Molecular Basis Of Heterosis Research Articles

Enriched partial correlations in genome-wide gene expression profiles of hybrids (A. thaliana): a systems biological approach towards the molecular basis of heterosis

Heterosis is a well-known phenomenon but the underlying molecular mechanisms are not yet established. To contribute to the understanding of heterosis at the molecular level, we analyzed genome-wide gene expression profile data of Arabidopsis thaliana in a systems biological approach. We used partial correlations to estimate the global interaction structure of regulatory networks. Our hypothesis states that heterosis comes with an increased number of partial correlations which we interpret as increased numbers of regulatory interactions leading to enlarged adaptability of the hybrids. This hypothesis is true for mid-parent heterosis for our dataset of gene expression in two homozygous parental lines and their reciprocal crosses. For the case of best-parent heterosis just one hybrid is significant regarding our hypothesis based on a resampling analysis. Summarizing, both metabolome and gene expression level of our illustrative dataset support our proposal of a systems biological approach towards a molecular basis of heterosis.

Identification of differentially expressed proteins between hybrid and parents in wheat (Triticum aestivum L.) seedling leaves

In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. To gain a better understanding of the molecular basis of wheat heterosis, we carried out a comparative proteomic analysis in seedling leaves between wheat hybrid and parents. Common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) Line 3338 and spelt wheat (Triticum spelta L., 2n = 6x = 42, AABBDD) Line 2463 were used to produce a heterotic F(1) hybrid. The expression patterns of the total proteins were compared in seedling leaves between hybrid and its parents by using two-dimensional gel electrophoresis with two pH ranges for the first dimension separation. Among ~900 protein spots reproducibly detected, 49 protein spots were identified as being differentially expressed between hybrid and its parental lines (P < 0.05) for more than 1.5-folds. Six possible modes of differential expression were observed, including high- and low-parent dominance, underdominance, and overdominance, uniparent silencing and uniparent dominance. Moreover, 30 of the 49 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that wheat hybridization can cause protein expression differences between hybrid and its parents; these proteins were involved in diverse physiological process pathways, which might be responsible for the observed heterosis.

Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue

Allelic differences in expression are important genetic factors contributing to quantitative trait variation in various organisms. However, the extent of genome-wide allele-specific expression by different modes of gene regulation has not been well characterized in plants. In this study we developed a new methodology for allele-specific expression analysis by applying Massively Parallel Signature Sequencing (MPSS), an open ended and sequencing based mRNA profiling technology. This methodology enabled a genome-wide evaluation of cis- and trans-effects on allelic expression in six meristem stages of the maize hybrid. Summarization of data from nearly 400 pairs of MPSS allelic signature tags showed that 60% of the genes in the hybrid meristems exhibited differential allelic expression. Because both alleles are subjected to the same trans-acting factors in the hybrid, the data suggest the abundance of cis-regulatory differences in the genome. Comparing the same allele expressed in the hybrid versus its inbred parents showed that 40% of the genes were differentially expressed, suggesting different trans-acting effects present in different genotypes. Such trans-acting effects may result in gene expression in the hybrid different from allelic additive expression. With this approach we quantified gene expression in the hybrid relative to its inbred parents at the allele-specific level. As compared to measuring total transcript levels, this study provides a new level of understanding of different modes of gene regulation in the hybrid and the molecular basis of heterosis.

Construction of a molecular functional map of rapeseed (Brassica napus L.) using differentially expressed genes between hybrid and its parents

Brassica napus L. is an important oilseed and fodder crop with significant heterosis for seed yield and other agronomic traits, but very little is known about the molecular basis of heterosis. As an initial step towards understanding the molecular events associated with this phenomenon, a molecular functional map of rapeseed was constructed using differentially expressed genes in hybrid identified by microarrays. Single-strand conformational polymorphism (SSCP) analysis was applied for genetic mapping in an F2 population of 184 individuals resulting from crossing ‘`SI-1300 × Eagle’'. A total of 162 markers including 154 loci corresponding to 98 differentially expressed genes assigned to 17 functional categories and 8 SSR markers were grouped into 21 linkage groups (LGs), covering a total map distance of 2267.3 cM. Subsequently, this map was aligned with Arabidopsis thaliana in silico. Comparative mapping shows that genes localized on each Arabidopsis chromosome have orthologs dispreading in different B. napus LGs. Similarly, a majority of LGs were made of homologous genes from different Arabidopsis chromosomes. In addition, a total of 25 syntenic regions were identified in B. napus, in most of which the gene order was not consistent between the two species, and each of the conserved regions in the A. thaliana genome was homologous to 1--5 distinct regions in the B. napus genome. These results indicate that it is not easy to exploit A. thaliana information for B. napus based on synteny.

