Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata

Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.

Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability

Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.

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.

Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids

F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns. Using a combination of multi-omic profiling and epigenetic mapping strategies we show that differentially methylated regions in parental pericentromeres act as major reorganizers of hybrid methylomes and transcriptomes, even in the absence of genetic variation. These parental differentially methylated regions are associated with hybrid methylation remodeling events at thousands of target regions throughout the genome, both locally (in cis) and distally (in trans). Many of these distally-induced methylation changes lead to nonadditive expression of nearby genes and associate with phenotypic heterosis. Our study highlights the pleiotropic potential of parental pericentromeres in the functional remodeling of hybrid genomes and phenotypes.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

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.

Epigenetic Changes Occurring in Plant Inbreeding

Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.

Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel

Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

High-frequency synthetic apomixis in hybrid rice

Introducing asexual reproduction through seeds - apomixis - into crop species could revolutionize agriculture by allowing F1 hybrids with enhanced yield and stability to be clonally propagated. Engineering synthetic apomixis has proven feasible in inbred rice through the inactivation of three genes (MiMe), which results in the conversion of meiosis into mitosis in a line ectopically expressing the BABYBOOM1 (BBM1) parthenogenetic trigger in egg cells. However, only 10-30% of the seeds are clonal. Here, we show that synthetic apomixis can be achieved in an F1 hybrid of rice by inducing MiMe mutations and egg cell expression of BBM1 in a single step. We generate hybrid plants that produce more than 95% of clonal seeds across multiple generations. Clonal apomictic plants maintain the phenotype of the F1 hybrid along successive generations. Our results demonstrate that there is no barrier to almost fully penetrant synthetic apomixis in an important crop species, rendering it compatible with use in agriculture.

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F₁ hybrid and parents, and of these, 4891 DMRs showed higher methylation in F₁ compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46–55% differentially expressed genes (DE-Gs) in the F₁ hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65–72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F₁ hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis in Capsicum.

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Global methylation identified significantly different proportions of mCs in hybrid

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Of common DMRs, 33.08% showed different methylation in hybrid from the mid-parental value

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Negatively correlated DEG pDMR-genes were enriched in metabolic pathways

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Significant higher expression of metabolites and DE-Gs were identified in the F₁ hybrid

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.

The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.

Additive and non-additive epigenetic signatures of natural hybridisation between fish species with different mating systems

Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.

Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

Background

Plants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramming process. The relationship of epigenomic changes to gene networks on a genome-wide basis has been elusive, particularly for intragenic DNA methylation repatterning.

Results

Epigenomic reprogramming is tractable to detailed study and cross-species modeling in the MSH1 system, where perturbation of the plant-specific gene MSH1 triggers at least four distinct nongenetic states to impact plant stress response and growth vigor. Within this system, we have defined RdDM target loci toward decoding phenotype-relevant methylome data. We analyze intragenic methylome repatterning associated with phenotype transitions, identifying state-specific cytosine methylation changes in pivotal growth-versus-stress, chromatin remodeling, and RNA spliceosome gene networks that encompass 871 genes. Over 77% of these genes, and 81% of their central network hubs, are functionally confirmed as RdDM targets based on analysis of mutant datasets and sRNA cluster associations. These dcl2/dcl3/dcl4-sensitive gene methylation sites, many present as singular cytosines, reside within identifiable sequence motifs. These data reflect intragenic methylation repatterning that is targeted and amenable to prediction.

Conclusions

A prevailing assumption that biologically relevant DNA methylation variation occurs predominantly in density-defined differentially methylated regions overlooks behavioral features of intragenic, single-site cytosine methylation variation. RdDM-dependent methylation changes within identifiable sequence motifs reveal gene hubs within networks discriminating stress response and growth vigor epigenetic phenotypes. This study uncovers components of a methylome “code” for de novo intragenic methylation repatterning during plant phenotype transitions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02731-w.

