Grasses have doubled pathways to synthesize lignin and starch

Amazing stuff!

"... Some of this success stems from grasses’ turbocharged growth: The plants can produce both energy-rich starch and structurally supportive lignin through two different metabolic pathways apiece, allowing them to grow faster and taller than their competitors. But researchers never knew how and when these innovations sprouted.

In a new Science study, botanists analyzed the genomes of the grass family’s closest relatives to reveal the evolutionary history of grasses’ key innovations. They found that the doubled starch production pathway was truly unique to grasses, having resulted from a previously documented whole-genome duplication event that also instilled the plants with some of their other world-conquering traits. This duplication “ likely gave a competitive advantage to grasses to grow in open habitat, where a lot of plants would love to grow because of all the sun,” ... 

By contrast, their sister groups had only one strategy to produce starch, restricting them to slow growth in the shade of their fast-rising relatives.

In addition, both grasses and related plants can also make lignin from two different precursor molecules, indicating that a separate gene duplication gave rise to the dual pathway before grasses split into their own lineage 100 million years ago. The researchers were able to track the specific genetic causes of the doubled route, potentially allowing them to introduce the mutation into other plants to help produce crops and feedstocks for bioenergy."

"One hundred million years ago, long before human intervention, ancestors of grasses, like wheat, rice and maize generated “bypasses” of chemical pathways that are used to create two critical compounds: lignin and starch. These more efficient pathways could explain why grass plants are so successful in nature and agriculture, according to a new paper recently published ...

Just as scientists use the chimpanzee’s genome as a comparison tool to study how humans evolved, Maeda’s group and their collaborators  ... turned to one of the closest relatives of grasses, Joinvillea ascendens. 

This long-leafed plant is found in wet forests of the South Pacific islands and grows much more slowly than many grasses. ..."

"... The researchers then mapped the genome of Joinvillea and three related species. Comparing the thousands of genes in these genomes revealed that, unlike grasses, Joinvillea has only one pathway to create starch.

“We knew that a common ancestor of all grasses doubled its gene content through a whole genome duplication,” ... “Some of the duplicated genes then enabled the evolution of an additional starch synthesis pathway, or a bypass route, which emerged in an early common ancestor of all grasses.”

As a result ... grasses are able to produce twice the amount of starch relative to Joinvillea and all other non-grass plants. ..."

From the editor's summary and abstract:

"Editor’s summary

Grasses include many economically important food crops and function as primary producers in diverse ecosystems. They also exhibit distinctive metabolic traits, such as the ability to synthesize starch in both plastids and cytosol and the synthesis of lignin from both phenylalanine and tyrosine.

However, the evolutionary origin of these traits has been unclear.

Takeda-Kimura et al. sequenced the genomes from grass sister clades and found that although some cytosolic starch synthesis genes emerged within grasses, a key plastid membrane transporter predates their evolution.

An earlier tandem duplication event predating a grass-specific whole-genome duplication gave rise to the bifunctional phenylalanine/tyrosine ammonia lyase, enabling dual lignin biosynthesis in grasses. ...

Structured Abstract

INTRODUCTION

The grass family (Poaceae) includes foundational primary producers in global ecosystems and economically important crops. Rice, wheat, and maize account for more than 40% of caloric intake for humans, and sugarcane, sorghum, and bamboo make abundant sugars and lignocellulosic biomass for renewable bioenergy and biomaterial production. Their genome assemblies have advanced our understanding of critical traits in agriculturally and ecologically important grass species. However, we still lack chromosomal assemblies for their closest relatives, which diverged from grass progenitors more than 100 million years ago, before the rho whole-genome duplication (ρWGD) in the ancestor of all grasses. This gap limits our understanding of how gene and genome duplications contributed to evolutionary innovations that define the grass lineage.

