Unlocking the Secrets: What Genetics Tells Us About Italy’s Unique Horse Breeds

Hey there, fellow horse enthusiasts and curious minds! Have you ever looked at a horse and wondered about its story? Not just its training or its lineage on paper, but the deep, genetic tale written over centuries? Well, I’ve been diving into just that, exploring the fascinating world of Italian native horse breeds and what their DNA can tell us about their past, present, and future. It’s like being a detective, but instead of fingerprints, we’re looking at tiny genetic markers!

Horses, as we know, haven’t just *happened*. They’ve been shaped by two powerful forces: Mother Nature herself, pushing them to adapt to tough environments, and us humans, carefully (or sometimes not so carefully!) selecting for traits we needed or admired. Think about it – from ancient warhorses and agricultural powerhouses to today’s sleek sport horses and sturdy companions, it’s all down to selection. Italy, with its incredibly diverse landscape and history, is a treasure trove of unique horse breeds, each with its own special quirks and strengths. We wanted to understand how this history, especially natural and artificial selection, has left its mark on their genetic makeup.

Now, many of these wonderful Italian breeds face a bit of a challenge. Their original jobs, like heavy farm work, aren’t as common anymore. This can lead to smaller populations, less genetic variety, and something called ‘inbreeding’ creeping in. This study, which I’m thrilled to share insights from, focused on five fantastic Italian characters: the Bardigiano, the Haflinger, the Maremmano, the Murgese, and the Italian Heavy Draught Horse (or TPR as they’re often called). Our mission? To peek into their genomes and see how selection has molded them over time and check out their genetic diversity status.

Gathering the Clues: How We Looked Inside

To do this, we got our hands on genetic data from a whopping 1620 horses from these five breeds. We used a special tool called an SNP chip – basically, a way to quickly read lots of tiny genetic variations (SNPs) across their DNA. After a bit of data cleaning (gotta make sure the info is reliable!), we ended up with data from 1498 horses and over 54,000 SNPs. That’s a lot of genetic dots to connect!

With this data, we did a few key things. We looked at the structure of the populations – how genetically similar or different the breeds are. We also identified ‘runs of homozygosity’ (ROH). Now, don’t let the fancy term scare you! Think of ROH as stretches of DNA where the horse has inherited identical copies from both parents. Longer ROH usually mean more recent shared ancestry or inbreeding, while shorter ones point to older, more distant relatedness. By looking at these ROH, we could calculate a genomic inbreeding coefficient (FROH) for each horse and each breed. And here’s a cool part: by looking at ROH that were *shared* by lots of horses within a breed (we set the bar at 70% or more), we could find ‘ROH islands’. These islands are like genetic hotspots that have likely been targeted by selection, either natural or artificial, because individuals with those specific genetic stretches were more successful and passed them on.

The Inbreeding Report: Who’s Who?

So, what did the inbreeding numbers tell us? The FROH values ranged from 0.15 to 0.23 across the five breeds. The Bardigiano and Haflinger breeds showed the highest average inbreeding (0.23 and 0.22, respectively). This isn’t necessarily a bad thing, but it often reflects focused selective breeding programs where certain desirable traits are emphasized, leading to a smaller effective breeding population over time. On the other hand, the Maremmano, Murgese, and Italian Heavy Draught Horse had lower FROH values (0.15, 0.16, and 0.18), suggesting they’ve maintained a bit more genetic diversity overall.

When we dug a little deeper into the ROH lengths, we found something interesting. Most of the ROH were quite short, which points to inbreeding events that happened a long, long time ago, perhaps when these breeds were first being established or went through ancient bottlenecks. However, the Bardigiano breed also showed a higher level of inbreeding due to *longer* ROH. This is a sign of more *recent* inbreeding, potentially linked to breeding decisions made in the last few generations, perhaps involving the heavy use of a few popular stallions to improve certain traits like height.

It seems like we can group these breeds based on their ROH patterns. The ‘cold-blooded’ types (Bardigiano, Haflinger, TPR), traditionally used for heavier work, tend to have a higher *number* of ROH segments compared to the ‘warm-blooded’ types (Maremmano, Murgese), which are often geared more towards sport. This could be because the warm-blooded breeds have had more genetic material introduced from other, international sport horse breeds to boost their athletic performance, which increases diversity and reduces homozygosity.

Finding the Genetic Hotspots: Where Selection Left Its Mark

Now for the really exciting part – the selection signatures, those ROH islands! We found 23 of these hotspots spread across 12 different chromosomes. Interestingly, the cold-blooded breeds had the majority of these islands, with the Haflinger showing the most (10), followed by the Bardigiano (7), and the TPR (4). The Maremmano and Murgese had just one each. A major hotspot area was Equine Chromosome 3 (ECA3), where almost all breeds (except Maremmano) had selection signatures.

These ROH islands weren’t just random stretches of DNA. They overlapped with regions known to contain genes and QTLs (Quantitative Trait Loci – areas linked to traits) associated with important characteristics. We found overlaps with 83 QTLs and 76 genes! These were linked to things like body shape, size, coat color, gaits, and importantly, health.

