Biology subjects

Leiboff, S.

Publications and source records attributed to Leiboff, S..

7 recordsLinked to original sources

bioRxiv2026

Ontogenetic and time-course transcriptomic analyses of maize leaf primordia reveal regulators of transverse vein development

Leaf vein patterning varies greatly among land plants and is linked to leaf structure and function. C4 plants, such as maize, have a denser arrangement of veins than C3 plants, which is hypothesized to be a pre-adaptive trait for C4 photosynthesis. Therefore, understanding how leaf veins are patterned has implications for maximizing photosynthetic efficiency. Major maize leaf veins, called longitudinal veins, are arranged in parallel and are interconnected by transverse veins. Recent work has established molecular factors controlling longitudinal vein development; however, it is unknown how transverse veins are patterned. Here, we investigated how transverse veins establish connections within the maize vascular network. We performed anatomical analyses of transverse veins and found that despite asynchronous development, transverse veins fully integrate into the longitudinal vein network. Tracing the ontogeny of transverse vein development using the marker PIN1a-YFP, we found that two sets of two initial cells on opposing sides of adjacent longitudinal veins recruit intervening ground cells to form the provascular strand. Treatment with auxin inhibitors did not abolish transverse vein initiation, suggesting an auxin-independent pre-pattern for transverse vein initiation. Through time-course RNAseq of leaf primordia, we identified a transcriptional signature that precedes transverse vein development. Two genes that belong to this gene cluster, EREB41 and EREB114, are necessary for transverse vein formation. Together, our studies establish the ontogeny of maize transverse vein development and reveal how new vascular connections are specified, assembled, and integrated into an existing vascular network.

plant biology↗

bioRxiv2026

BSA101: Unlocking Historical Mutant Collections with BSA-Seq

Forward genetics is a powerful approach for gene discovery, but identifying causal mutations becomes difficult when mutants are maintained in heterogeneous populations with uncertain pedigrees. This is exemplified by classical tasselseed (ts) mutants, which have long served as a genetic model for studying sex determination and carpel suppression. Decades of repeated outcrossing to diverse inbred lines have created substantial genetic heterogeneity, limiting the effectiveness of conventional bulked-segregant analysis sequencing (BSA-Seq). To address this, we developed a BSA-Seq framework that integrates flexible experimental designs, multiple reference genomes, and complementary statistical methods tailored for genetically heterogeneous populations. Applying this framework revealed that reference genome selection is critical for mapping success and that Euclidean distance raised to the fourth power (ED4) outperformed homozygosity mapping (HM). Furthermore, the framework enables simultaneous mapping of multiple mutations within a single population, eliminating the need for additional mapping populations. Applying this framework to 26 ts mutant stocks from the Maize Genetics Cooperation Stock Center, we successfully mapped 24 mutants to genomic intervals containing known ts genes, while the remaining mutants mapped to distinct genomic intervals, defining novel candidate regions underlying carpel suppression. Together, these results demonstrate that historical mutant collections represent an underutilized resource for gene discovery and establish a generalizable mapping strategy for unlocking their genetic potential across diverse species.

plant biology↗

bioRxiv2025

Spatial inheritance patterns across maize ears are associated with alleles that reduce pollen fitness

Significance StatementEarly studies noting uneven spatial distribution of progeny genotypes after pollination support a hypothesis where differences in pollen tube growth rate can bias inheritance. We used computer vision and statistical analysis to show alleles reducing maize pollen fitness are likely to produce statistically significant increasing, decreasing, or curvilinear spatial patterns from the apex of the inflorescence to the base, suggesting that differential pollen tube growth is not the only mechanism at play. SummaryOften, more pollen grains land on recipient flowers than there are ovules to fertilize. Consequently, the haploid male gametophyte engages in post-pollination competition, one way that pollen genotype can influence inheritance. The maize (Zea mays subsp. mays L.) inflorescence (ear), with its elongated stigma and style structures (silks), has a conspicuous spatial heterogeneity, with longer silks at the base of the ear than those at the apex. To evaluate the hypothesis that alleles with reduced pollen fitness influence the spatial distribution of progeny genotypes along the ear, we developed an updated phenotyping platform that maps mutant Ds-GFP kernel phenotypes on the ear via an implementation of the Faster R-CNN machine vision model (EarVision.v2) and a statistical pipeline that evaluates the relationship between kernel position and transmission ratio (EarScape). In our dataset (1384 ears) representing 58 Ds-GFP alleles, none with Mendelian inheritance (0/48) showed any significant pollen-conditioned spatial trend. In contrast, 50% of alleles with a pollen-specific transmission defect (5/10) exhibited significant spatial effects. An insertion into a gene encoding a putative actin-binding protein, base-to-apex gradient1* (bag1*), conditions increased mutant transmission at the ear apex relative to the base. Surprisingly, mutant alleles of two other pollen-expressed genes can generate the opposite pattern, decreased mutant transmission toward the ear apex; and two mutant alleles of the sperm-cell attachment factor, gamete expressed2 (gex2), can produce ears with transmission highest at both base and apex. We conclude that pollen fitness mutants have relatively common but heterogenous effects on the spatial distribution of progeny genotypes.

