Luis Herrera-Estrella

• PhD
• Professor Emeritus at Center for Research and Advanced Studies of the National Polytechnic Institute

Cotton fibers are single cells that develop from the epidermal cells in the outer integument of developing seeds. The processes regulating fiber cell development have been extensively studied; however, the spatiotemporal transcriptome and metabolome profiles during the early stages of fiber development remain largely unknown. In this study, we prof...

Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic e...

Extreme dryness is lethal for nearly all plants, excluding the so‐called resurrection plants, which evolved vegetative desiccation tolerance (VDT) by recruiting genes common in most plants. To better understand the evolution of VDT, we generated chromosome‐level assemblies and improved genome annotations of two Selaginella species with contrasting...

Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Sub...

Growth of the toxic alga Prymnesium parvum is hormetically stimulated with environmentally relevant concentrations of glyphosate. The mechanisms of glyphosate hormesis in this species, however, are unknown. We evaluated the transcriptomic response of P. parvum to glyphosate at concentrations that stimulate maximum growth and where growth is not dif...

Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and play a crucial role in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice ( Oryza sativa ssp. japonica ), a vital crop for more than half the...

Cuticular wax (CW) is the first defensive barrier of plants that forms a waterproof barrier, protects the plant from desiccation, and defends against insects, pathogens, and UV radiation. Sorghum, an important grass crop with high heat and drought tolerance, exhibits a much higher wax load than other grasses and the model plant Arabidopsis. In this...

Phosphite (Phi) has gained attention in agriculture due to its biostimulant effect on crops. This molecule has been found to benefit plant performance by providing protection against pathogens, improving yield and fruit quality as well as nutrient and water use efficiency. It is still unclear how Phi enhances plant growth and protects against multi...

The menace of drought has persistently loomed over global crop production, posing a serious threat to agricultural sustainability. Research on drought stress highlights the important role of the phytohormone abscisic acid (ABA) in orchestrating plant responses to drought conditions. ABA regulates various drought/dehydration-responsive genes, initia...

This review explores the integration of wild grass‐derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii , for improving resi...

In agriculture, mineral nutrient uptake and deposition profoundly influences plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) uptake and deposition alters plant physiology and particularly improves defense response and stress mitigation. While genetic and molecular mechanism...

Phosphite (Phi) has gained attention in agriculture due to its biostimulant effect on crops. This molecule has been found to benefit plant performance by providing protection against pathogens, improving yield and fruit quality, and improving nutrient and water use efficiency. It is still unclear how Phi enhances plant growth and protects against m...

Epidermal cells are the main avenue for signal and material exchange between plants and the environment. Leaf epidermal cells primarily include pavement cells, guard cells, and trichome cells. The development and distribution of different epidermal cells are tightly regulated by a complex transcriptional regulatory network mediated by phytohormones...

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understandin...

Introduction: Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) is a highly pathogenic soil-borne fungus responsible for Fusarium wilt in cotton (Gossypium spp.) and represents a continuing threat to cotton production in the southwest states of the United States, including California, New Mexico, and Texas. Pima (G. barbadense L.) cotton, w...

CLE14 belongs into a family of plant secreted peptides that interact with leucine-rich repeat receptor-like kinase (LRR-RLK) receptors to orchestrate plant morphogenesis. Previous studies indicated that CLE14 plays an important role in cell division, phosphate homeostasis, and senescence, but its specific involvement in cell fate determination and...

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and secondary meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understa...

Main conclusion In P. aeruginosa, mutation of the gene encoding N-acyl-L-homoserine lactone synthase LasI drives defense and plant growth promotion, and this latter trait requires adequate nitrate nutrition. Abstract Cross-kingdom communication with bacteria is crucial for plant growth and productivity. Here, we show a strong induction of genes fo...

Chia (Salvia hispanica) is an emerging crop considered a functional food containing important substances with multiple potential applications. However, the molecular basis of some relevant chia traits, such as seed mucilage and polyphenol content, remains to be discovered. This study generates an improved chromosome-level reference of the chia geno...

