Additive and over-dominant effects resulting from epistatic loci are the primary genetic basis of heterosis in rice

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.

AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds

In this study, we present AAQSP as an extension of existing NGS-BSA applications for identifying stable QTLs at high resolution. GhPAP16 and GhIQD14 fine mapped on chromosome D09 of upland cotton are identified as important candidate genes for lint percentage (LP). Bulked segregant analysis combined with next generation sequencing (NGS-BSA) allows rapid identification of genome sequence differences responsible for phenotypic variation. The NGS-BSA approach applied to crops mainly depends on comparing two bulked DNA samples of individuals from an F₂ population. Since some F₂ individuals still maintain high heterozygosity, heterosis will exert complications in pursuing NGS-BSA in such populations. In addition, the genetic background influences the stability of gene expression in crops, so some QTLs mapped in one segregating population may not be widely applied in crop improvement. The AAQSP (Association Analysis of QTL-seq on Semi-homologous Populations) reported in our study combines the optimized scheme of constructing BSA bulks with NGS-BSA analysis in two (or more) different parental genetic backgrounds for isolating the stable QTLs. With application of AAQSP strategy and construction of a high-density linkage map, we have successfully identified a QTL significantly related to lint percentage (LP) in cultivated upland cotton, followed by map-based cloning to dissect two candidate genes, GhPAP16 and GhIQD14. This study demonstrated that AAQSP can efficiently identify stable QTLs for complex traits of interest, and thus accelerate the genetic improvement of upland cotton and other crop plants.

Genetic Parameters for Selected Traits of Inbred Lines of Maize (Zea mays L.)

This paper presents an estimation of the parameters connected with the additive (a) effect, additive by additive (aa) epistatic effect, and additive by additive by additive (aaa) interaction gene effect for nine quantitative traits of maize (Zea mays L.) inbred lines. To our knowledge, this is the first report about aaa interaction of maize inbred lines. An analysis was performed on 252 lines derived from Plant Breeding Smolice Ltd. (Smolice, Poland)—Plant Breeding and Acclimatization Institute-National Research Institute Group (151 lines) and Małopolska Plant Breeding Ltd. (Kobierzyce, Poland) (101 lines). The total additive effects were significant for all studied cases. Two-way and three-way significant interactions were found in most analyzed cases with a considerable impact on phenotype. Omitting the inclusion of higher-order interactions effect in quantitative genetics may result in a substantial underestimation of additive QTL effects. Expanding models with that information may also be helpful in future homozygous line crossing projects.

Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies

The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.

Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding

Heterosis has historically been exploited in plants; however, its underlying genetic mechanisms and molecular basis remain elusive. In recent years, due to advances in molecular biotechnology at the genome, transcriptome, proteome, and epigenome levels, the study of heterosis in vegetables has made significant progress. Here, we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables. We summarize six hypotheses to explain the mechanism by which genes regulate heterosis, improve upon a possible model of heterosis that is triggered by epigenetics, and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables. We also discuss the contributions of yield-related traits, including flower, fruit, and plant architecture traits, during heterosis development in vegetables (e.g., cabbage, cucumber, and tomato). More importantly, we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants. The description of the strategy details how to obtain F1 hybrids that exhibit heterosis based on heterosis prediction, how to obtain elite lines based on molecular biotechnology, and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables. Finally, we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.

Cumulative and different genetic effects contributed to yield heterosis using maternal and paternal backcross populations in Upland cotton

Heterosis has been utilized in commercial production, but the heterosis mechanism has remained vague. Hybrid cotton is suitable to dissect the heterosis mechanism. In order to explore the genetic basis of heterosis in Upland cotton, we generated paternal and maternal backcross (BC/P and BC/M) populations. Data for yield and yield-component traits were collected over 2 years in three replicated BC/P field trials and four replicated BC/M field trials. At single-locus level, 26 and 27 QTLs were identified in BC/P and BC/M populations, respectively. Six QTLs shared in both BC populations. A total of 27 heterotic loci were detected. Partial dominant and over-dominant QTLs mainly determined yield heterosis in the BC/P and BC/M populations. QTLs for different traits displayed varied genetic effects in two BC populations. Eleven heterotic loci overlapped with QTLs but no common heterotic locus was detected in both BC populations. We resolved the 333 kb (48 genes) and 516 kb (25 genes) physical intervals based on 16 QTL clusters and 35 common QTLs, respectively, in more than one environment or population. We also identified 189 epistatic QTLs and a number of QTL × environment interactions in two BC populations and the corresponding MPH datasets. The results indicated that cumulative effects contributed to yield heterosis in Upland cotton, including epistasis, QTL × environment interaction, additive, partial dominance and over-dominance.

