The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato

Dt1 interacts with HB40 to affect lateral root primordium development by regulating CDC48 in soybean

Roots act as the plants' primary determinants of the uptake of water and nutrients, while the root structure largely depends on the repeated formation of new lateral roots (LR). Lateral root primordium (LRP) formation defines the organization and function of LRs. Therefore, lateral root formation is quite related to proper LRP morphogenesis to a great extent. Here, we identified the Arabidopsis TERMINAL FLOWER1 (TFL1) ortholog gene Dt1, which mediates soybean LRP development. The dt1 knock-out mutants showed reduced LRs with decreased LRPs. Further experiments proved that Dt1 interacted with the homeodomain-leucine zipper (HD-Zip) I family transcription factor HB40 to regulate Cell Division Control protein 48 (CDC48) expression and thus affect soybean LRP development. In summary, this study identified the Dt1-HB40-CDC48 regulatory modules to intricately control LRP development.

GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize

Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding. We analyzed plant height (PH), ear height (EH), and transcriptomic data from a maize hybrid population. Genome-wide association studies (GWASs) revealed that dominance effects of quantitative trait loci (QTLs) play a significant role in hybrid traits and mid-parent heterosis. By integrating GWAS, expression GWAS (eGWAS), and module eGWAS analysis, we prioritized six candidate heterotic genes underlying six QTLs, including one QTL that spans the bZIP29 gene. In the hybrid population, bZIP29 exhibits additive expression and dominance effects for both hybrid traits and mid-parent heterosis, with its favorable allele correlating positively with PH and EH. bZIP29 demonstrates dominance or over-dominance patterns in hybrids derived from crosses between transgenic and wild-type lines, contingent upon its expression. A tsCUT&Tag assay revealed that bZIP29 protein binds directly to a gene regulated by its associated expression QTL (eQTL) and six genes within expression modules governed by its associated module-eQTLs (meQTLs). Regulatory networks involving bZIP29 are more extensive in hybrid subpopulations than in the parental population. This study offers insights into key heterotic genes and networks that underpin the robust growth of hybrid maize.

A theory of heterosis

Heterosis refers to the superior performance of a hybrid over its parents. It is the basis for hybrid breeding particularly for maize and rice. Genetically, it is due to interactions between alleles of quantitative trait loci (dominance and epistasis). Despite enormous interest and efforts to study the genetic basis of heterosis, the relative contribution of dominance vs epistasis to heterosis is still not clear. This is because most published studies estimate quantitative trait loci effects in pieces, not able to put them together to assess the overall pattern adequately. We propose a theoretical framework that focuses on the inference of the relationship between genome and traits that includes the identification of multiple quantitative trait loci and estimation of the whole set of quantitative trait loci (additive, dominant, and epistatic) effects. Used for heterosis, it gives a clear genetic definition and interpretation of heterosis. We applied the theory and methods to a large maize dataset with a factorial design of many male and female inbred lines and their hybrid crosses. Heterosis of ear weight in maize is primarily due to quantitative trait loci dominant effects, many are overdominant. The contribution to heterosis due to epistasis is small and diffused. For comparison, we also analyzed a rice dataset that is an F2-type population derived from a cross between 2 inbred lines. The result indicates that dominance is still the main contributor to heterosis, and epistasis contribution is small.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

CsKIP1.7A, a gene involved in fruit development, contributes to the yield heterosis formation of hybrid F1 in cucumber

Heterosis has been widely applied in crops production. Nonetheless, how to determine the favorable recombination of non-alleles remains elusive. Due to the uncertainty of genetic recombination, hybrids with strong heterosis tend to be selected empirically, by developing and testing a tremendous number of combinations. Here, we found some individuals in recombinant inbred lines (RILs, F9) that were generated from hybrid F1 (HRF1) with heterosis performed transgressive segregation for yield in multiple environments. The result suggested that the formation of yield heterosis in hybrid was caused by the effective recombination of genes or QTLs. We performed multiple regression analysis (MRA) and redundancy analysis (RDA) using 11 traits measured in four environments. Of these traits, percentage of female flowers (PFF), fruit length (FL), fruit neck length (FNL), vine length (VL) and vine diameter (VD) contributed to increase yield. Moreover, the genes or QTL of yield contributor traits were identified by the molecular mapping strategy. We predicted a fl7.1 candidate gene that encoding a KIP1-like protein through correlation analysis between haplotype and fruit length phenotype. Based on the phenomenon some RILs individuals performed transgressive segregation and genetic theory, we proposed the model that the genetic sources of heterosis are contributed by combination of heterozygotic advantages and genetic recombination effects. Our work provides the theoretical basis for the pyramid of contributor genes or QTL for yield heterosis. This work also may facilitate Marker-assisted Selection for promote hybrid pyramid breeding and makes yield increasing more predictable in cucumber.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01551-7.

Optimization of Tomato Shoot Architecture by Combined Mutations in the Floral Activators FUL2/MBP20 and the Repressor SP

Shoot determinacy is a key trait affecting productivity in tomato, quantitatively governed by genes within the flowering pathway. Achieving an optimal balance of flowering signals is essential for shaping plant architecture and maximizing yield potential. However, the genetic resources and allelic diversity available for fine-tuning this balance remain limited. In this work, we demonstrate the potential for directly manipulating shoot architecture by simultaneously targeting the flowering activating FRUITFULL(FUL)-like genes, FUL2 and MADS-BOX PROTEIN 20 (MBP20), and the flowering-repressing gene SELFPRUNING (SP). Loss of MBP20 in the sp background leads to additional inflorescences, while determinacy is largely maintained. However, additional mutation of FUL2 results in mainly indeterminate plants, which have faster sympodial cycling, leading to more compact growth and increased flower production. Our results provide a path to quantitative tuning of the flowering signals with a direct impact on shoot architecture and productivity.