Expression Patterns Divergence of Reciprocal F1 Hybrids Between Gossypium hirsutum and Gossypium barbadense Reveals Overdominance Mediating Interspecific Biomass Heterosis

Hybrid breeding has provided an impetus to the process and achievement of a higher yield and quality of crops. Interspecific hybridization is critical for resolving parental genetic diversity bottleneck problems. The reciprocal interspecific hybrids and their parents (Gossypium hirsutum and Gossypium barbadense) have been applied in this study to elucidate the transcription regulatory mechanism of early biomass heterosis. Phenotypically, the seed biomass, plant height over parent heterosis, leaf area over parent heterosis, and fresh and dry biomass were found to be significantly higher in hybrids than in parents. Analysis of leaf areas revealed that the one-leaf stage exhibits the most significant performance in initial vegetative growth vigor and larger leaves in hybrids, increasing the synthesis of photosynthesis compounds and enhancing photosynthesis compound synthesis. Comparative transcriptome analysis showed that transgressive down-regulation (TDR) is the main gene expression pattern in the hybrids (G. hirsutum × G. barbadense, HB), and it was found that the genes of photosystem I and Adenosine triphosphate (ATP)-binding may promote early growth vigor. Transgressive up-regulation (TUR) is the major primary gene expression pattern in the hybrids (G. barbadense × G. hirsutum, BH), and photosystem II-related genes mediated the performance of early biomass heterosis. The above results demonstrated that overdominance mediates biomass heterosis in interspecific hybrid cotton and the supervisory mechanism divergence of hybrids with different females. Photosynthesis and other metabolic process are jointly involved in controlling early biomass heterosis in interspecific hybrid cotton. The expression pattern data of transcriptome sequencing were supported using the qRT-PCR analysis. Our findings could be useful in theoretical and practical studies of early interspecific biomass heterosis, and the results provide potential resources for the theoretical and applied research on early interspecific biomass heterosis.

Alien genome mobilization and fixation utilizing an apomixis mediated genome addition (AMGA) strategy in Pennisetum to improve domestication traits of P. squamulatum

An approach to release 'frozen' variability in apomictic species using sexuality of another species, eventually its utilization in crop improvement and de-novo domestication of crop wild relatives is presented. Pennisetum squamulatum, a secondary gene pool species of pearl millet (P. glaucum), harbours many desirable traits. However, it was neither utilized to improve pearl millet fodder traits nor improvement of its own domestication traits was attempted, due to the complexities of genomes and apomictic reproduction. To overcome this, we followed an Apomixis Mediated Genome Addition (AMGA) strategy and utilized the contrasting reproductive capacities (sexuality and apomixis) of both the species to access the otherwise un-available variability embedded in P. squamulatum. Segregating population of interspecific hybrids exhibited significant variability and heterosis for desired morphological, agronomical, and nutritional traits. Elite apomictic and perennial hybrids were evaluated in breeding trials, and eventually a novel grass cultivar was released for commercial cultivation in India. The performance of newly developed cultivar was superior to other adapted perennial grasses of arid and semi-arid rangelands. Through AMGA, the sexuality of one species was successfully utilized to 'release' the 'frozen' variability embedded in another species. Subsequently, the hybrids representing desirable trait combinations were again 'fixed' utilizing the apomixis alleles from the male parent in a back-and-forth apomixis-sexual-apomixis selection cycle. This study also demonstrated the potential of AMGA to improve crop relatives through genomes introgression as well as de novo domestication of new crops from wild species.

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.

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Simple Summary

Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses.

Abstract

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.

Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice

Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.

Grafting vigour is associated with DNA de-methylation in eggplant

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.

Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives

Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.

Revisiting Plant Heterosis-From Field Scale to Molecules

Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.

Advances in Research on the Mechanism of Heterosis in Plants

Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.

Integrated Analysis of mRNA and Non-coding RNA Transcriptome in Pepper (Capsicum chinense) Hybrid at Seedling and Flowering Stages

Pepper is an important vegetable in the world. In this work, mRNA and ncRNA transcriptome profiles were applied to understand the heterosis effect on the alteration in the gene expression at the seedling and flowering stages between the hybrid and its parents in Capsicum chinense. Our phenotypic data indicated that the hybrid has dominance in leaf area, plant scope, plant height, and fruit-related traits. Kyoto Encyclopedia of Genes and Genomes analysis showed that nine members of the plant hormone signal transduction pathway were upregulated in the seedling and flowering stages of the hybrid, which was supported by weighted gene coexpression network analysis and that BC332_23046 (auxin response factor 8), BC332_18317 (auxin-responsive protein IAA20), BC332_13398 (ethylene-responsive transcription factor), and BC332_27606 (ethylene-responsive transcription factor WIN1) were candidate hub genes, suggesting the important potential role of the plant hormone signal transduction in pepper heterosis. Furthermore, some transcription factor families, including bHLH, MYB, and HSF were greatly over-dominant. We also identified 2,525 long ncRNAs (lncRNAs), 47 micro RNAs (miRNAs), and 71 circle RNAs (circRNAs) in the hybrid. In particular, downregulation of miR156, miR169, and miR369 in the hybrid suggested their relationship with pepper growth vigor. Moreover, we constructed some lncRNA–miRNA–mRNA regulatory networks that showed a multi-dimension to understand the ncRNA relationship with heterosis. These results will provide guidance for a better understanding of the molecular mechanism involved in pepper heterosis.

