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LeapsOverRivers · Nov 29, 2020 3:27 PM

Anybody use COIs to monitor inbreeding? I just put all my breeding animals through a COI calculator (I used this one: https://bullypedigrees.com/inbreeding-calculator/) and got some pretty mixed results.
Highest is this girl:

blAH La Minimalista
at 31.25%. Which, if she were real, would be pretty crippling :(.
I have plenty of 0%s, mostly as a result of mixing my lines, which cancels any inbreeding in the dam or sire if there hasn't been any mixing earlier in the pedigree.

I also have a couple more interesting-looking pedigrees, like this girl:

gFsF La Acorde
whose COI is 8.59%, which is a bit high for a horse meant for athletics but is a lot lower than most purebred dogs. She has three paths back to Purpurina, who was a stud that I really liked and kept a lot of his fillies, and a few contributions from some others that were my first few attempts at breeding in the pasture. Unfortunately a lot of the duplicates aren't visible because the pedigree on here doesn't show enough generations.

I haven't really been avoiding inbreeding much, because I don't keep a lot of stallions around and I've been avoiding mixing lines. I only breed in the pasture as well, which makes it wayyy easier to stair-step my paper levels very high very quickly, but does mean that I can't use public studs or straws. I'm interested to see how common levels of inbreeding like mine are among people breeding for color.

BlueValley · Nov 29, 2020 5:33 PM

I thought this would be fun to try with one if my higher gens:

BV8 Snowfalls Pride SF

This guys is from my snowflake lines, and I'm quite surprised his COI was only 3.77%! With how many times he goes back to my original snowflake foundations, Mr Meteoric Milestone and Havasue Snow, I expected a higher number.

HTRanch · Nov 29, 2020 5:34 PM

Well this is interesting, because it actually helps me with an experiment I was already doing on my bootstrapping account. I've been having issues with stagnant PT scores over the past few years, and after conferring with some bootstrapping gurus, I was wondering if inbreeding was an issue. I got myself some new outside studs and I'm in the middle of breeding them with my current herd and testing AFPTs. None of these guys have been bred outside of my herd, so the results should be pretty accurate to my barns.

SG3 134 Lost in Loudon
My homebred guy with a COI of 4.69 and an AFPT of 13.08

SG4 135 Westbound
Wes has a slightly higher COI: 7.03 percent. He is the same paper quality as Lost in Loudon but has a slightly lower AFPT at 12.98.

SG3 131 Phoenician
Pho has the highest COI at 28.13%, but an AFPT of 13.08, which is actually higher than my other guys have. He also is ever so slightly lower quality in paper level.

So, because it seems like the COI did not significantly affect AFPT, I would guess that I just have a regular old mare lag problem :P

SpryOfJune · Nov 29, 2020 5:48 PM

I just used that site a bit ago, playing around.

6789915 Maybe

Inbreeding: F = 21.88%
12.50% through Crusty One (1 path)
9.38% through Crustacean (3 paths)

Haltanny · Nov 30, 2020 7:13 AM

Inbreeding has no negative effect in the game, last i heard. I'm certain my herd is highly inbred but i don't have the inclination to calculate anything. I have some horses that only have like 2 or 3 great grand parents. :-)) And in my bootstrap herd, a horse's sire, dam's sire and grand dam's sire might all be the same horse.

Inbreeding isn't terrible in real life unless someone is using inferior animals to begin with. Various methods of inbreeding are quite useful to breeders in real life and here.

LeapsOverRivers · Nov 30, 2020 3:24 PM

Haltanny, I'm just doing this for kicks, I find the statistics of it interesting :)>-

Now that I've run the numbers for the COIs, I found another site that calculates ALC (http://www.sobczyk.eu/inb/?lng=en), which I haven't seen before. It measures the percent value of how many ancestors don't repeat, but on either side of the pedigree, meaning that, unlike COI, ALC measures how inbred the parents are as well. Higher numbers are better.

