Muhammad Ilyas

Dr. Muhammad Ilyas

orcid

Research Focus & Metrics

Academic Career Length

8Years (2019-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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20 June 2019 in Plant Reproduction
Verified
Journal Article
Open access
PDF file
PSPauline Stephenson
Pauline Stephenson
NSNicola Stacey
Nicola Stacey
MBMarie Brüser
Marie Brüser
NPNick Pullen
Nick Pullen
MIMuhammad Ilyas
Muhammad Ilyas
LOLars Ostergaard
Lars Ostergaard
Elucidation of key regulators in Arabidopsis fruit patterning has facilitated knowledge-translation into crop species to address yield loss caused by premature seed dispersal (pod shatter).

12 April 2025 in The Plant Journal
Verified
Journal Article
Open access
ASAscenzo Salvati
Ascenzo Salvati
ADAlessandra Diomaiuti
Alessandra Diomaiuti
FLFederica Locci
Federica Locci
MGMatteo Gravino
Matteo Gravino
GGGiovanna Gramegna
Giovanna Gramegna
GLGiulia De Lorenzo
Giulia De Lorenzo
SUMMARY: Plant immunity is triggered by endogenous elicitors known as damage‐associated molecular patterns (DAMPs). Oligogalacturonides (OGs) are DAMPs released from the cell wall (CW) demethylated homogalacturonan during microbial colonization, mechanical or pest‐provoked mechanical damage, and physiological CW remodeling. Berberine bridge enzyme‐like (BBE‐l) proteins named OG oxidases (OGOXs) oxidize and inactivate OGs to avoid deleterious growth‐affecting hyper‐immunity and possible cell death. Using OGOX1 over‐expressing lines and ogox1/2 double mutants, we show that these enzymes determine the levels of active OGs vs. inactive oxidized products (ox‐OGs). The ogox1/2‐deficient plants have elevated levels of OGs, while plants overexpressing OGOX1 accumulate ox‐OGs. The balance between OGs and ox‐OGs affects disease resistance against Pseudomonas syringae pv. tomato, Pectobacterium carotovorum, and Botrytis cinerea depending on the microbial capacity to respond to OGs and metabolize ox‐OGs. Gene expression upon plant infiltration with OGs reveals that OGOXs orchestrate OG signaling in defense as well as upon mechanical damage, pointing to these enzymes as apoplastic players in immunity and tissue repair.

15 November 2025 in Plant Science
Verified
Journal Article
Open access
LFLudovica Fumelli
Ludovica Fumelli
MIMuhammad Ilyas
Muhammad Ilyas
FOFabrizio Olivieri
Fabrizio Olivieri
Barbara FarinonBarbara Farinon
Barbara Farinon
RFRoberto Forniti
Roberto Forniti
Andrea MazzucatoAndrea Mazzucato
Andrea Mazzucato
As agriculture and food systems are facing growing challenges because of extreme weather conditions and unstable socioeconomic landscapes, improving crop quality and agronomic traits has become an increasingly important goal in plant breeding. Preventing post-harvest losses and finding new genetic sources for pathogen resistance are vital for the development of resilient and competitive varieties. In tomato (Solanum lycopersicum L.), fruit softening plays a key role in determining the post-harvest quality, with a significant impact on both food waste and food safety. To elucidate the role of pectate lyase (SlPL, Solyc03g111690) in the softening process and in susceptibility-to-pathogen mechanisms, knock-out mutants have been generated in a Micro-Tom genetic background by CRISPR/Cas9. Two CAS-free edited mutant lines (carrying a 1 bp insertion and a 2 bp deletion, respectively) showed a significant increase in fruit firmness at two different ripening stages (breaker+4 and red ripe) and lower weight loss during post-harvest storage. Furthermore, the observed overall reduction in the activity of six cell wall remodeling enzymes (pectate lyase, pectin methylesterase, polygalacturonase, α-D-galactosidase, ꞵ-D-galactosidase and ꞵ-D-glucosidase) and the reduced susceptibility to leaf infection caused by Botrytis cinerea, Phytophthora capsici and Pseudomonas syringae pv. tomato pathogens suggested that the alteration of the cell wall metabolism limits the pathogen's ability to establish infection. The obtained results open the possibility of developing new tomato varieties that meet both agronomic and quality needs while helping to clarify the complexity of the cell wall-disassembly process.

