Biology subjects

Sidhu, J. S.

Publications and source records attributed to Sidhu, J. S..

10 recordsLinked to original sources

bioRxiv2026

Digging for meaningful connections: associations between root phenotypes and rhizosphere microbial diversity in maize

Drought threatens food security globally. Adaptive root phenotypes and microbiomes can improve maize (Zea mays L.) water uptake and tolerance to drought. However, synergisms between root phenotypes and microbiomes remain underexplored. We aimed to investigate the association between varying root phenotypes and rhizosphere microbiomes under field-scale drought. We grew 22 maize inbred lines in the field under optimal water availability and drought imposed by excluding rain with rainout shelters. We quantified grain yield and measured root architectural and anatomical phenotypes on root crown and cross-section images obtained by laser ablation tomography, respectively. We characterized rhizosphere prokaryotic and fungal communities with DNA metabarcoding of ribosomal markers. Rhizosphere microbial diversity predominantly associated with root anatomy rather than root architecture. Cortical parenchyma wall width explained 13.1% of the variance of the prokaryotic {beta}-diversity and correlated with grain yield under control conditions. Under the same conditions, number of cortical cell files and metaxylem vessels explained 1.4-2.1% of the variance of prokaryotic and fungal {beta}-diversities. No effect of the root phenotypes was observed under drought. We found 248 significant correlations between microbial taxa abundances and root anatomical phenotypes, especially cortex-related phenotypes such as number of cell files and living cortical area. Overall, a greater number of correlations was found under control conditions. We identified root phenotypes explaining a small but significant percentage of the variance of the microbial {beta}-diversity, mostly under optimal water availability. We showed that especially root anatomy is associated with rhizosphere microbial diversity in field-grown maize.

systems biology↗

bioRxiv2026

The MexMAGIC population reveals the genetic architecture of clinal trait variation in Mexican native maize

Defining the genetic basis of local adaptation is fundamental to evolutionary biology and crop improvement. Theory predicts that when selective pressures track differences in the environment, a cline will be established. Such clines might be exploited to uncover adaptive variation by association of alleles with environmental stressors. However, monotonic phenotypic change over a cline is not necessarily mirrored by adaptive genetic variants. Furthermore, population structure can complicate the interpretation of genotype-environment association. To test the assumptions of genotype-environment association in a crop species, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize varieties sourced from distinct agroecological zones. We mapped two clinal traits (tassel branching and flowering time) differing in genetic architecture. Variation in tassel branch number was dominated by a single QTL with allele effects that aligned well with a negative elevational cline. In contrast, we mapped 11 flowering time QTL with allele effects that were not consistently correlated with any one source environmental factor and distinct loci donated by highland and lowland early maturing varieties. Our observations support the theoretical result that genotype-environment association will be strongest under simple genetic architecture, although identification of adaptive alleles may still be confounded by population structure. Plain Language: Nine thousand years of careful selection and cultivation by indigenous farmers has generated a rich diversity of native Mexican maize (corn) varieties, grown from sea level to high mountains, and from jungle to semidesert. By crossing native varieties adapted to different locations, we can uncover important genetic variants conferring tolerance to environmental stressors.

genetics↗

bioRxiv2025

Ploidy alters root anatomy and shapes the evolution of wheat polyploids

Polyploidization played a crucial role in crop domestication and modern agriculture. While increased cell size in polyploids is known to enhance plant biomass and vigor, its impact on soil exploration remains poorly understood. Using wheat as a model, we identify a ploidy-induced belowground domestication syndrome, characterized by (a) increased root cortical cell size reducing root respiration, nitrogen content, and phosphorus content; (b) enlarged metaxylem vessels, increasing axial hydraulic conductance; and (c) blunter root tips, limiting penetration ability in compacted soils. Our empirical and in silico experiments show that reduced root respiration and reduced cellular nutrient content in wheat polyploids improved nutrient use and acquisition efficiency under suboptimal nitrogen and phosphorus availability. These adaptations would have been advantageous in nutrient-depleted agroecosystems of the Pre-Pottery Neolithic B (PPNB) Fertile Crescent, where continuous cultivation depleted soil fertility over time. Functional-structural modeling indicates that larger cortical cells in wheat polyploids increase vacuolar occupancy, reducing root metabolic costs. Enhanced axial hydraulic conducta nce may have improved water transport, an advantage in irrigated PPNB agroecosystems. However, polyploids have blunter root tips, which reduces their penetration ability in compacted soils, making them less suited for native soils with greater mechanical impedance. We propose that root anatomical changes driven by ploidy played an important role in adaptations of wheat domesticates to PPNB agriculture. One-Sentence SummaryPolyploidy induced changes in root anatomy may have improved adaptation of wheat to Neolithic agroecosystems.