Epigenetics for Crop Improvement in Times of Global Change

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future

For millennia, natural and artificial selection has combined favourable alleles for desirable traits in crop species. While modern plant breeding has achieved steady increases in crop yields over the last century, on the current trajectory we will simply not meet demand by 2045. Novel breeding strategies and sources of genetic variation will be required to sustainably fill predicted yield gaps and meet new consumer preferences. Here, we highlight that stepping up to meet this grand challenge will increasingly require thinking 'beyond the gene'. Significant progress has been made in understanding the contributions of both epigenetic variation and cis-regulatory variation to plant traits. This non-genic variation has great potential in future breeding, synthetic biology and biotechnology applications.

Parental variation in CHG methylation is associated with allelic-specific expression in elite hybrid rice

Heterosis refers to the superior performance of hybrid lines over inbred parental lines. Besides genetic variation, epigenetic differences between parental lines are suggested to contribute to heterosis. However, the precise nature and extent of differences between the parental epigenomes and the reprograming in hybrids that govern heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice (Oryza sativa) SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, for which high-quality reference genomic sequences are available. We showed that the parental varieties displayed substantial variation in genic methylation at CG and CHG (H = A, C, or T) sequences. Compared with their parents, the hybrids displayed dynamic methylation variation during development. However, many parental differentially methylated regions (DMRs) at CG and CHG sites were maintained in the hybrid. Only a small fraction of the DMRs displayed non-additive DNA methylation variation, which, however, showed no overall correlation relationship with gene expression variation. In contrast, most of the allelic-specific expression (ASE) genes in the hybrid were associated with DNA methylation, and the ASE negatively associated with allelic-specific methylation (ASM) at CHG. These results revealed a specific DNA methylation reprogramming pattern in the hybrid rice and pointed to a role for parental CHG methylation divergence in ASE, which is associated with phenotype variation and hybrid vigor in several plant species.

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.

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize

Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.

Epigenetic regulation of nitrogen and phosphorus responses in plants

Nitrogen (N) and phosphorus (P) are two of the most important nutrients for plant growth and crop yields. In the last decade, plenty of studies have revealed the genetic factors and their regulatory networks which are involved in N and/or P uptake and utilization in different model plant species, especially in Arabidopsis and rice. However, increasing evidences have shown that epigenetic regulation also plays a vital role in modulating plant responses to nutrient availability. In this review, we make a brief summary of epigenetic regulation including histone modifications, DNA methylation, and other chromatin structure alterations in tuning N and P responses. We also give an outlook for future research directions to comprehensively dissect the involvement of epigenetic regulation in modulating nutrient response in plants.

Genetic Rescue and the Plight of Ponui Hybrids

Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.

Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

BACKGROUND

Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood.

RESULTS

Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH.

CONCLUSIONS

Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.

Quantitative Epigenetics: A New Avenue for Crop Improvement

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.

Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement

Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.

MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification

Background

DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data.

Results

In this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes.

Conclusions

This study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.

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.

Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants

Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.

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.

Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea

Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

DNA methylation analysis in plants: review of computational tools and future perspectives

Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.

Understanding epigenomics based on the rice model

The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.

Exploring the molecular basis of heterosis for plant breeding

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena

Biological phenomena defined as having an "epigenetic" component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Molecular Biology builds on the work of its predecessor to describe cutting-edge tools for plant epigenetic and epigenomic research, and embrace crop and forestry species as well as natural populations and further insights from model species. In this chapter, the historical background to plant epigenetic and epigenomic research is summarized, and key considerations for the interpretation of current data are outlined.