Genetic basis of heterosis for yield and yield components explored by QTL mapping across four genetic populations in upland cotton

Background

Quantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying inbreeding depression and heterosis for yield and yield components of upland cotton was investigated in recombinant inbred line (RIL), immortalized F₂ (IF₂), and two backcross (BCF₁) populations based on a high-density SNP linkage map across four environments.

Results

Significant inbreeding depression of fruit branches per plant (FB), boll numbers per plant (BN), seed cotton yield (SY), and lint yield (LY) in RIL population and high levels of heterosis for SY, LY, and boll weight (BW) in IF₂ and two BCF₁ populations were observed. A total of 285 QTLs were identified in the four related populations using a composite interval mapping approach. In the IF₂ population, 26.60% partially dominant (PD) QTLs and 71.28% over-dominant (OD) QTLs were identified. In two BCF₁ populations, 42.41% additive QTLs, 4.19% PD QTLs, and 53.40% OD QTLs were detected. For multi-environment analysis, phenotypic variances (PV) explained by e-QTLs were higher than those by m-QTLs in each of the populations, and the average PV of m-QTLs and e-QTLs explained by QTL × environment interactions occupied a considerable proportion of total PV in all seven datasets.

Conclusions

At the single-locus level, the genetic bases of heterosis varied in different populations. Partial dominance and over-dominance were the main cause of heterosis in the IF₂ population, while additive effects and over-dominance were the main genetic bases of heterosis in two BCF₁ populations. In addition, the various genetic components to heterosis presented trait specificity. In the multi-environment model analysis, epistasis was a common feature of most loci associated with inbreeding depression and heterosis. Furthermore, the environment was a critical factor in the expression of these m-QTLs and e-QTLs. Altogether, additive effects, over-dominance, epistasis and environmental interactions all contributed to the heterosis of yield and its components in upland cotton, with over-dominance and epistasis more important than the others.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5289-2) contains supplementary material, which is available to authorized users.

Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations

Heterosis has been widely used to increase grain quality and yield, but its genetic mechanism remains unclear. In this study, the genetic basis of heterosis for four maize kernel traits was examined in two test populations constructed using a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058) in two environments. 63 and 57 different heterotic loci (HL) were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, respectively. Of these, nine HL and six HL were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, at the two locations simultaneously. Comparative analysis of the HL for the four kernel traits identified only 21 HL in the two test populations simultaneously. These results showed that most HL for the four kernel traits differed between the two test populations. The common HL were important loci from the Reid × Tangsipingtou heterotic model, and could be used to predict hybrid performance in maize breeding.

QTL Mapping and Heterosis Analysis for Fiber Quality Traits Across Multiple Genetic Populations and Environments in Upland Cotton

An "immortalized F₂" (IF₂) population and two reciprocal backcross (HSBCF₁ and MARBCF₁) populations were constructed to investigate the genetic bases of fiber quality traits in upland cotton across four different environments. A relatively high level of heterosis for micronaire (MIC) in IF₂ population as well as fiber length (FL) and MIC in MARBCF₁ population was observed. A total of 167 quantitative trait loci (QTLs) were detected in the three related experimental populations and their corresponding midparental heterosis (MPH) datasets using the composite interval mapping (CIM) approach. An analysis of genetic effects of QTLs detected in different populations and their MPH datasets showed 16 (24.24%) QTLs of partial dominance, and 46 (69.70%) QTLs of overdominance were identified in an IF₂ population; 89 (62.68%) additive QTLs, three (2.11%) partial dominant QTLs, and 49 (34.51%) over-dominant QTLs were detected in two BCF₁ populations. Multi-environment analysis showed 48 and 56 main-QTLs (m-QTLs) and 132 and 182 epistasis-QTLs (e-QTLs), by inclusive composite interval mapping (ICIM) in IF₂ and two BCF₁ populations, respectively. Phenotypic variance explained by e-QTLs, except for MARBCF₁ population, was higher than that by m-QTLs. Thus, the overdominant, partial dominant, and epistasis effects were the main causes of heterosis in the IF₂ population, whereas the additive, overdominant, and epistasis effects were the primary genetic basis of heterosis in the two BCF₁ populations. Altogether, additive effect, partial dominance, overdominance, and epistasis contributed to fiber quality heterosis in upland cotton, but overdominance and epistasis were the most important factors.

