Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems

DNA methylation remodeling in F1 hybrids

F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation patterns relative to their parents. To which extent these changes drive non-additive gene expression levels and phenotypic heterosis in F1 individuals is not fully resolved. Current mechanistic models propose that DNA methylation remodeling in hybrids is the result of epigenetic interactions between parental alleles via small interfering RNA (sRNA). These models have strong empirical support but are limited to genomic regions where the two parental lines differ in DNA methylation status. However, most remodeling events occur in parental regions with similar methylation patterns, and seem to be strongly conditioned by distally acting factors, even in isogenic hybrid systems. The molecular basis of these distal interactions is currently unknown, and will likely emerge as an active area of research in the future. Despite these gaps in our molecular understanding, parental DNA methylation states are statistically associated with heterosis, independent of genetic information, and may serve as biomarkers in crop breeding.

Heterotic growth of hybrids of Arabidopsis thaliana is enhanced by elevated atmospheric CO2

PREMISE

With the global atmospheric CO2 concentration on the rise, developing crops that can thrive in elevated CO2 has become paramount. We investigated the potential of hybridization as a strategy for creating crops with improved growth in predicted elevated atmospheric CO2.

METHODS

We grew parent accessions and their F1 hybrids of Arabidopsis thaliana in ambient and elevated atmospheric CO2 and analyzed numerous growth traits to assess their productivity and underlying mechanisms.

RESULTS

The heterotic increase in total dry mass, relative growth rate and leaf net assimilation rate was significantly greater in elevated CO2 than in ambient CO2. The CO2 response of net assimilation rate was positively correlated with the CO2 response of leaf nitrogen productivity and with that of leaf traits such as leaf size and thickness, suggesting that hybridization-induced changes in leaf traits greatly affected the improved performance in elevated CO2.

CONCLUSIONS

Vegetative growth of hybrids seems to be enhanced in elevated CO2 due to improved photosynthetic nitrogen-use efficiency compared with parents. The results suggest that hybrid crops should be well-suited for future conditions, but hybrid weeds may also be more competitive.

Self-incompatibility phenotypes of SRK mutants can be predicted with high accuracy

Only very limited information is available on why some non-synonymous variants severely alter gene function while others have no effect. To identify the characteristic features of mutations that strongly influence gene function, this study focused on S-locus receptor kinase, SRK, which encodes a highly polymorphic receptor kinase expressed in stigma papillary cells that underlies a female determinant of self-incompatibility in Brassicaceae. A set of 299 Arabidopsis thaliana transformants expressing mutated SRKb from A. lyrata was constructed and analyzed to determine the genotype and self-incompatibility phenotype of each transformant. Almost all the transformants showing the self-incompatibility defect contained mutations in AlSRKb that altered localization to the plasma membrane. The observed mutations occurred in amino acid residues that were highly conserved across S haplotypes and whose predicted locations were in the interior of the protein. These mutations were likely to underlie the self-incompatibility defect as they caused significant changes to amino acid properties. Such findings suggested that mutations causing the self-incompatibility defect were more likely to result from changes to AlSRKb biosynthesis than from loss of function. In addition, this study showed the RandomForest and Extreme Gradient Boosting methods could predict self-incompatibility phenotypes of SRK mutants with high accuracy.

Research on Physiological Characteristics and Differential Gene Expression of Rice Hybrids and Their Parents under Salt Stress at Seedling Stage

Soil salinization is one of the most important abiotic stresses which can seriously affect the growth and development of rice, leading to the decrease in or even loss of a rice harvest. Increasing the rice yield of saline soil is a key issue for agricultural production. The utilization of heterosis could significantly increase crop biomass and yield, which might be an effective way to meet the demand for rice cultivation in saline soil. In this study, to elucidate the regulatory mechanisms of rice hybrids and their parents that respond to salt stress, we investigated the phenotypic characteristics, physiological and biochemical indexes, and expression level of salt-related genes at the seedling stage. In this study, two sets of materials, encapsulating the most significant differences between the rice hybrids and their parents, were screened using the salt damage index and a hybrid superiority analysis. Compared with their parents, the rice hybrids Guang-Ba-You-Hua-Zhan (BB1) and Y-Liang-You-900 (GD1) exhibited much better salt tolerance, including an increased fresh weight and higher survival rate, a better scavenging ability towards reactive oxygen species (ROS), better ionic homeostasis with lower content of Na+ in their Na+/K+ ratio, and a higher expression of salt-stress-responsive genes. These results indicated that rice hybrids developed complex regulatory mechanisms involving multiple pathways and genes to adapt to salt stress and provided a physiological basis for the utilization of heterosis for improving the yield of rice under salt stress.

Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in Brassica rapa

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1. Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F1 plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa.

Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids

In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol  × clfC24 and clfC24  × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.)

BACKGROUND

Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages.

RESULTS

Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid.

CONCLUSIONS

These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.

Genetic and molecular regulation of increased photosynthetic cell number contributes to leaf size heterosis in Arabidopsis

Heterosis is an important genetic phenomenon that has been observed and widely utilized in agriculture. However, the genetic and molecular bases of heterosis are unclear. Through transcriptome-wide association studies (TWAS) and expression quantitative trait locus (eQTL) analysis to integrate genome, transcriptome, and heterotic phenotype of a half-sibling Arabidopsis hybrid population, we report that the genetic and molecular bases of variations in leaf growth heterosis can be explained by the varied expression levels of growth-regulating genes resulting from distinct sets of heterozygous eQTLs carried by the half-sibling hybrids. In F1 versus parent, the degree of up-regulated gene expression in the cell cycle pathway in the shoot apex and the photosynthesis pathway in true leaf positively correlates with true leaf area heterosis level, and this is affected by the accumulation of superior heterozygous eQTLs. This was further corroborated by the major contribution of increased photosynthetic cell number to leaf area heterosis.

Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis

Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F₁ hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F₁ hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F₁ hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F₁ hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.

Differences in the transcriptional immune response to Albugo candida between white rust resistant and susceptible cultivars in Brassica rapa L

Albugo candida causing white rust disease decreases the yield of Brassica rapa vegetables greatly. Resistant and susceptible cultivars in B. rapa vegetables have different immune responses against A. candida inoculation, however, the mechanism of how host plants respond to A. candida is still unknown. Using RNA-sequencing, we identified differentially expressed genes (DEGs) between A. candida inoculated [48 and 72 h after inoculation (HAI)] and non-inoculated samples in resistant and susceptible cultivars of komatsuna (B. rapa var. perviridis). Functional DEGs differed between the resistant and susceptible cultivars in A. candida inoculated samples. Salicylic acid (SA) responsive genes tended to be changed in their expression levels by A. candida inoculation in both resistant and susceptible cultivars, but different genes were identified in the two cultivars. SA-dependent systemic acquired resistance (SAR) involving genes were upregulated following A. candida inoculation in the resistant cultivar. Particular genes categorized as SAR that changed expression levels overlapped between A. candida and Fusarium oxysporum f. sp. conglutinans inoculated samples in resistant cultivar, suggesting a role for SAR in defense response to both pathogens particularly in the effector-triggered immunity downstream pathway. These findings will be useful for understanding white rust resistance mechanisms in B. rapa.

Performances of three-way cross hybrids over their respective single crosses and related heterosis of maize (Zea mays L.) hybrids evaluated in Ethiopia

Less attention had been given to the performances of three-way crosses and its comparative advantages of these hybrids over single crosses. This study was carried out to evaluate the performances of three-way crosses in comparison to single crosses for yield and related agronomic traits and to estimate the magnitude of heterosis. The trial was laid out in a simple alpha lattice design of 10 × 6 for lines, 6 × 5 for single crosses (SC), and 9 × 5 for three way-crosses and planted in adjacent plots in the 2019 cropping season in three locations namely Ambo, Abala-Farcha and Melkassa. Single cross hybrids showed a highly significant (P<1%) variation for grain yield, plant height, ear height, and ear length at three locations. These single cross hybrids had showed also a highly significant genotype by environment interaction (P < 1%) for grain yield, plant height, ear height and kernel per ear. Regarding three-way crosses, there was a significant variation (P<5%) on grain yield in Ambo and Melkassa but on ear height and rows per ear in Abala-Faracho. The genotype × environment interaction was significantly varied for grain yield, ear height and ear length. In the comparison, 80% crosses in Ambo, 73% in Abala-Faracho and 67% in Melkassa showed that three-way crosses were better in their performance than that of their respective single crosses. On the other hand, the single crosses that out-performed their respective three-way crosses were higher in Melkassa than Abala-Faracho and the least were reported from Ambo. Similarly, the maximum better and mid-parent heterosis was from single cross 1(769%) in Ambo and single cross 7 (104%) in Melkassa whereas TWC 14 (52%) and TWC 24 (78%) were the highest better and mid-parent heterosis, respectively in Ambo, TWC1 (56%), and TWC30 (25%) were the highest BPH, and MPH, respectively in Melkassa.

