Genome-wide analysis of the XTH gene family and functional analysis of DlXTH23.5/25 during early longan somatic embryogenesis

The bZIP20 transcription factor enhances thermotolerance in Dimocarpus longan by maintaining ROS homeostasis and involving the MeJA pathway

The basic-leucine zipper (bZIP) transcription factor (TF), which is abundant and highly conserved in eukaryotes, mainly participates in plant growth, development and adverse stress processes. However, the regulatory mechanisms of bZIP TFs under heat stress in Dimocarpus longan remain unclear. In this study, we reported a nuclear-localized bZIP TF, DlbZIP20, which was confirmed to be a positive regulator of thermotolerance in D. longan. It was identified as a strong interplay with hormone signalling pathways and oxidoreductase-related families. The transient overexpression DlbZIP20 could improve the thermotolerance of D. longan embryogenic callus (EC) and reduce the damage of cells under heat stress. Overexpression of DlbZIP20 in hairy roots significantly promoted roots elongation and photosystem II (PS II) responses in leaves, and significantly increased SOD and POD activities, promoted H2O2 scavenging, improved thermotolerance of D. longan by maintaining ROS homeostasis under heat stress. In addition, overexpression of DlbZIP20 increased endogenous MeJA content under heat stress. MeJA hormone synthesis genes DlMYC2 and DlCOI1 were up-regulated and DlJAZ3 was down-regulated in expression. This signalling pathway may play a role in the regulation of thermotolerance in D. longan. These results will provide a new insight into the molecular function of bZIP20 TF in response to heat stress in D. longan.

Temperature-induced variation in the transcriptome of maritime pine (Pinus pinaster Ait.) embryogenic masses modulates the phenotype of the derived plants

A number of studies show that combining somatic embryogenesis with environmental stimuli can induce plant defenses against abiotic stresses, offering a complementary strategy in tree breeding programs. In a previous study, we found that increasing/decreasing the standard temperature of 23 ˚C by 5 ˚C during maritime pine (Pinus pinaster) somatic embryo maturation resulted in epitypes, as the derived plants showed altered phenotypes regarding leaf histology, proline content, photosynthetic rates, and hormone profiles, and that also differentially respond after a short-term heat stress. To elucidate the mechanisms underlying these altered phenotypes, we sequenced the transcriptome of embryonal-suspensor masses (EMs) from the three epitypes, identifying 812 differentially expressed genes (DEGs). Ten genes involved in epigenetic regulation were specifically up-regulated in EMs of the cold epitype. While some of these genes have been linked with somatic embryo maturation, the increased expression of three of these genes, histone deacetylases HDA9, a histone-lysine methyl-transferase (HKMT) and an Argonaute (AGO7), was found to be low temperature-induced epigenetic marks. Among the genes up-regulated in the EMs from the warm epitype, we studied those related to abiotic stress response and observed greater variation in genes involved in abscisic acid (ABA)-mediated response such as those encoding Ras GTPase-activating protein-binding (G3BP) proteins, an AAA-ATPase, and an aspartyl protease (APF2). We also found differential expression in genes encoding for RING-type E3 ubiquitin-transferases, and DNAJ and BAG chaperones. Additionally, the biosynthetic pathways of jasmonic acid, cytokinins and the diterpene pimaradiene were also altered in the warm epitype. However, the increased ABA and cytokinin content observed in the plants derived from this warm epitype cannot be fully explained by the EMs transcriptome profile. Conversely, in the cold epitype, we observed downregulation of genes encoding for an ABA receptor (PYL3), and a xyloglucan endotrans-glucosylase/hydrolase (XTH6). These findings support the hypothesis that the previously reported heat-adapted phenotype of plants derived from the cold epitype (characterized by a faster and higher proline increase, lower increases in ABA levels, no reduction in active cytokinins, and a better net photosynthesis rate recovery) could be attributed to low-temperature-induced epigenetic marks that were absent in the warm epitype.

