Conservation & local programs

Comparison of traditional and gamma-based diversity metrics in dairy cattle breeds

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Abstract

During the last decade, the theory of metafounders has been used to overcome the assumption of unrelated base populations in genomic evaluations. In this theory, the gamma parameter can be used to estimate relationships within and across base populations. Interestingly, different genetic diversity metrics can be derived from the gamma parameter, including fixation index (Fst), Nei's minimum genetic distance (D), and different population inbreeding coefficients, e.g., based on average heterozygosity (Fb). However, the gamma-based and traditional formulas have never been compared in real populations. This study aimed to compare traditional and gamma-based diversity metrics by using the following formulas (shown as traditional and gamma-based): for fixation index, Fst = 1-Hwithin/Hbetween and Fst = (γb/8 + γb'/8 - γbb'/4)/(1/2 - γbb'/4); for Nei's Minimum genetic distance, D = 1/n∑(pb -pb')2 and D = γb/8+γb'/8-γbb'/4; and for inbreeding coefficient based on average heterozygosity, Fb = 1-4/n∑(2pbqb) and Fb = γb-1, with Hwithin the within population heterozygosity, Hbetween the between population heterozygosity, γb and γb' the within population gamma estimates, γbb' the across-populations gamma estimate, n the number of SNPs, pb and pb' the allelic frequencies in the different populations, pb(t) and pb(0) the current and initial allelic frequencies, respectively, and q = 1-p. For Fst, we assumed that heterozygosity between populations (Hbetween) corresponds to total heterozygosity. We estimated these different metrics on five dairy cattle breeds (number of genotyped animals): Ayrshire (1,981), Brown Swiss (10,521), Guernsey (3,871), Holstein (19,996) and Jersey (19,982). The average allelic frequencies at the base population were: 0.4818 for Ayrshire, 0.4824 for Brown Swiss, 0.4825 for Guernsey, 0.4823 for Holstein and 0.4825 for Jersey. The average differences between traditional and gamma-based diversity metrics were: -0.0022 for Fst , -0.0007 for D and 1.388 × 10-5 for Fb; while the mean squared errors were: 5.278 × 10-6 for Fst , 5.052 × 10-7 for D and 2.745 × 10-8 for Fb. Therefore, traditional and gamma-based Fb, Fst, and D were similar. To conclude, our results showed that it is possible to use formulas based on gamma to estimate Fb, Fst, and D in base populations of dairy cattle breeds.

Keywords: 2026

How to Cite:

Bermann, M., Legarra, A., Lourenco, D. & Wilmot, H., (2026) “Comparison of traditional and gamma-based diversity metrics in dairy cattle breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2266355. doi: https://doi.org/10.31274/wcgalp.23395

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