Genetic Basis Of Heterosis Research Articles

Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L.

Quantitative trait loci (QTL) mapping provides a powerful tool for unraveling the genetic basis of yield and yield components as well as heterosis in upland cotton. In this research, a molecular linkage map of Xiangzamian 2 (Gossypium hirsutum L.)-derived recombinant inbred lines (RILs) was reconstructed based on increased expressed sequence tag–simple sequence repeat markers. Both the RILs and immortalized F2s (IF2) developed through intermating between RILs were grown under multiple environments. Yield and yield components including seed-cotton yield, lint yield, bolls/plant, boll weight, lint percentage, seed index, lint index and fruit branch number were measured and their QTL were repeatedly identified across environments by the composite interval mapping (CIM) method. From a total of 111 non-redundant QTL, 23 were detected in both two populations. In the meantime, multi-marker joint analyses showed that 16 of these QTL had significant environmental interaction. QTL for correlated traits tended to be collocated and most of the QTL for seed-cotton yield and lint yield were associated with QTL for at least one yield component, consistent with the results observed in correlation analyses. For many QTL with significant additive effects, positive alleles from CRI12, the inferior parent with lower yield performance, were associated with trait improvement. Trait performance of IF2s and the large number of QTL with positive dominant effects implied that dominance plays an important role in the genetic basis of heterosis in Xiangzamian 2 and that non-additive inheritance is also an important genetic mode for lint percentage in the population. These QTL can provide the bases for marker-assisted breeding programs of upland cotton.

Dissecting Genetic Networks Underlying Complex Phenotypes: The Theoretical Framework

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many ‘downstream’ loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and “co-adapted” gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.

Genetic analysis of heterotic loci detected in a cross between indica and japonica rice (Oryza sativa L.)

The study on the genetic basis of heterosis has received significant attention in recent years. In this study, using a set of introgression lines (ILs) and corresponding testcross F1 populations, we investigated heterotic loci (HL) associated with six yield-related traits in both Oryza sativa L. subsp. indica and japonica. A total of 41 HL were detected on the basis of mid-parent heterosis values with single-point analysis. The F1 test-cross population showed superiority in most yield-related traits and was characterized by a high frequency of overdominant HL. Thirty-eight of the 41 HL were overdominant, and in the absence of epistasis, three HL were dominant, suggesting that heterotic effects at the single-locus level mainly appeared to be overdominant in rice. Twenty-four HL had a real positive effect, suggesting that they are viable candidates for the improvement of rice yield potential. Compared with the quantitative trait loci (QTLs) detected in the ILs, only six out of the 41 (14.6%) HL were detected in QTL analysis under the same statistical threshold, indicating that heterosis and trait performance may be conditioned by different sets of loci.

Primary analysis of QTG contribution to heterosis in upland cotton

In this paper, we analyzed the contribution of pure DNA factors to heterosis using quantitative trait genes (QTG) in two randomly selected strains from a recombinant inbred line of Gossypium hirsutum. According to a set of QTL mapping results, combined with analysis of DNA recombinant fragment sources in the two strains and QTL association analysis with their field traits, we hypothesize a view of “dominance + overdominance + epistasis”. That is, additive and additive epistasis may be the genetic basis of heterosis, and dominance, overdominance and epistasis may be the modes of heterosis action. Based on the heterosis results of this study, we also suggest a molecular mechanism for heterosis, and explain, in detail, with two randomly selected strains as examples. The male and female parent-derived additive epistatic QTLs of upper half mean length in LG01 and LG03 produced a trait variance of 2.99–3.52 compared with the female parent-derived loci. The trait of bolls per plant was controlled by two pairs of additive epistatic QTLs in LG02 and LG07, which were derived from both female and male parents. The QTLs were reciprocally interacted and produced a trait variance of 0.86. An initial concept of “super-hybrid cotton” was raised according to the nature of additive effect, that is genetic stability.

High congruency of QTL positions for heterosis of grain yield in three crosses of maize

The genetic basis of heterosis in maize has been investigated in a number of studies but results have not been conclusive. Here, we compare quantitative trait loci (QTL) mapping results for grain yield, grain moisture, and plant height from three populations derived from crosses of the heterotic pattern Iowa Stiff Stalk Synthetic x Lancaster Sure Crop, investigated with the Design III, and analyzed with advanced statistical methods specifically developed to examine the genetic basis of mid-parent heterosis (MPH). In two populations, QTL analyses were conducted with a joint fit of linear transformations Z (1) (trait mean across pairs of backcross progenies) and Z (2) (half the trait difference between pairs of backcross progenies) to estimate augmented additive and augmented dominance effects of each QTL, as well as their ratio. QTL results for the third population were obtained from the literature. For Z (2) of grain yield, congruency of QTL positions was high across populations, and a large proportion of the genetic variance (~70%) was accounted for by QTL. This was not the case for Z (1) or the other two traits. Further, almost all congruent grain yield QTL were located in the same or an adjacent bin encompassing the centromere. We conclude that different alleles have been fixed in each heterotic pool, which in combination with allele(s) from the opposite heterotic pool lead to high MPH for grain yield. Their positive interactions very likely form the base line for the superior performance of the heterotic pattern under study.