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

KEY MESSAGE

Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F₁ hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

Correlation between Parental Transcriptome and Field Data for the Characterization of Heterosis in Chinese Cabbage

In Chinese cabbage breeding, hybrids have made a terrific contribution due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new, top-performing hybrids requires a large scale of human and material resources, the prediction of hybrid performance is of utmost interest to plant breeders. In our research, leaf transcriptome data from eight parents were used to investigate if they might be employed as markers to predict hybrid performance and heterosis. In Chinese cabbage, heterosis of plant growth weight (PGW) and heterosis of head weight (HW) were more obvious than other traits. The number of differential expression genes (DEGs) between parents was related to the PGW, length of the biggest outer leaf (LOL), leaf head height (LHH), leaf head width (LHW), HW, leaf number of head (LNH) and plant height (PH) of hybrids, and up-regulated DEGs number was also associated with these traits. Euclidean and binary distances of parental gene expression levels were significantly correlated with the PGW, LOL, LHH, LHW, HW and PH of hybrids. Additionally, there was a significant correlation between the parental expression levels of multiple genes involved in the ribosomal metabolic pathway and hybrid observations and heterosis in PGW, with the BrRPL23A gene showing the highest correlation with the MPH of PGW(r = 0.75). Therefore, leaf transcriptome data can preliminarily predict the hybrid performance and select parents in Chinese cabbage.

Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage

Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.

Overdominant expression of genes plays a key role in root growth of tobacco hybrids

Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F₁ hybrids, all of which showed strong heterosis, indicating that tobacco F₁ hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids. In addition, Nitab4.5_0011528g0020、Nitab4.5_0003282g0020、Nitab4.5_0004384g0070 may be the genes involved in root growth. Genome-wide comparative transcriptome analysis enhanced our understanding of the regulatory network of tobacco root development and provided new ideas for studying the molecular mechanisms of tobacco root development.

Comparative Transcriptome Analysis of the Heterosis of Salt Tolerance in Inter-Subspecific Hybrid Rice

Soil salinity is one of the major abiotic stresses limiting rice growth. Hybrids outperform their parents in salt tolerance in rice, while its mechanism is not completely understood. In this study, a higher seedling survival was observed after salt treatment in an inter-subspecific hybrid rice, Zhegengyou1578 (ZGY1578), compared with its maternal japonica Zhegeng7A (ZG7A) and paternal indica Zhehui1578 (ZH1578). A total of 2584 and 3061 differentially expressed genes (DEGs) with at least twofold changes were identified between ZGY1578 and ZG7A and between ZGY1578 and ZH1578, respectively, in roots under salt stress using the RNA sequencing (RNA-Seq) approach. The expressions of a larger number of DEGs in hybrid were lower or higher than those of both parents. The DEGs associated with transcription factors, hormones, and reactive oxygen species (ROS)-related genes might be involved in the heterosis of salt tolerance. The expressions of the majority of transcription factors and ethylene-, auxin-, and gibberellin-related genes, as well as peroxidase genes, were significantly higher in the hybrid ZGY1578 compared with those of both parents. The identified genes provide valuable clues to elucidate the heterosis of salt tolerance in inter-subspecific hybrid rice.

Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids

BACKGROUND

Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F₁ hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis.

RESULTS

In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM.

CONCLUSIONS

The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.

Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid

Rice productivity has considerably improved due to the effective employment of heterosis, but the genetic basis of heterosis for grain shape and weight remains uncertain. For studying the genetic dissection of heterosis for grain shape/weight and their relationship with grain yield in rice, quantitative trait locus (QTL) mapping was performed on 1,061 recombinant inbred lines (RILs), which was developed by crossing xian/indica rice Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM). Whereas, BC₁F₁ (a backcross F₁) was developed by crossing RILs with Quan9311A (Q9311A) combined with phenotyping in Hefei (HF) and Nanning (NN) environments. Overall, 114 (main-effect, mQTL) and 359 (epistatic QTL, eQTL) were identified in all populations (RIL, BC₁F₁, and mid-parent heterosis, H_MPs) for 1000-grain weight (TGW), grain yield per plant (GYP) and grain shape traits including grain length (GL), grain width (GW), and grain length to width ratio (GLWR). Differential QTL detection revealed that all additive loci in RILs population do not show heterotic effects, and few of them affect the performance of BC₁F₁. However, 25 mQTL not only contributed to BC₁F₁'s performance but also contributed to heterosis. A total of seven QTL regions was identified, which simultaneously affected multiple grain traits (grain yield, weight, shape) in the same environment, including five regions with opposite directions and two regions with same directions of favorable allele effects, indicating that partial genetic overlaps are existed between different grain traits. This study suggested different approaches for obtaining good grain quality with high yield by pyramiding or introgressing favorable alleles (FA) with the same direction of gene effect at the QTL regions affecting grain shape/weight and grain yield distributing on different chromosomes, or introgressing or pyramiding FA in the parents instead of fixing additive effects in hybrid as well as pyramiding the polymorphic overdominant/dominant loci between the parents and eliminating underdominant loci from the parents. These outcomes offer valuable information and strategy to develop hybrid rice with suitable grain type and weight.

Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield

We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.

Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

BACKGROUND

Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F₁ (BCF₁) hybrids derived from QYSM's parents across three environments and gene-based analyses.

RESULTS

Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF₁ hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM.

CONCLUSIONS

The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus

Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.

Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression

Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus

BACKGROUND

Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear.

RESULTS

In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones.

CONCLUSION

Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.

Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower

INTRODUCTION

Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood.

OBJECTIVES

This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments.

METHODS

Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F₁ hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing.

RESULTS

Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses.

CONCLUSION

Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.

Selection for early shoot vigour in wheat increases root hair length but reduces epidermal cell size of roots and leaves

Six cycles of recurrent selection for early shoot vigour in wheat resulted in significant increases in leaf width and shoot biomass. Here, in replicated controlled-environment studies, the effect of early shoot vigour on root biomass, rhizosheath size, root hair length, and cell size in the roots and leaves was examined across different cycles of selection. Increased shoot vigour was associated with greater root biomass, larger rhizosheath size, and longer root hairs. Our findings demonstrate that rhizosheath size was a reliable surrogate for root hair length in this germplasm. Examination of the root epidermis revealed that the 'cell body' of the trichoblasts (hair-forming cells) and the atrichoblasts (non-hair-forming cells) decreased in size as shoot vigour increased. Therefore, in higher vigour germplasm, longer root hairs emerged from smaller trichoblasts so that total trichoblast volume (root hair plus cell body) was generally similar regardless of shoot vigour. Similarly, the sizes of the four main cell types on the leaf epidermis became progressively smaller as shoot vigour increased, which also increased stomatal density. The relationship between shoot vigour and root traits is considered, and the potential contribution of below-ground root traits to performance and competitiveness of high vigour germplasm is discussed.

Transcriptome Profiling in the Marine Red Alga Neopyropia yezoensis Under Light/Dark Cycle

Many organisms are subjected to a daily cycle of light and darkness, which significantly influences metabolic and physiological processes. In the present study, Neopyropia yezoensis, one of the major cultivated seaweeds used in "nori," was harvested in the morning and evening during light/dark treatments to investigate daily changes in gene expression using RNA-sequencing. A high abundance of transcripts in the morning includes the genes associated with carbon-nitrogen assimilations, polyunsaturated fatty acid, and starch synthesis. In contrast, the upregulation of a subset of the genes associated with the pentose phosphate pathway, cell cycle, and DNA replication at evening is necessary for the tight control of light-sensitive processes, such as DNA replication. Additionally, a high abundance of transcripts at dusk encoding asparaginase and glutamate dehydrogenase imply that regulation of asparagine catabolism and tricarboxylic acid cycle possibly contributes to supply nitrogen and carbon, respectively, for growth during the dark. In addition, genes encoding cryptochrome/photolyase family and histone modification proteins were identified as potential key players for regulating diurnal rhythmic genes.

Environment dependence of the expression of mutational load and species' range limits

Theoretical and empirical research on the causes of species’ range limits suggest the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline towards range edges and enhance the expression of load. Here, we tested whether the expression of mutational load associated with range limits in the North American plant Arabidopsis lyrata was enhanced under stressful environmental conditions by comparing the performance of within‐ versus between‐population crosses at common garden sites across the species’ distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range‐edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress‐dependent load linked to general heterozygote deficiency, but there is no synergistic effect between them.