Impact of structural variations and genome partitioning on bread wheat hybrid performance

The agronomical interest of hybrid wheat has long been a matter of debate. Compared to maize where hybrids have been successfully grown for decades, the mixed results obtained in wheat have been attributed at least partially to the lack of heterotic groups. The wheat genome is known to be strongly partitioned and characterized by numerous presence/absence variations and alien introgressions which have not been thoroughly considered in hybrid breeding. The objective was to investigate the relationships between hybrid performance and genomic diversity. For this, we characterized a set of 124 hybrids as well as their 19 female and 16 male parents. Phenotyping for yield and yield components was conducted during two years in three locations. Parental lines were genotyped using a 410 K SNP array as well as through sequence capture of roughly 200,000 loci. This led to the identification of 180 structural variations including presence-absence variations and alien introgressions. Twenty-six of them were associated to hybrid performance through either additivity or dominance effects. While no correlation was observed at the whole genome level, the genetic distance for 25 genomic regions resulting from the structural and functional partitioning of the chromosomes shown positive or negative correlation with agronomic traits including yield. Large introgressions, like the Aegilops ventricosa 2NS-2AS translocation, can correspond to entire chromosomal regions, such as the R1 region, with an impact on yield. Our results suggest hybrid breeding should consider both structural variations and chromosome partitioning rather than maximizing whole-genome genetic distance, and according to genomic regions to combine homozygosity and heterozygosity.

Marker-assisted selection in segregating populations of tomatoes for resistance to TYLCV, ToMV, and Fusarium wilt

BACKGROUND

Tomato yellow leaf curl virus (TYLCV), tomato mosaic virus (ToMV), and Fusarium wilt are three of tomatoes' most important viral and fungal diseases.

METHODS AND RESULTS

In this study, the application of molecular markers associated with tomato yellow leaf curl virus resistance gene (Ty1), tomato mosaic virus resistance gene (Tm2), and Fusarium wilt resistance gene (I-1) (linked marker) were evaluated. In order to optimize and use SNP markers (by HRM diagnostic method) and SCAR markers, segregating populations of tomatoes were produced by self-pollination of commercial hybrid cultivars. For Ty1 and Tm2, a part of the gene was isolated from F3 populations by PCR reaction. After the sequencing of amplicons, the SNPs were identified between genotypes. According to the previous sequences, the proper site of the gene was determined and new primers were designed for PCR and HRM analysis. The results showed that among the genotypes tested for the resistance against the TYLCV virus, Comodoro, Speedy, and Matin genotypes were heterozygous and showed differentiation in the F3 generation, while Namib and SV8320 genotypes were resistant homozygous and their progeny did not show segregation. Regarding the ToMV virus, in the F3 generation of Matin, Comodoro, and Speedy 30, 12.5 and 12.5% of resistant plants were homozygous, respectively. Although a small number of resistant plants were observed among the F3 generation of SV8320 and Speedy, it can be concluded that these two genotypes were also heterozygous for this gene.

CONCLUSIONS

Finally, concerning Fusarium wilt disease, in the F5 generation, Matin, Comodoro, Speedy, SV8320, and Namib genotypes were all homozygous. In the field experiment of F1, F2, and F3 generation of SV8320 high heritability was observed for yield per plant, days to flowering, and fruit shelf life. Overall, the findings of this study can inform tomato breeding programs aimed at producing resistant inbred lines.

Molecular concepts to explain heterosis in crops

Heterosis describes the superior performance of hybrid plants compared with their genetically distinct parents and is a pillar of global food security. Here we review the current status of the molecular dissection of heterosis. We discuss how extensive intraspecific structural genomic variation between parental genotypes leads to heterosis by genetic complementation in hybrids. Moreover, we survey how global gene expression complementation contributes to heterosis by hundreds of additionally active genes in hybrids and how overdominant single genes mediate heterosis in several species. Furthermore, we highlight the prominent role of the microbiome in improving the performance of hybrids. Taken together, the molecular understanding of heterosis will pave the way to accelerate hybrid productivity and a more sustainable agriculture.

Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives

Heterosis, or hybrid vigor, refers to the phenomenon where hybrid progenies outperform their parents in traits such as yield and resistance. This phenomenon has been widely applied in plant breeding. Recent advances in high-throughput genomics have significantly advanced our understanding of heterosis. This review systematically summarizes the genetic, molecular, and epigenetic mechanisms underlying heterosis. Furthermore, we discuss recent advances in predictive methods for heterosis and their applications in improving growth rate, resistance to abiotic stresses, and wood yield in tree species. We also explore the role of tree genomics in unraveling the mechanisms underlying heterosis, emphasizing the potential of integrating high-resolution genomics, single-cell sequencing, and spatial transcriptomics to achieve a comprehensive understanding of heterosis from the molecular to spatial levels. Building on this, CRISPR-based gene-editing technologies can be employed to precisely edit heterotic loci, enabling the study of allele function. Additionally, molecular marker-assisted selection (MAS) can be utilized to identify heterotic loci in parental lines, facilitating the selection of optimal hybrid combinations and significantly reducing the labor and time costs of hybrid breeding. Finally, we review the utilization of heterosis in tree breeding and provide a forward-looking perspective on future research directions, highlighting the potential of integrating multi-omics approaches and emerging gene-editing tools to revolutionize tree hybrid breeding.