So some of my horses coming from mixed lines but inbred parents that have a COI of 0% are going to have much worse ALC, like this filly.

6955070
You can see some of the repeat ancestors early in the pedigree, and there's a few more further in, so her ALC is 88.71%.

Or this mare, with a COI of 28.13%.

gFsF La Delgada
She has an ALC of 80% square. Janky!

FeldingFields · Dec 1, 2020 11:01 AM

So I figured go big or go home, and I'm doing my best in Pasture 7g mare...

L7G Red Comet BiP

one, lots of horses. two, didn't realize that she has so many outside line horses in her pedigree. Not sure how I feel about that. Makes it feel less "my" accomplishment. three, I mislabeled a horse back in 3G and she's uneven aaaaaalll the way back there and this bothers me so much. I genuinely don't know what I'm going to do with her. Like half of my L7 mares have the same great-granddam. Argh.

Anyway, her COI is lower than I expect the rest of my horses will be and is 28.59%
14.23% through L6S Star of Winter BiP (1 path)
10.25% through L5A Lucid Dreamer BiP (3 paths)
1.66% through L4A Stacked Deck Memory (2 paths)
1.14% through AdL Rhaegar (93 paths)
0.59% through L3Bl PromiseMeNed BoP (3 paths)
0.44% through L3A DragonFire liv (2 paths)
0.15% through AdL John Snow 2A (3 paths)
0.098% through AdL Summerhall 2A (2 paths)
0.037% through sT AdL Drink With Me RaS (3 paths)

I suspect my others will be higher - I have several horses that have Rhaegar as the foundation sire in all but one slot.

I am ridiculously angry over this though, and will go get lunch before doing any others.

BlueValley · Dec 1, 2020 11:36 AM

@FeldingFields I made a similar discovery when I was revamping my sixth and seventh gen mares. It was an oopsy pasture breeding that I missed a long time ago. Luckily for me, most of the mares didn't fit my breeding goals anymore, so I wasn't too upset to just spay them and add them to my show herd.

If you choose to no longer breed with those mares, I know there's quite a few bootstrap breeders about--perhaps they would take her off your hands. :)

FeldingFields · Dec 1, 2020 11:45 AM

@BlueValley That's a thought. I have my own little bootstrap herd and have been trying to decrease the bone size for a while. Adding her and her sisters to those pastures might ease the sting a little bit.

FeldingFields · Dec 1, 2020 1:34 PM

Double or Nothing has only one grandfather (who has been an absolutely stellar sire, and I keep procrasinating replacing him), and Rhaegar is his foundation sire eight times.

L5S Double or Nothing
His stats: Inbreeding: F = 23.44%
14.06% through L3A Leroy Jenkins liv (1 path)
9.38% through AdL Rhaegar (12 paths)

(Not sure why its says 1 path to Leroy Jenkins when there are two... is it a phrasing/terminology I'm not sure of?)

The other site lists
Inbreeding: 0.21875 (21.875%)
AVK (ancestor loss coefficient): 60% (Ouch!)

Double or Nothing will be replaced as my G5 sire in January by his half-brother Lost Chances, who is not only sup but also less inbred.

L5S Lost Chances
His stats: Inbreeding: F = 0.0%

From the other site:
Inbreeding: 0.1171875 (11.71875%)
AVK (ancestor loss coefficient): 73.333333333333%

FollysFantasies · Dec 4, 2020 12:26 PM

This is an interesting exercise...
This boy has a COI of 2.34%, a descendant of my very first stallion with Watercolor.

KS05s Stremonar 5895007 KitMhWC

Since I breed this line for genes first, I'm super surprised to find that this fellow has COI 0.0%! I tracked him back 7 generations (as far as that calculator will go without a pro subscription), leaving all foundation horses blank.
Then I realized that I picked his dam up in the auction. I need to do that more often, even if it results in uneven pedigrees.

NX05s Delde 6691659 OXNXWC

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