plant biology↗

bioRxiv2024

In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacan

Roots are essential for plant adaptation to changing environments, yet the role of roots in crop domestication remains unclear. This study examines the evolution of root phenotypes from teosinte to maize, a transition resulting in reduced nodal root number (NRN), multiseriate cortical sclerenchyma (MCS), and increased seminal root number (SRN). We reconstructed the root phenotypes of maize and teosinte, as well as the environments of the Tehuacan Valley over the last 18,000 years using a combination of ancient DNA, paleobotany, and functional-structural modeling. Our models reveal that increasing Holocene atmospheric CO2 concentrations favored the appearance of reduced NRN and MCS between 12000 to 8000 years before present (yBP), promoting deeper root systems. The advent of irrigation by 6000 yBP switched nitrogen distribution from topsoil to subsoil domains, a change which increased the utility of reduced NRN and MCS. Comparison of allelic frequencies among ancient samples ranging from 5500 to 500 yBP suggest that increased SRN may have appeared around 3500 yBP, coinciding with a period of increased human population, agricultural intensification, and soil degradation. Our results suggest that root phenotypes that enhance plant performance under nitrogen stress were important for maize adaptation to changing agricultural practices in the Tehuacan Valley. ClassificationPhysiology & Development

plant biology↗

bioRxiv2024

Xylem perforation plate phenotypes affect water use and drought adaptation in maize (Zea mays L.)

O_LIRationale: Xylem morphology in annual monocots is important for water use strategies in many agronomically important species. C_LIO_LIMethods: We assess how xylem perforation plates affect water use strategies in maize (Zea mays L.) through in silico modeling, empirical studies under water deficit in controlled environments, and in the field. C_LIO_LIKey Result: Significant genotypic variation for the prominence and frequency of perforation plates was observed in maize germplasm. Perforation plate phenotypes had high heritability, were associated with several QTL, and were pleiotropic across leaves, aerial nodal roots, and subterranean nodal roots. Perforation plate phenotypes did not affect vulnerability to cavitation, but modeling predicted that they should affect axial water transport, which was supported by in situ measurements of root segments. Metaxylem vessel length was correlated with the rate of root elongation, root depth, and deep-water utilization in mesocosms. Under drought stress in the field, variation in xylem vessel length was associated with leaf roll, leaf temperature, transpiration, photosynthesis, and grain yield. C_LIO_LIMain Conclusion: Phenotypic variation for xylem perforation plate phenotypes in maize directly affects axial water conductance and is part of a pleiotropic syndrome with greater root elongation and deeper rooting that improves adaptation to water deficit stress. C_LI

plant biology↗

bioRxiv2023

Cortical parenchyma wall width (CPW) regulates root metabolic cost and maize performance under suboptimal water availability

We describe how increased root cortical parenchyma wall width (CPW) can improve tolerance to drought stress in maize by reducing the metabolic costs of soil exploration. Significant variation (1.0 to 5.0 {micro}m) for CPW was observed within maize germplasm. The functional-structural model RootSlice predicts that increasing CPW from 2 to 4 {micro}m is associated with ca. 15% reduction in root cortical cytoplasmic volume, respiration rate, and nitrogen content. Analysis of genotypes with contrasting CPW grown with and without water stress in the field confirms that increased CPW is correlated with ca. 32 to 42% decrease in root respiration. Under water stress in the field, increased CPW is correlated with 125% increased stomatal conductance, 325% increased leaf CO2 assimilation rate, 73 to 78% increased shoot biomass, and 92 to 108% increased grain yield. CPW was correlated with leaf mesophyll midrib parenchyma wall width, indicating pleiotropy. GWAS analysis identified candidate genes underlying CPW. OpenSimRoot modeling predicts that a reduction in root respiration due to increased CPW would also benefit maize growth under suboptimal nitrogen, which requires empirical testing. We propose CPW as a new phene that has utility under edaphic stress meriting further investigation. Significance StatementSuboptimal water availability is a primary constraint for global crop production that is intensifying due to climate change. The metabolic cost of soil exploration is a critical factor in plant performance under suboptimal water availability. This study highlights how increased root cortical parenchyma wall width (CPW) reduces root metabolic cost and improves crop adaptation to water deficit. Modeling results also indicate that increased CPW would be beneficial under suboptimal nitrogen availability. Therefore, CPW is a promising target for breeding crops with improved water and nitrogen use efficiency.

