Inbreeding depression is caused mainly due to:
Genetic load comprising numerous mildly deleterious partially recessive alleles dispersed across coding regions for enzymes in photosynthesis, respiration and hormone biosynthesis remains hidden in heterozygous condition due to dominance masking. During random mating most individuals heterozygous Aa, functional allele compensates. Inbreeding increases homozygosity, exposing aa genotypes expressing reduced fitness such as chlorosis, dwarfing or sterility. Estimates in Drosophila and maize suggest each diploid carries hundreds of lethal equivalents affecting quantitative traits additively. Purgi
Ref: Charlesworth D Nature Review Genetics recessive load; Falconer Quantitative Genetics Ch Inbreeding; PubMed genomic basis inbreeding depression.