plant biology↗

bioRxiv2025

Partial retention of ancient function increases genetic pleiotropy in grass evolution

Changes in form are driven by the differential, context-dependent regulation of pleiotropic genes. How genetic pleiotropy itself emerges, however, remains unclear. The maize genes GRASSY TILLERS1 (GT1) and RAMOSA3 (RA3) are required for axillary meristem suppression, a deeply conserved trait across angiosperms, and for floral organ suppression, a trait which evolved within the grass family. To determine how these pleiotropic functions are regulated, we first established a high-throughput method for quantitative phenotyping of grass flowers. Using this method, we show that distinct environmental mechanisms regulate axillary meristem versus floral organ suppression. In line with these differences, we find upstream regulation of GT1 and RA3 has diverged, consistent with their redeployment in flowers. Our results show that, rather than wholesale adoption of genetic networks, developmental genes can retain ancient functions and be recruited into other programs in the evolution of form, thereby increasing genetic pleiotropy.

plant biology↗

bioRxiv2023

Comparing hormone dynamics in cereal crops via transient expression of hormone sensors

Plant hormones are small molecules which elicit profound physiological responses. Although plant hormone biosynthesis and response genes have been critical for agricultural improvement, it has been difficult to experimentally compare hormone biology across species because of complex phenotypic outputs. We used transient expression of genetic hormone sensors and transcriptomics to quantify tissue-specific gibberellic acid (GA) and auxin responses across tissues and genotypes in cereal crops. We found that the FRET-based GPS2 biosensor detects exogenous GA treatments in maize, barley, sorghum, and wheat, in both vegetative and floral tissues. Measuring GPS2 output across GA dosages revealed tissue- and genotype-specific differences in GA sensor response. We observed marked differences in maize vs barley leaves and floral tissues and an unexpected drop in GPS2 output in the maize d1 GA biosynthesis mutant after GA treatment, likely reflecting differences in bioactive GA content, GA transport, and mechanisms of GA response. We then used RNAseq to measure transcriptional responses to GA treatment in leaves from maize wildtype, d1, and barley as well as floral tissues from maize and barley for a cross-tissue, cross-genotype, and cross-species GA-response comparison. After orthology prediction and analysis of within- and cross-species GO-term enrichment, we identified core sets of GA-responsive genes in each species as well as maize- barley orthogroups. Our analysis suggests that downregulation of GA-INSENSITIVE DWARF1 (GID1) and upregulation of -Expansin1 (EXPA1) orthologs comprises a universal GA-response mechanism that is independent of GA biosynthesis, and identifies F-Box proteins, hexokinase, and AMPK/SNF1 protein kinase orthologs as unexpected cross-tissue, cross-genotype, and cross-species GA-responsive genes. We then compared the transient expression of the DR5, DR5v2, and DII-mDII auxin reporters in barley and maize and find that although DR5 did not respond to exogenous auxin in barley, DR5v2 responded to auxin treatment with a similar magnitude as in maize. Both species display auxin-mediated DII degradation that requires the 26S proteasome.

plant biology↗

bioRxiv2020

Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in protein translation

TARGET OF RAPAMYCIN (TOR) is a deeply conserved protein kinase that coordinates eukaryotic metabolism with nutrient availability. In mammals, TOR specifically promotes translation of ribosomal protein mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. Here, we took parallel global profiling approaches to define the in planta TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on the canonical 5' oligopyrimidine tract motif (5'TOP) found in mammalian ribosomal protein mRNAs. To investigate this further, we focused on a putative TOR substrate identified in our phosphoproteome: LARP1, a eukaryotic RNA-binding protein that is proposed to mediate TOR translational control of 5'TOP mRNAs in humans and that has gained increased interest because it associates with SARS-CoV-2. By conducting parallel global profiling experiments with larp1 mutants, we discovered that the TOR-LARP1 signaling axis controls 5'TOP mRNA translation in plants and defined a set of conserved eukaryotic 5'TOP mRNAs that encode cyclins, importins/karyopherins, translation elongation factors, and TCTP1, among others. We then identified novel, plant-specific 5'TOP mRNAs involved in critical biological processes, including ribosome biogenesis, chromatin remodeling, and auxin signaling. Our study illuminates the ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1 in eukaryotic cells.

plant biology↗

bioRxiv2019

Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely-related species with architecturally distinct inflorescences, we collected RNAseq profiles encompassing inflorescence body plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BTx623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNAseq. We used two descriptions of transcriptional conservation to identify hourglass-like developmental stages. Despite short evolutionary ancestry of 12 million years, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an inverse-hourglass model of development. We discuss if agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.\n\nHighlightsO_LITranscript dynamics identify maize tassel and sorghum panicle developmental stages\nC_LIO_LIRandom forest predicts developmental age by gene expression, providing molecular markers and an in silico staging application\nC_LIO_LIMaize and sorghum inflorescences are most similar when committing stem cells to a determinant fate\nC_LIO_LIExpression conservation identifies hourglass-like stage, but transcriptomes diverge, similar to inverse hourglass observations in cross-phyla animal embryo comparisons\nC_LI

plant biology↗