plant biology↗

bioRxiv2023

Cortical cell size regulates root metabolic cost

It has been hypothesized that vacuolar occupancy in mature root cortical parenchyma cells regulates root metabolic cost and thereby plant fitness under conditions of drought, suboptimal nutrient availability, and soil mechanical impedance. However, the mechanistic role of vacuoles in reducing root metabolic cost was unproven. Here we provide evidence to support this hypothesis. We first show that root cortical cell size is determined by both cortical cell diameter (CCD) and cell length (CCL). Significant genotypic variation for both CCD ([~]1.1 to 1.5- fold) and CCL ([~] 1.3 to 7-fold) was observed in maize and wheat. GWAS and QTL analyses indicate CCD and CCL are heritable and under independent genetic control. We identify candidate genes for both phenes. Empirical results from isophenic lines contrasting for CCD and CCL show that increased cell size, due to either CCD or CCL, is associated with reduced root respiration, root nitrogen content, and root phosphorus content. RootSlice, a functional-structural model of root anatomy, predicts that an increased ratio of vacuolar to cytoplasmic volume causes reduced root respiration and tissue nutrient content. Ultrastructural imaging of cortical parenchyma cells with varying CCD and CCL confirms the in-silico predictions and shows that an increase in cell size is correlated with increased vacuolar volume and reduced cytoplasmic volume. Phylogenetic analysis of terrestrial plants reveals that CCD has not significantly changed throughout plant evolution. Vacuolar occupancy and its relationship with CCD/CCL merits further investigation as a phene for improving crop adaptation to edaphic stress. Significance StatementCortical cell size is an important phene determining root metabolic cost, but the underlying physiological mechanism is unclear. Here, using in silico and empirical approaches, we provide evidence that supports the hypothesis that vacuolar occupancy in cortical parenchyma cells regulates root metabolic cost. We also show that vacuolar occupancy is associated with cortical cell diameter and cell length, phenes that are under distinct genetic control and hold the potential for improving crop yields under edaphic stress.

plant biology↗

bioRxiv2022

RootSlice: a novel functional-structural model for root anatomical phenotypes

Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes. Summary statementRoot anatomy remains an underutilized target for crop breeding. RootSlice, a multicellular functional-structural model of root anatomy, simulates the costs and benefits of diverse root anatomical phenotypes to estimate their utility for plant fitness in unfavorable soil environments.

plant biology↗

bioRxiv2021

Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster

Facial eczema (FE) in grazing ruminants is a debilitating liver syndrome induced by ingestion of sporidesmin, a toxin belonging to the epipolythiodioxopiperazine class of compounds. Sporidesmin is produced in spores of the fungus Pseudopithomyces chartarum, a microbe which colonises leaf litter in pastures. New Zealand has a high occurrence of FE in comparison to other countries as animals are fed predominantly on ryegrass, a species that supports high levels of Pse. chartarum spores. The climate is also particularly conducive for Pse. chartarum growth. Here, we present the genome of Pse. chartarum and identify the putative sporidesmin gene cluster. The Pse. chartarum genome was sequenced using single molecule real-time sequencing (PacBio) and gene models identified. Loci containing genes with homology to the aspirochlorine, sirodesmin PL and gliotoxin cluster genes of Aspergillus oryzae, Leptosphaeria maculans and Aspergillus fumigatus, respectively, were identified by tBLASTn. We identified and annotated an epipolythiodioxopiperazine cluster at a single locus with all the functionality required to synthesise sporidesmin. HighlightsO_LIThe whole genome of Pseudopithomyces chartarum has been sequenced and assembled. C_LIO_LIThe genome is 39.13 Mb, 99% complete, and contains 11,711 protein coding genes. C_LIO_LIA putative sporidesmin A toxin (cause of facial eczema) gene cluster is described. C_LIO_LIThe genomes of Pse. chartarum and the Leptosphaerulina chartarum teleomorph differ. C_LIO_LIComparative genomics is required to further resolve the Pseudopithomyces clade. C_LI

genomics↗

bioRxiv2019

Developmentally Regulated Genome Editing in Terminally Differentiated N2-Fixing Heterocysts of Anabaena cylindrica ATCC 29414

Some vegetative cells of Anabaena cylindrica are programed to differentiate semi-regularly spaced, single heterocysts along filaments. Since heterocysts are terminally differentiated non-dividing cells, with the sole known function for solar-powered N2-fixation, is it necessary for a heterocyst to retain the entire genome ({approx}7.1 Mbp) from its progenitor vegetative cell? By sequencing the heterocyst genome, we discovered and confirmed that at least six DNA elements ({approx}0.12 Mbp) are deleted during heterocyst development. The six-element deletions led to the restoration of five genes (nifH1, nifD, hupL, primase P4 and a hypothetical protein gene) that were interrupted in vegetative cells. The deleted elements contained 172 genes present in the genome of vegetative cells. By sequence alignments of intact nif genes (nifH, nifD and hupL) from N2-fixing cyanobacteria (multicellular and unicellular) as well as other N2-fixing bacteria (non-cyanobacteria), we found that interrupted nif genes all contain the conserved core sequences that may be required for phage DNA insertion. Here, we discuss the nif genes interruption which uniquely occurs in heterocyst-forming cyanobacteria. To our best knowledge, this is first time to sequence the genome of heterocyst, a specially differentiated oxic N2-fixing cell. This research demonstrated that (1) different genomes may occur in distinct cell types in a multicellular bacterium; and (2) genome editing is coupled to cellular differentiation and/or cellular function in a heterocyst-forming cyanobacterium.

microbiology↗