What Traits Were Under the Spotlight?

Let’s break down some of the traits that seem to have been shaped by selection in these breeds:

Morphology and Size: Built for a Purpose

Physical attributes have always been key in horse breeding. We found several ROH islands overlapping with QTLs related to exterior measurements like height at withers and body size. ECA3, that busy chromosome, was a big player here, with shared signatures between the TPR and Murgese. These breeds were historically used for heavy work, needing strength and size.

For the TPR, selection has focused on traits like muscle mass and body dimensions, particularly for meat production and heavy draft work. This aligns with selection signatures found in other draft breeds. The Murgese, while also historically a draft horse, is now increasingly selected for height, especially for military and riding purposes, aiming for horses over 170 cm. So, while they share a chromosome hotspot, the *reasons* for selection might differ slightly today.

Within the ECA3 hotspot, we found the LCORL gene, known to influence skeletal size and height. We looked at a specific SNP near this gene and found that in the Bardigiano breed, the frequency of a particular allele (the ‘G’ allele) increased over time, mirroring an increase in average height in the breed. This suggests selection for height is happening, and this SNP could be a useful marker for breeders.

Other genes linked to body size, like ZC3H18 and FAM184B, were also found in selection signature regions, further supporting the idea that selection for size and build has been a major force, particularly in the heavier breeds.

The Maremmano breed had its own private selection signature on ECA9, also linked to height at withers. This breed, known as Italy’s first sport horse, has long had height as a key selection trait in its breeding program, using morphological scoring systems. It’s fascinating how different breeds achieve similar goals (like height) through selection on different parts of their genome.

Coat Color: Looking Good for the Job

Coat color is a defining trait for some breeds. The Haflinger is famous for its chestnut coat, and the Murgese is primarily black or gray. We looked at genes known to control coat color, MC1R and ASIP, and found selection signatures nearby in the Haflinger and TPR (for MC1R) and the Murgese (for ASIP). This isn’t surprising – breeders have actively selected for these specific colors. We also found that certain SNPs near these genes showed strong associations with the expected coat colors, suggesting they could be used as handy markers for breeders without needing extra specific tests.

Health and Adaptation: Built Tough

Native breeds are often praised for their robustness and adaptation to their local environments. Our study found selection signatures linked to health traits, particularly in the Bardigiano and Haflinger breeds. On ECA3 and ECA10, we found hotspots overlapping with QTLs for conditions like osteochondrosis (a skeletal issue) and navicular bone morphology, and even genes related to hoof health (like WWP2).

Considering these breeds often live in challenging mountain terrain and are sometimes kept barefoot, selection for strong, healthy hooves makes perfect sense! It seems their environment and traditional use have really shaped their genetics for resilience.

The Haflinger also showed a private selection signature on ECA3 and ECA11 linked to insect bite hypersensitivity (IBH). Since Haflingers live in high-altitude, colder areas, selection might favor horses naturally more resistant to the insects that cause this condition, or perhaps selection for thicker hair density (which helps against both cold and insects) is the real driver here.

Interestingly, selection signatures related to osteochondrosis were found in most of the heavier breeds (Bardigiano, Haflinger, TPR, Murgese) but *not* the lighter Maremmano. Osteochondrosis is more common in heavier horses that grow quickly. This suggests that selection in the heavier breeds might be working to mitigate the risk of this condition, while the Maremmano’s lighter build and historical selection against skeletal issues (through performance tests and X-rays since the 1990s) might explain the absence of a detectable signature.

Performance: Ready for Action

While not as intensely selected for sport as some international breeds, performance is becoming more important for native breeds like the Haflinger, especially for endurance events. We found a selection signature on ECA7 in the Haflinger, near genes linked to bone remodeling (ACP5) and heart muscle development (ECSIT). A larger heart size is beneficial for endurance, so this finding aligns nicely with the Haflinger’s increasing role in performance sports.

Bringing It All Together

This study gives us a fantastic window into the genetic history of these five unique Italian horse breeds. By looking at inbreeding levels and identifying those special ROH islands, we can see how both natural adaptation and human selection have shaped them. The differences we see between the cold-blooded and warm-blooded types, in terms of inbreeding and selection hotspots, really highlight their distinct breeding histories and purposes.

For breeders and breed associations, this information is incredibly valuable. Understanding which genetic regions are linked to specific traits – whether it’s size, coat color, hoof health, or performance – can help them make more informed decisions. This is crucial for maintaining the genetic diversity that *is* present, preserving the unique characteristics of each breed, and improving their health and suitability for modern uses. It’s about honoring their history while securing their future.

Think of it as giving breeders a genetic roadmap. They can use this knowledge to select breeding pairs that will help preserve desirable traits, avoid potential health issues, and manage inbreeding levels. It’s a powerful tool for conservation and improvement, ensuring these wonderful Italian horse breeds continue to thrive for generations to come.

Source: Springer