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Understanding of the molecular mechanisms of heterosis
Heterosis, also referred to as hybrid vigor, is generally defined as the phenotypic superiority of a heterozygous hybrid over its genetically diverse parents in terms of many traits such as biomass, growth rate and yield (1). There are many different examples of the heterotic species in both animals and plants. For instance, a mule is reproduced from an interspecific cross between a female horse and a male donkey. Besides, some crop plants such as maize and rice are also heterotic species commonly found in modern agricultural plantation. In fact, the extensive exploitation of heterosis has made great contributions to breeding together with agronomic production of many crop and livestock varieties. Therefore, the significant phenotypic manifestations of heterotic hybrids and their associated tremendous economic importance of hybrid strains have triggered a large variety of research that have made efforts to elucidate the genetic basis of heterosis in order to better utilize it for the current food production (2). However, in spite of the obvious importance of heterosis, the biological mechanisms underlying heterosis have been debated and remain obscured over the past century.
In accordance with previous research findings, there are three major genetic hypotheses/models to explain heterosis which are termed dominance, overdominance and epistasis, respectively. Briefly, the dominance hypothesis attributes heterosis to the complementation of superior dominant alleles from both parental inbred lines at multiple loci over the corresponding inferior recessive alleles. (3) In another word, this model depends on the idea that slightly different deleterious recessive homozygous alleles from two parental lines can complement in the hybrid progeny by their corresponding dominant alleles, which leads to better phenotypic traits (4). On the other hand, the overdominance hypothesis assumes that the heterozygous combination of the alleles at a single locus is superior to either of the homozygous combinations of the alleles at that locus (5), similarly resulting in better performance in the heterozygous hybrids compared to the homozygous parental inbred lines. Additionally, the epistasis hypothesis proposes that epistatic interactions between non-allelic genes at two or more loci are major factors for the superior phenotypic expression of a trait in hybrids. (3)
Even with more knowledge about heterosis, nonetheless, there is still no consensus on the molecular basis of it not only because of the limitations of the abovementioned hypotheses but also the complexity of genetic inheritance. Thus the elusive mechanisms have promoted extensive approaches to explore the nature of heterosis through different biological models. The following sections typically provide some practical evidences to support each hypothesis with respect to different research backgrounds and focuses.
Case of the dominance hypothesis
Xiao et al. (5) derived a group of 194 F7 lines from a subspecific cross using two elite homozygous rice lines, indica 9024 (I) and Japonica LH422 (J) and backcrossed them to their two parents. The procedures to acquire materials for genetic analysis are schematically shown in Fig.1. In short, I and J were crossed to produce F1 hybrids and 194 F7 lines were generated from the F1 hybrids through six times of consecutive self-fertilization. Then each single F7 plant was chosen randomly to backcross to either of the two parental lines to produce F8 progeny. The obtained lines respectively designated BC1F7, F8 and two parental lines were all phenotyped for 12 quantitative traits. The results demonstrated that among a total of 37 quantitative trait loci (QTLs) detected in the BC1F7 populations, 27 (73%) QTLs were examined in only one of the populations. Moreover, 82% heterozygotes from these measurements exhibited superiority over the recessive homozygotes. Other 10 (23%) QTLs existed in both BC1F7 populations and these heterozygotes showed a phenotypic performance at the level between two recessive homozygotes. Finally, no cases were detected that the heterozygotic phenotypes exceeded both homozygotes. In summary, these observations provided evidences supporting dominance as the major genetic mechanism of heterosis in rice. Furthermore, their findings were opposite to the overdominance model of heterosis because there was not relationship between the overall genome heterozygosity and most traits tested concurrent with the absence of significant digenic epistatic interactions.
Despite of numerous examples favoring the dominance hypothesis, there are still observations that cannot be explained by the model alone. It turns out that in some hybrids, the performance of them exceeds the sum of their parents-a result not supposed to appear since the maximal phenotypic performance of the hybrid would equal to the sum of the parents when considering complete dominance. (2) Hence, perhaps the overdominance hypothesis may play an essential role in other species.
Examples of overdominance hypothesis
The utilization of molecular linkage maps brought convenience to dissect genetic basis of heterosis more completely. By using molecular markers, Stuber et al. analyzed the genetic factors beneficial to heterosis formation in maize based on two elite inbred lines (6). They discovered that the heterozygotes of almost all QTLs for grain yield exhibited better phenotypic performance relative to the respective homozygotes. Accordingly, they proposed that the overdominance factor plays an important role in regulating heterosis of this type of maize.
When considering the simplest pattern of overdominance in hybrid vigor, there are many examples of heterosis concerning developmental transition that can be attributed to heterozygote advantage exhibited at a single locus. Krieger et al. have successfully specified a single overdominant gene for yield and suggested that single heterozygous mutations may improve productivity in other agricultural organisms (7). In their study of tomato, heterozygotes with loss-of-function alleles of a gene termed SINGLE FLOWER TRUSS (SFT) showed elevated yield because SFT can perform negative functions on regulation of growth termination. Nevertheless, they subsequently figured out that the yield trait in heterozygotes was not associated with the expression level of SFT. Hence, the outcome of those heterozygotes may result from regulatory interactions between SFT and its correlated acting factors. To sum up, heterosis originated from single-locus theory may regulate developmental processes through alterations within the established networks.
