Breeding goals & design

How does the continuous addition of new traits affect U.S. selection indices?

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Abstract

Selective breeding has been practiced since domestication, but early breeders commonly selected on appearance (e.g., coat color or pattern) rather than performance traits. A breeding index combines information about many traits into a single value, representing total economic merit, that can be used for selection. The first USDA selection index was released in 1971 and included only milk and fat yield, while the 2025 revision of the Lifetime Net Merit (NM$) index includes 17 traits and composites. Many dairy farmers, semen salespeople, sire analysts, and genetics regularly express concern that, as the number of traits in the index grows, it becomes less effective because selection response is "diluted" (index efficiency decreases). The response for individual traits changes as new items are added to the index, but the direction of the selection response for those traits remains favorable. Correlated response to selection for 24 traits and composites currently evaluated by the Council on Dairy Cattle Breeding (Bowie, MD) and Holstein Association USA (Brattleboro, VT) was calculated for 12 USDA selection indices and their changes over time were examined. Indices including only yield (milk, fat, and protein) traits had the highest heritabilities (0.272-0.290), while NM$ had heritabilities ranging from 0.188 in 2010 to 0.243 in 2025. Rates of selection response have changed over time but are in favorable directions for most traits. While selection response has slowed for some traits (e.g., production) as new traits were added to the index they remained favorable (positive). Other traits, most notably fertility, now have favorable trends when they had unfavorable (negative) trends in earlier versions of the selection index. There is some reranking within birth year cohorts for genetic merit and reliabilities because older animals were selected using different criteria than contemporary animals. Rank correlations are high across indices, ranging from 0.8746 to 0.9994, suggesting that sires rank similarly despite the increasing complexity of the index. Selection gains for fat, protein, longevity, and body weight composite have the greatest economic value regardless of how responses are calculated. As new traits are added to selection indices, genetic and phenotypic (co)variance matrices grow in dimension and estimation of all elements can be difficult. This is compounded for traits collected in research trials, in which some but not all phenotypes used in the index are collected. Off-diagonal elements of the genetic and phenotypic (co)variance matrices were permuted withing trait groups to determine the effect of errors in (co)variances on the NM$ selection index. While it is important that (co)variance matrices are properly estimated, results show that modest errors in those values do not substantially affect index weights or realized genetic gain. Properly constructed selection indices produce desirable rates and directions of gain for many traits at once.

Keywords: 2026

How to Cite:

Cole, J., (2026) “How does the continuous addition of new traits affect U.S. selection indices?”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285432. doi: https://doi.org/10.31274/wcgalp.23704

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