Heterosis in root development and differential gene expression between hybrids and their parental inbreds in wheat (Triticum aestivum L.)

In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. In this study, heterosis was estimated for eight root traits in 20 wheat hybrids derived from a NC Design II mating scheme. Positive mid-parent heterosis was detected in 96 of 160 hybrid-trait combinations, and positive high-parent heterosis was detected in 79 of 160 hybrid-trait combinations. Improved differential display was used to analyze alterations in gene expression between hybrids and their parents in roots at the jointing stage. More than 990 fragments were repeatedly displayed, among which 27.52% were differentially expressed between hybrids and their parents. Four differential expression patterns were observed. Thirty differentially expressed cDNA fragments and three genes with open reading frames were cloned, and their expression patterns were confirmed by reverse-northern blot and semi-quantitative RT-PCR analysis, respectively. We concluded that these differentially expressed genes, though mostly with unknown function, could play important roles for hybrids to demonstrate heterosis in root system traits.

Isolation, cloning and sequence analysis of differentially expressed genes in the backfat tissue between hybrids and parents in pigs

AbstractIn order to reveal the molecular basis of heterosis, Large White (LW), an introduced European pig breed, and Meishan (MS), a Chinese indigenous pig breed, were selected to hybridize directly and reciprocally in the present experiment. mRNA differential display (DD) technique was performed to identify genes that were differentially expressed in the backfat tissues of hybrids (LW×MS, MS×LW) and purebred (LW×LW, MS×MS) pigs. The ten anchor primers in combination with ten arbitrary primers (100 sets in total) were used and nearly 1500 reproducible bands were observed in polyacrylamide gels. The 40 differentially displayed bands were selected for cloning and sequencing. Thirty-six out of 40 expressed sequence tags (ESTs) proved to be novel and the sequences were submitted to GenBank (accession No. CV507051-CV507087); the other four showed similarity to known genes published in GenBank. Three among 36 novel ESTs were chosen for further identification with semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR). The result showed that two ESTs were differentially expressed, and the third showed no obvious difference between hybrids and purebreds. In order to reduce the percentage of false-positive DD, RNA pools of four types of pigs were constructed, by mixing samples from six pigs of the same genotype, and subjected to DD. Stringent annealing temperature was applied and only bands that could be repeated in duplicate PCR were used for further study. The results showed that the expression pattern of these 36 ESTs differed among the four genotypes of pigs, suggesting that the genes corresponding to these differentially expressed ESTs might be related to the heterosis occurring in fat tissue.

Cloning and Characterization of Liver cDNAs That Are Differentially Expressed between Chicken Hybrids and Their Parents

Using mRNA differential display technique, we investigated differential gene expression in hybrids relative to their parents in a diallel cross involving four chicken breeds in order to provide an insight into the molecular basis of heterosis in chicken. The results indicated that there was extensive differential gene expression between chicken F1 hybrids and their parents which was classified into four kinds of patterns as following: (1) bands only detected in hybrid F1; (2) bands only absent in hybrid F1; (3) bands only detected in parent P1 or P2; (4) bands absent in parent P1 or P2. Forty-two differentially expressed cDNAs were cloned and sequenced, and their expression patterns were confirmed by Reverse-Northern dot blot. Sequence analysis and database searches revealed that genes showed differential expression between hybrid and parents were regulatory and functional genes involved in metabolism, mRNA splicing, transcriptional regulation, cell cycles and protein modification. These results indicated that hybridization between two parents can cause changes in expression of a variety of genes. In conclusion, that the altered pattern of gene expression in hybrids may be responsible for heterosis in chickens. (Asian-Aust. J. Anim. Sci. 2005. Vol 18, No. 12 : 1684-1690)

Inheritance mode of fruit traits in melon: Heterosis for fruit shape and its correlation with genetic distance

Fruit quality traits were studied in 12 exotic accessions and their hybrids with a “Piel de Sapo” inodorus melon cultivar. The genetic relationships among these genotypes were assessed with 16 microsatellite markers, which agreed with the classification of Cucumis callosus, C. pubescens and C. trigonus as accessions within C. melo. There were very large differences between all the exotic accessions and “Piel de Sapo” genotype for fruit traits. When the hybrids were analysed, three different situations regarding mid parent heterosis were found, depending on the trait: no heterosis (soluble solid concentration), highly variable, from negative to positive (fruit weight and fruit diameter) and general positive heterosis (ovary shape, fruit length and fruit shape). Best parent heterosis for fruit shape was also common among hybrids. A highly significant correlation (r = 0.81) was detected between fruit shape and fruit length heterosis, suggesting that fruit shape heterosis is caused mainly by the enlargement of the fruit longitudinally. A highly significant correlation (r = 0.84) between heterosis for fruit shape and genetic distance, as estimated with microsatellites, was also found. These results, together with the previously reported observation that melon fruit shape is polygenic and highly heritable, makes the genetics of melon fruit shape a suitable system for dissecting the genetic and molecular basis of heterosis.