Lonicera macranthoides (LM) and L. japonica (LJ) are medicinal plants widely used in treating viral diseases, such as COVID-19. Although the two species are morphologically similar, their secondary metabolite profiles are significantly different. Here, metabolomics analysis showed that LM contained ~86.01 mg/g hederagenin-based saponins, 2000-fold...

Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or...

Background Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) is a highly pathogenic soil-borne fungus responsible for Fusarium wilt in cotton (Gossypium spp.) and represents a continuing threat to cotton production in the southwest states of the U.S., including California, New Mexico, and Texas. Even though the Pima (G. barbadense L.) cotto...

Throughout evolution, only two known primary photosynthetic endosymbiosis occurred, which originated the Archaeplastida and the Paulinella spp. Fundamental questions regarding primary endosymbiosis remain unsolved, but may now be addressed with the recent development of chimeric photosynthetic life-form. Cournoyer et al. could establish artificial...

There are feedforward and feedback loops along the microbiota-root-shoot axis to maintain plant growth or defense under environmental stresses. Here, we highlight a reciprocal interaction between the endodermis and the plant-bacterial community, which stabilizes the diffusion barriers to maintain nutrient homeostasis under nutritional stress.

As a finite and non-renewable resource, phosphorus (P) is essential to all life and crucial for crop growth and food production. The boosted agricultural use and associated loss of P to the aquatic environment are increasing environmental pollution, harming ecosystems, and threatening future global food security. Thus, recovering and reusing P from...

Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or...

Verticillium wilt caused by Verticillium dahliae is a serious vascular disease in cotton (Gossypium spp.). V. dahliae induces the expression of the CAROTENOID CLEAVAGE DIOXYGENASE 7 (GauCCD7) gene involved in strigolactone (SL) biosynthesis in Gossypium australe, suggesting a role for SLs in Verticillium wilt resistance. We found that the SL analog...

Background Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome assembl...

Genetic modification allows engineering of important traits in crops through expensive and tedious procedures to alter their genetic background. Recently, Thagun et al. developed a nanocarrier-based foliar spray method to translocate bioactive molecules of interest into plant cells to engineer important traits without introducing a transgene.

Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to hi...

Titanium is a ubiquitous element with a wide variety of beneficial effects in plants, including enhanced nutrient uptake and resistance to pathogens and abiotic stresses. While there is numerous evidence supporting the beneficial effects that Ti fertilization give to plants, there is little information on which genetic signaling pathways the Ti app...

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive...

Cotton fibers develop from epidermal cells in the outer integument of ovules. The regulatory process underlying fiber cell development has been extensively studied, little is known about the spatio-temporal profiles of transcriptomes and metabolomes during its development. Here we characterized the dynamics of transcriptome and metabolome during th...

Cotton fibers develop from epidermal cells in the outer integument of ovules. The regulatory process underlying fiber cell development has been extensively studied, little is known about the spatio-temporal profiles of transcriptomes and metabolomes during its development. Here we characterized the dynamics of transcriptome and metabolome during th...

Somatic embryogenesis is a major pathway for the regeneration of cotton in tissue culture, and a major technique used for cotton breeding and improvement. The signaling pathway regulating the process of somatic embryogenesis in cotton are extremely complex and still poorly characterized. Little is known about the mechanisms regulating the changes t...

Somatic embryogenesis is a major pathway for the regeneration of cotton in tissue culture, and a major technique used for cotton breeding and improvement. The signaling pathway regulating the process of somatic embryogenesis in cotton are extremely complex and still poorly characterized. Little is known about the mechanisms regulating the changes t...

Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount...

Plant roots recruit most prokaryotic members of their root microbiota from the locally avail- able inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to character...

SignificanceInterspecific hybridization is a widespread phenomenon, but measuring its extent, directionality, and adaptive importance remains challenging. Ancient genomes, however, can help illuminate the history of modern organisms. Here, we present a genome retrieved from a 130,000- to 115,000-y-old polar bear and perform genome analyses of moder...

Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome-assemblies. The an...