RATIONALE

This study generated reference-quality genomes for Joinvillea ascendens and Ecdeiocolea monostachya, which represent the sister lineage to all grasses, along with Pharus latifolius and Typha latifolia, which represent sister lineages to core grasses and all other members of the order Poales, respectively. Using these new genomic resources, we traced the evolutionary history of two distinctive metabolic traits of grasses: dual starch and lignin biosynthetic pathways. These grass-specific metabolic innovations contribute to the starch-rich endosperm of cereals and substantial lignin deposition in the vasculatures and fibers of grasses.

RESULTS

In this study, the new high-quality genome assemblies and annotations enabled comparative genomic analyses to place the timing of the ρWGD event just after the divergence of ancestral lineages leading to the grasses and their sister clade, including Joinvilleaceae and Ecdeiocoleaceae. Phylogenetic and molecular evolutionary analyses of more than 20 gene families involved in starch biosynthesis across many Poaceae and Poales species revealed that ρWGD contributed to the duplication of several of these genes, which now support cytosolic starch biosynthesis in grass endosperms. By contrast, genome comparisons and biochemical analyses of the lignin biosynthesis pathway revealed that an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) before the ρWGD and the origin of grasses, enabling grasses to synthesize lignin and other phenylpropanoid compounds from two aromatic amino acid precursors, phenylalanine and tyrosine. Precise determination of the timing of the plant PTAL evolution, combined with site-directed mutagenesis and x-ray crystal structural analyses, further identified two key residues, Ile112 and His140, that are responsible for the neofunctionalization of plant PAL into PTAL, providing a promising gene-editing strategy to enhance diverse phenylpropanoid production in plants.

CONCLUSION

Our integrated genomic, biochemical, and structural analyses, supported by robust phylogenetic resolution of grasses and their relatives, have unveiled the evolutionary history and molecular basis of key metabolic innovations predating the emergence of grasses. Our findings highlight critical roles for both WGDs and tandem gene duplications as drivers of evolutionary innovation. The nonmodel, noncrop Poales reference genomes generated for this study now offer valuable resources for dissecting the diverse and complex traits that contribute to the ecological and economic importance of grasses. The evolutionary basis of grass-specific traits will inform efforts to conserve grass-dominated ecosystems and accelerate breeding and engineering of cereals and other grass crops for sustainable production of food, feed, bioenergy, and biomaterials."

ScienceAdviser

Molecular “bypasses” improve grass plants’s synthesis of lignin and starch, laying the early groundwork for evolutionary success (original news release)

Grass plant ancestors evolved metabolic pathway to ecological success (original news release)

Genomes of Poaceae relatives reveal key metabolic innovations preceding the evolution of grasses (no public access)

Genomes of Poaceae sisters reveal key metabolic innovations preceding the evolution of grasses (preprint, open access, published already in December 2024 and never updated recently)

Metabolic innovations that predate the origin of grasses.

Fig. 1: Sequencing genomes of Poaceae sisters to trace the evolutionary history of grass metabolic innovations.

Fig. 2. Alteration of starch and fatty acid biosynthesis during the grass evolution.

Saudi Aramco backs India's Mitti Labs to make Asia's rice farming more water-resilient

Good news, but older news!

Let's not forget Methane is a trace gas! Associations between methane in the atmosphere and climate change/global warming are tenuous!

"As rising temperatures and shifting rainfall patterns put Asia’s water-intensive rice farming under pressure, Mitti Labs, a New York- and Bengaluru-headquartered climate-tech startup, has raised $9.5 million in an investment led by Aramco Ventures, Saudi Aramco’s venture arm, to expand across Asia with a platform that combines satellite imagery, AI, and field operations to help farmers cut water use and methane emissions. ...

Since launching its first programs in 2023, Mitti Labs has sought to tackle the heavy water use and methane emissions associated with rice farming through its platform that fuses satellite radar imagery with years of field data collected by its teams. The startup says the technology creates digital twins of individual rice fields, allowing it to monitor crop conditions, water use, and methane emissions across thousands of smallholder farms, where the average holding is about one hectare.

