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In crop production heterosis is widely exploited, its genetic and molecular basis is still not fully understood. It is supposed that heterosis results in crosses between genetically and /or epigenetically distant parents. Various models have been proposed to explain heteroses such as dominance and overdominance hypothesis. With the recent advances in functional genomics, epigenetics, transcriptomics, proteomics, and metabolomics related technologies, system-level approaches have been adopted to understand its molecular basis. In this review, we gather a brief account of findings from various studies in order to better understand the genetic and molecular basis of heterosis.
Heterosis has been commonly observed in many plants. It is formed as a result of the cross between different varieties. Heterosis refers to the superior performance of a hybrid in biomass, Size, Yield, growth rate or fertility in comparison to its parents. Joseph Koelreuter 1776 for the first time described that some plants hybrids show superior growth than their parents. Charles Darwin in 1876 concluded that the crossed plants when fully grown were more plainly taller and even vigorous than the self-fertilized ones. He reported the growth patterns in more than 60 plant species. George H.Shull, in 1914 rediscovered the phenomena and coined the term heterosis for it. Since then the term heterosis has been widely used in crops breeding especially in maize. In the late 1990s, it was reported that 65% OF the world maize (Zea mays) area was planted as hybrids and the yield of maize had increased six-fold since the use of hybrids started in the 1930s. 5. The economic importance of heterosis has led to an extensive research to understand its basis. However, the genetic and molecular mechanism of heterosis is still elusive. In this review, we present a brief account of findings in various heterosis studies.
Genetic basis for heterosis has been studied for more than a century and numerous hypothesis has been proposed to explain it, but minimum progress has been made for its genetic basis. Dominance and Overdominance are the two most prominent genetic hypothesis to explain the phenomena. According to dominance hypothesis complementation of two corresponding deleterious alleles leads to heterosis in hybrids. In accordance with overdominance hypothesis heterozygous allelic interactions result in heterosis in a hybrid. Overall these hypothesis explains the genetic difference between hybrids and inbred lines. Though it is difficult to associate directly the favorable alleles that dominant and overdominant predicts with the phenotypic traits in crop breeding, including maize.
To correlate the gene expression changes between hybrids and its parent’s various transcriptomics analysis have been performed. On the basis of gene action in the hybrid, the genes have been classified as Additive (dominance) and Nonadditive (Overdominance ) expression patterns.
The Additive expression patterns in the hybrid, represent mid-parental expression pattern whereas the dominance model suggests both low and high parent expression. In Overdominance, the gene expression level in hybrids can be higher or lower than the level in a parent. Numerous aspects of plant development and different organs have been analyzed at the transcriptomic level, Overall there is no uniform global expression detected in these studies. Several studies indicate that nonadditive gene expression was prevalent between parent and hybrids. Whereas additive gene expression was detected in other studies.
In addition, a similar number of genes followed additive and nonadditive expression model was also observed. This is interesting that of the two heterotic rice hybrids, nonadditive gene expression was prevalent in one hybrid, while additive gene expression in the other in the younger stages of development. Though the mode of gene expression is found different in different studies, the global; l tends are similar. For example, Heterosis is a genome-wide phenomenon involves a global change in gene expression. More significant expression difference is found in the related species than those within species.
In many plant hybrids, allelic expression variation was further detected such rice and maize. Some genes in maize showed maternal or paternal-like expression patterns, which are suggested to be associated with genomic imprinting. In some studies, the minimal parent of origin effects on allele-specific expression was detected. A recent study gives the mechanism that allelic diversity is sensitive to dosage sensitive factors. Besides genetic factors, Epigenetic factors were also suggested to play a potential role in allelic expression in the hybrid. Recently small RNA levels were measured in inbreds and hybrids. The differential expression patterns of small RNAs have been linked to heterosis.
The expression of proteins in inbreds and hybrids have been having been measured in various studies. Some of which indicated a strong correlation between protein patterns and heterosis. Proteomic analysis of rice and maize suggested that more frequency of nonadditive protein expressional variation than nonadditive gene expressional variation in hybrids.
