BREEDER’S BLOG

Genetic vs. Physical Maps – Why distances don’t always match

A 𝗽𝗵𝘆𝘀𝗶𝗰𝗮𝗹 𝗺𝗮𝗽 shows the actual DNA sequence of a chromosome, measured in base pairs (bp or kb). It tells us where genes and markers are located along the chromosome in physical space.
A 𝗴𝗲𝗻𝗲𝘁𝗶𝗰 𝗺𝗮𝗽, on the other hand, is based on recombination frequencies, measured in centimorgans (cM). It reflects how often two markers are inherited together, not how many base pairs separate them.

While the order of markers is usually the same in both maps, the distances between them often don’t align.
📌 Examples:
In Arabidopsis, 1 cM can represent 30–550 kb.
In rice, the average is 258.5 kb per cM, but ranges from 120 to 1000 kb.
In wheat, variation is extreme: 118 kb to 22,000 kb per cM!

This means two markers genetically close may be physically far apart (or vice versa), depending on recombination patterns.

Why? 🌍
Recombination isn’t random: it happens more in “hot spots” (gene-rich regions) and less in “cold spots” (repetitive, gene-poor regions).
In wheat, over 85% of genes lie in just 5–10% of the chromosomal space, and these regions recombine much more frequently.

🌾 Implications For breeding:
Understanding recombination hot spots is more than a technical detail — it directly impacts how easily unwanted traits can be removed, especially when working with exotic or non-commercial germplasm.

It allows correct placement of flanking markers around a desirable gene.
This ensures that the target locus is captured with minimal linkage drag, avoiding the inheritance of unwanted neighboring traits.

🔑 Takeaway: Knowing how recombination is distributed across genomes is crucial for breeders to design the marker strategy and introduce valuable traits while keeping their elite material clean.

✨ At AgroSynapsis, we offer training workshops and coaching on topics of molecular breeding, explaining complex concepts with clarity and simplicity.

👉 If you’d like to be informed about our upcoming workshops, and receive early access and discounts, f𝗶𝗹𝗹 𝗼𝘂𝘁 𝗼𝘂𝗿 𝘀𝗵𝗼𝗿𝘁 𝘁𝗿𝗮𝗶𝗻𝗶𝗻𝗴 𝗶𝗻𝘁𝗲𝗿𝗲𝘀𝘁 𝗳𝗼𝗿𝗺 here:

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