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1, BPH-resistant genes Bph6 and Bph9, fertility restorer genes Rf3, Rf4, Rf5, and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

Detection of QTLs for Yield Heterosis in Rice Using a RIL Population and Its Testcross Population

Analysis of the genetic basis of yield heterosis in rice was conducted by quantitative trait locus mapping using a set of 204 recombinant inbred lines (RILs), its testcross population, and mid-parent heterosis dataset (H_MP). A total of 39 QTLs for six yield traits were detected, of which three were detected in all the datasets, ten were common to the RIL and testcross populations, six were common to the testcross and H_MP, and 17, 2, and 1 were detected for RILs, testcrosses, and H_MP, respectively. When a QTL was detected in both the RIL and testcross populations, the difference between TQ and IR24 and that between Zh9A/TQ and Zh9A/IR24 were always in the same direction, providing the potential to increase the yield of hybrids by increasing the yield of parental lines. Genetic action mode of the 39 QTLs was inferred by comparing their performances in RILs, testcrosses, and H_MP. The genetic modes were additive for 17 QTLs, dominance for 12 QTLs, and overdominance for 10 QTLs. These results suggest that dominance and overdominance are the most important contributor to yield heterosis in rice, in which the accumulative effects of yield components play an important role.

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.

Genetic analysis of Upland cotton dynamic heterosis for boll number per plant at multiple developmental stages

Yield is an important breeding target. As important yield components, boll number per plant (BNP) shows dynamic character and strong heterosis in Upland cotton. However, the genetic basis underlying the dynamic heterosis is poorly understood. In this study, we conducted dynamic quantitative trait loci (QTL) analysis for BNP and heterosis at multiple developmental stages and environments using two recombinant inbred lines (RILs) and two corresponding backcross populations. By the single-locus analysis, 23 QTLs were identified at final maturity, while 99 QTLs were identified across other three developmental stages. A total of 48 conditional QTLs for BNP were identified for the adjacent stages. QTLs detected at later stage mainly existed in the partial dominance to dominance range and QTLs identified at early stage mostly showed effects with the dominance to overdominance range during plant development. By two-locus analysis, we observe that epistasis played an important role not only in the variation of the performance of the RIL population but also in the expression of heterosis in backcross population. Taken together, the present study reveals that the genetic basis of heterosis is dynamic and complicated, and it is involved in dynamic dominance effect, epistasis and QTL by environmental interactions.

Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton

Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.

Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton

Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.

Epistasis together with partial dominance, over-dominance and QTL by environment interactions contribute to yield heterosis in upland cotton

QTL mapping based on backcross and RIL populations suggests that epistasis together with partial dominance, over-dominance and their environmental interactions of QTLs play an important role in yield heterosis in upland cotton. A backcross population (BC) was constructed to explore the genetic basis of heterosis in upland cotton (Gossypium hirsutum L.). For yield and yield components, recombinant inbred line (RIL) and BC populations were evaluated simultaneously at three different locations. A total of 35 and 30 quantitative trait loci (QTLs) were detected based on the RILs and BC data, respectively. Six (16.7 %) additive QTLs, 19 (52.8 %) partial dominant QTLs and 11 (30.6 %) over-dominant QTLs were detected by single-locus analysis using composite interval mapping in BC population. QTLs detected for mid-parent heterosis (MPH) were mostly related to those detected in the BC population. No significant correlation was found between marker heterozygosity and performance. It indicated that heterozygosity was not always favorable for performance. Two-locus analysis revealed 46, 25 and 12 QTLs with main effects (M-QTLs), and 55, 63 and 33 QTLs involved in digenic interactions (E-QTLs) were detected for yield and yield components in RIL, BC and MPH, respectively. A large number of M-QTLs and E-QTLs showed QTL by environment interactions (QEs) in three environments. These results suggest that epistasis together with partial dominance, over-dominance and QEs all contribute to yield heterosis in upland cotton.

Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids

Based on two recombinant inbred line (RIL) populations, two corresponding backcross (BC) populations were constructed to elucidate the genetic basis of heterosis in Upland cotton (Gossypium hirsutum L.). The yield, and yield components, of these populations were evaluated in three environments. At the single-locus level, 78 and 66 quantitative trait loci (QTL) were detected using composite interval mapping in RIL and BC populations, respectively, and 29 QTL were identified based on mid-parental heterosis (MPH) data of two hybrids. Considering all traits together, a total of 50 (64.9%) QTL with partial dominance effect, and 27 (35.1%) QTL for overdominance effect were identified in two BC populations. At the two-locus level, 120 and 88 QTL with main effects (M-QTL), and 335 and 99 QTL involved in digenic interactions (E-QTL), were detected by inclusive composite interval mapping in RIL and BC populations, respectively. A large number of QTL by environment interactions (QEs) for M-QTL and E-QTL were detected in three environments. For most traits, average E-QTL explained a larger proportion of phenotypic variation than did M-QTL in two RIL populations and two BC populations. It was concluded that partial dominance, overdominance, epistasis, and QEs all contribute to heterosis in Upland cotton, and that partial dominance resulting from single loci and epistasis play a relatively more important role than other genetic effects in heterosis in Upland cotton.

Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications

Hybrids are broadly used in plant breeding and accurate estimation of variance components is crucial for optimizing genetic gain. Genome-wide information may be used to explore models designed to assess the extent of additive and non-additive variance and test their prediction accuracy for the genomic selection. Ten linear mixed models, involving pedigree- and marker-based relationship matrices among parents, were developed to estimate additive (A), dominance (D) and epistatic (AA, AD and DD) effects. Five complementary models, involving the gametic phase to estimate marker-based relationships among hybrid progenies, were developed to assess the same effects. The models were compared using tree height and 3303 single-nucleotide polymorphism markers from 1130 cloned individuals obtained via controlled crosses of 13 Eucalyptus urophylla females with 9 Eucalyptus grandis males. Akaike information criterion (AIC), variance ratios, asymptotic correlation matrices of estimates, goodness-of-fit, prediction accuracy and mean square error (MSE) were used for the comparisons. The variance components and variance ratios differed according to the model. Models with a parent marker-based relationship matrix performed better than those that were pedigree-based, that is, an absence of singularities, lower AIC, higher goodness-of-fit and accuracy and smaller MSE. However, AD and DD variances were estimated with high s.es. Using the same criteria, progeny gametic phase-based models performed better in fitting the observations and predicting genetic values. However, DD variance could not be separated from the dominance variance and null estimates were obtained for AA and AD effects. This study highlighted the advantages of progeny models using genome-wide information.

The regulatory network mediated by circadian clock genes is related to heterosis in rice

Exploitation of heterosis in rice (Oryza sativa L.) has contributed greatly to global food security. In this study, we generated three sets of reciprocal F1 hybrids of indica and japonica subspecies to evaluate the relationship between yield heterosis and the circadian clock. There were no differences in trait performance or heterosis between the reciprocal hybrids, indicating no maternal effects on heterosis. The indica-indica and indica-japonica reciprocal F1 hybrids exhibited pronounced heterosis for chlorophyll and starch content in leaves and for grain yield/biomass. In contrast, the japonica-japonica F1 hybrids showed low heterosis. The three circadian clock genes investigated expressed in an above-high-parent pattern (AHP) at seedling stage in all the hybrids. The five genes downstream of the circadian clock, and involved in chlorophyll and starch metabolic pathways, were expressed in AHP in hybrids with strong better-parent heterosis (BPH). Similarly, three of these five genes in the japonica-japonica F1 hybrids showing low BPH were expressed in positive overdominance, but the other two genes were expressed in additive or negative overdominance. These results indicated that the expression patterns of circadian clock genes and their downstream genes are associated with heterosis, which suggests that the circadian rhythm pathway may be related to heterosis in rice.