Heterosis Is Prevalent for Multiple Traits in Diverse Maize Germplasm

BackgroundHeterosis describes the superior phenotypes observed in hybrids relative to their inbred parents. Maize is a model system for studying heterosis due to the high levels of yield heterosis and commercial use of hybrids.MethodsThe inbred lines from an association mapping panel were crossed to a common inbred line, B73, to generate nearly 300 hybrid genotypes. Heterosis was evaluated for seventeen phenotypic traits in multiple environments. The majority of hybrids exhibit better-parent heterosis in most of the hybrids measured. Correlations between the levels of heterosis for different traits were generally weak, suggesting that the genetic basis of heterosis is trait-dependent.ConclusionsThe ability to predict heterosis levels using inbred phenotype or genetic distance between the parents varied for the different traits. For some traits it is possible to explain a significant proportion of the heterosis variation using linear modeling while other traits are more difficult to predict.

Mapping an Overdominant Quantitative Trait Locus for Heterosis of Body Weight in Mice

The genetic basis of heterosis has not been elucidated. Previously, a congenic mouse strain with a 44-Mb genomic region of proximal chromosome 2 containing the allele derived from wild Mus musculus castaneus at Pbwg1, a quantitative trait locus (QTL) for body weight and growth, has been developed. In this study, to fine-map and characterize body weight QTLs on the congenic region, QTL analysis of body weight at 1, 3, 6, and 10 weeks after birth was performed on a population of 265 F(2) intercross mice between the developed congenic strain and its background strain C57BL/6J. A significant QTL (named Pbwg1.10) affecting body weight at 6 and 10 weeks of age was identified within an approximately 21-Mb support interval. Surprisingly, Pbwg1.10 had an overdominance effect and caused heterosis for body weight. This result supported the overdominance hypothesis explaining heterosis.

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that has been used for estimating the average degree of dominance of quantitative trait loci (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selfing. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive x additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions (INDELs), many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

Progress in Research and Development on Hybrid Rice: A Super-domesticate in China

BackgroundChina has been successful in breeding hybrid rice strains, but is now facing challenges to develop new hybrids with high-yielding potential, better grain quality, and tolerance to biotic and abiotic stresses. This paper reviews the most significant advances in hybrid rice breeding in China, and presents a recent study on fine-mapping quantitative trait loci (QTLs) for yield traits.ScopeBy exploiting new types of male sterility, hybrid rice production in China has become more diversified. The use of inter-subspecies crosses has made an additional contribution to broadening the genetic diversity of hybrid rice and played an important role in the breeding of super rice hybrids in China. With the development and application of indica-inclined and japonica-inclined parental lines, new rice hybrids with super high-yielding potential have been developed and are being grown on a large scale. DNA markers for subspecies differentiation have been identified and applied, and marker-assisted selection performed for the development of restorer lines carrying disease resistance genes. The genetic basis of heterosis in highly heterotic hybrids has been studied, but data from these studies are insufficient to draw sound conclusions. In a QTL study using stepwise residual heterozygous lines, two linked intervals harbouring QTLs for yield traits were resolved, one of which was delimited to a 125-kb region.ConclusionsAdvances in rice genomic research have shed new light on the genetic study and germplasm utilization in rice. Molecular marker-assisted selection is a powerful tool to increase breeding efficiency, but much work remains to be done before this technique can be extended from major genes to QTLs.

Relationship Between Differential Gene Expression and Heterosis During Ear Development in Maize ( Zea mays L.)

Maize ( Zea mays L.) is one of the most important crops because of the remarkable properties of its hybrid, which is responsible for the high commercial value of hybrid maize. The genetic basis of heterosis (hybrid vigor) is not well understood. A differential display technique was performed to identify genes with differential expression across twelve maize inbred lines and thirty-three hybrids during ear development. An incomplete diallel design was used to investigate the relationship between the global framework of differential gene expression and heterosis. It was found that the genes belonging to MONO pattern (i.e., genes expressed in both parental lines and in hybrid) was the highest in percentage among the total five patterns and illustrated that the properties of differentially expressed genes are not entirely responsible for heterosis. Furthermore, a larger number of differentially expressed genes in hybrid, which serves as a major reservoir for generating novel phenotypes that exhibit heterosis of certain agronomic traits during early development and differentiation of maize ear. Moreover, there were some silent genesin hybrids that are responsible for the arrest or abortion of spikelets and for the increase in kernels weight.

