Biology subjects

Perez-Perez, J. M.

Publications and source records attributed to Perez-Perez, J. M..

6 recordsLinked to original sources

bioRxiv2026

Multi-trait evaluation of a tomato MAGIC population identifies promising lines with improved nitrogen use efficiency (NUE)

Nitrogen-use efficiency (NUE) is a pivotal breeding target in tomato (Solanum lycopersicum L.) to sustain production under reduced N inputs. Here, we leveraged a recently developed tomato multi-parent advanced generation inter-cross (ToMAGIC) population to identify lines with superior performance under reduced N availability. The eight founders and a core subset of 118 ToMAGIC lines were characterized with 10,684 SNP markers and evaluated under optimal (opN, 15 mM) and suboptimal (subN, 8 mM) N supply in an experiment totalling 1,576 plants, generating 48,068 data points across 61 phenotypic variables. Under both N treatments, ToMAGIC lines exhibited transgressive segregation for most traits, confirming the value of this population as a reservoir of untapped variation. Notably, under subN conditions, harvest index (Hi) increased by 29-44%, suggesting adaptive resource redistribution toward reproductive sinks. Variance partitioning revealed that agronomic and NUE-related traits were largely under genetic control, with heritability estimates frequently above 0.80 and broadly conserved across N treatments. Multivariate trait analysis identified fruit yield N concentration (NUE component, CN,y), shoot biomass N content (NAb), and shoot growth-related traits as the main drivers of treatment differentiation. Finally, proxy traits were prioritized by integrating response magnitude, heritability, trait correlations, and treatment-discriminatory power into multi-trait selection indices. This strategy generated favorable predicted genetic gains, reaching 158% for high-performance lines and 170% for subN-adapted lines, and consistently identified lines 402, 428, 518, 800, and 816 as promising pre-breeding materials. Overall, this study supports ToMAGIC as a powerful resource for developing N-efficient cultivars suited for sustainable agriculture.

plant biology↗

bioRxiv2026

Arabidopsis RETINOBLASTOMA-RELATED controls cell size during plant development in a dose-dependent manner

The RETINOBLASTOMA-RELATED (RBR) protein in plants functions as a cell-cycle inhibitor, regulating cell numbers in developing organs and establishing cellular quiescence during growth. Although the role of RBR counterparts in animals also involves regulating cell size, this potential function remains unexplored in plants. We investigated transgenic Arabidopsis plants with altered RBR levels and observed corresponding changes in cell size from embryogenesis through organ development. In addition, stomatal meristemoid cells with reduced RBR levels divided beyond the size threshold, whereas elevated RBR levels increased their size. RBR stimulated terminal differentiation in the stomatal lineage by inducing MUTE and CYCLIN D5;1 expression, whereas reduced RBR levels maintained asymmetric divisions through high SPEECHLESS and CYCLIN D3;1 expression. Interestingly, the cell proliferation-dependent phosphorylation of RBR at the conserved 911Ser site positively correlated with RBR protein levels in the transgenic lines and aligned with the effect of RBR on cell size. This study discusses the potential link between RBRs control of cell proliferation and cell size, providing new insights into the coordinated regulation of plant development.

plant biology↗

bioRxiv2025

Role of the tomato MARS1/ROUGH gene encoding a LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 in adventitious root and fruit skin formation

In contrast to animals, plants have a high regenerative capacity, and they can form new organs and even complete individuals from a few cells present in adult tissues, either in response to injury or to the alteration of their environment. In this study, we describe the isolation and characterization of the more adventitious roots1-1 (mars1-1) mutant, which exhibits enhanced regenerative potential upon wounding in tomato hypocotyl explants. Additionally, the mars1-1 fruits exhibited a rough surface due to the ectopic proliferation of subepidermal cells, which formed callus-like structures on the cuticle. The MARS1/ROUGH gene encodes a conserved lysine-specific histone demethylase, SlLSD1, which regulates a variety of processes in metazoans, including cell proliferation, stem cell pluripotency, and embryogenesis. Two CRISPR/Cas9 null alleles, mars1-2 and mars1-3, were generated and their pleiotropic phenotype was characterized. We found elevated levels of H3K4me1 in mars1/rough seedlings, which suggests that SlLSD1 is required for the demethylation of this histone mark. To ascertain the impact of altered epigenetic marks in the mars1/rough mutants on gene expression regulation, we conducted a transcriptome analysis using a variety of RNA-Seq studies on tomato hypocotyls. By employing specific bioinformatic workflows and leveraging on the resolution of directional RNA-Seq data, we have identified over several dozen distinct genomic regions that exhibit de novo expression in the mars1/rough mutants. One such region includes a novel B-type cyclin gene, which is upregulated in the mars1/rough mutants and may account for the observed phenotypes. Our findings indicate that SlLSD1 plays a role in the establishment and maintenance of silencing in specific genomic regions that are essential for tissue-specific reprogramming.