Mitti Labs’ GeoAI platform uses synthetic aperture radar (SAR) imagery from commercial and public satellites, with resolutions ranging from 50 centimeters to 10 meters, alongside years of field measurements collected by its teams. The startup’s edge lies less in the satellite imagery itself than in the proprietary datasets it has built to train its AI models, allowing it to monitor crop growth, soil moisture, and flooding across smallholder farms remotely, co-founder Xavier Laguarta said in an interview. ..."

"Rice feeds half the world every day, but growing it is putting an outsized strain on the planet's water supply. As the most water-intensive crop on Earth, rice consumes more than 30% of all irrigation water. Traditional paddies, kept continuously flooded to suppress weeds, also generate huge volumes of methane, a greenhouse gas now responsible for roughly a quarter of the warming the planet [???] has experienced to date. ...

We are proud to announce that we have raised a $9.5 million Series A to accelerate an answer to that problem. The round was led by Aramco Ventures, with participation from Lightspeed India, Godrej Industries Group, Cisco Foundation, Francis Family Fund, and Volta Circle. ..."

Saudi Aramco backs India's Mitti Labs to make Asia's rice farming more water-resilient | TechCrunch

Mitti Labs raises $9.5M to build water resilience in Asia's rice fields (original news release)

Really!

Mexico Sends 1,500 Troops To Its Avocado Heartland After US Halts Imports

Very recommendable! 

Incredible, organized crime in Mexico has also infiltrated the Avocado business of Mexico. Will the current President Sheinbaum do more to fight organized crime in Mexico?

(1207) Mexico Sends 1,500 Troops To Its Avocado Heartland After US Halts Imports | FP Explains - YouTube

Studying grass grow

Amazing stuff!

"Watching grass grow gets a bad name—studying how grass grows is anything but boring. Grasses include many of our most critical food sources including wheat, rice, and corn. And until recently, nobody was quite sure what factors caused these plants to grow tall.

In a new study, a team of researchers revealed that temperature, not light, determines when grass stems harden, allowing for vertical growth.

To monitor growth, the scientists merged a gene important for the development of the secondary cell wall—the structure that causes grass stems to become rigid—with the gene that makes fireflies glow.

Then, they exposed the plant to a variety of light and temperature conditions and watched how they responded with a time-lapse camera. ...

Neither daylight nor any sort of internal clock had an impact on grass growth. But when the biologists varied the temperature, their grasses responded. In cooler conditions, plants started slowly before rapidly growing; in the heat, grass growth initially spiked but soon dropped to a slower pace.

In addition, pulses of warmth in cool temperatures prompted the greatest growth rates, while cold blasts in the heat ground growth to nearly a halt.

What the study might mean for crop growth, including in the context of climate change, remains unknown. Nevertheless, the findings present new insights into the unexpectedly fascinating process of how grass grows.  ..."

From the highlights and abstract:

"Highlights

• Thermocycles, not light or the circadian clock, drive CESA8 rhythms

• CESA8 expression increases during cool nights and declines during warm days

• Secondary-wall gene expression is coordinated with stem elongation

• Warm and cold pulses trigger opposing responses, explained by an incoherent feedforward loop model

Summary

Secondary cell wall thickening is essential for plant structural development, providing the mechanical strength and rigidity required for upright growth. However, direct observation of this process in its endogenous developmental context within living plants has remained limited.

Cellulose, the predominant component of secondary walls and the most abundant biopolymer on Earth, is synthesized at the plasma membrane by complexes containing CELLULOSE SYNTHASE A (CESA) proteins.

Despite its central role, the precise timing and regulation of cellulose deposition during plant development remain unclear.

To address this gap, we developed a real-time bioluminescence imaging system in the model grass Brachypodium distachyon using a luciferase transcriptional reporter driven by the CESA8 cis-regulatory region.

