Genome-wide transcriptome analysis reveals the molecular mechanism of high temperature-induced floral abortion in Litchi chinensis

The SOC1 gene plays an important role in regulating litchi flowering time

Litchi (Litchi chinensis Sonn.) is a valuable subtropical fruit tree with high-quality fruit. However, its economic benefits and sustainable development are restrained by a number of challenges. One major challenge is the lack of extremely early and late maturing high-quality varieties due to limited availability of varieties suitable for commercial cultivation and outdated breeding methods, resulting in an imbalanced supply and low price of litchi. Flowering time is a crucial genetic factor influencing the maturation period of litchi. Our previous research has highlighted the pivotal role of the LcFT1 gene in regulating the flowering time of litchi and identified a gene associated with LcFT1 (named as LcSOC1) based on RNA-Seq and weight gene co-expression network (WGCNA) analysis. This study further investigated the function of LcSOC1. Subcellular localization analysis revealed that LcSOC1 is primarily localized in the nucleus, where it acts as a transcription factor. LcSOC1 overexpression in Nicotiana tabacum and Arabidopsis thaliana resulted in significant early flowering. Furthermore, LcSOC1 was found to be expressed in various tissues, with the highest expression in mature leaves. Analysis of spatial and temporal expression patterns of LcSOC1 in litchi varieties with different flowering time under low temperature treatment and across an annual cycle demonstrated that LcSOC1 is responsive to low temperature induction. Interestingly, early maturing varieties exhibited higher sensitivity to low temperature, with significantly premature induction of LcSOC1 expression relative to late maturing varieties. Activation of LcSOC1 triggered the transition of litchi into the flowering phase. These findings demonstrate that LcSOC1 plays a pivotal role in regulating the flowering process and determining the flowering time in litchi. Overall, this study provides theoretical guidance and important target genes for molecular breeding to regulate litchi production period.

Comparative transcriptome and metabolome profiles of the leaf and fruits of a Xianjinfeng litchi budding mutant and its mother plant

Background: Litchi (Litchi chinensis) is an important sub-tropical fruit in the horticulture market in China. Breeding for improved fruit characteristics is needed for satisfying consumer demands. Budding is a sustainable method for its propagation. During our ongoing breeding program, we observed a litchi mutant with flat leaves and sharp fruit peel cracking in comparison to the curled leaves and blunt fruit peel cracking fruits of the mother plant. Methods: To understand the possible molecular pathways involved, we performed a combined metabolome and transcriptome analysis. Results: We identified 1,060 metabolites in litchi leaves and fruits, of which 106 and 101 were differentially accumulated between the leaves and fruits, respectively. The mutant leaves were richer in carbohydrates, nucleotides, and phenolic acids, while the mother plant was rich in most of the amino acids and derivatives, flavonoids, lipids and organic acids and derivatives, and vitamins. Contrastingly, mutant fruits had higher levels of amino acids and derivatives, carbohydrates and derivatives, and organic acids and derivatives. However, the mother plant's fruits contained higher levels of flavonoids, scopoletin, amines, some amino acids and derivatives, benzamidine, carbohydrates and derivatives, and some organic acids and derivatives. The number of differentially expressed genes was consistent with the metabolome profiles. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enriched gene expressions showed consistent profiles as of metabolome analysis. Conclusion: These results provide the groundwork for breeding litchi for fruit and leaf traits that are useful for its taste and yield.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.

Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size

Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.

Identification of Chilling-Responsive Genes in Litchi chinensis by Transcriptomic Analysis Underlying Phytohormones and Antioxidant Systems

Litchi (Litchi chinensis Sonn.) is an important subtropical and tropical evergreen fruit tree that is seriously affected by chilling stress. In order to identify genes that may be involved in the response to chilling in litchi, we investigate the physiological and biochemical changes under chilling stress and construct 12 RNA-Seq libraries of leaf samples at 0, 4, 8, and 12 days of chilling. The results show that antioxidant enzymes are activated by chilling treatments. Comparing the transcriptome data of the four time points, we screen 2496 chilling-responsive genes (CRGs), from which we identify 63 genes related to the antioxidant system (AO-CRGs) and 54 ABA, 40 IAA, 37 CTK, 27 ETH, 21 BR, 13 GA, 35 JA, 29 SA, and 4 SL signal transduction-related genes. Expression pattern analysis shows that the expression trends of the 28 candidate genes detected by qRT-PCR are similar to those detected by RNA-Seq, indicating the reliability of our RNA-Seq data. Partial Least Squares Structural Equation Modeling (PLS-SEM) analysis of the RNA-Seq data suggests a model for the litchi plants in response to chilling stress that alters the expression of the plant hormone signaling-related genes, the transcription factor-encoding genes LcICE1, LcCBFs, and LcbZIPs, and the antioxidant system-related genes. This study provides candidate genes for the future breeding of litchi cultivars with high chilling resistance, and elucidates possible pathways for litchi in response to chilling using transcriptomic data.

