Tissue-specific Gene Expression Analysis Research Articles

Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time.

111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

Characterization of cinnamate 4-hydroxylase (CYP73A) and p-coumaroyl 3′-hydroxylase (CYP98A) from Leucojum aestivum, a source of Amaryllidaceae alkaloids

Biosynthesis of Amaryllidaceae alkaloids (AA) starts with the condensation of tyramine with 3,4-dihydroxybenzaldehyde. The latter derives from the phenylpropanoid pathway that involves modifications of trans-cinnamic acid, p-coumaric acid, caffeic acid, and possibly 4-hydroxybenzaldehyde, all potentially catalyzed by hydroxylase enzymes. Leveraging bioinformatics, molecular biology techniques, and cell biology tools, this research identifies and characterizes key enzymes from the phenylpropanoid pathway in Leucojum aestivum. Notably, we focused our work on trans-cinnamate 4-hydroxylase (LaeC4H) and p-coumaroyl shikimate/quinate 3ʹ-hydroxylase (LaeC3′H), two key cytochrome P450 enzymes, and on the ascorbate peroxidase/4-coumarate 3-hydroxylase (LaeAPX/C3H). Although LaeAPX/C3H consumed p-coumaric acid, it did not result in the production of caffeic acid. Yeasts expressing LaeC4H converted trans-cinnamate to p-coumaric acid, whereas LaeC3′H catalyzed specifically the 3-hydroxylation of p-coumaroyl shikimate, rather than of free p-coumaric acid or 4-hydroxybenzaldehyde. In vivo assays conducted in planta in this study provided further evidence for the contribution of these enzymes to the phenylpropanoid pathway. Both enzymes demonstrated typical endoplasmic reticulum membrane localization in Nicotiana benthamiana adding spatial context to their functions. Tissue-specific gene expression analysis revealed roots as hotspots for phenylpropanoid-related transcripts and bulbs as hubs for AA biosynthetic genes, aligning with the highest AAs concentration. This investigation adds valuable insights into the phenylpropanoid pathway within Amaryllidaceae, laying the foundation for the development of sustainable production platforms for AAs and other bioactive compounds with diverse applications.

Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses.

Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) genes encode a subfamily of receptor-like kinases (RLK) that regulate diverse processes during plant growth, development, and stress responses. The first CrRLK1L was identified from the Catharanthus roseus, commonly known as Madagascar periwinkle. Subsequently, CrRLK1L gene families have been characterized in many plants. The genome of T. aestivum encodes 15 CrRLK1L genes with 43 paralogous copies, with three homeologs each, except for -2-D and -7-A, which are absent. Chromosomal localization analysis revealed a markedly uneven distribution of CrRLK1L genes across seven different chromosomes, with chromosome 4 housing the highest number of genes, while chromosome 6 lacked any CrRLK1L genes. Tissue-specific gene expression analysis revealed distinct expression patterns among the gene family members, with certain members exhibiting increased expression in reproductive tissues. Gene expression analysis in response to various abiotic and biotic stress conditions unveiled differential regulation of gene family members. Cold stress induces CrRLK1Ls -4-B and -15-A while downregulating -3-A and -7B. Drought stress upregulates -9D, contrasting with the downregulation of -7D. CrRLK1L-15-B and -15-D were highly induced in response to 1 hr of heat, and combined drought and heat stress, whereas -10-B is downregulated. Similarly, in response to NaCl stress, only CrRLK1L1 homeologs were induced. Fusarium graminearum and Claviceps purpurea inoculation induces homeologs of CrRLK1L-6 and -7. The analysis of cis-acting elements in the promoter regions identified elements crucial for plant growth and developmental processes. This comprehensive genome-wide analysis and expression study provides valuable insights into the essential functions of CrRLK1L members in wheat.

The genetic regulation of the gastric transcriptome is associated with metabolic and obesity-related traits and diseases.