Bioluminescence imaging revealed a consistent spatial pattern of CESA8 expression within elongating internodes, coinciding with regions undergoing secondary wall deposition and progressive increases in cellulose crystallinity. Time-lapse imaging showed that expression follows a robust daily rhythm driven by temperature cycles, independent of light or endogenous circadian signals. Temperature-pulse experiments uncovered rapid, transient inverse responses that were accurately predicted by a mathematical model based on an incoherent feedforward loop.

CESA8 expression correlated strongly with stem elongation, linking structural reinforcement with temperature-driven shoot growth in grasses."

ScienceAdviser

Grasses provide most of the world’s calories—but we’re only now starting to learn how they grow

Grasses Provide Most of the World’s Calories—But We’re Only Now Starting to Learn How They Grow (original news release) "UMass Amherst researchers devise technique to show grasses don’t grow like most other plants"

Temperature signals drive grass secondary cell wall thickening (partial public access)

Graphical abstract

A microRNA for perennial rice traits

Amazing stuff!

"Most grain crops die after completing one life cycle, meaning that new plants must be sown each year. However, some wild relatives of rice are perennial and can live through multiple yearly cycles.

Dai et al. identified a locus coding for a duplicated microRNA with expression that is regulated by DNA methylation status. Some alleles of this locus confer the ability to propagate rice vegetatively. By generating rice lines harboring this microRNA, as well as genes for other perennial traits, the authors developed rice that could grow for more than a year. Although alleles of additional loci will be needed to make fully fertile perennial rice plants, this work provides insights into perennial traits in rice and is a step forward in genetic engineering efforts."

From the abstract:

"Structured Abstract

INTRODUCTION

Plants exhibit a wide variety of life history strategies. Rice (Oryza sativa), one of the most widely grown staple crops worldwide, is cultivated as an annual species, whereas several of its wild relatives, such as Oryza rufipogon, display a perennial growth habit characterized by sustained vegetative growth and repeated reproduction. During domestication, this perennial growth habit was largely lost, representing an important shift in the life history strategy of rice. However, the genetic basis responsible for this transition remains poorly understood.

RATIONALE

To address this question, we investigated the traits associated with the perennial growth habit using 446 accessions of perennial wild rice. In O. rufipogon, one of the key traits linked to its perennial growth habit is a grasslike plant architecture, characterized by extensive tillering, floral reversion, and vegetative propagation—a phenotype largely absent in modern cultivated rice. To delineate the genetic basis underlying this trait, we used a set of single-segment substitution lines derived from both wild and cultivated rice and identified a gene locus that harbors tandem microRNA156 genes (MIR156BC). Through expression pattern analysis and epigenomic profiling, we investigated how dynamic changes in miR156 abundance promote a vegetative perennial growth habit in O. rufipogon. Finally, we explored whether we could reproduce the vegetative perennial growth habit of O. rufipogon in cultivated rice by introgressing this gene locus along with loci associated with prostrate growth.

RESULTS

We identified Endless Branches and Tillers 1 (EBT1) as a key gene locus controlling vegetative propagation and floral reversion in O. rufipogon W1943. The EBT1 locus harbors two tandem MIR156BC genes and has been positively selected for. Whereas wild-type cultivars senesce after seed setting, plants carrying the EBT1 allele from O. rufipogon W194 (EBT1W1943) exhibit vigorous tiller bud outgrowth and sustained vegetative growth after flowering. Mechanistically, unlike MIR156BC in modern annual cultivars, MIR156BC expression in O. rufipogon can be reset in developing tiller buds after flowering. This expression pattern is associated with increased chromatin accessibility and a reduction in the repressive epigenetic marker H3K27me3 at a regulatory region of EBT1. The combination of PROSTRATE GROWTH 1, TILLER INCLINED GROWTH 1, and EBT1W1943 enables annual cultivated rice to largely recapitulate the vegetative perennial growth habit of O. rufipogon.