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants

DNA methylation is involved in many different biological processes in the development and well-being of crop plants such as transposon activation, heterosis, environment-dependent transcriptome plasticity, aging, and many diseases. Whole-genome bisulfite sequencing is an excellent technology for detecting and quantifying DNA methylation patterns in a wide variety of species, but optimized data analysis pipelines exist only for a small number of species and are missing for many important crop plants. This is especially important as most existing benchmark studies have been performed on mammals with hardly any repetitive elements and without CHG and CHH methylation. Pipelines for the analysis of whole-genome bisulfite sequencing data usually consists of four steps: read trimming, read mapping, quantification of methylation levels, and prediction of differentially methylated regions (DMRs). Here we focus on read mapping, which is challenging because un-methylated cytosines are transformed to uracil during bisulfite treatment and to thymine during the subsequent polymerase chain reaction, and read mappers must be capable of dealing with this cytosine/thymine polymorphism. Several read mappers have been developed over the last years, with different strengths and weaknesses, but their performances have not been critically evaluated. Here, we compare eight read mappers: Bismark, BismarkBwt2, BSMAP, BS-Seeker2, Bwameth, GEM3, Segemehl, and GSNAP to assess the impact of the read-mapping results on the prediction of DMRs. We used simulated data generated from the genomes of Arabidopsis thaliana, Brassica napus, Glycine max, Solanum tuberosum, and Zea mays, monitored the effects of the bisulfite conversion rate, the sequencing error rate, the maximum number of allowed mismatches, as well as the genome structure and size, and calculated precision, number of uniquely mapped reads, distribution of the mapped reads, run time, and memory consumption as features for benchmarking the eight read mappers mentioned above. Furthermore, we validated our findings using real-world data of Glycine max and showed the influence of the mapping step on DMR calling in WGBS pipelines. We found that the conversion rate had only a minor impact on the mapping quality and the number of uniquely mapped reads, whereas the error rate and the maximum number of allowed mismatches had a strong impact and leads to differences of the performance of the eight read mappers. In conclusion, we recommend BSMAP which needs the shortest run time and yields the highest precision, and Bismark which requires the smallest amount of memory and yields precision and high numbers of uniquely mapped reads.

Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses

DNA methylation through the activity of cytosine-5-methyltransferases (C5-MTases) and DNA demethylases plays important roles in genome protection as well as in regulating gene expression during plant development and plant response to environmental stresses. In this study, we report on a genome-wide identification of six C5-MTases (SmelMET1, SmelCMT2, SmelCMT3a, SmelCMT3b, SmelDRM2, SmelDRM3) and five demethylases (SmelDemethylase_1, SmelDemethylase_2, SmelDemethylase_3, SmelDemethylase_4, SmelDemethylase_5) in eggplant. Gene structural characteristics, chromosomal localization and phylogenetic analyses are also described. The transcript profiling of both C5-MTases and demethylases was assessed at three stages of fruit development in three eggplant commercial F1 hybrids: i.e. 'Clara', 'Nite Lady' and 'Bella Roma', representative of the eggplant berry phenotypic variation. The trend of activation of C5-MTases and demethylase genes varied in function of the stage of fruit development and was genotype dependent. The transcription pattern of C5MTAses and demethylases was also assessed in leaves of the F1 hybrid 'Nite Lady' subjected to salt and drought stresses. A marked up-regulation and down-regulation of some C5-MTases and demethylases was detected, while others did not vary in their expression profile. Our results suggest a role for both C5-MTases and demethylases during fruit development, as well as in response to abiotic stresses in eggplant, and provide a starting framework for supporting future epigenetic studies in the species.

Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites

In Brassica oleracea, heterosis is the most efficient tool providing impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of genomic-SSRs and EST-SSRs based genetic distance (GD) and agronomic trait based phenotypic distance (PD) for predicting heterosis in F₁ hybrids using CMS and DH based parents. 120 F₁ hybrids derived from 20Ogura based CMS lines and 6 DH based testers were evaluated for 16 agronomic traits along with the 26 parental lines and 4 commercial standard checks. The genomic-SSRs and EST-SSRs based genetic structure analysis grouped the 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing early maturity hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for the heterotic response of hybrids. Less than unity value of σ²A/D coupled with σ²_gca/σ²_sca indicated the predominance of non-additive gene action in the expression of studied traits. The correlation analysis of genetic distance with heterosis for commercial traits suggested that microsatellites based genetic distance estimates can be helpful in heterosis prediction to some extent.