Global agriculture and food security face paramount challenges due to climate change and land degradation. Human-induced soil compaction severely affects soil fertility, impairing root system development and crop yield. There is a need to design compaction-resilient crops that can thrive in degraded soils and maintain high yields. To address plausi...

In the context of plant evolution, pteridophytes, which is comprised of lycophytes and ferns, occupy an intermediate position between bryophytes and seed plants, sharing characteristics with both groups. Pteridophytes is a highly diverse group of plant species that occupy a wide range of habitats including ecosystems with extreme climatic condition...

Epidermal cells are the main avenue for signal and material exchange between plants and the environment. Leaf epidermal cells primarily include pavement cells (PCs), guard cells, and trichomes cells (TCs), which differentiate from protodermal cells or meristemoids. The development and distribution of different epidermal cells are tightly regulated...

Cotton (Gossypium spp.) is the most important renewable source of natural textile fiber and one of the most cultivated crops around the world. Plant-parasitic nematode infestations, such as the southern Root-Knot Nematode (RKN) Meloidogyne incognita, represent a threat to cotton production worldwide. Host-plant resistance is a highly effective stra...

While most plants die below a threshold of water content, desiccation-tolerant species display specific responses that allow them to survive extreme dehydration. Some of these responses are activated at critical stages during water loss and could represent the difference between desiccation tolerance (DT) and death. Here, we report the development...

Arsenite regulates the uptake and detoxification of arsenate in plants under low-phosphate conditions by governing the stability of PHOSPHATE STARVATION RESPONSE 1, as reported in a recent study by Navarro and colleagues. This finding opens new opportunities for research into developing mitigation strategies to deal with arsenic toxicity in plants.

The polar bear ( Ursus maritimus ) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population...

Significance The regulatory roles of cytokinin (CK) signaling on metabolic plasticity of plant response to salt stress remain widely unknown. A comprehensive metabolome and transcriptome analysis of CK-signaling–defective Arabidopsis thaliana histidine-containing phosphotransfer protein ahp2,3,5 and type-B Arabidopsis response regulator arr1,10,12...

Photosynthetic microalgae hold great potential as light-driven heterologous protein expression hosts. In particular, the algal chloroplast is an ideal sub-cellular site for the compartmentalized synthesis and accumulation of high-value recombinant proteins. However, full integration of transplastomic algal biotechnology in the large-scale productio...

Significance Low phosphate (Pi) availability is a major constraint for plant productivity in both natural and agricultural environments. Over the course of evolution, plants acquired a complex cascade of transcriptional responses that enhance their capacity to survive and reproduce in phosphate-poor soils. However, it is unclear to what extent chro...

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding R...

Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexic...

Low‐molecular‐weight organic acids (OAs) extrusion by plant roots is critical for plant nutrition, tolerance to cations toxicity, and plant‐microbe interactions. Therefore, methodologies for the rapid and precise quantification of OAs are necessary to be incorporated in the analysis of roots and their exudates. The spatial location of root exudates...

Plants can tolerate some degree of dehydration but below a threshold of water content most plants die. However, some species display specific physiological, biochemical, and molecular responses that allow survival to desiccation. Some of these responses are activated at critical stages during water loss and could represent the difference between de...

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs...

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation. Because the compact genome size of the carniv...

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne ro...

Plant hormones are master regulators of developmental and genetic mechanisms to deal with diverse environmental cues. Upon phosphate (Pi) limitation, vascular plants modify phytohormone metabolism to coordinate diverse mechanisms to overcome such stress. However, the transcriptional program underlying the hormonal signaling in response to Pi scarci...

Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phyloge...

Phosphate (Pi) is a critical macronutrient for the biochemical and molecular functions of cells. Under phosphate limitation, plants manifest adaptative strategies to increase phosphate scavenging. However, how low phosphate sensing links to the transcriptional machinery remains unknown. The role of the MEDIATOR (MED) transcriptional co‐activator, t...