CONCLUSION

We have identified MIR156BC as a key determinant of perenniality in rice. The distinctive epigenetic state at the MIR156BC locus in O. rufipogon facilitates its resetting after flowering, which subsequently leads to floral reversion and vegetative perennial growth. Our findings not only offer fresh insights into the genetic basis of perenniality in cereals but also pave the way for the development of sustainable perennial rice cultivars in the future."

In Science Journals | Science

Resetting of a tandem microRNA156 enables vegetative perennial growth in rice (no public access)

Chinese researchers have developed a revolutionary form of high yield hybrid rice that can replicate itself through seeds that are clones

Good news! This could be a breakthrough!

"Hybrid rice, produced by crossing two genetically distinct parent varieties, typically produces much higher yields through a phenomenon called heterosis, or “hybrid vigor.” However, the benefit doesn’t extend to the next generation of seeds, which lose their yield advantage when replanted, forcing farmers to buy new seed every season. Scientists at the China National Rice Research Institute now claim they’ve solved that problem by creating hybrid rice that produces seeds that are genetically identical to itself, a long-sought breakthrough in rice breeding."

From the abstract:

"Apomixis, a form of clonal seed reproduction, offers a transformative approach to agriculture by enabling the stable fixation of hybrid vigor and elite heterozygosity across generations.

However, the practical implementation of synthetic apomixis has been hindered by highly variable clonal efficiency or significant yield penalties.

In this study, through integrated transcriptomic analyses, we identified a sperm-specific transcription factor in rice that likely functions as a key initiator of embryogenesis.

Ectopic expression of this factor in egg cells effectively induces parthenogenesis and produces haploid progeny. When combined with clonal gametogenesis, this system achieved nearly complete synthetic apomixis, with clonal seed production rates exceeding 99% across all derived hybrid rice lines. Moreover, we generated apomictic hybrid lines that not only consistently produced over 99% clonal seeds but also exhibited seed yields comparable to conventional F1 hybrids. These findings establish a scalable and agriculturally viable platform for synthetic apomixis, achieving stable fixation of heterosis through clonal seeds and paving the way for the commercial deployment of self-perpetuating hybrid crops."

Doomslayer: Progress Roundup - by Malcolm Cochran

World’s First Clone-Hybrid Rice Could Double Global Output

Fixing Hybrid Rice: >99% Efficient Apomixis with Near-Normal Seed Set (open access)

Fig. 1 Ectopic expression of HUAXU in egg cells efficiently induces parthenogenesis and haploid progeny formation.

Wheat ‘cries for help’ when it experiences drought

Amazing stuff!

"An Australian study has revealed an ingenious tactic used by wheat to withstand drought conditions – it calls in reinforcements.

The plant sends out a chemical signal to attract specialised soil bacteria which release beneficial compounds that help it resist drought and continue to grow. ...

[team] revealed that, under drought conditions, wheat releases the compound 4-oxoproline from its roots to recruit the bacteria Streptomyces coeruleorubidus and Leifsonia shinshuensis which produce osmolytes – which preserve osmotic balance in cells – plant hormones, and nutrient solubilisers.

When the research team reintroduced these microbes to wheat plants in dry soils, the plants grew bigger, stayed healthier, and produced more grain, even in the next generation of crops. ...

“S. coeruleorubidus enhances wheat drought resistance by promoting plant biomass and yield through multiple mechanisms,” the authors write, “including increased hydrogen peroxide contents in the leaves, increased leaf stomatal density, and upregulated drought-resistant genes in wheat leaves.” ..."

From the highlights and abstract:

"Highlights

• Drought enriches Streptomyces and Leifsonia spp. in the plant microbiome

• Plant-produced 4-oxoproline recruits beneficial microbes under drought conditions

• Microbial rimJ gene is linked to drought response and plant metabolite levels

• Microbial reintroduction improves plant drought resistance and yield

Summary

Plant-microbiome interactions are crucial in maintaining plant health and productivity under stress; however, little is known about these interactions under drought.