Differential gene expression in liver of inbred chickens and their hybrid offspring

Differential display of mRNA was used to analyse the differences of gene expression in liver between chicken hybrids and their parents in a 4 x 4 diallel crosses in order to study the molecular basis of heterosis in chickens. The results indicated that patterns of gene expression in hybrids differ significantly from their parents. Four patterns of differential gene expression were revealed, which included: (i) bands only detected in the hybrid F1s (UNF1); (ii) bands only absent in the hybrid F1s (ABF1); (iii) bands only detected in the parental P1 or P2 lines (UNP1 and UNP2) and (iv) bands absent in the parental P1 or P2 lines (ABP1 and ABP2). In addition, correlations between patterns of gene expression and heterosis percentages of nine carcass traits of 8-week-old chickens were evaluated. Statistical results showed that negative correlations between heterosis percentages and the percentage of F1-specific bands (UNF1) were significant at P < 0.01 for breast muscle yield, leg muscle yield, wing weight, eviscerated weight and eviscerated weight with giblet of 8-week-old chickens, and at P < 0.05 for intermuscular fat width. Heterosis percentage was negatively correlated with ABP (bands present in the hybrid F1s and one parental line but absent in the other parental line, ABP1 and ABP2) for breast muscle yield, leg muscle yield, wing weight, eviscerated weight and eviscerated weight with giblet of 8-week-old chickens (P < 0.01). Bands detected only in the hybrid F1s but not in either of the parental lines (UNF1) and bands absent in parental P1 or P2 lines (which includes ABP1 and ABP2) may play important roles in chicken heterosis.

Differential gene expression patterns in leaves between hybrids and their parental inbreds are correlated with heterosis in a wheat diallel cross

In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. Improved differential display was used in this study to analyze alterations in gene expression between hybrid and parents in leaves at jointing stage and heading stage in a wheat diallel cross involving 20 hybrids and nine parents, with the purpose of determining the relationship of differential expression patterns with heterosis in nine agronomic traits. About 2800 fragments were displayed from each hybrid and its parents, among which about 30% were differentially expressed between hybrids and their parents. Four patterns of differential expression were observed: (i) fragments observed in both parents but not in F 1 (BPnF 1); (ii) fragments that occurred in either of the parents but not in F 1 (UPnF 1); (iii) fragments observed only in F 1 but not in either of the parents (F 1nBP); (iv) fragments present in one of the parents and F 1 (UPF 1). UPnF 1 pattern is negatively correlated with heterosis in seven traits, while F 1nBP pattern is positively correlated with heterosis in six traits, and UPF 1 pattern is positively correlated with heterosis in three traits. BPnF 1 is not correlated with heterosis in any of the nine traits. We conclude that these differentially expressed genes, though functionally not known yet, play an important role for hybrids to demonstrate heterosis.

Differential gene expression between wheat hybrids and their parental inbreds in seedling leaves

Differential display of mRNA was used to analyze the differences of gene expression in seedling leaves between heterotic hybrid/nonheterotic hybrid and their parental inbreds in order to study the molecular basis of heterosis in wheat. The results indicated that patterns of gene expression in hybrids differ significantly from their parents. Both quantitative and qualitative differences were observed. The quantitative differences include gene over-expression, gene under-expression in hybrid and dominant expression of highly-expressed parental genes in hybrids. The qualitative differences include silencing in hybrids of genes expressed either in male or female parent, and silencing in hybrids of genes expressed in both parents. Expression in hybrid of genes only expressed either in male or female parent was also observed. It was also found that some genes expressed at high level in heterotic hybrid were underexpressed or expressed at low level in nonheterotic hybrid. One differentially expressed cDNA fragment 4B was cloned and sequenced after being confirmed through Northern blot analysis. Homology search in GenBank proved that the cDNA fragment is a new sequence. The selection of primers for differential RNA display in wheat and the relationship between wheat heterosis and alteration of gene expression in hybrids as compared to their parental inbreds were also discussed.