Rewards and dangers of regulatory innovation

Adaptive evolution often involves structural variation affecting genes or cis-regulatory changes that engender novel and favorable gain-of-function gene regulation. Such mutation could result in a favorable dominant trait. At the same time, the gene product could be dosage sensitive if its change in concentration disrupts another trait. As a result, the mutant allele would display dosage-sensitive pleiotropy (DSP). By minimizing imbalance while conserving the favorable dominant effect, heterozygosity can increase fitness and result in heterosis. The properties of these alleles are consistent with evidence from multiple studies that indicate increased fitness of heterozygous regulatory mutations. DSP can help explain mysterious properties of heterosis as well as other effects of hybridization.

One Hundred Years of Progress and Pitfalls: Maximising Heterosis through Increasing Multi-Locus Nuclear Heterozygosity

The improvement in quantitative traits (e.g., yield, size) in F1 offspring over parent lines is described as hybrid vigour, or heterosis. There exists a fascinating relationship between parental genetic distance and genome dosage (polyploidy), and heterosis effects. The contribution of nuclear heterozygosity to heterosis is not uniform across diploid and polyploid crops, even within same species, thus demonstrating that polyploid crops should be part of any discussion on the mechanisms of heterosis. This review examines the records of correlating heterosis with parental genetic distance and the influence of adding supplementary genomes in wide crosses. Increasing nuclear heterozygosity through parental genetic distance has been shown to be an imperfect predictor for heterosis in a variety of commercial crops such as maize, rice, and pepper. However, increasing the ploidy level raises the maximum number of alleles that can be harboured at any one locus, and studies on crops such as oilseed rape, potato, alfalfa, maize, and rice have demonstrated that heterosis may be maximised upon increasing multi-locus nuclear heterozygosity. The novel heterotic phenotypes observed above the diploid level will contribute to our understanding on the mechanisms of heterosis and aid plant breeders in achieving the righteous goal of producing more food with fewer inputs.

Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding.

Hybrid Prediction in Horticulture Crop Breeding: Progress and Challenges

In the context of rapidly increasing population and diversified market demands, the steady improvement of yield and quality in horticultural crops has become an urgent challenge that modern breeding efforts must tackle. Heterosis, a pivotal theoretical foundation for plant breeding, facilitates the creation of superior hybrids through crossbreeding and selection among a variety of parents. However, the vast number of potential hybrids presents a significant challenge for breeders in efficiently predicting and selecting the most promising candidates. The development and refinement of effective hybrid prediction methods have long been central to research in this field. This article systematically reviews the advancements in hybrid prediction for horticultural crops, including the roles of marker-assisted breeding and genomic prediction in phenotypic forecasting. It also underscores the limitations of some predictors, like genetic distance, which do not consistently offer reliable hybrid predictions. Looking ahead, it explores the integration of phenomics with genomic prediction technologies as a means to elevate prediction accuracy within actual breeding programs.

Non-additive expression genes play a critical role in leaf vein ratio heterosis in Nicotiana tabacum L

Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies.

Ergothioneine Improves Seed Yield and Flower Number through FLOWERING LOCUS T Gene Expression in Arabidopsis thaliana

Biostimulants are a new category of materials that improve crop productivity by maximizing their natural abilities. Out of these biostimulants, those that increase seed production are considered to be particularly important as they contribute directly to the increase in the yield of cereals and legumes. Ergothioneine (EGT) is a natural, non-protein amino acid with antioxidant effects that is used in pharmaceuticals, cosmetics, and foods. However, EGT has not been used in agriculture. This study investigated the effect of EGT on seed productivity in Arabidopsis thaliana. Compared with an untreated control, the application of EGT increased the seed yield by 66%. However, EGT had no effect on seed yield when applied during or after bolting and did not promote the growth of vegetative organs. On the other hand, both the number of flowers and the transcript levels of FLOWERING LOCUS T (FT), a key gene involved in flowering, were increased significantly by the application of EGT. The results suggest that EGT improves seed productivity by increasing flower number through the physiological effects of the FT protein. Furthermore, the beneficial effect of EGT on flower number is expected to make it a potentially useful biostimulant not only in crops where seeds are harvested, but also in horticultural crops such as ornamental flowering plants, fruits, vegetables.

Orthogonal genome editing and transcriptional activation in tomato using CRISPR-Combo systems

KEY MESSAGE

The CRISPR-Combo systems (Cas9-Combo and CBE-Combo) are designed for comprehensive genetic manipulation, enabling Cas9-based targeted mutagenesis or cytosine base editing with simultaneous gene activation in tomato stable lines.