Here, using wheat as a model, we combine genomics and culture-dependent methods to investigate the interactions between the soil, root, and rhizosphere microbiomes with rhizosphere metabolomes and plant phenotypes.

We find that drought conditions promote microbial colonization in plant microbiomes, enriching Streptomyces coeruleorubidus and Leifsonia shinshuensis, while also increasing 4-oxoproline levels in the rhizosphere, potentially attracting S. coeruleorubidus.

Consistently, genes facilitating microbial responses to drought, including the N-terminal acetyltransferase rimJ, are enriched, while S. coeruleorubidus and L. shinshuensis reintroduction promotes host drought resistance. Drought-legacy-effect experiments further support these benefits, with increased plant biomass and yield in the subsequent growth cycle under drought. Collectively, this study informs how drought-induced microbial and metabolite enrichments improve plant adaptation to abiotic stresses, potentially informing development of bio-based tools to mitigate drought effects."

Wheat ‘cries for help’ when it experiences drought

Drought-induced plant microbiome and metabolic enrichments improve drought resistance (no public access)

Graphical abstract

Heatwave-tolerant potatoes the latest climate change ready crops. Really!

What about heatwave-tolerant couch potatoes?

Keep in mind: Global warming is a hoax and climate change is a religion! It is being used as a pretext by Big Government and the elite to interfere with our lives. It is among the greatest scams and scandals of at least the last 30 years!

"Engineering plants to thrive in warmer and drier conditions associated with climate change is an exploding field of scientific study, as researchers all over the world work to stave off the threat of food insecurity. ..."

Heatwave-tolerant potatoes the latest climate ready crops

Shortcutting Photorespiration Protects Potato Photosynthesis and Tuber Yield Against Heatwave Stress (open access)

The lead author of the study

Fig. 1 The native and introduced alternative photorespiratory pathway (AP3). 

Asia Combats Rice Inflation: Can India Come to The Rescue? with Palki Sharma

Recommendable! However, you have to subtract this nonsense about climate change!

Gene-Editing An Ancient Crop To Help Feed The World

Good news! Hunger be damned! Food for all!

"Cowpea is a staple in sub-Saharan Africa, where it has always been picked by hand. The stalks don’t naturally stand upright, making it impossible to harvest by machine.

Until now. The agri-tech company BetterSeeds has re-coded the plant’s genetic makeup, so it’s suitable for mechanized harvesting, and can help address the world’s food security concerns."

"... The first Cowpea plant made suitable for mechanized harvesting is being developed by BetterSeeds, an Agri-Tech company that genetically enhances agricultural crops by using its proprietary genome editing technology. BetterSeeds is set to plant their enhanced Cowpea seeds in the United States in the Spring of 2023, in order to test its potential for mass scale cultivation. ...
Cowpea, also called Lubia or black-eyed peas, is the most ancient crop known to have been farmed by man. Due to its high protein content, heat tolerance and highly efficient water and fertilizer consumption ..."

Gene-Editing An Ancient Crop To Help Feed The World A crop that has been farmed for thousands of years has been gene-edited by Israeli scientists – so it can be cultivated on a large scale.

https://finance.yahoo.com/news/first-successful-gene-editing-cowpea-140000658.html

Cowpea pods and beans.

UAE farms the desert in quest for food security with wheat

Making up for the Ukraine!

Ethiopia begins to export wheat in the Horn of Africa

Making up for the Ukraine! For a region that has suffered from hunger for decades this is very encouraging!

Fonio, a Drought-Resistant Grain from West Africa Could Feed a Warmer World

Recommendable!

New IPCC Baloney About Crops

Just read http://www.technologyreview.com/news/525891/un-climate-report-warns-of-increased-risk-to-crops/

Even the MIT Technology Review cannot resist to regurgitate this nonsense. This has been thoroughly debunked. Crops actually appreciate the increased CO2.

As if We The People are fools, the IPCC warns that by 2030 dire things will happen. We cannot even predict weather with any certainty for up to 10 days.