29 September 2019 in Pakistan Journal of Botany
Verified
Journal Article
Closed access
HQHuma Qamar
Huma Qamar
GSGhulam Shabbir
Ghulam Shabbir
MIMuhammad Ilyas
Muhammad Ilyas
Adnan ArshadAdnan Arshad
Adnan Arshad
SMSaad Imran Malik
Saad Imran Malik
HMHafiz Saad Bin Mustafa
Hafiz Saad Bin Mustafa

2 July 2024 in bioRxiv
Verified
Preprint
Open access
PDF file
ASAscenzo Salvati
Ascenzo Salvati
ADAlessandra Diomaiuti
Alessandra Diomaiuti
FLFederica Locci
Federica Locci
MGMatteo Gravino
Matteo Gravino
GGGiovanna Gramegna
Giovanna Gramegna
GLGiulia De Lorenzo
Giulia De Lorenzo
Plant immunity is triggered by endogenous elicitors known as damage-associated molecular patterns (DAMPs). Oligogalacturonides (OGs) are DAMPs released from the cell wall (CW) demethylated homogalacturonan during microbial colonization, mechanical or pest-provoked tissue damage, and physiological CW remodeling. Berberine Bridge Enzyme-like (BBE-l) proteins named OG oxidases (OGOXs) have been proposed to govern OGs homeostasis, which is necessary to avoid deleterious growth-affecting hyper-immunity and possible cell death. Using OGOX1 over-expressing lines and ogox1/2 double mutants, we show that these enzymes determine the levels of active OGs vs. inactive oxidized products (oxOGs). The ogox1/2 -deficient plants have elevated levels of OGs, while plants overexpressing OGOX1 accumulate oxOGs. The balance between OGs and oxOGs affect disease resistance against Pseudomonas syringae pv tomato , Pectobacterium carotovorum, and Botrytis cinerea depending on the microbial capacity to respond to OGs and metabolize oxOGs. Gene expression upon plant infiltration with OGs reveals that OGOXs orchestrate OG signaling in defense as well as upon tissue damage, pointing to these enzymes as apoplastic players in immunity and tissue repair. Teaser: Oxidases control the homeostasis of oligogalacturonides in the cell wall and play a pivotal role in the plant immunity.

6 July 2026 in Earth
Verified
Journal Article
Open access
PDF file
Roberta FarinaRoberta Farina
Roberta Farina
MIMuhammad Ilyas
Muhammad Ilyas
Mariangela DiaconoMariangela Diacono
Mariangela Diacono
Claudia Di BeneClaudia Di Bene
Claudia Di Bene
VBValentina Baratella
Valentina Baratella
SVSilvia Vanino
Silvia Vanino
Mediterranean agroecosystems are highly vulnerable to climate change, soil degradation, and declining soil organic carbon (SOC), threatening long-term agricultural sustainability. Carbon farming and regenerative agriculture have emerged as complementary approaches to restore soil functionality while contributing to climate change mitigation. This review synthesizes peer-reviewed literature published between 2015 and 2025 to assess the agronomic effectiveness of key regenerative and carbon farming practices in Mediterranean systems. A structured bibliographic analysis using Scopus and Web of Science evaluated practices influencing SOC dynamics, erosion control, water regulation, and associated ecosystem services. Evidence indicates that the introduction of cover crops in the crop rotation and reduced or no-tillage are the most consistently effective practices for enhancing SOC stocks, particularly when combined with organic amendments and diversified rotations. Crop diversification, intercropping, and agroforestry further support SOC accumulation and erosion control, especially in perennial systems such as vineyards and olive orchards. Organic inputs stimulate microbial-mediated carbon stabilization, while regenerative grazing contributes to nutrient cycling under context-specific conditions. Across practices, integrated management consistently delivers greater and more stable benefits than single interventions. Regenerative agriculture thus provides a systems-based foundation for carbon farming in Mediterranean agroecosystems. Long-term field experiments and improved monitoring frameworks remain essential to quantify carbon persistence and support policy implementation.