cases, reduced radial growth was marked by reduced surface area and volume, more dramatically for P than N deficiency. GWAS identified SNPs associated with these RSA adaptations, some of which were in regions encoding genes such as: ILR3-like, bHLH, and a LEUNIG homolog all with known roles in root growth regulation. These findings provide novel genetic insights into sorghum root adaptation to nutrient limitations and offer potential targets for breeding resource-efficient crop varieties. SummaryPlants absorb water and nutrients from the soil through their roots, yet for most crops, little is known about how root shape and structure adapt to stressful conditions such as poor soil fertility. In this study, we used a globally diverse collection of sorghum genotypes to investigate how sorghum roots respond to nitrogen and phosphorus deficiency. Specific genotypes showed strong root adaptations under these conditions, leading us to identify genetic factors significantly associated with these responses. Our findings improve our understanding of root adaptation to nutrient stress and highlight promising genetic targets for breeding more nutrient-efficient crops.

genomics↗

bioRxiv2022

A transcriptome atlas of Striga hermonthica germination

Societal Impact StatementWitchweeds, parasitic plants of the genus Striga, are nicknamed "cereal killers" because of their devasting destruction of Africas most staple cereals, including maize, sorghum, millets, and upland rice. The parasite relies on biomolecules emitted from the host roots to germinate and therefore initiate its infectious lifecycle. Some sorghum varieties have evolved to not produce effective germination stimulants, making them resistant to the parasite. Here, we assess genetic factors that underpin Striga germination. We discuss how such knowledge can be used to develop new Striga management strategies through the disruption of host-parasite communication exchange. SummaryO_LISeeds of the parasitic plant Striga are dormant. They only germinate in response to biomolecules emitted from the hosts root exudate, strigolactones (SL). But, it is now emerging that Striga germination is a much more complex process regulated by crosstalk of hormone signaling pathways. C_LIO_LITo further understand the genetic basis of the communication exchange between Striga and its host sorghum, we performed a comparative transcriptomic analysis. We sought to identify major transcriptomic changes that define the germination process in Striga and a set of genes that may contribute to the differences in germination rates. C_LIO_LIResults showed that germination proceeds immediately after SL perception and is marked by a wave of transcriptional reprogramming to allow for metabolic processes of energy mobilization. Cluster analysis using self-organizing maps (SOMs) revealed a time-phased and genotype-differentiated response to germination stimulation. The variation in germination was also a function of hormonal crosstalk. The early germination stage was associated with significant repression of genes in the abscisic acid (ABA) biosynthesis pathway. Other hormones influenced germination as follows: (i) ABA and auxin repressed germination, (ii) brassinosteroid, ethylene and jasmonic acid promoted germination, and (iii) cytokinin had a more prominent role post-germination rather than during germination. Perception of SL sets the germination programme leading to different rates of germination in sorghum followed by a complex hormonal regulation network that acts to either repress or enhance germination. These results have far-reaching implications for developing Striga management strategies by disrupting hormonal communication exchange. C_LI

plant biology↗

bioRxiv2022

Resolving intergenotypic Striga resistance in sorghum

Genetic underpinnings of host-pathogen interactions in the parasitic plant Striga hermonthica,a root parasitic plant that ravages cereals in sub-Saharan Africa, are unclear. We performed a comparative transcriptome study on five genotypes of sorghum exhibiting diverse resistance responses to S. hermonthica using weighted gene co-expression network analysis (WGCNA). We found that S. hermonthica elicits both basal and effector-triggered immunity - like a bona fide pathogen. Resistance response was genotype-specific. Some resistance responses followed the salicylic acid-dependent signaling pathway for systemic acquired resistance characterized by cell wall reinforcements, lignification and callose deposition while in others the WRKY-dependent signaling pathway was activated leading to a hypersensitive response (HR). In some genotypes, both modes of resistance were activated while in others, either mode dominated the resistance response. Cell-wall-based resistance was common to all sorghum genotypes but strongest in IS2814, while HR-based response was specific to N13, IS9830 and IS41724. WGCNA further allowed for pinpointing of S. hermonthica resistance causative genes in sorghum. Some highlights include a Glucan synthase-like 10, a pathogenesis-related thaumatin-like family, and a phosphoinositide phosphatase gene. Such candidate genes will form a good basis for subsequent functional validation and possibly future resistance breeding. HighlightParasitic plants of the Striga genus are major pests to cereals in Africa. We pinpointed genetic causes of Striga resistance in sorghum that can be harnessed for future resistance breeding.

plant biology↗

bioRxiv2020

Physiological and ecological warnings that Dodder pose an exigent threat to farmlands in Eastern Africa

Invasive holoparasitic plants of the genus Cuscuta (dodder) threaten Africas ecosystems, due to their rapid spread and attack on various host plant species. Most Cuscuta species cannot photosynthesize, hence rely on host plants for nourishment. After attachment through a peg-like organ called a haustorium, the parasites deprive hosts of water and nutrients leading to their death. Despite their rapid spread in Africa, dodders have attracted limited research attention, although data on their taxonomy, host range and epidemiology are critical for their management. Here, we combine taxonomy and phylogenetics to reveal presence of field dodder (Cuscuta campestris) and C. kilimanjari (both either naturalized or endemic to East Africa), and for the first time in continental Africa, presence of the giant dodder (C. reflexa) a south Asian species. These parasites have a wide host range, parasitizing species across 13 angiosperm orders. Evaluating the possibility of C. reflexa to expand this host range to tea, coffee, and mango, crops of economic importance to Africa, revealed successful parasitism, following haustorial formation and vascular bundle connections in all three crops. However, only mango mounted a successful post-attachment resistance response. Furthermore, species distribution models predicted high habitat suitability for all three Cuscuta species across major tea- and coffee-growing regions of Eastern Africa, suggesting an imminent risk to these crops. Our findings provide relevant insights into a little-understood threat to biodiversity and economic wellbeing in Eastern Africa, and providing critical information to guide development of management strategies to avert their spread. Sentence SummaryMicroscopy and habitat suitability modeling provide an early warning that dodders invasion in Eastern Africa poses a threat to important cash crops

ecology↗