Intra-canopy LED lighting outperformed top LED lighting in improving tomato yield and expression of the genes responsible for lycopene, phytoene and vitamin C synthesis

Greenhouses located at high latitudes and in cloudy areas often experience a low quality and quantity of light, especially during autumn and winter. This low daily light integral (DLI) reduces production rate, quality, and nutritional value of many crops. This study was conducted on Sakhiya RZ F1 tomato plants to evaluate the impact of LED lights on the growth and nutritional value of tomatoes in a greenhouse with low daily light due to cloudy weather. The treatments included LED growth lights in three modes: top lighting, intra-canopy lighting, and combined top and intra-canopy lighting. The results showed that although the combined top and intra-canopy lighting reached the maximum increase in tomato yield, exposure to intra-canopy LED lighting alone outperformed in tomato fruit yield increase (28.46%) than exposure to top LED lighting alone (12.12%) when compared to no supplemental lighting during the entire production year. Intra-canopy exposure demonstrated the highest increase in tomato lycopene (31.3%), while top and intra-canopy lighting exhibited the highest increase in vitamin C content (123.4%) compared to the control. The LED light treatment also had a very positive effect on the expression of genes responsible for metabolic cycles, including Psy1, LCY-β, and VTC2 genes, which had collinearity with the increase in tomato fruit production.

Refining flowering date enhances sesame yield independently of day-length

BACKGROUND

The transition from vegetative to reproductive growth is a key factor in yield maximization. Sesame (Sesamum indicum), an indeterminate short-day oilseed crop, is rapidly being introduced into new cultivation areas. Thus, decoding its flowering mechanism is necessary to facilitate adaptation to environmental conditions. In the current study, we uncover the effect of day-length on flowering and yield components using F2 populations segregating for previously identified quantitative trait loci (Si_DTF QTL) confirming these traits.

RESULTS

Generally, day-length affected all phenotypic traits, with short-day preceding days to flowering and reducing yield components. Interestingly, the average days to flowering required for yield maximization was 50 to 55 days, regardless of day-length. In addition, we found that Si_DTF QTL is more associated with seed-yield and yield components than with days to flowering. A bulk-segregation analysis was applied to identify additional QTL differing in allele frequencies between early and late flowering under both day-length conditions. Candidate genes mining within the identified major QTL intervals revealed two flowering-related genes with different expression levels between the parental lines, indicating their contribution to sesame flowering regulation.

CONCLUSIONS

Our findings demonstrate the essential role of flowering date on yield components and will serve as a basis for future sesame breeding.

Flowering time genes branching out

Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.

Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection

Ginseng, an important medicinal plant, is characterized by its main active component, ginsenosides. Among more than 40 ginsenosides, Rg1 is one of the ginsenosides used for measuring the quality of ginseng. Therefore, the identification and characterization of genes for Rg1 biosynthesis are important to elucidate the molecular basis of Rg1 biosynthesis. In this study, we utilized 39,327 SNPs and the corresponding Rg1 content from 344 core ginseng cultivars from Jilin Province. We conducted a genome-wide association study (GWAS) combining weighted gene co-expression network analysis (WGCNA), SNP-Rg1 content association analysis, and gene co-expression network analysis; three candidate Rg1 genes (PgRg1-1, PgRg1-2, and PgRg1-3) and one crucial candidate gene (PgRg1-3) were identified. Functional validation of PgRg1-3 was performed using methyl jasmonate (MeJA) regulation and RNAi, confirming that this gene regulates Rg1 biosynthesis. The spatial-temporal expression patterns of the PgRg1-3 gene and known key enzyme genes involved in ginsenoside biosynthesis differ. Furthermore, variations in their networks have a significant impact on Rg1 biosynthesis. This study established an accurate and efficient method for identifying candidate genes, cloned a novel gene controlling Rg1 biosynthesis, and identified 73 SNPs significantly associated with Rg1 content. This provides genetic resources and effective tools for further exploring the molecular mechanisms of Rg1 biosynthesis and molecular breeding.

Transcriptome analysis reveals the key role of overdominant expression of photosynthetic and respiration-related genes in the formation of tobacco(Nicotiana tabacum L.) biomass heterosis

BACKGROUND

Leaves are the nutritional and economic organs of tobacco, and their biomass directly affects tobacco yield and the economic benefits of farmers. In the early stage, our research found that tobacco hybrids have more leaves and larger leaf areas, but the performance and formation reasons of biomass heterosis are not yet clear.

RESULTS

This study selected 5 parents with significant differences in tobacco biomass and paired them with hybrid varieties. It was found that tobacco hybrid varieties have a common biomass heterosis, and 45 days after transplantation is the key period for the formation of tobacco biomass heterosis; By analyzing the biomass heterosis of hybrids, Va116×GDH94 and its parents were selected for transcriptome analysis. 76.69% of the differentially expressed genes between Va116×GDH94 and its parents showed overdominant expression pattern, and these overdominant expression genes were significantly enriched in the biological processes of photosynthesis and TCA cycle; During the process of photosynthesis, the overdominant up-regulation of genes such as Lhc, Psa, and rbcl promotes the progress of photosynthesis, thereby increasing the accumulation of tobacco biomass; During the respiratory process, genes such as MDH, ACO, and OGDH are overedominantly down-regulated, inhibiting the TCA cycle and reducing substrate consumption in hybrid offspring; The photosynthetic characteristics of the hybrid and its parents were measured, and the net photosynthetic capacity of the hybrid was significantly higher than that of the parents.

CONCLUSION

These results indicate that the overdominant expression effect of differentially expressed genes in Va116×GDH94 and its parents plays a crucial role in the formation of tobacco biomass heterosis. The overdominant expression of genes related to photosynthesis and respiration enhances the photosynthetic ability of Va116×GDH94, reduces respiratory consumption, promotes the increase of biomass, and exhibits obvious heterosis.

