BOTANIC?
Living Models

Use case

What to take home, a Plant Biologist Perspective

Understanding the genomic mechanisms behind a trait observed in the field can take years of work, thousands of plants and a pinch of luck. Genetics can help narrow the search to a region of the genome. But within that region, large blocks of DNA are inherited together, making it hard to separate the causal variant from all the variants that sit next to it. To separate them and get to the “genomic” resolution biologists need to draw a conclusion, more crosses, more plants and more seasons in the field are usually required.

BOTANIC-1 separates co-inherited variants in a different way. Instead of waiting for a recombination event to fall between them, it reads each in its sequence context and scores how much damage the change is likely to cause, a judgement grounded in the DNA grammar learned from 320 plant genomes. That score ignores if two variants are inherited together; it can tell them apart even when no plant in a field separates them.

In a published melon sex-determination study, experimental mapping left 3,061 candidate variants on chromosome 2 that segregated together. From that list only, BOTANIC-1 ranked first the experimentally validated causal mutation, a single substitution in the ethylene-signalling gene CmEIN3.

Botanic1 / A causal variant in melon

From thousands of variants to CmEIN3

The G124R mutation changes melon flowers from female to hermaphrodite.

  1. 47,492Starting variantsAcross 12 chromosomes
  2. 3,061After genetic mappingChromosome 2 · 2,494 SNPs score-able by BOTANIC1
  3. #1CmEIN3 · G124RRanked first
From 47,492 starting variants to the causal CmEIN3 mutation The dots are schematic, not one per variant. The grey region occupies 3,061 / 47,492 of the dot field. Dot positions are not genomic coordinates.

Schematic. Dots stand for the starting variants, not one each. The grey region is the chromosome 2 candidates at their true share of the field (1 in 15.5); the green dot is CmEIN3. Layout is not genomic position.

Retrospective case studyCmEIN3 Paper: Rashid et al. 2023 ↗

“The real opportunity is not to replace genetics or experimental validation, but to dramatically reduce the search space, telling us which variants to test first, rather than having to separate them one by one through thousands of plants”

Adnane Boualem, Research Director @ INRAE

The genetics still tells you where to look. BOTANIC-1 tells you what to test first, and you no longer have to grow your way to the answer.

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