LcNAC13 Is Involved in the Reactive Oxygen Species-Dependent Senescence of the Rudimentary Leaves in Litchi chinensis

Litchi is an important evergreen fruit tree. Floral formation in litchi is induced by low temperatures (LTs). However, unstable flowering is a challenge for litchi production in times of global warming and climate change. Previous studies have shown that the methyl viologen dichloride hydrate-generated reactive oxygen species (ROS) could promote flowering. Leaves in the panicles may affect the development of the inflorescence in litchi under high-temperature condition. In this study, potted litchi trees were transferred to growth chambers at LT and high temperature (HT). From a previous dataset of the RNA sequencing of the ROS-treated rudimentary leaves, a NAC transcription factor-encoding gene LcNAC13 was identified. By genetic transformation of LcNAC13 to Arabidopsis thaliana and tobacco, it was found that the ROS-induced senescence of the leaves was accelerated. Silencing LcNAC13 by virus-induced gene silencing (VIGS) delayed ROS-dependent senescence. Our results suggested that LcNAC13 regulates rudimentary leaf senescence. Our study provided a new target gene for the future molecular breeding of new cultivars that could flower under global warming conditions.

Comparative physiological and transcriptomic analysis of sesame cultivars with different tolerance responses to heat stress

High temperature is the main factor affecting plant growth and can cause plant growth inhibition and yield reduction. Here, seedlings of two contrasting sesame varieties, i.e., Zheng Taizhi 3 (heat-tolerant) and SP19 (heat-sensitive), were treated at 43 °C for 10 days. The results showed that the relative electrical conductivity, hydrogen peroxide levels, and superoxide anion radical levels of both varieties increased significantly under high temperature stress. Additionally, dry matter accumulation and chlorophyll content decreased significantly, and the activities of peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) increased. However, under HT stress, the content of reactive oxygen species in Zheng Taizhi 3 was lower than that in SP19, and the activities of SOD, CAT, and POD as well as the chlorophyll content in Zheng Taizhi 3 were higher than those in SP19. Comparative transcriptome analysis identified 6736 differentially expressed genes (DEGs); 5526 DEGs (2878 up and 2648 down) were identified in Zheng Taizhi 3, and 5186 DEGs (2695 up and 2491 down) were identified in SP19, with 3976 overlapping DEGs. These DEGs included stress tolerance-related heat-shock proteins, as well as genes related to carbohydrate and energy metabolism, signal transduction, endoplasmic reticulum protein processing, amino acid metabolism, and secondary metabolism. Overall, our results showed that the heat tolerance of Zheng Taizhi 3 was attributed to a stronger antioxidant defense system, enabling the variety to avoid oxidative damage compared with the heat-sensitive SP19. Moreover, some specifically expressed and high-abundance genes in Zheng Taizhi 3 were involved in regulatory mechanisms related to heat tolerance, including plant hormone signal transduction and heat shock protein regulation, thereby enhancing heat tolerance. The study contributes to a deeper understanding of the underlying complex molecular mechanisms involved in the responses of sesame seedlings to heat stress and provides a potential strategy for heat-resistant new varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01195-3.

The Halophyte Species Solanum chilense Dun. Maintains Its Reproduction despite Sodium Accumulation in Its Floral Organs

Salinity is a growing global concern that affects the yield of crop species, including tomato (Solanum lycopersicum). Its wild relative Solanum chilense was reported to have halophyte properties. We compared salt resistance of both species during the reproductive phase, with a special focus on sodium localization in the flowers. Plants were exposed to NaCl from the seedling stage. Salinity decreased the number of inflorescences in both species but the number of flowers per inflorescence and sepal length only in S. lycopersicum. External salt supply decreased the stamen length in S. chilense, and it was associated with a decrease in pollen production and an increase in pollen viability. Although the fruit set was not affected by salinity, fruit weight and size decreased in S. lycopersicum. Concentrations and localization of Na, K, Mg, and Ca differed in reproductive structures of both species. Inflorescences and fruits of S. chilense accumulated more Na than S. lycopersicum. Sodium was mainly located in male floral organs of S. chilense but in non-reproductive floral organs in S. lycopersicum. The expression of Na transporter genes differed in flowers of both species. Overall, our results indicated that S. chilense was more salt-resistant than S. lycopersicum during the reproductive phase and that differences could be partly related to dissimilarities in element distribution and transport in flowers.

Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIP-Seq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars 'Daqiandi' (DQD) and 'Longyan' (LY), which showed that the majority of DNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.