Assessing inbreeding networks from partial correlations and information theory in rabbits

Overview & Synopsis

Accurate estimates of inbreeding (F) are crucial for the management of populations inselection schemes. Traditionally, inbreeding has been estimated from pedigree-basedinformation. Currently, genome-based estimates of inbreeding can be obtained fromSNP chip data. The correlation between pedigree and different genome-based estimatesof inbreeding is usually discussed in the literature. However, some of these correlationscould be spurious. Using partial correlations and information theory (PCIT) it ispossible to distinguish a significant association between two variables which isindependent from associations with a third variable. The objective of this study is toimplement PCIT to assess the relationship between different estimates of inbreeding andphenotypes using a selected population of rabbits. Pedigree data and genomicinformation from a 200K chip were available. After applying filtering criteria, the dataset constituted 490 animals genotyped for 114,604 autosomal SNPs. Phenotypic recordsfor average dairy gain (ADG) were also accessible for full (f) and restricted (r) feeding.Pedigree-based inbreeding estimates (ped) were decomposed in ancient (A),intermediate (I) and recent (R) inbreeding. Accordingly, genomic estimates ofinbreeding based on runs of homozygosity (roh) were also decomposed in A, I and R.Other genomic estimates of inbreeding were also evaluated: VanRaden (van),proportion of homozygous SNPs (snp), proportion of homozygous SNPs for the minorallele frequency (PHoMA) and the compression efficiency (CE). The results indicatethat FrohR is an essential node with 6 edges, one of which is negative with FrohA (-0.31). CE is a balanced node with 2 positive (Fsnp and FrohR) and 2 negative (FrohAand FpedI) edges. Fvan is the less related node with only one positive edge withPHoMA (0.70). When including phenotypic information, FpedI is correlated negativelywith ADGf (-0.11) and positively with ADGr (0.10). In addition, ADGr has a negativeedge with FrohA (-0.11). These results indicate that PCIT approach allows inferringmeaningful associations between estimates of inbreeding.