Unlocking the secrets of pineapple DNA to understand plant evolution, domestication, and climate resilience
When Christopher Columbus first encountered the pineapple in the Caribbean during his 1493 voyage, he and his sailors were delighted by its "astonishing flavor and fragrance" 7 . Little could he have imagined that this exotic fruit would one day become a cornerstone of genomic research, offering insights into plant evolution, domestication, and climate resilience.
Pineapple ranks as the third most important tropical fruit worldwide, with an annual production value approaching $9 billion 1 .
Cultivation spans over 80 countries, making it a truly global crop 7 .
Today, beyond its economic significance and culinary appeal, pineapple has emerged as an unlikely hero in the world of genomics, helping scientists unravel mysteries that stretch back millions of years and could shape our agricultural future.
What makes this spiky tropical fruit so genetically fascinating? Pineapple offers a unique window into plant evolution for several compelling reasons.
As the most economically valuable crop possessing crassulacean acid metabolism (CAM) photosynthesis, pineapple serves as a model for understanding this water-efficient adaptation 7 .
The pineapple lineage diverged from the grasses approximately 82-100 million years ago, providing an invaluable evolutionary reference point for investigating cereal genome evolution 7 .
Pineapple's long history of clonal propagation has created distinctive genetic patterns that illuminate how humans have shaped crops through centuries of cultivation 7 .
Expert Insight: "Pineapple has outstanding nutritional and medicinal properties and is a model for studying the evolution of CAM photosynthesis" - Professor Ray Ming from the University of Illinois 7 .
For years, pineapple geneticists worked with incomplete genomic maps that contained substantial gaps, representing only two of the five known pineapple varieties 1 . That changed dramatically in 2024 when an international team of scientists achieved a major breakthrough: the first gap-free reference genome for pineapple 1 .
This telomere-to-telomere assembly represents a monumental technical achievement. The researchers sequenced three distinct varieties:
By combining multiple sequencing technologies and manually revising each gene structure annotation, they identified 26,656 protein-coding genes with exceptional completeness of 99.2% as evaluated by BUSCO benchmarking 1 .
Protein-coding genes identified in the pineapple genome
Research Impact: "The construction of this gap-free reference genome with high-quality gene structure annotations provides a solid foundation for pineapple genomics and a valuable reference for pineapple breeding" 1 .
Perhaps the most fascinating revelation from pineapple genomics concerns how this fruit came to be domesticated. Unlike seed-propagated crops that require generations of selective breeding, clonally propagated plants like pineapple can be domesticated through what scientists call a "one-step operation" 4 6 .
Prehistoric forager encounters a wild pineapple plant with desirable traits
Takes a cutting (such as the leafy crown) to propagate an exact genetic duplicate
In one single step, creates a domesticated variety without years of selective breeding 4
Professor Ming's team developed a novel bioinformatic method that looked for long strings of similar genetic sequences at the ends of chromosomes, called "runs of homozygosity" 4 6 .
"To our surprise and delight," Ming reported, "extensive terminal runs of homozygosity were detected in cultivar 'Singapore Spanish'" 6 .
This genetic pattern is best explained by many years of exclusive clonal propagation, supporting the single-step domestication hypothesis 6 .
Scientific Implications: "The co-existence of punctuated sexual reproduction and 'one-step operation' in domestication of clonally propagated crops implies rapid domestication of clonally propagated crops is possible" - Professor Ming 6 .
To appreciate how modern genomic research unfolds, let's examine a specific experiment that reveals the power of these approaches. A key study sought to understand the genetic basis of anthocyanin production—the pigments that create red, purple, and blue colors in many fruits and vegetables—in different pineapple varieties 1 .
The research revealed that approximately 30.8% of pineapple genes were located within range of structural variations that might influence their function, including 30 genes associated with anthocyanin synthesis 1 .
| Tissue Type | AcMYB528 Expression Level | Anthocyanin Accumulation | Key Genetic Factor |
|---|---|---|---|
| Leaves with high pigment | High | Significant | 1.9-kb insertion fragment |
| Leaves with low pigment | Low | Minimal | Absence of insertion |
Further analysis and functional experiments demonstrated that high expression of a specific gene called AcMYB528 correlated with anthocyanin accumulation in leaves, likely influenced by a 1.9-kb insertion fragment 1 .
Practical Application: Understanding the genetic control of anthocyanin production has implications for developing new ornamental varieties and potentially enhancing stress resistance in fruit-producing cultivars, since anthocyanins are linked to plant defense mechanisms .
Modern genomic research relies on sophisticated technologies and reagents. Here are some key tools that enabled the pineapple genomic breakthroughs:
| Tool/Reagent | Function in Research | Specific Application in Pineapple Studies |
|---|---|---|
| PacBio Long-Read Sequencing | Generates long DNA sequences | Enabled contiguous genome assembly |
| Illumina Sequencing | Produces high-accuracy short reads | Used for polishing genome assemblies |
| Hi-C Technology | Captures chromosomal conformation | Anchored sequences to chromosomes |
| BUSCO | Assesses genome completeness | Evaluated quality of gene annotations 1 |
| RepeatMasker | Identifies repetitive elements | Characterized transposable elements 7 |
| MAKER | Annotates gene models | Predicted protein-coding genes 7 |
| RNA-seq | Measures gene expression | Revealed diel expression of CAM genes 7 |
The genomic journey of pineapple—from Columbus's delight to today's chromosome-scale assemblies—demonstrates how modern biology can transform our understanding of the natural world. The complete pineapple genome provides more than just insights into a single fruit species; it offers a reference point for cereal crops, a model for climate-resilient agriculture through CAM photosynthesis, and a window into domestication history 7 4 .
Understanding CAM photosynthesis in pineapple could help develop drought-resistant crops in a changing climate.
Genomic resources may help address pressing challenges like reducing food waste through by-product valorization 2 .
As we stand at the threshold of a new era in plant breeding, the pineapple's crown, once merely an ornamental feature, now symbolizes its regal position in the genomic revolution—truly making it the "king of tropical fruits."
The author is a science writer specializing in making complex biological concepts accessible to general audiences. This article is based on analysis of recent scientific publications from leading research institutions.
Crassulacean Acid Metabolism (CAM) is a water-efficient photosynthetic adaptation that allows pineapple to:
Indigenous peoples cultivate pineapple in South America
Columbus encounters pineapple in the Caribbean
Pineapple spreads to Europe and becomes status symbol
First telomere-to-telomere pineapple genome completed