Progressive DNA demethylation in epigenetic hybrids between parental plants with and without methylation of the transgene promoter

Crosses of parents that differ in their DNA methylation states leads to progressive demethylation in the F₁ hybrids. In plant breeding research, hybrid vigor in F₁ hybrids is known to be a very important phenomenon. Hybrid vigor, or heterosis, refers to the fact that F₁ hybrids from crosses with a certain combination of parents have traits that are superior to those of the parents. In addition, DNA methylation is an important factor that affects gene expression in plant genomes and contributes to hybrid vigor. We introduced the 35S promoter sequence into the cucumber mosaic virus (CMV)-based vector and inoculated the GFP-expressing transgenic Nicotiana benthamiana line 16c with the recombinant virus specifically to induce DNA methylation on the 35S promoter. For plants that had transcriptional gene silencing (TGS) of GFP established by methylation of the 35S promoter (35S-TGS), TGS was fully maintained in their later self-pollinated generations. When the 35S-TGS plants were crossed with 16c, which does not contain DNA methylation in the 35S promoter, the F₁ hybrids unexpectedly became progressively DNA demethylated as the plants grew. We hypothesis that in F₁ hybrids that are produced by a cross between parents with extremely different gene methylation states, the methylation state of the genes in question may shift more and more to hypomethylation as the plants grow. This progressive demethylation phenomenon observed in this study may be important in plant breeding to reactivate the genes which were silenced by DNA methylation.

Genetic Basis of Sexual Maturation Heterosis: Insights From Ovary lncRNA and mRNA Repertoire in Chicken

Sexual maturation is fundamental to the reproduction and production performance, heterosis of which has been widely used in animal crossbreeding. However, the underlying mechanism have long remained elusive, despite its profound biological and agricultural significance. In the current study, the reciprocal crossing between White Leghorns and Beijing You chickens were performed to measure the sexual maturation heterosis, and the ovary lncRNAs and mRNAs of purebreds and crossbreeds were profiled to illustrate molecular mechanism of heterosis. Heterosis larger than 20% was found for pubic space and oviduct length, whereas age at first egg showed negative heterosis in both crossbreeds. We identified 1170 known lncRNAs and 1994 putative lncRNAs in chicken ovary using a stringent pipeline. Gene expression pattern showed that nonadditivity was predominant, and the proportion of nonadditive lncRNAs and genes was similar between two crossbreeds, ranging from 44.24% to 49.15%. A total of 200 lncRNAs and 682 genes were shared by two crossbreeds, respectively. GO and KEGG analysis showed that the common genes were significantly enriched in the cell cycle, animal organ development, gonad development, ECM-receptor interaction, calcium signaling pathway and GnRH signaling pathway. Weighted gene co-expression network analysis (WGCNA) identified that 7 out of 20 co-expressed lncRNA-mRNA modules significantly correlated with oviduct length and pubic space. Interestingly, genes harbored in seven modules were also enriched in the similar biological process and pathways, in which nonadditive lncRNAs, such as MSTRG.17017.1 and MSTRG.6475.20, were strongly associated with nonadditive genes, such as CACNA1C and TGFB1 to affect gonad development and GnRH signaling pathway, respectively. Moreover, the results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. Integrated with positive heterosis of serum GnRH and melatonin content detected in crossbreeds, we speculated that nonadditive genes involved in the GnRH signaling pathway elevated the gonad development, leading to the sexual maturation heterosis. We characterized a systematic landscape of ovary lncRNAs and mRNAs related to sexual maturation heterosis in chicken. The quantitative exploration of hybrid transcriptome changes lays foundation for genetic improvement of sexual maturation traits and provides insights into endocrine control of sexual maturation.

Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice

Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to DNA methylation differences between the hybrid and its parents. Inter-subspecific hybrid rice combinations of indica × japonica have great potential to broaden genetic diversity and enhance the heterosis. The genetic and epigenetic molecular mechanism of its heterosis is not completely understood. Here, the dissection of gene expression and epigenetic regulation of an elite inter-subspecific hybrid rice were reported. In the hybrid, plant height, flag leaf area and Pn showed significant heterosis at the heading stage. Chloroplast-related differentially expressed genes (DEGs) and 530 allele-specific expression genes in hybrid were identified. Analysis of the genome-wide distribution of DNA methylation (5-methylcytosine, 5mC) and its association with transcription showed that there were variant DNA methylation maps and that the regulation of gene expression levels was negatively regulated by DNA methylation in the inter-subspecific hybrid rice. Differentially methylated DEGs were significantly enriched in photosynthetic functions. Moreover, distinct 5mC sequence contexts and distinct functional elements (promoter/gene body) may have different influences on heterosis related genes. The data identified heterosis related molecular mechanisms in inter-subspecific hybrid rice and suggested that epigenetic changes could extensively influence the flag leaf gene expression and heterosis.

Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L

Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc.

Transcriptome profiling revealed the growth superiority of hybrid pufferfish derived from Takifugu obscurus ♀ × Takifugu rubripes ♂

Hybridization is an efficient method to breed new strains of aquatic animals. In the present study, we produced a hybrid puffer by crossing female obscure puffer with male tiger puffer. The hybrid puffer could live in fresh water like obscure puffer and exhibited growth superiority. The averaged body weight of 4- and 6-month-old hybrid puffer were respectively 38.06% and 38.93% higher than that of obscure puffer. Then, we analyzed the underlying genetic basis for the growth advantage of hybrid puffer by comparative transcriptome analysis. A total number of 4264 and 1285 differentially expressed genes (DEGs) were respectively identified from pituitary and liver transcriptome profiles between hybrid puffer and obscure puffer. Comprehensive analysis showed that the DEGs related with cell proliferation and differentiation, and protein synthesis and export, specifically showed higher expression levels in hybrid puffer, such as "ECM-receptor interaction", "focal adhesion", "protein export" and "protein processing in endoplasmic reticulum". While the DEGs involved in gametogenesis and carbohydrate and energy metabolism highly expressed in obscure puffer, such as "oxidative phosphorylation", "citrate cycle", "progesterone-mediated oocyte maturation" and "oocyte meiosis". Furthermore, a series of candidate genes related to the growth superiority of hybrid puffer were identified, such as fn1a, ptprc, plcg2, igf1, tgfβ1, bmp4, abl1, col1a2, col1a1a, and myl9a. These results will be beneficial to understand the molecular basis of growth superiority and helpful to the hybrid breeding of pufferfish.

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus

Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.

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.

Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables

In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F₂ populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F₂ populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.

Genetic dissection of heterosis of indica-japonica by introgression line, recombinant inbred line and their testcross populations

The successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F₁s (TCF₁s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF₁s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF₁s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2, qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.

The dominance model for heterosis explains culm length genetics in a hybrid sorghum variety

Heterosis helps increase the biomass of many crops; however, while models for its mechanisms have been proposed, it is not yet fully understood. Here, we use a QTL analysis of the progeny of a high-biomass sorghum F₁ hybrid to examine heterosis. Five QTLs were identified for culm length and were explained using the dominance model. Five resultant homozygous dominant alleles were used to develop pyramided lines, which produced biomasses like the original F₁ line. Cloning of one of the uncharacterised genes (Dw7a) revealed that it encoded a MYB transcription factor, that was not yet proactively used in modern breeding, suggesting that combining classic dw1or dw3, and new (dw7a) genes is an important breeding strategy. In conclusion, heterosis is explained in this situation by the dominance model and a combination of genes that balance the shortness and early flowering of the parents, to produce F₁ seed yields.

Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton (Gossypium hirsutum L.)

Background

Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F₁, derived from NCII mating scheme. The hybrids, their parents and two check cultivars were evaluated for two years. Performance of F₁, mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits, including plant height, boll weight, boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index.

Results

Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F₁ performances. The F₁ performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits, including boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F₁ performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. The correlation between GD and F₁ performance, MPH and BPH were significant for lint percentage and micronaire.

Conclusions

Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07431-6.

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.

Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

BACKGROUND

Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.

RESULTS

Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value.