A Boolean gene regulatory model of heterosis and speciation

BACKGROUND

Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor: crossing individuals from genetically distinct populations often results in improvements in quantitative traits, such as growth rate, biomass production and stress resistance. Heterosis has become a very useful tool in global agriculture, but its genetic basis remains controversial and its effects hard to predict. We have taken a computational approach to studying heterosis, developing a simulation of evolution, independent reassortment of alleles and hybridization of Gene Regulatory Networks (GRNs) in a Boolean framework. These artificial regulatory networks exhibit topological properties that reflect those observed in biology, and fitness is measured as the ability of a network to respond to external inputs in a pre-defined way.

RESULTS

Our model reproduced common experimental observations on heterosis using only biologically justified parameters, such as mutation rates. Hybrid vigor was observed and its extent was seen to increase as parental populations diverged, up until a point of sudden collapse of hybrid fitness. Thus, the model also describes a process akin to speciation due to genetic incompatibility of the separated populations. We also reproduce, for the first time in a model, the fact that hybrid vigor cannot easily be fixed by within a breeding line, currently an important limitation of the use of hybrid crops. The simulation allowed us to study the effects of three standard models for the genetic basis of heterosis: dominance, over-dominance, and epistasis.

CONCLUSION

This study describes the most detailed simulation of heterosis using gene regulatory networks to date and reproduces several phenomena associated with heterosis for the first time in a model. The level of detail in our model allows us to suggest possible warning signs of the impending collapse of hybrid vigor in breeding. In addition, the simulation provides a framework that can be extended to study other aspects of heterosis and alternative evolutionary scenarios.

Hierarchical additive effects on heterosis in rice (Oryza sativa L.)

Exploitation of heterosis in crops has contributed greatly to improvement in global food and energy production. In spite of the pervasive importance of heterosis, a complete understanding of its mechanisms has remained elusive. In this study, a small test-crossed rice population was constructed to investigate the formation mechanism of heterosis for 13 traits. The results of the relative mid-parent heterosis and modes of inheritance of all investigated traits demonstrated that additive effects were the foundation of heterosis for complex traits in a hierarchical structure, and multiplicative interactions among the component traits were the framework of heterosis in complex traits. Furthermore, new balances between unit traits and related component traits provided hybrids with the opportunity to achieve an optimal degree of heterosis for complex traits. This study dissected heterosis of both reproductive and vegetative traits from the perspective of hierarchical structure for the first time. Additive multiplicative interactions of component traits were proven to be the origin of heterosis in complex traits. Meanwhile, more attention should be paid to component traits, rather than complex traits, in the process of revealing the mechanism of heterosis.

Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton

In the present study, a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F₁ populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL). A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBS-D7-1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects (partial-, full-, over-dominant) were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.

Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

Hybridization can lead to phenotypic differences arising from changes in gene expression patterns or new allele combinations. Variation in gene expression is thought to be controlled by differences in transcription regulation of parental alleles, either through cis- or trans-regulatory elements. A previous study among brook charr hybrids from different populations (Rupert, Laval, and domestic) showing distinct length at age during early life stages also revealed different patterns in transcription regulation inheritance of transcript abundance. In the present study, transcript abundance using RNA-sequencing and quantitative real-time PCR, single-nucleotide polymorphism (SNP) genotypes and allelic imbalance were assessed in order to understand the molecular mechanisms underlying the observed transcriptomic and differences in length at age among domestic × Rupert hybrids and Laval × domestic hybrids. We found 198 differentially expressed genes between the two hybrid crosses, and allelic imbalance could be analyzed for 69 of them. Among these 69 genes, 36 genes exhibited cis-acting regulatory effects in both of the two crosses, thus confirming the prevalent role of cis-acting regulatory elements in the regulation of differentially expressed genes among intraspecific hybrids. In addition, we detected a significant association between SNP genotypes of three genes and length at age. Our study is thus one of the few that have highlighted some of the molecular mechanisms potentially involved in the differential phenotypic expression in intraspecific hybrids for nonmodel species.

A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice

A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties. In this study, we generated an F₂ population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64), an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10, resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364(th) amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.

Genetic-basis analysis of heterotic loci in Dongxiang common wild rice (Oryza rufipogon Griff.)