Background Desiccation tolerant Selaginella species evolved to survive extreme environmental conditions. Studies to determine the mechanisms involved in the acquisition of desiccation tolerance (DT) have focused on only a few Selaginella species. Due to the large diversity in morphology and the wide range of responses to desiccation within the genu...

Acidic soils constrain plant growth and development in natural and agricultural ecosystems because of the combination of multiple stress factors including high levels of Fe³⁺, toxic levels of Al³⁺, low phosphate (Pi) availability and proton rhizotoxicity. The transcription factor SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) has been reported to underl...

Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phyloge...

High‐temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because competing microbial activities are inhibited at elevated temperatures and thermostable cell wall degrading enzymes are superior to mesophilic enzymes. Here, we report on the development o...

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne ro...

Phosphate (P i) is a critical macronutrient for the biochemical and molecular functions of cells. Under phosphate limitation, plants manifest adaptative strategies to increase phosphate scavenging. However, how low phosphate sensing links to the transcriptional machinery remains unknown. The role of the MEDIATOR (MED) transcriptional co-activator,...

Background: The use of cyanobacteria and microalgae as cell factories to produce biofuels and added-value bioproducts has received great attention during the last two decades. Important investments have been made by public and private sectors to develop this field. However, it has been a challenge to develop a viable and cost-effective platform fo...

Significance Low availability of nitrogen (N), mainly nitrate in aerobic soils, is a primary limiting factor for crop production. Most terrestrial plants live in symbiosis with arbuscular mycorrhizal (AM) fungi to increase nutrient uptake, including N, from soil. Research on the AM symbiosis field has focused almost exclusively on ammonium as the f...

High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. mi...

Plants adapt to soil injury and biotic stress via cell regeneration. In Arabidopsis, root tip damage by genotoxic agents, antibiotics, UV light and cutting induces a program that recovers the missing tissues through activation of stem cells and involves ETHYLENE RESPONSE FACTOR 115 (ERF115), which triggers cell replenishment. Here, we show that mut...

Background The use of cyanobacteria and microalgae as cell factories to produce biofuels and added-value bioproducts has received great attention during the last two decades. Important investment has been made by public and private sectors to develop this field. However, it has been a challenge to develop a viable and cost-effective platform for cu...

Background: The use of cyanobacteria and microalgae as cell factories to produce biofuels and added-value bioproducts has received great attention during the last two decades. Important investments have been made by public and private sectors to develop this field. However, it has been a challenge to develop a viable and cost-effective platform for...

Gene expression patterns are controlled by cis regulatory elements (CRE) present in promoters. To understand how CRE are responsible for transcriptional activity and shape the architecture of a promoter, it is necessary to identify them and associate them with specific responses. Comparative studies of Dof promoters have focused on analyzing these...

Background: The genus Utricularia belongs to Lentibulariaceae, the largest family of carnivorous plants, which includes terrestrial, epiphytic and aquatic species. The development of specialized structures that evolved for carnivory is a feature of this genus that has been of great interest to biologists since Darwin's early studies. Utricularia g...

Heterologous expression of the NAD+-dependent phosphite dehydrogenase (PTXD) bacterial enzyme from Pseudomonas stutzerii enables selective growth of transgenic organisms by using phosphite as sole phosphorous source. Combining phosphite fertilization with nuclear expression of the ptxD transgene was shown to be an alternative to herbicides in contr...

Abiotic stresses and soil nutrient limitations are major environmental conditions that reduce plant growth, productivity and quality. Plants have evolved mechanisms to perceive these environmental challenges, transmit the stress signals within cells as well as between cells and tissues, and make appropriate adjustments in their growth and developme...

I had the fortune to start my scientific carrier during the early stages of the development of plant transformation in one of the leading laboratories in the field. Here, I describe my personal experience in the laboratory of Marc van Montagu and Jeff Schell, and some important contributions that the group made to the development of the technology...

Background: Trichoderma species are among the most effective cell factories to produce recombinant proteins, whose productivity relies on the molecular toolkit and promoters available for the expression of the target protein. Although inducible promoter systems have been developed for producing recombinant proteins in Trichoderma, constitutive pro...