Breeding goals & design

The Genomic Selection Index: A Tool for Enhancing Improvement in Low Heritability Traits

---

Abstract

Genomic Selection Index (GSI) is a method proposed to enhance long-term genetic gains by optimizing the use of dense marker information available in the genomic selection era. Unlike Genomic Selection (GS), which applies economic weights directly to trait-level genomic estimated breeding values (GEBVs), GSI first divides markers into groups based on their directional effects on different traits. The GEBVs of these marker groups are then combined into an overall selection index, with coefficients derived from selection index theory to maximize the correlation with the true aggregate genotype (H). This approach provides optimum and group-specific weights based on their relative importance in the aggregate genotype. The long-term effect of GSI compared to standard GS, demonstrated significant differences when adverse correlations were present. The results of simulated data sets showed that when traits were negatively correlated (-0.5, standard GS resulted in a negative selection response for the low heritability trait, While, the GSI method yielded a positive genetic gain. This represents a 137% higher genetic gain for GSI for the low heritable trait compared to GS. Furthermore, when traits were negatively correlated, GSI yielded a 9% higher gain for the aggregate genotype (H) compared to GS. Even with a zero genetic correlation, GSI still achieved a 22% higher response for the low heritability trait. The superiority of GSI decreased as the correlation increased positively, showing a similar response to GS when the correlation was 0.5. GSI outperforms GS in scenarios with antagonistic trait relationships because it explicitly accounts for marker-level pleiotropic effects. By differentially weighting marker groups, such as those with opposing effects on two traits, GSI mitigates the unintended suppression of low-heritability traits that often occurs under conventional genomic selection. The evidence overwhelmingly suggests the utility of GSI rather than standard genomic selection, especially for breeding programs where traits with low heritability are included in the aggregate genotype and exhibit a negative correlation with high heritability traits.

Keywords: 2026

How to Cite:

Foroutanifar, S., (2026) “The Genomic Selection Index: A Tool for Enhancing Improvement in Low Heritability Traits”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2282737. doi: https://doi.org/10.31274/wcgalp.23468

Rights: 1