Which genes commonly contribute to inbreeding depression?

Inbreeding depression is primarily caused by deleterious recessive alleles and certain overdominant loci that become homozygous due to mating between genetically related individuals. The genes contributing to this phenomenon affect essential plant functions such as growth, fertility, stress tolerance, and survival.

1. Genetic Mechanisms Involved

There are two main theoretical models explaining how genes contribute to inbreeding depression:

• Partial Dominance (Recessive Deleterious Allele) Hypothesis: Inbreeding increases homozygosity, exposing partially recessive harmful alleles that reduce plant fitness. These alleles, normally hidden in heterozygous states, become expressed when homozygous, causing lower seed viability, growth defects, or sterility.
• Overdominance (Heterozygote Advantage) Hypothesis: Certain loci confer higher fitness when heterozygous (e.g., for enzyme efficiency or stress resistance). Inbreeding reduces heterozygosity at such loci, leading to diminished overall vigor and adaptability.

2. Gene Categories Commonly Involved

Empirical and genomic studies have identified several functional classes of genes associated with inbreeding depression:

• Developmental and Growth Genes: Mutations in genes regulating embryo development (e.g., LEC1, FUS3, ABI3) lead to poor germination and plant stature.
• Reproductive Genes: Deleterious alleles affecting pollen formation, ovule viability, and gametophyte competition—such as S-locus genes and tapetum-development regulators—reduce fertility.
• Metabolic and Stress Response Genes: Loss-of-function mutations in genes involved in oxidative stress response, photosynthesis, and respiration can impair plant metabolism and abiotic stress resistance.
• Defense-Related and Pathogenesis-Response Genes: Inbred plants often express reduced disease resistance, partly due to homozygosity at loci controlling pathogen recognition (e.g., NBS-LRR gene families).

3. Role of Epigenetic Modifications

Recent research highlights the contribution of epigenetic changes, such as altered DNA methylation patterns, to inbreeding depression intensity. Epigenetic silencing of key regulatory genes following selfing can amplify or mitigate depression effects independent of DNA sequence variation.

4. Genomic Insights

High-throughput sequencing in model plants like Arabidopsis thaliana and crops like maize, rice, and soybean shows that inbreeding depression is polygenic, involving hundreds of loci with small effects rather than single major genes. These loci cumulatively increase “mutational load,” leading to the decline in fitness with repeated selfing