Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

Characterization of tomato autophagy-related SlCOST family genes

Autophagy is a eukaryote-specific cellular process that can engulf unwanted targets with double-membrane autophagosomes and subject them to the vacuole or lysosome for breaking down and recycling, playing dual roles in plant growth and environmental adaptions. However, perception of specific environmental signals for autophagy induction is largely unknown, limiting its application in agricultural usage. Identification of plant-unique DUF641 family COST1 (Constitutively Stressed 1) protein directly links drought perception and autophagy induction, shedding light on manipulating autophagy for breeding stress tolerant crops. In this study, we performed a genome-wide analysis of DUF641/COST family in tomato, and identified five SlCOST genes SlCOST1, -2, -3, -4, and -5. SlCOST genes show both overlapping and distinct expression patterns in plant growth and stress responding. In addition, SlCOST1, -3, -4, -5 proteins demonstrate co-localization with autophagy adaptor protein ATG8e, and all five SlCOST proteins show interactions ATG8e in planta. However, only SlCOST1, the closest ortholog of Arabidopsis AtCOST1, can restore cost1 mutant to WT level, suggesting conserved role of COST1 and functional diversification of SlCOST family in tomato. Our study provides clues for future investigation of autophagy-related COST family and its promising implementations in breeding crops with robust environmental plasticity.

A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.)

Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.

Data-driven approaches to improve water-use efficiency and drought resistance in crop plants

With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.

Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis

The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.

Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress

Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid, and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene coexpression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development.

Gene expression variation explains maize seed germination heterosis

BACKGROUND

Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis.

RESULTS

In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

BACKGROUND

Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break.

RESULTS

Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions.

CONCLUSION

In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.

Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing

Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.

Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels

Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.

Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit

The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.

Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population

Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay-Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.

Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato

Water deficit (WD) leads to significant phenotypic changes in crops resulting from complex stress regulation mechanisms involving responses at the physiological, biochemical and molecular levels. Tomato growth and fruit quality have been shown to be significantly affected by WD stress. Understanding the molecular mechanism underlying response to WD is crucial to develop tomato cultivars with relatively high performance under low watering conditions. Transcriptome response to WD was investigated through the RNA sequencing of fruit and leaves in eight accessions grown under two irrigation conditions, in order to get insight into the complex genetic regulation of WD response in tomato. Significant differences in genotype WD response were first observed at the phenotypic level for fruit composition and plant development traits. At the transcriptome level, a total of 14,065 differentially expressed genes (DEGs) in response to WD were detected, among which 7393 (53%) and 11,059 (79%) were genotype- and organ-specific, respectively. Water deficit induced transcriptome variations much stronger in leaves than in fruit. A significant effect of the genetic background on expression variation was observed compared to the WD effect, along with the presence of a set of genes showing a significant genotype × watering regime interaction. Integrating the DEGs with previously identified WD response quantitative trait loci (QTLs) mapped in a multi-parental population derived from the crossing of the eight genotypes narrowed the candidate gene lists to within the confidence intervals surrounding the QTLs. The results present valuable resources for further study to decipher the genetic determinants of tomato response to WD.

The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions

Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in barley. We used RNA sequencing to examine allele-specific expression in hybrids between wild and domesticated barley. Our results show that most genes have conserved regulation. In contrast to studies of allele-specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

Phylogenetic Origin of Primary and Secondary Metabolic Pathway Genes Revealed by C. maxima and C. reticulata Diagnostic SNPs

Modern cultivated Citrus species and varieties result from interspecific hybridization between four ancestral taxa. Among them, Citrus maxima and Citrus reticulata, closely associated with the pummelo and mandarin horticultural groups, respectively, were particularly important as the progenitors of sour and sweet oranges (Citrus aurantium and Citrus sinensis), grapefruits (Citrus paradisi), and hybrid types resulting from modern breeding programs (tangors, tangelos, and orangelos). The differentiation between the four ancestral taxa and the phylogenomic structure of modern varieties widely drive the phenotypic diversity's organization. In particular, strong phenotypic differences exist in the coloration and sweetness and represent important criteria for breeders. In this context, focusing on the genes of the sugar, carotenoid, and chlorophyll biosynthesis pathways, the aim of this work was to develop a set of diagnostic single-nucleotide polymorphism (SNP) markers to distinguish the ancestral haplotypes of C. maxima and C. reticulata and to provide information at the intraspecific diversity level (within C. reticulata or C. maxima). In silico analysis allowed the identification of 3,347 SNPs from selected genes. Among them, 1,024 were detected as potential differentiation markers between C. reticulata and C. maxima. A total of 115 SNPs were successfully developed using a competitive PCR technology. Their transferability among all Citrus species and the true citrus genera was very good, with only 0.87% of missing data. The ancestral alleles of the SNPs were identified, and we validated the usefulness of the developed markers for tracing the ancestral haplotype in large germplasm collections and sexually recombined progeny issued from the C. reticulata/C. maxima admixture gene pool. These markers will pave the way for targeted association studies based on ancestral haplotypes.

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets

Statistical and machine learning (ML)-based methods have recently advanced in construction of gene regulatory network (GRNs) based on high-throughput biological datasets. GRNs underlie almost all cellular phenomena; hence, comprehensive GRN maps are essential tools to elucidate gene function, thereby facilitating the identification and prioritization of candidate genes for functional analysis. High-throughput gene expression datasets have yielded various statistical and ML-based algorithms to infer causal relationship between genes and decipher GRNs. This review summarizes the recent advancements in the computational inference of GRNs, based on large-scale transcriptome sequencing datasets of model plants and crops. We highlight strategies to select contextual genes for GRN inference, and statistical and ML-based methods for inferring GRNs based on transcriptome datasets from plants. Furthermore, we discuss the challenges and opportunities for the elucidation of GRNs based on large-scale datasets obtained from emerging transcriptomic applications, such as from population-scale, single-cell level, and life-course transcriptome analyses.