Biology subjects

Devos, K. M.

Publications and source records attributed to Devos, K. M..

5 recordsLinked to original sources

bioRxiv2025

Pan-genome analyses of 226 finger millet-infecting Magnaporthe oryzae strains from eastern Africa reveal two lineages that differ in their genetic make-up, virulence and effector gene content with gene loss driven by homologous recombination between Pot2 elements

Blast disease, caused by the filamentous ascomycete Magnaporthe oryzae, is the main biotic constraint to finger millet production in eastern Africa. M. oryzae is a pathogen on many grass species, but the high host-specificity of blast isolates underscores the need to study pathogen diversity and virulence at the host level. Here, we fill a void on knowledge on finger millet-infecting strains of M. oryzae by sequencing 226 isolates pure-cultured from infected tissues, mainly peduncles and panicles, sampled from field-grown finger millet accessions across Ethiopia, Kenya, Tanzania and Uganda. Phylogenetic analysis showed that eastern African isolates are genetically distinct from Asian isolates, and differentiated into two groups potentially driven by climate variables. One group was dominated by isolates from Kenya and Uganda (KU group), and the other by isolates from Ethiopia and Tanzania (ET group). Analysis of the portfolio of 887 predicted effector genes showed that the KU group had significantly fewer effectors, concomitant with higher virulence levels on the two finger millet accessions tested. We demonstrate that homologous recombination between transposable elements, leading to genomic deletions, plays a key role in gene removal. Transcript profiling of fungal genes in compatible and incompatible interactions revealed upregulation in the incompatible interaction as a characteristic of an estimated 30% of effector genes, including seven of the eight homologs of known avirulence genes from rice-infecting M. oryzae identified in our study. Prioritization of these effectors for functional validation will pave the way for identifying cognate resistance genes and improving finger millet for resistance to blast disease.

plant biology↗

bioRxiv2025

Exploring eco-evolutionary and temporal patterns of arbuscular mycorrhizal fungal communities colonizing Sorghum bicolor across sites of contrasting land use history and climate

Societal Impact StatementSorghum bicolor is a globally important crop, having endpoint uses ranging from human food to animal feed to biofuel production. Sorghum is stress-tolerant and can be grown on marginal land that may be otherwise unsuitable for large-scale food production. Sorghum is therefore a promising candidate for agricultural strategies focused on maximizing production on these marginal lands through beneficial interactions with arbuscular mycorrhizal fungi and other microbes. This study investigates how sorghum genotypes and their interactions with the environment can be leveraged to foster particular AMF assemblages which can be investigated further for their effect on the host plant. Arbuscular mycorrhizal fungal (AMF) symbiosis can influence crop production, but can be variable across environmental conditions, host-partner complementarity and temporal dynamics. Understanding how these factors interact to shape AMF community assembly allows for the selection of crop genotypes that may maximally utilize AMF associations in agricultural systems. We assessed the development of AMF communities colonizing the roots of eight genetically diverse genotypes of Sorghum bicolor across a growing season. We used two field sites with contrasting environments and management histories. Sorghum cultivated in Arizona (AZ) contained low diversity AMF communities, while in Georgia (GA) sorghum harbored more diverse and evenly distributed AMF communities. We observed evidence of host-filtering of AMF communities, though with genotypes displaying more distinct associations in GA than AZ. AZ showed rapid shifts from early Funneliformis mosseae dominance to dominance by either Entrophospora etunicata or Diversispora aurantia. In GA, such drastic abundance shifts were not observed. Instead, consistent temporal turnover was associated more with higher level family abundance patterns driven by the combination of minor variations in multiple low-abundance taxa. Our findings demonstrate that there is potential for leveraging intra-species genetic variation in AMF community assembly as an extended plant phenotype.

ecology↗

bioRxiv2025

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with [~]8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer x Zoysia matrella acc. PI 231146 F2 population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes a MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F1 population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F1 population co-mapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in a MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica x Z. matrella F2 genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

genetics↗

bioRxiv2021

The genome of stress tolerant crop wild relativePaspalum vaginatum leads to increased biomassproductivity in the crop Zea mays

A number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum Paspalum vaginatum is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologous conserved in 6 related grass species placed paspalum as an outgroup of the maize-sorghum clade demonstrating paspalum as their closest sequenced wild relative. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibited significant increases in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, resulting in autophagy dependent increases in biomass accumulation.

plant biology↗

bioRxiv2020

Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ~1920 bin markers spanning ~875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