Heterosis is widely used in genetic crop improvement; however, the genetic basis of heterosis is incompletely understood. The use of whole-genome segregating populations poses a problem for establishing the genetic basis of heterosis, in that interactions often mask the effects of individual loci. However, introgression line (IL) populations permit the partitioning of heterosis into defined genomic regions, eliminating a major part of the genome-wide epistasis. In our previous study, based on mid-parental heterosis (HMP) value with single-point analysis, 42 heterotic loci (HLs) associated with six yield-related traits were detected in wild and cultivated rice using a set of 265 ILs of Dongxiang common wild rice (Oryza rufipogon Griff.). In this study, the genetic effects of HLs were determined as the combined effects of both additive and dominant gene actions, estimated from the performance values of testcross F1s and the dominance effects estimated from the HMP values of testcross F1s. We characterized the gene action type at each HL. Thirty-eight of the 42 HLs were over-dominant, and in the absence of epistasis, four HLs were dominant. Therefore, we favour that over-dominance is a major genetic basis of 'wild-cultivar' crosses at the single functional Mendelian locus level.

The statistical power of inclusive composite interval mapping in detecting digenic epistasis showing common F2 segregation ratios

Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits, which could maintain additive variance and therefore assure the long-term genetic gain in breeding. Inclusive composite interval mapping (ICIM) is able to identify epistatic quantitative trait loci (QTLs) no matter whether the two interacting QTLs have any additive effects. In this article, we conducted a simulation study to evaluate detection power and false discovery rate (FDR) of ICIM epistatic mapping, by considering F2 and doubled haploid (DH) populations, different F2 segregation ratios and population sizes. Results indicated that estimations of QTL locations and effects were unbiased, and the detection power of epistatic mapping was largely affected by population size, heritability of epistasis, and the amount and distribution of genetic effects. When the same likelihood of odd (LOD) threshold was used, detection power of QTL was higher in F2 population than power in DH population; meanwhile FDR in F2 was also higher than that in DH. The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR. In simulated populations, ICIM achieved better mapping results than multiple interval mapping (MIM) in estimation of QTL positions and effect. At the end, we gave epistatic mapping results of ICIM in one actual population in rice (Oryza sativa L.).

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 F(1) 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 F(1) 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.

Tissue culture-induced variation at simple sequence repeats in sorghum (Sorghum bicolor L.) is genotype-dependent and associated with down-regulated expression of a mismatch repair gene, MLH3

Somaclonal variation is a common phenomenon associated with plant tissue culture. Microsatellites or simple sequence repeats (SSRs) are ubiquitous components of eukaryotic genomes, and are intrinsically unstable under various stress conditions including tissue culture. Here, we assessed genetic stability of a set of 29 mapped SSR loci in calli and regenerated plants derived from a pair of reciprocal sorghum inter-strain F1 hybrids and their pure line parents. We further measured the steady-state transcripts of a set of nine mismatch repair (MMR)-encoding genes and a DEMETER (DME), a DNA glycosylase domain protein-encoding gene in these lines, and tested for a possible relationship between altered expression of a given MMR or DME gene and the SSR variations. We found that SSR variations occurred in calli and regenerated plants of both the studied pure lines though at sharply different frequencies (20.7 vs. 6.9%), but no variation was detected in calli and regenerated plants of the pair of F1 hybrids. Compared with the donor seed plants, markedly altered expression of all nine studied MMR genes and the DME gene was observed in calli, and more conspicuously, in the regenerated plants. However, only one gene, i.e., MLH3, showed an altered expression pattern that is genotype specific and significantly correlated with the occurrence of SSR instability.

The genetics of inbreeding depression

Inbreeding depression - the reduced survival and fertility of offspring of related individuals - occurs in wild animal and plant populations as well as in humans, indicating that genetic variation in fitness traits exists in natural populations. Inbreeding depression is important in the evolution of outcrossing mating systems and, because intercrossing inbred strains improves yield (heterosis), which is important in crop breeding, the genetic basis of these effects has been debated since the early twentieth century. Classical genetic studies and modern molecular evolutionary approaches now suggest that inbreeding depression and heterosis are predominantly caused by the presence of recessive deleterious mutations in populations.