Factors affecting accuracy of estimated effective number of chromosome segments for numerically small breeds

For numerically small breeds, obtaining a sufficiently large breed-specific reference population for genomic prediction is challenging or simply not possible, but may be overcome by adding individuals from another breed. To prioritize among available breeds, the effective number of chromosome segments (M_e) can be used as an indicator of relatedness between individuals from different breeds. The M_e is also an important parameter in determining the accuracy of genomic prediction. The M_e can be estimated both within a population and between two populations or breeds, as the reciprocal of the variance of genomic relationships. However, the threshold for number of individuals needed to accurately estimate within or between populations M_e is currently unknown. It is also unknown if a discrepancy in number of genotyped individuals in two breeds affects the estimates of M_e between populations. In this study, we conducted a simulation that mimics current domestic cattle populations in order to investigate how estimated M_e is affected by number of genotyped individuals, single-nucleotide polymorphism (SNP) density and pedigree availability. Our results show that a small sample of 10 genotyped individuals may result in substantial over or underestimation of M_e. While estimates of within population M_e were hardly affected by SNP density, between population M_e values were highly dependent on the number of available SNPs, with higher SNP densities being able to detect more independent chromosome segments. When subtracting pedigree from genomic relationships before computing M_e, estimates of within population M_e were three to four times higher than estimates with genotypes only; however, between M_e estimates remained the same. For accurate estimation of within and between population M_e, at least 50 individuals should be genotyped per population. Estimates of within M_e were highly affected by whether pedigree was used or not. For within M_e, even the smallest SNP density (~11k) resulted in accurate representation of family relationships in the population; however, for between M_e, many more markers are needed to capture all independent segments.