Contributed by Nisha Joy @JoyNish65839026, Former postdoctoral fellow (MSCA) at the University of Dundee, Scotland, United Kingdom
Orphan crops, as the name implies, are often ignored. Yet, they have great potential to improve global food security. These underutilised plants, primarily grown in Africa, Asia, and South America, are staples in local diets but receive minimal attention in modern agriculture. Due to limited research and breeding advancements, they remain vulnerable to biotic and abiotic stresses.
The Importance of black pepper
One orphan crop that needs special attention is black pepper (Piper nigrum). It is often called the ‘Black Gold’ of India’s Malabar Coast. People globally cherish this spice for its pungency, which comes from the naturally occurring alkaloid ‘piperine.’ Historically, black pepper has been used in everything from mummification rituals to currency. It gained recognition for its commercial, nutritional, and medicinal significance.
Susceptibility and resistance
This hidden gold comes from the Western Ghats of India and serves as a vital income source for small farmers in Vietnam, India, and Indonesia. It has long relied on traditional selection based on traits like pungency and pest tolerance. However, it is very vulnerable to the harmful oomycete Phytophthora capsici. This can lead to “slow decline” and “quick wilt” (foot rot) diseases. Historically propagated through cuttings, its predominantly self-pollinating nature and vulnerability to diseases like foot rot have led to declining yields. This poses challenges to food security and market demand. Despite repeated efforts in black pepper, including integrated disease management, germplasm screening for pest resistance, and interspecific hybridisation, researchers have not found an effective solution to boost crop production. A striking revelation is that the only known source of pathogen resistance comes from a distant wild relative, Piper colubrinum, native to South America.
The key question remains: How does the same pathogen evade plant signalling responses in black pepper, causing susceptibility, while its wild relative, P. colubrinum, exhibits resistance? This mystery warrants further investigation.
The power of third generation Nanopore Technologies to transform orphan genomes
Pocket-sized Nanopore machines have revolutionised real-time DNA/RNA sequencing, enabling analysis anywhere. Cutting-edge Nanopores from Oxford Nanopore Technologies (ONT) are transforming orphan crop annotation and diversifying human diets. Thanks to Hagan Bayley, a Professor of Chemical Biology at the University of Oxford, and his team, they have developed a new technique. This method allows for real-time reading of individual molecules, such as DNA or RNA bases. These molecules pass through tiny holes called ‘nanopores’ in an electro-resistant membrane found in ONT flow cell devices. Each nanopore corresponds to its own electrode linked to a channel and sensor chip, which can measure the electric current that flows through the nanopore.
We all know that no two individuals are the same and differ in their genetic constitution by 0.1%. The ONT technology unravels such characteristic ‘mark’ of every individual by measuring the change in current produced when a molecule passes through a nanopore. This ‘mark’ is then decoded with base-calling algorithms to read the DNA or RNA sequence.
Successful crop breeding relies on ‘omics’—the blend of genomics, proteomics, transcriptomics, and metabolomics. ONT technology provides a strong ‘omics’ platform for orphan crops. It delivers ultra-long read data that helps identify important agronomic genes. This goes beyond traditional phenotype-based selection. No matter the crop’s complexity, this third-generation sequencing is a rapid, real-time gold standard for studying neglected species. The remarkable pathogen resistance of P. colubrinum offers a key opportunity to unravel the regulatory and evolutionary mechanisms behind plant defence. Understanding these dynamics could help mitigate the decline in black pepper cultivation, enhance crop resilience, and contribute to global food security (UN SDG 2: Zero Hunger) while promoting planetary sustainability.
Concluding thoughts
Food and technology are two significant ends that must be met with rapid revolutionary stunning approaches for a better hunger-free future generation with healthy mind and body. Global food security is a matter of concern when it comes to increased food demand in the modern world. Good food always promises a good life, which well fits into the saying of the famous innovative English writer Virginia Woolf:
‘One cannot think well, love well, sleep well, if one has not dined well.’
Acknowledgements
- HORIZON EUROPE Marie Sklodowska-Curie Actions (OCNANO; Grant agreement ID 896598).
- University of Dundee, Scotland, United Kingdom.
References
- 1Ravindran, P. N. Black Pepper. Hardwood academic publishers (2000).
- 2 Garalde, D. R. et al.Highly parallel direct RNA sequencing on an array of nanopores. Nature Methods (2018) http://dx.doi.org/10.1038/nmeth.4577