Recently, the Expression level of protein was compared using heterotic and nonheterotic maize hybrids, It was interesting that differential expression of proteins detected in heterotic hybrids was mainly involved in stress response, Protein and carbon metabolism. In addition, the degree of heterosis was suggested to be linked to the frequency of protein isoforms and modifications. Although the different mode of gene action, as well as protein expression patterns, were observed in hybrids and they supported the genetic models of dominance and overdominance, the molecular basis of heterosis is still largely unknown.
In the same nucleus combination of diverged maternal and paternal genomes may lead to genomic instability, epigenetic and gene expression changes, which ultimately caused the changes of phenotypes in the hybrid. Numerous studies have been carried out in the past to find out the role of epigenetics in heterosis. Genome-wide methylation, sRNAs expression, gene expression and physiological index have been analyzed comprehensively in both hybrids and its parents. The variation of DNA methylation and sRNA were observed between parents and its progeny. Shen et al 2012 found that hybrids had increased cytosine methylation compared with the parents, In contrast to the higher methylation levels, more down-regulated genes existed in the hybrids then the parental lines. The down-regulated genes including the circadian clock genes CCA, LHY, have been shown to be involved in heterosis previously.
Shen et al 2012 Greaves et al 2012 also found altered methylomes between hybrids and its parents in Arabidopsis. 23.In both studies, changes occur most frequently at loci where parental methylation levels are markedly different.
A recent study by Chodavarapu et al 2012 found that regions of altered methylation are often correlated with changes in sRNA levels. Using Arabidopsis, Greaves et al 2012 and Shen et al 2012 also found a strong correlation between DNA methylation and sRNA. It is interesting that research by Shen et 2012 found that the growth vigor was compromised in the F1 hybrids of hen1(RNA methyltransferase, HUA ENH-ANCEF1) mutants which further supported that the notion that sRNA plays a role in heterosis, perhaps by guiding methylation of DNA via the RNA directed DNA –methylation pathway. Differential expression patterns of small RNAs were observed in rice, wheat and tomato hybrids recently. For example, In Rice hybrids, sRNAs showed more down-regulated the upregulated. Previously, various studies have proved that sRNAs play an important role in gene regulation and genome integrity maintaining. 29.30. It is possible that the changes in sRNAs profiling could result in the expression patterns of the gene that they control in hybrids, Which might be related to the phenotypes of the hybrids.
Energy model proposed for heterosis Goff 2011 proposed an energy model to explain the difference in growth and yield between inbreds and hybrids. In this model, he explains that allele-specific gene expression is linked to protein folding and stability and helps to conserve energy and allows faster cell division. It is possible that that allelic choice available in hybrids but not inbreds provide the opportunity for hybrids to express the favorable allele and use energy efficiency to accelerate crop improvement. Heterosis is a common phenomenon is main rice and other species.6. It is likely that a common biological mechanism underlying heterosis exists in a wide variety of different species. Dominance and overdominance models have been proposed to explain single trait heterosis, A gene expression level additive and nonadditive mode of differential gene actions have been shown to be involved in the manifestation of heterosis. Genes influencing heterosis could be affected by genome dosage. Recently mounting evidence of the epigenetic machinery was provided to explain heterosis. Quantitative trait locus studies indicated many QTLs associated with specific efficiency plays an important role in heterosis. Taken together it is likely that the combination of many mechanisms across many genes accounts for the complex heterosis traits.
To date, there are still many things which are not clear but with promising for a future breakthrough in uncovering the heterosis, first what is the relationship between genome combination and gene activity at a single gene level? It is known that the differential expression of a large number of genes emerges when two different genomes come together in a hybrid. Do all these changed transcriptome in hybrid have biological functions? What proportion of the altered hybrid transcriptome could have a major influence on heterosis besides the circadian clock genes? What factors affect on the variable profile of these key genes, mechanisms? Second, how to choose the best combination of parents for producing ‘super hybrids to meet the growing demand for food and biofuels?
As we know, the degree of heterosis is proportional to the genetic difference in two parental strains. However many interspecific hybrids especially distant hybrids cannot survive, which causes hybrids incompatibility, A better understanding of the mechanism for hybrid vigor will help us effectively select the best combinations of parents for the predicting breeding goals, such as the increased production of seeds, fruits, and metabolites.
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