Overdominant quantitative trait loci for yield and fitness in tomato

Heterosis, or hybrid vigor, is a major genetic force that contributes to world food production. The genetic basis of heterosis is not clear, and the importance of loci with overdominant (ODO) effects is debated. One problem has been the use of whole-genome segregating populations, where interactions often mask the effects of individual loci. To assess the contribution of ODO to heterosis in the absence of epistasis, we carried out quantitative genetic and phenotypic analyses on a population of tomato (Solanum lycopersicum) introgression lines (ILs), which carry single marker-defined chromosome segments from the distantly related wild species Solanum pennellii. The ILs revealed 841 quantitative trait loci (QTL) for 35 diverse traits measured in the field on homozygous and heterozygous plants. ILs showing greater reproductive fitness were characterized by the prevalence of ODO QTL, which were virtually absent for the nonreproductive traits. ODO can result from true ODO due to allelic interactions of a single gene or from pseudoODO that involves linked loci with dominant alleles in repulsion. The fact that we detected dominant and recessive QTL for all phenotypic categories but ODO only for the reproductive traits indicates that pseudoODO due to random linkage is unlikely to explain heterosis in the ILs. Thus, we favor the true ODO model involving a single functional Mendelian locus. We propose that the alliance of ODO QTL with higher reproductive fitness was selected for in evolution and was domesticated by man to improve yields of crop plants.

Unraveling the genetic basis of hybrid vigor

The study of hybrid vigor and inbreeding depression traces back to Charles Darwin, who was the first scientist to examine the phenomenon in a systematic manner (1). Hybrid vigor, or heterosis, is the increase in stature, biomass, and fertility that characterizes the progeny of crosses between diverse parents such that the F1 is superior to the better of the two parents. In plants, this is basically achieved by a greater proliferation of cells in some but not all tissues (2). Inbreeding depression refers to the decline in the quantitative measure of these characters upon self-fertilization or other forms of homozygosis of alleles (inbreeding). The genetic basis of heterosis has been debated for nearly a hundred years without an emerging consensus (3–5) (Fig. 1). An early view was that the combination of different alleles in an organism resulted in a superior state for growth and vigor compared with the presence of identical alleles (3). As genetic knowledge increased, the concept that inferior alleles of different genes in the two parents were complemented in the hybrid (6), thus leading to the superior characteristics, gained favor. Although the latter explanation is simple and easily envisioned, results that seemed to favor interactions of diverse alleles have been repeatedly found. In this issue of PNAS, the work of Semel et al. (7) examined an extensive set of quantitative traits in partial hybrids of domesticated tomato and a wild relative. They conclude that most traits that exhibit heterosis do so as a result of heterozygosity of the controlling genomic regions to produce traits superior to the better parent. They also suggest that heterosis was selected over evolutionary time for characteristics that impact reproductive success.

Correlations of Genic Heterozygosity and Variances with Heterosis in a Pig Population Revealed by Microsatellite DNA Marker

Correlation of microsatellite heterozygosity with performance or heterosis was reported in wild animal populations and domestic animal populations, but the correlation with heterosis in a crossbreeding F1 pig population remained uncertain. To explore this, we had random selected and mated Yorkshire×Meishan (F, n = 82) and their reciprocal (G, n = 47) to F1, and used the two straightbreds as control groups (Yorkshire = 34, Meishan = 55), and observed the heterosis of birth weight (BWT), average daily gain (ADG) and feed and meat ratio (FMR). Two Kinds of measurement-individual heterozygosity (IH) and individual mean d 2 (lg value, ID) were used as index of heterozygosity and variance from 39 microsatellite marker loci to perform univariate regression analysis against heterosis. We detected significant correlation of IH with BWT in all of F1 (F+G) and in F. We observed significant correlation of ID with ADG in all of F1 (F+G), and with FMR in all of F1 (F+G) and in F. There was significant maternal effect on heterosis, which was indicated by significant difference of means and distribution of heterosis between F and G. This difference was consistent with distributions of IH and ID, and with difference of means in F and G. From this study, it would be suggested that the two kinds of genetic index could be used to explore the genetic basis of heterosis in crossbreeding populations but could not determine which is better. (Asian-Aust. J. Anim. Sci. 2005. Vol 18, No. 5 : 620-625)

Genetic basis of heterosis and inbreeding depression in rice (Oryza sativa L.).

