An ancient gene times avocado flowers
A genomic study links avocado's complementary A- and B-type flower schedules to two SDMYB haplotypes maintained for more than 42 million years, while stopping short of direct gene-editing proof.
The 60-second version
Genome mapping and time-series expression data link avocado's A/B flower schedules to two ancient SDMYB haplotypes.
Key points
- The primary association analysis used 374 resequenced offspring and found one strong locus on chromosome 10.
- The dominant allele's expression rhythm lagged by about two hours, matching the delayed second flower opening in A-type trees.
- Comparative genomics estimates the haplotypes have persisted for more than 42 million years and occur in at least 26 non-avocado species.
- Markers may classify seedlings before the crop's five-to-twelve-year juvenile phase ends, but yield gains have not been demonstrated.
Verdict. SDMYB is the strongest supported regulator and a useful marker candidate, while direct functional conversion and field benefit remain to be tested.
A PNAS study links avocado's complementary A- and B-type flowering schedules to two ancient haplotypes around SDMYB, a flower-specific transcription factor. The evidence could let breeders identify flowering type in seedlings, but it does not yet show that changing this gene alone rewires the schedule or raises orchard yields.
The flower clockOne flower, two phases
An avocado flower is hermaphroditic. It first opens in a female phase, closes, and reopens the next day in a male phase. Under typical conditions, A-type trees begin the female phase in the morning; B-type trees follow the complementary schedule.
How it was foundA signal on chromosome 10
The researchers ran a genome-wide association study in 374 resequenced offspring from an open-pollinated cross between A-type Gem and B-type Luna UCR trees. One strong association appeared on chromosome 10. Read-depth patterns in a broader group of 504 phenotyped and resequenced relatives supported a structural difference at the same locus.
Additional avocado genomes narrowed the associated interval to one leading candidate: SDMYB, a member of a transcription-factor family involved in late flower maturation. A separate mapping panel published while this study was under review independently pointed to the same gene region.
MechanismExpression moves with the schedule
The team sampled flowers from three biological replicates of each type about every three hours across a daily cycle. SDMYB expression was rhythmic in both types. In A-type trees, the dominant A1 allele's expression rhythm lagged the A2 allele by about two hours, close to the delay in the flowers' second opening.
| Mapping | A single chromosome 10 region tracked A- versus B-type flowering in the primary family. |
|---|---|
| Structure | Read depth and assembled genomes showed distinct haplotypes around the locus. |
| Expression | SDMYB was flower-specific and its two alleles followed different daily phases. |
| Function | No reported knockout or allele-swap experiment directly converted one flowering schedule into the other. |
The result is a chain of converging evidence, not a one-experiment proof of a solitary genetic switch.
EvolutionA polymorphism older than the crop
Comparative genomes and a fossil-calibrated phylogeny place the divergence of the two haplotype lineages more than 42 million years ago. Diagnostic variants occur in at least 26 non-avocado species in the Perseeae tribe.
The proposed stabilizer is negative frequency-dependent selection. A rare flowering type can gain more compatible pollen partners, preventing either schedule from taking over. The 42-million-year figure is a molecular-clock estimate with model and calibration assumptions, not a direct measurement.
What changesSeedlings could be screened early
Avocado's juvenile phase lasts roughly five to twelve years. Genetic markers at the SD locus could identify A- or B-type seedlings before they flower, reducing the time and land needed to evaluate crosses and choose pollen donors.
Bottom lineUse the marker, test the outcome
Breeders can now test the locus as an early screening marker instead of waiting years for every seedling to flower. The next evidence should show whether that shortcut improves crossing efficiency and orchard performance across climates.