Epistasis hypothesis-An emerging regulatory mechanism in heterosis
For this relative less prominent model, Yu et al. collected data of yield and three yield-associated component traits from 250 F2:3 families over two years and examined the interactions between year and genotypic manifestation (8). Their results demonstrated that among all 32 QTLs detected based on the aforementioned four traits, 12 QTLs existed in both years and the rest of 20 QTLs were present in only one year. The data also indicated the low associations between trait expression and heterozygosity, suggesting that heterosis in this case was merely induced by heterozygosity. In addition, three types of digenic interactions defined as additive by additive, dominance by dominance and additive by dominance were discovered in the experimental population generated in their design. Through the analysis of genetic components together with detection of digenic interactions among 150 different loci which distribute along the entire genome, they eventually concluded that epistasis is the genetic basis of heterosis in these elite rice hybrids (8).
In consistent with the epistasis hypothesis, Hua et al. (9) generated and assessed a so-called “immortalized F2” elite rice population based on intermating of 240 recombinant-inbred lines and by conducting the similar experiments, they emphasized the importance of epistasis in dominance by dominance epistatic interactions for the formation of heterosis. Moreover, though they claimed that their results were helpful to reconcile the debate concerning the mechanisms of heterosis, it has recently been demonstrated in tomato introgression lines that heterosis is manifested even in the absence of epistasis (3). These again illustrated that no single genetic hypothesis of heterosis can generalize every situation among different species or provide comprehensive explanations to clarify hybrid superiority.
Relevant study implications
Recent studies have made use of various methods to determine the molecular basis of heterosis in terms of different aspects. Yao et al. reported in their study that by comparison of heterosis within several different maize lines, a major component of heterosis is a mechanism that is modulated by dosage-sensitive factors that involves allelic diversity across the genome (4).
Li et al. have explored the correlations among heterosis of Larix Kaempferi, and DNA sequence variations, changes in the DNA methylation status and gene expression in a set of intraspecific parental lines and their reciprocal hybrids (10). They reported that when reproducing hybrids from a cross between the two intraspecific parental lines indicated in their experiment, DNA methylation status in particular contributes to the heterosis formation.
Given the implication that different levels of heterosis can be ascribed to the variety of environments, Dahal et al. examined the alterations of protein expression which may be associated with variance among F1 hybrids. They revealed through proteomics studies that expression of specific alleles and/or post-translational modification of specific proteins correlate with higher levels of heterosis (11).
Discussion and perspectives
It has been shown that recent studies using various omics approaches including transcriptomics, proteomics, metabolomics and epigenomics and so forth have provided innovative insights into the systematical mechanisms underlying heterosis of hybrids. These advanced highthroughput measures make it possible to go further beyond the classic mechanisms of heterosis. Emerging genomic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids. For example, epigenetic modifications of key regulatory genes in hybrids and allopolyploids can alter complex regulatory networks of physiology and metabolism, thus modulating biomass and leading to heterosis (2).
Although epigenetic regulations give rise to the understanding of the essentials of heterosis, several unsolved questions still need to be answered in the future studies. For example, in order to provide direct evidence to confirm the involvement of epigenetic modifications in heterosis of hybrids, we may observe and determine the impacts of various genes associated with epigenetic regulation on phenotypic traits of hybrids via generating loss-of-function gene models. Further, the universality of epigenetic variations in hybrids remains undecided. The contribution of the allelic bias in epigenetic states to the allelic bias in gene expressions in hybrids and thus to the divergent gene activity between hybrids and parents needs to be explored extensively (1). Also, comparative epigenomic analyses in different tissues at different developmental stages from various hybrid crosses should be conducted to elucidate the conservation and divergence of epigenetic variations in hybrids. In addition, how epigenetic variations interact with genetic variations to lead to transcriptomic polymorphisms in hybrids is unclear (1). Combinatorial analysis of variations in genomic sequences and in epigenomic states at each genomic locus should be conducted to distinguish between obligatory, facilitated, and pure epigenetic variations (1). This will help in assessing the importance of epigenetic regulation of global variation of gene expression in hybrids (1).
In a word, it is well known that many diverse molecular mechanisms can translate DNA into phenotype and it is highly possible that the combination of all these mechanisms across many genes produces heterosis in complex traits. (2) There is no doubt that the future studies will gradually focus on heterosis to elucidate how different mechanisms work in concert to impact hybrid phenotypic traits (13, 14). Taken together, only the comprehensive analysis of both the genetic and epigenetic effects on regulation of gene expression variation in hybrids can we have a better understanding of the molecular mechanisms of heterosis among different species.