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. Purging through selection removes severe alleles but small effect alleles persist due to drift and linkage. Molecular cloning of inbreeding depression QTL in rice shows clusters of nonsynonymous substitutions in defense genes. Hence primary cause remains expression of harmful recessives rather than dominance of beneficial alleles. This understanding supports competitive exam preparation for NEET, GATE and CSIR NET concepts linking genotype with phenotype through molecular pathways involving transcription factors, hormones and metabolic enzymes that regulate development, adaptation and reproductive biology in applied breeding programs.
Ref: Charlesworth D Nature Review Genetics recessive load; Falconer Quantitative Genetics Ch Inbreeding; PubMed genomic basis inbreeding depression.