Molecular basis of heterosis in hybrid rice and hybrid maize revealed by mRNA amplification

Molecular basis of heterosis in hybrid rice and hybrid maize revealed by mRNA amplification

Relationship between gene expression and hybrid vigor in primary root tips of young maize (Zea mays L.) plantlets

To provide an insight into the molecular basis of heterosis, we investigated gene expression in primary root tips of a heterotic maize hybrid (B73 × Mo17) and its parental lines (B73 and Mo17). This analysis was carried out (i) by differential plaque hybridization of a recombinant cDNA library made to poly(A) RNA isolated from B73 × Mo17 primary root tips, and (ii) by comparing with two-dimensional gel electrophoresis proteins synthesized in vitro in the rabbit reticulocyte system by poly(A) RNA isolated, at different stages of development, from the three genotypes. The results showed that there are sets of proteins and mRNAs that are differentially synthesized and expressed in the F1 primary root tips in comparison to the parental lines. Moreover, results from the survey of 21 major in-vitrosynthesized polypeptide variants, from mRNAs of primary root tips of the parental lines and their F1 hybrid, indicated that in seven instances hybrid proteins translated in vitro were more abundant or possibly new. In most of the remaining cases, hybrid spots were similar in intensity to the same protein produced by one of the two parental lines.

Subunit interaction: a molecular basis of heterosis.

Acid phosphatase, a dimeric enzyme, in Drosophila malerkotliana was studied in isogenic flies to explore the molecular basis of heterosis. As the enzyme activity in heterozygotes is 34% more than that in the better parent (S/S), heterosis is indicated. Vmax, Km, and Ki values are 14.60, 3.6 X 10(-4) M, and 0.45 X 10(-4) M, respectively, for the enzyme from F/S flies and 11.80, 4.0 X 10(-4) M, and 0.37 X 10(-4) M, respectively, for the enzyme from S/S flies. Thus heterosis for enzyme activity results from a better enzyme in F/S flies. The higher efficiency and better quality of the enzyme in F/S flies were traced to the heterodimeric allozyme, present only in heterozygotes. Enzyme activity, Vmax, Km, and Ki values are 0.739, 42.1; 3.6 X 10(-4) M, and 0.50 X 10(-4) M, respectively, for the heterodimeric and 0.513, 36.8; 4.1 X 10(-4) M, and 0.37 X 10(-4) M, respectively, for the better parental homodimeric allozyme. On an equimolar basis the enzyme activity of the heterodimer is 44% higher than that of the better homodimer. The better performance of the heterodimer is probably a reflection of superior conformation resulting from interaction between component subunits (F and S polypeptides).

Molecular basis for heterosis in the chicken-quail hybrid

1. 1. Electrophoretical and immunological comparative study of blood proteins and enzymes of the cock-quail hybrid and the parental blood was performed. 2. 2. The investigated blood proteins and enzymes of the hybrid fall into following three categories: mainly one of the parental components is present; both parental components are present: a hybrid molecule is present showing intermediate electrophoretic migration. 3. 3. These three categories correspond to the three mechanisms of heterosis, respectively the dominance, the codominance and the overdominance.

A Genetic and Molecular Basis for Heterosis in Arabidopsis and Drosophila

Experimental evidence is consistent in showing that a considerable proportion of the heterotic expression for a character is a function of the temperature. There is relatively little heterosis at temperatures below the growth optimum, but as the temperature is increased above the optimum, so also is the heterosis. This is so for growth rate in Arabidopsis; and in Drosophila for frequency of heterozygous chromosomes, for wing and thorax length, for body weight and for various components of fitness (larval survival, total viability, egg production, longevity). The temperature-heterosis relation also holds for fluctuating temperatures (larval survival in Drosophila) and for high temperature shocks (growth rate in Arabidopsis and survival in Drosophila). The genetic basis for this phenomenon can be found in the common occurrence of high temperature sensitive alleles in natural populations. Such alleles have been demonstrated in Arabidopsis and in a large number of microorganisms. Different strains of these organisms possess different series of temperature unstable alleles. These alleles constitute a burden unavoidable by the organism because they are a frequent consequence of mutation and are relatively resistant to natural selection. The fraction of temperature sensitive alleles produced by forward mutation probably exceeds one-tenth of the total mutations. Many of the loci whose activity is restored by back-mutation are unstable to high temperature. The molecular basis of temperature sensitive mutants rests on the production of unstable enzymes by the affected loci. Such enzymes are usually unstable at any temperature, but the high thermal coefficient for inactivation leads to mutant expression only at elevated temperatures. It is suggested that mutational alteration of the amino acids of an enzyme, other than those comprising the catalytic center, sensitizes the enzyme to thermal denaturation. This interpretation of heterosis is intended only for organisms whose internal temperature adjusts to the environmental temperature.