A higher-yield hybrid rice is achieved by assimilating a dominant heterotic gene in inbred parental lines

The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR-Cas9, which accounted for approximately 34.1%-47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene-edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two-line hybrid rice Guang-liang-you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene-modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three-line hybrid rice Quan-you-si-miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR-Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield-related heterosis and provided a promising strategy for breeding higher-yielding rice varieties above what is currently achievable.

ETHYLENE RESPONSE FACTOR 070 inhibits flowering in Pak-choi by indirectly impairing BcLEAFY expression

APETALA2/ethylene responsive factors respond to ethylene and participate in many biological and physiological processes, such as plant morphogenesis, stress resistance, and hormone signal transduction. Ethylene responsive factor 070 (BcERF070) is important in flowering. However, the underlying molecular mechanisms of BcERF070 in floral transition in response to ethylene signaling have not been fully characterized. Herein, we explored the function of BcERF070 in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Ethylene treatment induced BcERF070 expression and delayed flowering in Pak-choi. Silencing of BcERF070 induced flowering in Pak-choi. BcERF070 interacted with major latex protein-like 328 (BcMLP328), which forms a complex with helix-loop-helix protein 30 (BcbHLH30) to enhance the transcriptional activity of BcbHLH30 on LEAFY (BcLFY), ultimately promoting flowering. However, BcERF070 impaired the BcMLP328-BcbHLH30 complex activation of LEAFY (BcLFY), ultimately inhibiting flowering in Pak-choi. BcERF070 directly promoted the expression of the flowering inhibitor gene B-box 29 (BcBBX29) and delayed flowering by reducing FLOWERING LOCUS T (BcFT) expression. These results suggest that BcERF070 mediates ethylene-reduced flowering by impairing the BcMLP328-BcbHLH30 complex activation of BcLFY and by directly promoting the gene expression of the flowering inhibition factor BcBBX29 to repress BcFT expression. The findings contribute to understanding the molecular mechanisms underlying floral transition in response to ethylene in plants.

Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.

Strigolactones promote flowering by inducing the miR319-LA-SFT module in tomato

Strigolactones are a class of phytohormones with various functions in plant development, stress responses, and in the interaction with (micro)organisms in the rhizosphere. While their effects on vegetative development are well studied, little is known about their role in reproduction. We investigated the effects of genetic and chemical modification of strigolactone levels on the timing and intensity of flowering in tomato (Solanum lycopersicum L.) and the molecular mechanisms underlying such effects. Results showed that strigolactone levels in the shoot, whether endogenous or exogenous, correlate inversely with the time of anthesis and directly with the number of flowers and the transcript levels of the florigen-encoding gene SINGLE FLOWER TRUSS (SFT) in the leaves. Transcript quantifications coupled with metabolite analyses demonstrated that strigolactones promote flowering in tomato by inducing the activation of the microRNA319-LANCEOLATE module in leaves. This, in turn, decreases gibberellin content and increases the transcription of SFT. Several other floral markers and morpho-anatomical features of developmental progression are induced in the apical meristems upon treatment with strigolactones, affecting floral transition and, more markedly, flower development. Thus, strigolactones promote meristem maturation and flower development via the induction of SFT both before and after floral transition, and their effects are blocked in plants expressing a miR319-resistant version of LANCEOLATE. Our study positions strigolactones in the context of the flowering regulation network in a model crop species.

Nuclear factor Y-A3b binds to the SINGLE FLOWER TRUSS promoter and regulates flowering time in tomato

The control of flowering time is essential for reproductive success and has a major effect on seed and fruit yield and other important agricultural traits in crops. Nuclear factors Y (NF-Ys) are transcription factors that form heterotrimeric protein complexes to regulate gene expression required for diverse biological processes, including flowering time control in plants. However, to our knowledge, there has been no report on mutants of individual NF-YA subunits that promote early flowering phenotype in plants. In this study, we identified SlNF-YA3b, encoding a member of the NF-Y transcription factor family, as a key gene regulating flowering time in tomato. Knockout of NF-YA3b resulted in an early flowering phenotype in tomato, whereas overexpression of NF-YA3b delayed flowering in transgenic tomato plants. NF-YA3b was demonstrated to form heterotrimeric protein complexes with multiple NF-YB/NF-YC heterodimers in yeast three-hybrid assays. Biochemical evidence indicated that NF-YA3b directly binds to the CCAAT cis-elements of the SINGLE FLOWER TRUSS (SFT) promoter to suppress its gene expression. These findings uncovered a critical role of NF-YA3b in regulating flowering time in tomato and could be applied to the management of flowering time in crops.

Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.

A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials

BACKGROUND

Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation.

RESULTS

Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks.

CONCLUSIONS

Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.

The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

Hybrid rice (Oryza sativa) generally outperforms its inbred parents in yield and stress tolerance, a phenomenon termed heterosis, but the underlying mechanism is not completely understood. Here, we combined transcriptome, proteome, physiological, and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000 (CY1000). In addition to surpassing the mean values for its two parents (mid-parent heterosis), CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents (over-parent heterosis or heterobeltiosis). Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance, acting in an overdominant fashion in CY1000. Furthermore, we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30. The salt-sensitive phenotypes were associated with the OsWRKY72paternal genotype or the OsAAT30maternal genotype in core rice germplasm varieties. OsWRKY72paternal specifically repressed the expression of OsGSTU26 under salt stress, leading to salinity sensitivity, while OsWRKY72maternal specifically repressed OsAAT30, resulting in salinity tolerance. These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice, providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length changes. Seed weight is one of the key traits determining the soybean yield; however, the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly understood. In this study, we identify SW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1, an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit, as the causal gene of the SW19 locus. We showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in soybean. Further analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo, thus modulating seed weight under long days. However, Dt1 does not function in seed development under short days due to its very low expression. Importantly, we discovered a novel natural allelic variant of Dt1 (H4 haplotype) that decouples its pleiotropic effects on seed size and growth habit; i.e., this variant remains functional in seed development but fails to regulate the stem growth habit of soybean. Collectively, our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes, offering an ideal genetic component for improving soybean's yield by manipulating its seed weight and growth habit.

