Banana: Genetics and the Sequenced Genome
The Musa acuminata genome was sequenced in 2012: ~523 Mb with approximately 36,500 protein-coding genes across 11 chromosomes. Commercial Cavendish bananas are sterile triploids (AAA) with 33 chromosomes, making seed production impossible.
Banana Genetics: The Sequenced Genome
🍌 The banana genome was fully sequenced in 2012, making Musa acuminata one of the early large genomes to be decoded in the monocot lineage. The project was led by Angélique D’Hont and colleagues at CIRAD (France) and published in Nature. The sequenced reference genome has since become the foundation for disease resistance research and banana breeding programs worldwide.
The 2012 Sequencing Paper
Reference: D’Hont, A. et al. (2012). “The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.” Nature, 488, 213–217. doi:10.1038/nature11241
The sequenced accession was a doubled haploid (DH Pahang) derived from Musa acuminata ssp. malaccensis — a diploid wild banana from Malaysia used as the reference because of its genetic tractability. Key genomic statistics from the 2012 assembly:
| Genomic Feature | Value |
|---|---|
| Genome size (assembly) | ~523 Mb |
| Estimated total genome size | ~500–600 Mb |
| Chromosomes (haploid) | 11 |
| Protein-coding genes | ~36,500 |
| Transposable elements | ~42% of genome |
| Gene density | ~70 genes per Mb |
| Sequencing coverage | ~16× Sanger + high-coverage Illumina |
The banana genome is notably gene-rich compared to other crop genomes of similar size. The ~36,500 predicted genes exceed the human gene count (~20,000–25,000 protein-coding genes), though many banana gene models are small or represent tandem duplications.
Chromosome Numbers and Ploidy
The base chromosome number for Musa is x = 11. All wild and cultivated banana chromosome counts are multiples of 11.
| Genome Group | Ploidy | Chromosome Count | Fertility | Example |
|---|---|---|---|---|
| AA (diploid) | 2x | 2n = 22 | Fertile | Wild M. acuminata |
| BB (diploid) | 2x | 2n = 22 | Fertile | Wild M. balbisiana |
| AB (diploid hybrid) | 2x | 2n = 22 | Partially fertile | Some wild accessions |
| AAA (triploid) | 3x | 2n = 33 | Sterile | Cavendish, Gros Michel |
| AAB (triploid) | 3x | 2n = 33 | Sterile | French Plantain, Horn Plantain |
| ABB (triploid) | 3x | 2n = 33 | Sterile | Bluggoe, Pisang Awak |
| AAAA (tetraploid) | 4x | 2n = 44 | Partially fertile | Some bred varieties |
| AABB (tetraploid) | 4x | 2n = 44 | Low fertility | Experimental hybrids |
Why Triploids Are Sterile
Commercial Cavendish bananas are triploid (3x) — each cell carries three copies of every chromosome (33 total) rather than the usual two. This arises from historical crosses between diploid and tetraploid M. acuminata ancestors during domestication.
Sterility in triploids results from the mechanics of meiosis — the cell division process that produces gametes (pollen and egg cells). Normal meiosis requires chromosomes to pair up in homologous pairs (bivalents) and then segregate cleanly. In a triploid, chromosomes must form trivalents (groups of three), which cannot segregate evenly. The result is:
- Gametes with unbalanced chromosome numbers
- Non-viable pollen and non-viable egg cells
- No fertilization possible
- No seed development
This is why Cavendish bananas contain only tiny, vestigial black specks where seeds would form — the seeds initiated but could not develop. Parthenocarpy (fruit development without fertilization) fills the ecological niche: the fruit grows anyway, without seeds.
Polyploidy and the A/B Genome Distinction
🍌 The M. acuminata (A) and M. balbisiana (B) genomes are distinct enough to be classified as different species yet similar enough to produce viable (if sterile) hybrids. The A and B genomes diverged approximately 4.6–5.6 million years ago based on molecular clock estimates.
The A-genome contributes traits associated with sweet, soft dessert fruit. The B-genome contributes starchiness, drought tolerance, and disease resistance. Breeders working to develop post-Cavendish varieties (resistant to Tropical Race 4 / TR4 Fusarium wilt) are using genomic data to introgress B-genome disease resistance traits into A-genome dessert types.
| Genome Feature | A genome (M. acuminata) | B genome (M. balbisiana) |
|---|---|---|
| Origin | Southeast Asia / Australasia | South / Southeast Asia |
| Fruit quality | Sweet, dessert | Starchy, cooking |
| TR4 resistance | Susceptible | More resistant |
| Genome size | ~523 Mb (haploid) | ~553 Mb (estimated) |
| Divergence from A | — | ~5 Mya |
Significance for Disease Resistance Breeding
The 2012 genome sequence identified candidate resistance gene analogs (RGAs) and NBS-LRR disease resistance genes in Musa. Subsequent genomic work has:
- Mapped TR4 resistance loci in M. balbisiana and resistant diploid accessions
- Enabled molecular marker-assisted selection in breeding programs (CIRAD, CARBAP, IITA)
- Supported CRISPR-based approaches targeting susceptibility genes in Cavendish
- Provided the reference for transcriptomic studies of banana ripening and stress response
The MGIS (Musa Germplasm Information System) curates genomic, phenotypic, and passport data for over 7,000 accessions, providing breeders with the full breadth of Musa genetic diversity.
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Related Pages
- Banana Taxonomy — genus Musa, genome group system, species classification
- Banana Varieties — major cultivars and the genome groups they belong to
- Wild Bananas vs. Cultivated Varieties — domestication and the loss of seeds
- Cavendish Crisis — Tropical Race 4 and why genetics matters for the future