The genetic basis of heterosis was studied through mid-parent, standard variety and better parent for 11 quantitative traits in 17 parental lines and their 10 selected hybrids in rice (Oryza sativa L.). The characters were plant height, days to flag leaf initiation, days to first panicle initiation, days to 100% flowering, panicle length, flag leaf length, days to maturity, number of fertile spikelet/panicle, number of effective tillers/hill, grain yield/10-hill, and 1000-grain weight. In general the hybrids performed significantly better than the respective parents. Significant heterosis was observed for most of the studied characters. Among the 10 hybrids, four hybrids viz., 17Ax45R, 25Ax37R, 27Ax39R, 31Ax47R, and 35Ax47R showed highest heterosis in 10-hill grain yield/10-hill. Inbreeding depression of F2 progeny was also studied for 11 characters of 10 hybrids. Both positive and negative inbreeding depression were found in many crosses for the studied characters, but none was found significant. Selection of good parents was found to be the most important for developing high yielding hybrid rice varieties.

Analysis of heterosis by a direct method using the concept of heritability.

The presence of heterosis has been observed in many species at both phenotypic and gene levels. Strangely, the genetic basis of heterosis was and still is largely unknown. In this study, we extended and simplified some formulas that we reported previously. The foundation of our model was based on partitioning the F1 phenotypic variance of the cross between two pure lines into additive, dominance and epistasis components, which lead to the estimation of effective factors, crossheritability in the broad and narrow sense and heterotic power. In the model, we assume that all polygenes controlling a quantitative trait have an equal genetic effect and are independent of each other. By extension of the heritability to a cross population, new features appear. The word 'crossheritability' acquires the status of a new genetic parameter that suffices to deal with the problem of crossbreeding and clarifies the picture of heterosis. Lastly, an example of employing the proposed method in analyzing the crossing data from Drosophila melanogaster is given to illustrate its application.

Importance of over-dominance as the genetic basis of heterosis in rice

In populations derived from commercial hybrid rice combination Shanyou 10, F(1) heterosis and F(2) inbreeding depression were observed on grain yield (GYD) and number of panicles (NP). Using marker loci evenly distributed on the linkage map as fixing factors, the F(2) population was divided into sub-populations. In a large number of sub-populations, significant correlations were observed between heterozygosity and GYD, and between heterozygosity and NP. This was especially true in type III sub-populations in which the genotype of a fixing factor was heterozygotes. In type III sub-populations, 15 QTL for GYD and 13 QTL for NP were detected, of which the majority exhibited over-dominance effects for increasing the trait values. This study showed that over-dominance played an important role in the genetic control of heterosis in rice.

Biotechnology in the 1930s: the development of hybrid maize.

Hybrid maize was one of the first examples of genetic theory successfully applied to food production. When first introduced, it seemed almost miraculous; study hybrids convinced skeptical farmers that 'the professors' and their arcane science could do them some good. Strangely, the genetic basis of heterosis (hybrid vigour) was and still is unknown. But to this day, newer hybrids continue to outyield their predecessors; they do so because they are tougher and healthier.

Epistasis plays an important role as genetic basis of heterosis in rice

The genetic basis of heterosis in rice was studied in a cross between Zhenshan 97 and Minghui 63, the parents of the best hybrid widely used in rice production in China. Field data for yield and yield components traits were collected over two years from 240 F(2:3) families of this cross planted in replicated field trials. These families were assayed with 151 marker loci that were polymorphic between the parents and a linkage map was constructed with Mapmaker analysis. A total of 32 quantitative trait loci (QTLs) were identified for yield and the three component traits: 12 QTLs were detected in both years and the remaining 20 QTLs were observed in only one year. A search for the entire genome by using two-way analyses of variance with all possible two-locus combinations detected a very large number of significant digenic interactions involving both the QTLs resolved by single-locus analysis and loci that did not show significant effects by single-locus analysis. Many of the interactions were simultaneously detected in both years. Partitioning of the epistatic interactions recovered all three types of interactions, i. e. additive by additive, additive by dominance and dominance by dominance, for all the traits. Some of the epistatic interactions even showed pleiotropic effects by simultaneously affecting two or more traits. The results clearly indicate that epistasis plays a significant role in the inheritance of yield traits as well as in the genetic basis of heterosis.

Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid.

The genetic basis of heterosis was investigated in an elite rice hybrid by using a molecular linkage map with 150 segregating loci covering the entire rice genome. Data for yield and three traits that were components of yield were collected over 2 years from replicated field trials of 250 F(2:3) families. Genotypic variations explained from about 50% to more than 80% of the total variation. Interactions between genotypes and years were small compared with the main effects. A total of 32 quantitative trait loci (QTLs) were detected for the four traits; 12 were observed in both years and the remaining 20 were detected in only one year. Overdominance was observed for most of the QTLs for yield and also for a few QTLs for the component traits. Correlations between marker heterozygosity and trait expression were low, indicating that the overall heterozygosity made little contribution to heterosis. Digenic interactions, including additive by additive, additive by dominance, and dominance by dominance, were frequent and widespread in this population. The interactions involved large numbers of marker loci, most of which individually were not detectable on single-locus basis; many interactions among loci were detected in both years. The results provide strong evidence that epistasis plays a major role as the genetic basis of heterosis.