EARLY FLOWERING is a dominant gain-of-function allele of FANTASTIC FOUR 1/2c that promotes early flowering in tomato

Flowering time, an important factor in plant adaptability and genetic improvement, is regulated by various genes in tomato (Solanum lycopersicum). In this study, we characterized a tomato mutant, EARLY FLOWERING (EF), that developed flowers much earlier than its parental control. EF is a dominant gain-of-function allele with a T-DNA inserted 139 bp downstream of the stop codon of FANTASTIC FOUR 1/2c (FAF1/2c). The transcript of SlFAF1/2c was at elevated levels in the EF mutant. Overexpressing SlFAF1/2c in tomato plants phenocopied the early flowering trait of the EF mutant. Knocking out SlFAF1/2c in the EF mutant reverted the early flowering phenotype of the mutant to the normal flowering time of the wild-type tomato plants. SlFAF1/2c promoted the floral transition by shortening the vegetative phase rather than by reducing the number of leaves produced before the emergence of the first inflorescence. The COP9 signalosome subunit 5B (CSN5B) was shown to interact with FAF1/2c, and knocking out CSN5B led to an early flowering phenotype in tomato. Interestingly, FAF1/2c was found to reduce the accumulation of the CSN5B protein by reducing its protein stability. These findings imply that FAF1/2c regulates flowering time in tomato by reducing the accumulation and stability of CSN5B, which influences the expression of SINGLE FLOWER TRUSS (SFT), JOINTLESS (J) and UNIFLORA (UF). Thus, a new allele of SlFAF1/2c was discovered and found to regulate flowering time in tomato.

Precise fine-turning of GhTFL1 by base editing tools defines ideal cotton plant architecture

BACKGROUND

CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and crop genetic improvement. However, the editing efficiency of base editors at different targets varies greatly.

RESULTS

Here, we develop a set of highly efficient base editors in cotton plants. GhABE8e, which is fused to conventional nCas9, exhibits 99.9% editing efficiency, compared to GhABE7.10 with 64.9%, and no off-target editing is detected. We further replace nCas9 with dCpf1, which recognizes TTTV PAM sequences, to broaden the range of the target site. To explore the functional divergence of TERMINAL FLOWER 1 (TFL1), we edit the non-coding and coding regions of GhTFL1 with 26 targets to generate a comprehensive allelic population including 300 independent lines in cotton. This allows hidden pleiotropic roles for GhTFL1 to be revealed and allows us to rapidly achieve directed domestication of cotton and create ideotype germplasm with moderate height, shortened fruiting branches, compact plant, and early-flowering. Further, by exploring the molecular mechanism of the GhTFL1L86P and GhTFL1K53G+S78G mutations, we find that the GhTFL1L86P mutation weakens the binding strength of the GhTFL1 to other proteins but does not lead to a complete loss of GhTFL1 function.

CONCLUSIONS

This strategy provides an important technical platform and genetic information for the study and creation of ideal plant architecture.

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.

Heterosis in crop improvement

Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F1 hybrids over both inbred parents. The development of high-yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self-pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis-associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis-associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (Hordeum vulgare) as the model self-pollinating crop species, and a few heterosis-associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.

The genetic and molecular basis of haploinsufficiency in flowering plants

In diploid organisms, haploinsufficiency can be defined as the requirement for more than one fully functional copy of a gene. In contrast to most genes, whose loss-of-function alleles are recessive, loss-of-function alleles of haploinsufficient genes are dominant. However, forward and reverse genetic screens are biased toward obtaining recessive, loss-of-function mutations, and therefore, dominant mutations of all types are underrepresented in mutant collections. Despite this underrepresentation, haploinsufficient loci have intriguing implications for studies of genome evolution, gene dosage, stability of protein complexes, genetic redundancy, and gene expression. Here we review examples of haploinsufficiency in flowering plants and describe the underlying molecular mechanisms and evolutionary forces driving haploinsufficiency. Finally, we discuss the masking of haploinsufficiency by genetic redundancy, a widespread phenomenon among angiosperms.

Virus-induced overexpression of heterologous FLOWERING LOCUS T for efficient speed breeding in tomato

Potato virus X (PVX) vectors expressing the Arabidopsis thaliana FLOWERING LOCUS T (FT) or tomato FT ortholog SINGLE-FLOWER TRUSS (SFT) shortened the generation time in tomato due to accelerated tomato flowering and ripening by 14-21 d, and caused a 2-3-fold increase in the number of flowers and fruits, compared with non-infected or empty vector-infected plants. The Arabidopsis FT was more effective than the tomato orthologue SFT and there was no alteration of the flower or fruit morphology. The virus was not transmitted to the next generation; therefore viral vectors with expression of a heterologous FT will be a useful approach to speed breeding in tomato and other species.

