Biology subjects

Bennetzen, J. L.

Publications and source records attributed to Bennetzen, J. L..

7 recordsLinked to original sources

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

Leaf stage and roasting shape methylxanthine levels, chlorogenic acid, and overall metabolic profile of Ilex vomitoria leaf extracts

Yaupon holly (Ilex vomitoria) is a shrub native to the southeastern US whose leaves can be roasted and brewed into a caffeinated infusion. While production and consumption of yaupon tea is growing, not much is known about what influences downstream levels of caffeine and other metabolites within the leaf. To address this question, we used ultra-high performance liquid chromatography-mass spectrometry to measure the effect of leaf stage and roasting on the metabolome of yaupon leaves. We found caffeine levels strongly decreased with leaf stage but were not significantly affected by roasting. We also tentatively identified 100 chemicals that were dramatically increased by roasting, including several lactones and probable Maillard products related to known flavor compounds. These findings will help the yaupon tea industry produce a more consistent and tailored product, as well as lend insight into how leaf biochemistry changes over time.

biochemistry↗

bioRxiv2024

Microbial Partner (MiPner) Analysis

Although a few bacteria have been studied in great depth, relatively little is known about the characteristics of microbe-microbe interactions that occur within ecosystems on a daily basis. A simple, robust technique was developed to set up the foundation for investigating pairwise bacterial-bacterial interactions, using cell-cell binding as a self-selective mechanism to identify interesting bacterial species pairs. Using a Serratia marcescens strain (SMC43) isolated from Georgia soil as a "bait", specific bacteria were purified by their specificity in binding SMC43 bacteria that were themselves attached to a wooden applicator stick. The isolated Microbial Partners (MiPners) were greatly enriched for members of the genera Sphingobium and Caulobacter. Two out of 24 streaked MiPners were unable to be separated from, and grow on the plate type tested without, SMC43. This suggests that the MiPner technology will be one strategy for purifying bacteria that were previously recalcitrant to culturing.

microbiology↗

bioRxiv2024

Iron-induced Transcriptional and Microbiome Changes in Host Roots Associated with Drought Tolerance in Sorghum

Drought stress significantly impairs growth, and microbial interactions in sorghum. This study explores the transcriptional and microbial shifts in sorghum under drought, revealing key adaptations to water deficit. LC-MS (Liquid Chromatography-Mass Spectrometry) analyses revealed that drought stress induced abscisic acid while significantly reducing jasmonic acid levels in sorghum roots, likely due to resource conservation strategies during drought. Transcriptional reprogramming highlighted the upregulation of genes in the roots involved in mineral homeostasis (Ferritin 1, Iron dehydrogenase, Nitrate transporter 1), hormone signaling (Ethylene-insensitive protein 3, Gibberellin 2-oxidase), and osmotic regulation (Aquaporin, Dehydrin), underlining key adaptive responses to maintain nutrient uptake, redox status, and cellular turgor. In Fe-supplemented plants, increased Fe in roots correlated with increased Ferritin 1 expression, improved plant health, and reduced Fenton reaction rate and H O levels. This suggests that ferritin helps minimize oxidative stress under drought in sorghum. Drought reduced root-associated bacterial diversity and richness while enriching drought tolerance-associated genera, such as Burkholderia, Caballeronia and Paraburkholderia, known for promoting plant growth through auxin production, phosphate solubilization, and siderophore-mediated iron acquisition. In contrast, fungal diversity and richness remained unchanged, dominated by Talaromyces, which showed a statistically non-significant increase under drought. Random forest models could not identify functional predictors for fungi but revealed a shift in bacterial functional groups under drought, with enrichment in phototrophy, methylotrophy, and nitrate reduction, traits emphasizing microbial roles in nutrient cycling and drought adaptation of sorghum. This study provides insights into the role of ferritin and potential bacterial bioinoculants that could enhance sorghum resilience to drought. Future research should validate these findings to integrate them into breeding programs and biofertilizer formulation for drought-tolerant sorghum and climate-resilient agriculture.

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↗

bioRxiv2019

Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Despite its overall importance to small-scale farmers and communities in Africa, teff suffers from low production compared to other cereals because of limited intensive selection and molecular breeding. Here we report a chromosome-scale genome assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintained as syntenic gene pairs. Through analyzing the history of transposable element activity, we estimate the teff polyploidy event occurred [~]1.1 million years ago (mya) and the two subgenomes diverged [~]5.0 mya. Despite this divergence, we detected no large-scale structural rearrangements, homoeologous exchanges, or bias gene loss, contrasting most other allopolyploid plant systems. The exceptional subgenome stability observed in teff may enable the ubiquitous and recurrent polyploidy within Chloridoideae, possibly contributing to the increased resilience and diversification of these grasses. The two teff subgenomes have partitioned their ancestral functions based on divergent expression patterns among homoeologous gene pairs across a diverse expression atlas. The most striking differences in homoeolog expression bias are observed during seed development and under abiotic stress, and thus may be related to agronomic traits. Together these genomic resources will be useful for accelerating breeding efforts of this underutilized grain crop and for acquiring fundamental insights into polyploid genome evolution.

plant biology↗

bioRxiv2017

Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

plant biology↗