Genome-Wide Analysis of the Xyloglucan Endotransglucosylase/Hydrolase (XTH) Gene Family: Expression Pattern during Magnesium Stress Treatment in the Mulberry Plant (Morus alba L.) Leaves

Mulberry (Morus alba L.), a significant fruit tree crop, requires magnesium (Mg) for its optimal growth and productivity. Nonetheless, our understanding of the molecular basis underlying magnesium stress tolerance in mulberry plants remains unexplored. In our previous study, we identified several differential candidate genes associated with Mg homeostasis via transcriptome analysis, including the xyloglucan endotransglucosylase/hydrolase (XTH) gene family. The XTH gene family is crucial for plant cell wall reconstruction and stress responses. These genes have been identified and thoroughly investigated in various plant species. However, there is no research pertaining to XTH genes within the M. alba plant. This research systematically examined the M. alba XTH (MaXTH) gene family at the genomic level using a bioinformatic approach. In total, 22 MaXTH genes were discovered and contained the Glyco_hydro_16 and XET_C conserved domains. The MaXTHs were categorized into five distinct groups by their phylogenetic relationships. The gene structure possesses four exons and three introns. Furthermore, the MaXTH gene promoter analysis reveals a plethora of cis-regulatory elements, mainly stress responsiveness, phytohormone responsiveness, and growth and development. GO analysis indicated that MaXTHs encode proteins that exhibit xyloglucan xyloglucosyl transferase and hydrolase activities in addition to cell wall biogenesis as well as xyloglucan and carbohydrate metabolic processes. Moreover, a synteny analysis unveiled an evolutionary relationship between the XTH genes in M. alba and those in three other species: A. thaliana, P. trichocarpa, and Zea mays. Expression profiles from RNA-Seq data displayed distinct expression patterns of XTH genes in M. alba leaf tissue during Mg treatments. Real-time quantitative PCR analysis confirmed the expression of the MaXTH genes in Mg stress response. Overall, this research enhances our understanding of the characteristics of MaXTH gene family members and lays the foundation for future functional genomic study in M. alba.

Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis

Introduction

An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security.

Methods

In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season.

Results

The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation.

Discussion

The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.

Genome-Wide Identification and Expression Analysis Reveal bZIP Transcription Factors Mediated Hormones That Functions during Early Somatic Embryogenesis in Dimocarpus longan

The basic leucine zip (bZIP) transcription factors (TFs) are a group of highly conserved gene families that play important roles in plant growth and resistance to adversity stress. However, studies on hormonal regulatory pathways and functional analysis during somatic embryogenesis (SE) in Dimocarpus longan is still unavailable. In this study, a total of 51 bZIP family members were systematically identified in the whole genome of longan, a comprehensive bioinformatics analysis of DlbZIP (bZIP family members of D. longan) was performed, and subcellular localization and profiles patterns after transiently transformed DlbZIP60 were analyzed. The combined analysis of RNA-seq, ATAC-seq and ChIP-seq showed that four members have different H3K4me1 binding peaks in early SE and differentially expressed with increased chromatin accessibility. Comparative transcriptome analysis of bZIPs expression in early SE, different tissues and under 2,4-D treatment revealed that DlbZIP family might involved in growth and development during longan early SE. The qRT-PCR results implied that DlbZIP family were subjected to multiple hormonal responses and showed different degrees of up-regulated expression under indole-3-acetic acid (IAA), abscisic acid (ABA) and methyl jasmonate (MeJA) treatments, which indicated that they played an important role in the hormone synthesis pathways associated with the early SE of longan. Subcellular localization showed that DlbZIP60 was located in the nucleus, and the contents of endogenous IAA, MeJA and ABA were up-regulated in transiently DlbZIP60 overexpressed cell lines. These results suggest that DlbZIP60 may mediate hormones pathways that functions the development during early SE in longan.