Bet you never heard that before. But it is a statistical fact that pedigree inbreeding coefficients and AI selection by “one size fits all” index ranking go hand in hand.
Why? Because a composite index establishes an “ideal genotype” (a process that is much accelerated by Genomics, which is 60% based on “ideal” marker gene possession). If you insist on the highest affordable level of “ranking” you will be breeding “like to likes” at the level that will express inbreeding depression in some form by third or fourth generation.
Under “matrix” selection you monitor each generation for its results, and change the traits on which you can see the emerging needs before they get out of hand. In this way, genotypes over multiple generations remain heterozygous (as in more capable of hybrid vigor than we see from homozygous genotype selection defined by a sire ranking index).
Mating to balance the physique improves adaptability of your replacements
Many dairymen utilizing “matrix” sire selection also utilize “aAa” concepts for the choice of matching cows in the herd to sires found through the matrix screening. The idea here is that most of our involuntary culling losses come from physiques that had extreme characteristics leading to structural failure of the udder, the legs and/or feet, or major body organic systems (circulation, respiration, spinal nerve signals, pelvic calving dimensions, energy metabolism)
A major review of the impact of “aAa” concepts on the performance and longevity of 1980s purebred Holsteins (utilizing data provided by Holstein USA) indicated a 5000 pounds per lactation difference between “getting it right” and “breeding likes to likes” according to how aAa perceives those differences in cattle physiques.
Nothing developed as a result of Genomic technology (including the very interesting work being done by Zoetis on “wellness” trait correlations) has changed any aspect of breeding that is beyond the limited “reductionist” focus of trait and composite indexes. Thus either “index selection” or “matrix selection” results can still be improved by adding the physical mating selection to the genetic trait selection, especially on the side of “cost control”.
Ranking indexes keep changing
CDCI will soon incorporate the “Livability” trait at a 1% level into Net Merit. AJCA has announced a major revamp of Jersey Performance Index. All this tinkering with indexes that are the basis for AI studs’ young sire selection is evidence that “one size fits all” does not fit anyone very well. Just as cows have unique genotypes, herds have unique genetic trait bundles. The job of the breeding industry is not to tell you what to use, it is to help you find what best fits your current needs, and to recognize when needs change before our herds suffer declining economic competitiveness and physical adaptability.
Genetic selection is important; compensatory mating is equally important; when these work together you insure your future herd can deal with changing economic and environmental conditions. Breeding should be under your hands-on control, not left to the theorizing of mathematicians who fail to see the tremendous random variability that exists in biology at levels they are not factoring into their equations.