Engineering homoeologs provide a fine scale for quantitative traits in polyploid

Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.

Mainstreaming production and nutrient resilience of vegetable crops in megacities: pre-breeding for terrace cultivation

Modern megacities offer convenient lifestyles to their citizens. However, agriculture is becoming increasingly vulnerable, especially during unexpected public health emergencies such as pandemics. Fortunately, the adaptability of terrace vegetables cultivation presents an opportunity to grow horticultural crops in residential spaces, bringing numerous benefits to citizens, including enhanced nutrition and recreational engagement in the cultivation process. Although certain planting skills and equipment have been developed, the citizens tend to sow some seeds with unknown pedigree, it is rare to find new plant varieties specifically bred for cultivation as terrace vegetables. To expand the genetic basis of new breeding materials, elite parents, and varieties (pre-breeding) for terrace cultivation, this review not only discusses the molecular breeding strategy for the identification, creation, and application of rational alleles for improving horticultural characteristics including plant architecture, flavor quality, and ornamental character, but also assesses the potential for terrace cultivation of some representative vegetable crops. We conclude that the process of pre-breeding specifically for terrace cultivation environments is vital for generating a genetic basis for urban terrace vegetable crops.

Multi-year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity

Tomato (Solanum lycopersicum) is a prominent fruit with rich genetic resources for crop improvement. By using a phenotype-guided screen of over 7900 tomato accessions from around the world, we identified new associations for complex traits such as fruit weight and total soluble solids (Brix). Here, we present the phenotypic data from several years of trials. To illustrate the power of this dataset we use two case studies. First, evaluation of color revealed allelic variation in phytoene synthase 1 that resulted in differently colored or even bicolored fruit. Secondly, in view of the negative relationship between fruit weight and Brix, we pre-selected a subset of the collection that includes high and low Brix values in each category of fruit size. Genome-wide association analysis allowed us to detect novel loci associated with total soluble solid content and fruit weight. In addition, we developed eight F2 biparental intraspecific populations. Furthermore, by taking a phenotype-guided approach we were able to isolate individuals with high Brix values that were not compromised in terms of yield. In addition, the demonstration of novel results despite the high number of previous genome-wide association studies of these traits in tomato suggests that adoption of a phenotype-guided pre-selection of germplasm may represent a useful strategy for finding target genes for breeding.

Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis

Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica-indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica-japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing

BACKGROUND

Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association studies (GWAS) assume alleles act additively.

RESULTS

We systematically investigate both dominance-here representing any non-additive within-locus interaction-and additivity across 574 physiological and gene expression traits in three mammalian stocks: F2 intercross pigs, rat heterogeneous stock, and mice heterogeneous stock. Dominance accounts for about one quarter of heritable variance across all physiological traits in all species. Hematological and immunological traits exhibit the highest dominance variance, possibly reflecting balancing selection in response to pathogens. Although most quantitative trait loci (QTLs) are detectable as additive QTLs, we identify 154, 64, and 62 novel dominance QTLs in pigs, rats, and mice respectively that are undetectable as additive QTLs. Similarly, even though most cis-acting expression QTLs are additive, gene expression exhibits a large fraction of dominance variance, and trans-acting eQTLs are enriched for dominance. Genes causal for dominance physiological QTLs are less likely to be physically linked to their QTLs but instead act via trans-acting dominance eQTLs. In addition, thousands of eQTLs are associated with alternatively spliced isoforms with complex additive and dominant architectures in heterogeneous stock rats, suggesting a possible mechanism for dominance.

CONCLUSIONS

Although heritability is predominantly additive, many mammalian genetic effects are dominant and likely arise through distinct mechanisms. It is therefore advantageous to consider both additive and dominance effects in GWAS to improve power and uncover causality.

Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids

BACKGROUND

Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we turn to hybrids, which provide a facile means for creating many novel allele combinations.

RESULTS

We focus on the interaction between alleles of the same locus, i.e., dominance, and perform a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive, dominant gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below the parental average. Unlike in the additive genes, regulatory rare-allele burden in the dominant gene set is strongly correlated with F1 rosette size, even though it only mildly covaries with the expression level of these genes.

CONCLUSIONS

Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.

Plant biochemical genetics in the multiomics era

Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.

Marker assisted early generation identification of root knot disease resistant orange tomato segregants with multiple desirable alleles

Enhanced bioavailability of cis-isomers of lycopene, accumulated in orange-fruited tangerine mutant has broadened the scope of nutritional enrichment in tomato. At the same time, advancements in the field of marker assisted selection (MAS) have made the stacking of multiple desirable alleles through molecular breeding to develop superior tomato genotypes possible. Here we report seedling stage MAS from 146 F2 plants, to identify 3 superior performing, root knot disease resistant orange-fruited segregants. In the selected segregants, fruit weight ranged from 39.2 to 54.6 g, pericarp thickness ranged from 4.56 to 6.05 mm and total soluble solid content ranged from 3.65 to 4.87° Brix. Presence of parental diversity allowed identification of the other desirable alleles of the genes governing late blight and mosaic disease resistance, growth habit (determinate and indeterminate) as well as fruit elongation and firmness. Resistance to root knot disease of the selected 3 segregants was also validated through a unique method employing in vitro rooted stem cuttings subjected to artificial inoculation, where the resistant parent and the selected segregants developed no galls in comparison to ~ 24 galls developed in the susceptible parent. The selected segregants form the base for development of multiple disease resistant, nutritionally enriched orange-fruited determinate/indeterminate tomato lines with superior fruit quality. The study also highlights the utility of early generation MAS for detailed characterization of segregants, through which multiple desirable alleles can be precisely targeted and fixed to develop superior tomato genotypes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01361-1.

Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

The long and intricate domestication history of the tomato (Solanum lycopersicum) includes selection sweeps that have not been fully explored, and these sweeps show significant evolutionary trajectories of domestication traits. Using three distinct selection strategies, we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium (PIM) and 166 S. lycopersicum (BIG) accessions, which are defined as pseudo-domestication in this study. We identified 390 potential selection sweeps, some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process. During tomato pseudo-domestication, we discovered a minor-effect allele of the SlLEA gene related to fruit weight (FW), as well as the major haplotypes of fw2.2/cell number regulator (CNR), fw3.2/SlKLUH, and fw11.3/cell size regulator (CSR) in cultivars. Furthermore, 18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated BRI1-EMS-SUPPRESSOR 1.2 (SlBES1.2), a gene that may affect flavonoid content by modulating the MYB12 expression profile. Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.

Molecular dissection of heterosis in cereal roots and their rhizosphere

Heterosis is already manifested early in root development. Consistent with the dominance model of heterosis, gene expression complementation is a general mechanism that contributes to phenotypic heterosis in maize hybrids. Highly heterozygous F1-hybrids outperform their parental inbred lines, a phenomenon known as heterosis. Utilization of heterosis is of paramount agricultural importance and has been widely applied to increase yield in many crop cultivars. Plant roots display heterosis for many traits and are an important target for further crop improvement. To explain the molecular basis of heterosis, several genetic hypotheses have been proposed. In recent years, high-throughput gene expression profiling techniques have been applied to investigate hybrid vigor. Consistent with the classical genetic dominance model, gene expression complementation has been demonstrated to be a general mechanism to contribute to phenotypic heterosis in diverse maize hybrids. Functional classification of these genes supported the notion that gene expression complementation can dynamically promote hybrid vigor under fluctuating environmental conditions. Hybrids tend to respond differently to available nutrients in the soil. It was hypothesized that hybrid vigor is promoted through a higher nutrient use efficiency which is linked to an improved root system performance of hybrids in comparison to their inbred parents. Recently, the interaction between soil microbes and their plant host was added as further dimension to disentangle heterosis in the belowground part of plants. Soil microbes influenced the performance of maize hybrids as illustrated in comparisons of sterile soil and soil inhabited by beneficial microorganisms.

Integrated approaches for increasing plant yield under salt stress

Salt stress affects large cultivated areas worldwide, thus causing remarkable reductions in plant growth and yield. To reduce the negative effects of salt stress on plant growth and yield, plant hormones, nutrient absorption, and utilization, as well as developing salt-tolerant varieties and enhancing their morpho-physiological activities, are some integrative approaches to coping with the increasing incidence of salt stress. Numerous studies have been conducted to investigate the critical impacts of these integrative approaches on plant growth and yield. However, a comprehensive review of these integrative approaches, that regulate plant growth and yield under salt stress, is still in its early stages. The review focused on the major issues of nutrient absorption and utilization by plants, as well as the development of salt tolerance varieties under salt stress. In addition, we explained the effects of these integrative approaches on the crop's growth and yield, illustrated the roles that phytohormones play in improving morpho-physiological activities, and identified some relevant genes involve in these integrative approaches when the plant is subjected to salt stress. The current review demonstrated that HA with K enhance plant morpho-physiological activities and soil properties. In addition, NRT and NPF genes family enhance nutrients uptake, NHX1, SOS1, TaNHX, AtNHX1, KDML, RD6, and SKC1, maintain ion homeostasis and membrane integrity to cope with the adverse effects of salt stress, and sd1/Rht1, AtNHX1, BnaMAX1s, ipal-1D, and sft improve the plant growth and yield in different plants. The primary purpose of this investigation is to provide a comprehensive review of the performance of various strategies under salt stress, which might assist in further interpreting the mechanisms that plants use to regulate plant growth and yield under salt stress.

Genome-Wide Identification of PEBP Gene Family in Solanum lycopersicum

The PEBP gene family is crucial for the growth and development of plants, the transition between vegetative and reproductive growth, the response to light, the production of florigen, and the reaction to several abiotic stressors. The PEBP gene family has been found in numerous species, but the SLPEBP gene family has not yet received a thorough bioinformatics investigation, and the members of this gene family are currently unknown. In this study, bioinformatics was used to identify 12 members of the SLPEBP gene family in tomato and localize them on the chromosomes. The physicochemical characteristics of the proteins encoded by members of the SLPEBP gene family were also examined, along with their intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements. In parallel, a phylogenetic tree was built and the collinear relationships of the PEBP gene family among tomato, potato, pepper, and Arabidopsis were examined. The expression of 12 genes in different tissues and organs of tomato was analyzed using transcriptomic data. It was also hypothesized that SLPEBP3, SLPEBP5, SLPEBP6, SLPEBP8, SLPEBP9, and SLPEBP10 might be related to tomato flowering and that SLPEBP2, SLPEBP3, SLPEBP7, and SLPEBP11 might be related to ovary development based on the tissue-specific expression analysis of SLPEBP gene family members at five different stages during flower bud formation to fruit set. This article's goal is to offer suggestions and research directions for further study of tomato PEBP gene family members.