Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Genomic measures of inbreeding based on identical-by-descent (IBD) segments are increasingly used to measure inbreeding and mostly estimated on SNP arrays and whole-genome sequencing (WGS) data. However, some softwares recurrently used for their estimation assume that genomic positions which have not been genotyped are nonvariant. This might be true for WGS data, but not for reduced genomic representations and can lead to spurious IBD segments estimation. In this project, we simulated the outputs of WGS, two SNP arrays of different sizes and RAD-sequencing for three populations with different sizes and histories. We compare the results of IBD segments estimation with two softwares: runs of homozygosity (ROHs) estimated with PLINK and homozygous-by-descent (HBD) segments estimated with RZooRoH. We demonstrate that to obtain meaningful estimates of inbreeding, RZooRoH requires a SNPs density 11 times smaller compared to PLINK: ranks of inbreeding coefficients were conserved among individuals above 22 SNPs/Mb for PLINK and 2 SNPs/Mb for RZooRoH. We also show that in populations with simple demographic histories, distribution of ROHs and HBD segments are correctly estimated with both SNP arrays and WGS. PLINK correctly estimated distribution of ROHs with SNP densities above 22 SNPs/Mb, while RZooRoH correctly estimated distribution of HBD segments with SNPs densities above 11 SNPs/Mb. However, in a population with a more complex demographic history, RZooRoH resulted in better distribution of IBD segments estimation compared to PLINK even with WGS data. Consequently, we advise researchers to use either methods relying on excess homozygosity averaged across SNPs or model-based HBD segments calling methods for inbreeding estimations.