My experience with the anatomy of the boy bits is it also goes with the placement of his teats as well. I agree your herd sire has the best scrotal confirmation and pedro has the worst. His cleft is pronounced. But.... In the past (I do similar to you... Breeding my own landrace from nubian, spanish, boer, and a Nigerian dwarf in 4-5th generation) my Spanish doe was so worm resistant (I'm in fl) that even though she produced bucklings with a cleft, and her only doeling had a lopsided udder despite my diligence at keeping things even. I kept a male and used him anyway. I have a small herd and just now have yearlings by him... but the one of those I did breed had fabulous buckling and milked perfectly and had the attributes I bred for. (Nice udder and teats, worm resistance, good appetite, quiet on the stand) There's 2 more that I waited to breed and they are now bred for Feb and April kidding.
Its my opinion that experimenting is okay... Especially when highly desirable traits exist and you accept that not all offspring need bred in the future. We have to weigh the highly desirable traits with the acceptable traits with the undesirable traits....
I haven't logged in in a long time but retirement is near so hopefully I'll be back
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