We’re all aware of the severe genetic and unpleasant physical consequences that result from reproducing with a closely related relative. Aside from unfortunate aesthetics, inbreeding can also lead to the extinction of small organismal populations. This decrease of reproductive success is referred to as “inbreeding depression” and mechanisms that cause it are still being debated by biologists.



A study led by Ken Paige at the University of Illinois at Urbana-Champaign, contributes to the understanding of the mechanisms associated with inbreeding depression, and his results are surprising. Paige’s study shows that two different mechanisms are responsible for reproductive decline, and even more surprisingly, alleles affected by inbreeding are not random and can be grouped into three categories of cellular function. Furthermore, these alleles are regulated by only a few key genes.



Currently, there are two mechanisms that are considered to be responsible for inbreeding depression—loss of dominant alleles and the loss of overdominance.



The loss of dominant alleles and subsequent unmasking of recessive alleles, is generally thought to be the predominant mechanism responsible for a population’s loss of fitness. Recessive alleles typically do not cause the organism harm unless two identical copies are inherited. During inbreeding, the frequency of inheriting two recessive alleles increases.



Overdominance occurs when two different alleles inherited together causes a higher level of gene expression than that of the offspring’s parents. Since inbreeding reduces genetic diversity, the odds of an offspring inheriting different alleles decreases. Therefore, any advantage that is conferred by overdominance is lost.



Although scientists have known for more than a century that small inbred populations are likely to suffer from low reproductive success, biologists have long wondered which mechanisms are responsible. Also, the impact of inbreeding on an organism’s entire genome had not been studied.



In order to clarify these unknowns, researchers at the University of Illinois mated genetically identical fruit flies and analyzed gene expression via microarray analysis.



To start, six different lines of inbred fruit flies were created. All six strains were genetically identical to each other except for chromosome three. The degree of inbreeding depression observed in the six fly lines was highly variable—24 to 59 percent when compared to non-inbred flies.



Paige’s Conservation Biology study is the first to analyze the impact of inbreeding on an entire genome. In oligonucleotide microarray analysis, gene expression of a whole genome can be studied all at once. Paige and colleagues compared the different inbred lines by determining if each individual gene was either more active (up-regulated) or less active (down-regulated).



In the fruit fly lines that suffered the greatest percentage of inbreeding depression, 567 genes were identified as up-regulated or down-regulated in comparison to lines that exhibited a lower percentage of inbreeding depression. Only 62 percent of the 567 genes expressing differences were located on the non-genetically identical chromosome three. This means that 38 percent of the genes differentially expressed on other chromosomes had been modified by chromosome three.



“These results suggest that a significant amount of inbreeding depression is due to a few key genes that affect the expression of other genes,” explains animal biology professor and department head Ken Paige.



Overall, microarray analysis showed that a relatively small amount of genes were affected by inbreeding directly, however, these genes in turn regulated the overall expression of other genes which significantly increases the total genes affected at the whole genome level.



To answer the question of which mechanisms are involved, Paige found that approximately 75 percent of the reproductive declines seen in the inbred flies could be attributed to the loss of dominant alleles while 25 percent of the declines were due to the loss of overdominance.



“This means we have two mechanisms ongoing. One does predominate, but the other may be important too,” Paige said.



Furthermore, the 567 genes found to be associated with inbreeding depression can be grouped into three broad categories of cellular function; metabolism, defense and stress. A significant amount of metabolic genes as well as genes that fight pathogens were up-regulated in the most inbred flies. The other group of genes that protect cells from damaging reactive molecules was down-regulated. These changes in gene regulation divert energy away from reproduction and undermine other basic cellular functions.



“This is a surprising finding,” Paige said, “because we think of inbreeding as a random process.”



Genetic drift is the loss of genetic diversity within a population due to chance and occurs during inbreeding. Therefore, we would expect genetic drift to cause the random fixation of different alleles within the different inbred fly lines as opposed to the same alleles affected in each fly line.



Paige further explains the significance of his findings, “Given the number of replicate lines and the fact that the set of genes found to be differentially expressed is not a random sampling of the gene pool but primarily related to metabolism and stress resistance, we find it unlikely that genetic drift alone can explain our results.”



Overall, the fact that a relatively large number of genes are affected by inbreeding is bad news for conservational biologists that are trying to preserve small populations of plants or animals on the brink of extinction. Clearly there is no quick and easy fix for saving small populations and the best approach still is to maintain genetic diversity in natural populations long before the risk of extinction emerges.