plant biology↗

bioRxiv2022

Mapping of the Classical Mutation rosette Highlights a Role for Calcium in Wound-induced Rooting

Removal of the root system induces the formation of new roots from the remaining shoot. This process is primarily controlled by the phytohormone auxin which interacts with other signals in a yet unresolved manner. Here, we study the classical tomato mutation rosette (ro) which lacks shoot-borne roots. ro plants were severely inhibited in the formation of wound-induced roots and have reduced rates of auxin transport. We mapped ro to the tomato ortholog of the Arabidopsis thaliana BIG and the mammalians UBR4/p600. RO/BIG is a large protein of unknown biochemical function. In A. thaliana, BIG was implicated in the regulation of auxin transport and calcium homeostasis. We show that exogenous calcium inhibits wound-induced root formation in both tomato and A. thaliana ro/big mutants. Exogenous calcium antagonized the root-promoting effects of the auxin IAA, but not of 2,4-D, an auxin analog that is not recognized by the polar transport machinery, and accumulation of the auxin transporter PIN1 was sensitive to calcium levels in the ro/big mutants. Consistent with a role for calcium in mediating auxin transport, both ro/big mutants and calcium-treated wild-type plants were hypersensitive to treatment with polar auxin transport inhibitors. Subcellular localization of BIG suggests that like its mammalian ortholog, it is associated with the endoplasmic reticulum (ER). Analysis of subcellular morphology revealed that ro/big mutants exhibited disruption in cytoplasmic streaming. We suggest that RO/BIG maintain auxin flow by stabilizing PIN membrane localization, possibly by attenuating the inhibitory effect of Ca2+ on cytoplasmic streaming.

plant biology↗

bioRxiv2021

Methods for in situ quantitative root biology

When dealing with plant roots, a multi-scale description of the functional root structure is needed. Since the beginning of XXI century, new devices like laser confocal microscopes have been accessible for coarse root structure measurements, including 3D reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitatively determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for three-dimensional (3D) analysis of root features at single cell resolution, including root asymmetry, lateral root analysis, xylem and phloem structure, cell cycle kinetics, and chromatin determination. Quantitative maps of the distal and proximal root meristems are shown for different species, including Arabidopsis thaliana, Nicotiana tabacum and Medicago sativa. A 3D analysis of the primary root tip showed divergence in chromatin organization and cell volume distribution between cell types and precisely mapped root zonation for each cell file. Detailed protocols are also provided. Possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

plant biology↗

bioRxiv2021

Tissue-specific metabolic reprogramming during wound induced de novo organ formation in tomato hypocotyl explants

O_LIPlants have remarkable regenerative capacity, which allows them to survive tissue damaging after biotic and abiotic stress. Some of the key transcription factors and the hormone crosstalk involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ regeneration. C_LIO_LIHere, we performed detailed transcriptome analysis and targeted metabolomics approach during de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways after wounding. C_LIO_LIOur results indicate that callus growth in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of the photorespiratory pathway and the differential regulation of photosynthesis-related genes and of the gluconeogenesis pathway. C_LIO_LIThe endogenous pattern of ROS accumulation in the apical and basal region of the hypocotyl during the time-course were dynamically regulated, and contributed to tissue-specific wound-induced regeneration. C_LIO_LIOur findings provide a useful resource for further investigation on the molecular mechanisms involved in wound-induced organ formation in a crop species such as tomato. C_LI One-sentence SummaryMetabolic switch during wound-induced regeneration

plant biology↗