CONCLUSIONS

Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular biology have revolutionized traditional plant breeding based on visual phenotype assessment: the development of different types of molecular markers has made genotype selection possible. Marker-assisted breeding can significantly accelerate the breeding process, but this method has not been shown to be effective for selection of complex traits on forest trees. This new method of genomic selection is based on the analysis of all effects of quantitative trait loci (QTLs) using a large number of molecular markers distributed throughout the genome, which makes it possible to assess the genomic estimated breeding value (GEBV) of an individual. This approach is expected to be much more efficient for forest tree improvement than traditional breeding. Here, we review the current state of the art in the application of genomic selection in forest tree breeding and discuss different methods of genotyping and phenotyping. We also compare the accuracies of genomic prediction models and highlight the importance of a prior cost-benefit analysis before implementing genomic selection. Perspectives for the further development of this approach in forest breeding are also discussed: expanding the range of species and the list of valuable traits, the application of high-throughput phenotyping methods, and the possibility of using epigenetic variance to improve of forest trees.

DNA methylation changes in clonally propagated oil palm

Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling. One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the "mantled" phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC₃-poor genes) were increasingly methylated towards their 3' region, while GC₃-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5' UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.

Transcriptome analysis of biological pathways associated with heterosis in Chinese cabbage

Chinese cabbage is an important vegetable in Asia, and high-yielding hybrids are needed to cope with the growing demand. A comparative transcriptome profiling was conducted to reveal the differentially expressed genes (DEGs) associated with heterosis in two hybrids relative to their parents. Our data suggests that heterosis is underlined by a significant upregulation of gene expression. High expression of DEGs in glycolysis and photosynthesis pathways in hybrids depicted their relation with growth and hybrid vigor. Besides, DEGs related to auxin, abscisic acid, ethylene and gibberellin were identified, implying that these hormones may boost the mechanisms of growth and developmental processes in the hybrids. Furthermore, transcription factors, including bHLH, ERF, MYB and WRKY were predicted to regulate downstream genes linked to hybrid vigor. Collectively, the present study will be helpful for a better understanding of the regulation mechanisms of heterosis to aid cabbage yield improvement.

Hybrid breeding in wheat: how shaping floral biology can offer new perspectives

Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.

Exploitation of Heterosis in Pearl Millet: A Review

The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.

Large-Scale Analysis of Combining Ability and Heterosis for Development of Hybrid Maize Breeding Strategies Using Diverse Germplasm Resources

Understanding combining ability and heterosis among diverse maize germplasm resources is important for breeding hybrid maize (Zea mays L.). Using 28 temperate and 23 tropical maize inbreds that represent different ecotypes and worldwide diversity of maize germplasm, we first developed a large-scale multiple-hybrid population (MHP) with 724 hybrids, which could be divided into three subsets, 325 temperate diallel hybrids and 136 tropical diallel hybrids generated in Griffing IV, and 263 temperate by tropical hybrids generated in NCD II. All the parental lines and hybrids were evaluated for 11 traits in replicated tests across two locations and three years. Several widely used inbreds showed strong general combining ability (GCA), and their derived hybrids showed strong specific combining ability (SCA). Heterosis is a quantifiable, trait-dependent and environment-specific phenotype, and the response of parental lines and their hybrids to environments resulted in various levels of heterosis. For all the tested traits except plant height and hundred grain weight (HGW), NCD II (temperate × tropical) hybrids showed higher average heterosis than the temperate and tropical diallel hybrids, with higher hybrid performance for ear length, ear diameter, and HGW. Tropical maize germplasm can be used to improve the yield potential for temperate lines. Grain number per row and grain number per ear were two most important traits that determined yield heterosis, which can be used as direct selection criteria for yield heterosis. The hybrids from heterotic groups, Reid × SPT, Reid × LRC, SPT × PA, and Lancaster × LRC, contributed highly significant positive SCA effects and strong heterosis to yield-related traits, and the heterotic patterns identified in this study were potentially useful for commercial maize breeding. Heterosis was more significantly and positively correlated with SCA than GCA, indicating that SCA can be used in heterosis prediction to develop potential hybrids in commercial maize breeding. The results of the present study not only contribute to developing breeding strategies, but also improve targeted breeding efficiency by using both temperate and tropical maize to broaden genetic basis. Large sets of parental lines with available genotypic information can be shared and used in worldwide hybrid breeding programs through an open-source breeding strategy. Potential applications of the reported results in developing hybrid maize breeding strategies were also discussed.

In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F1 Hybrid Population

Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F₁ hybrid cultivars in many crops. A similar level of heterosis in all F₁ individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F₁ plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F₁ plants had 26.1% larger leaf area in the first and second leaves than medium-sized F₁ plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F₁ plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F₁ plants could generate the variation in plant size of individual F₁ plants in A. thaliana.