Tissue-specific gene expression and gene regulation lead to a better understanding of tissue-specific physiology and pathophysiology. We analyzed the transcriptome and genetic regulatory profiles of two distinct gastric sites, corpus and antrum, to identify tissue-specific gene expression and its regulation. Gastric corpus and antrum mucosa biopsies were collected during routine gastroscopies from up to 431 healthy individuals. We obtained genotype and transcriptome data and performed transcriptome profiling and expression quantitative trait locus (eQTL) studies. We further used data from genome-wide association studies (GWAS) of various diseases and traits to partition their heritability and to perform transcriptome-wide association studies (TWAS). The transcriptome data from corpus and antral mucosa highlights the heterogeneity of gene expression in the stomach. We identified enriched pathways revealing distinct and common physiological processes in gastric corpus and antrum. Furthermore, we found an enrichment of the single nucleotide polymorphism (SNP)-based heritability of metabolic, obesity-related, and cardiovascular traits and diseases by considering corpus- and antrum-specifically expressed genes. Particularly, we could prioritize gastric-specific candidate genes for multiple metabolic traits, like NQO1 which is involved in glucose metabolism, MUC1 which contributes to purine and protein metabolism or RAB27B being a regulator of weight and body composition. Our findings show that gastric corpus and antrum vary in their transcriptome and genetic regulatory profiles indicating physiological differences which are mostly related to digestion and epithelial protection. Moreover, our findings demonstrate that the genetic regulation of the gastric transcriptome is linked to biological mechanisms associated with metabolic, obesity-related, and cardiovascular traits and diseases. NEW & NOTEWORTHY We analyzed the transcriptomes and genetic regulatory profiles of gastric corpus and for the first time also of antrum mucosa in 431 healthy individuals. Through tissue-specific gene expression and eQTL analyses, we uncovered unique and common physiological processes across both primary gastric sites. Notably, our findings reveal that stomach-specific eQTLs are enriched in loci associated with metabolic traits and diseases, highlighting the pivotal role of gene expression regulation in gastric physiology and potential pathophysiology.

Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus).

SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.

Identification, Characterization, and Expression Profiling of Maize GATA Gene Family in Response to Abiotic and Biotic Stresses

GATA transcription factor is crucial for plant growth and development, physiological metabolism, and environmental response, which has been reported in many plants. Although the identification of maize GATA genes has been reported previously, the number of maize GATA genes was incomplete, and the expression patterns of maize GATA genes were not analyzed. Therefore, in this study, the GATA gene family of maize (Zea mays L.) was systematically analyzed. Forty-one GATA family genes were identified in the maize and were divided into four groups. The gene structure of each subgroup was basically consistent with that of the motif. The maize GATA genes were distributed on 10 chromosomes, including 3 and 17 pairs of tandem and segmental duplication genes, respectively. Fourteen types of cis-acting elements were identified in the promoter sequences of maize GATA family genes, involving four categories: light response, stress, hormone, and growth and development. The tissue-specific expression analysis of maize GATA family genes revealed that 4 GATA genes were highly expressed in almost all the maize tissues, and 11 GATA genes were not expressed in almost all tissues. The other maize GATA family genes showed a tissue-specific expression pattern. The results of RNA-seq reanalysis of publicly available transcriptome sequencing big data revealed that the gene ZmGATA37 was significantly down-regulated in response to abiotic stresses including high temperature, low temperature, drought, waterlogging, and salt, and significantly up-regulated in response to biotic stresses including smut disease, Maize Iranian mosaic virus infection, beet armyworm and aphid infestations. This indicated that the ZmGATA37 gene plays an important role in maize growth and development. Our findings offer new insight into the potential role of GATA transcription factors in abiotic and biotic stresses and provide a theoretical groundwork for the molecular mechanisms underlying maize adaptation to such stress.

A comprehensive investigation of lipid-transfer proteins from Cicer arietinum disentangles their role in plant defense against Helicoverpa armigera-infestation.

Lipid Transfer Proteins (LTPs) play a crucial role in synthesizing lipid barrier polymers and are involved in defense signaling during pest and pathogen attacks. Although LTPs are conserved with multifaceted roles in plants, these are not yet identified and characterized in Cicer arietinum. In this study, a genome-wide analysis of LTPs was executed and their physiochemical properties, biochemical function, gene structure analysis, chromosomal localization, promoter analysis, gene duplication, and evolutionary analysis were performed using in silico tools. Furthermore, tissue-specific expression analysis and gene expression analysis during pest attack was also conducted for the LTPs. A total of 48 LTPs were identified and named as CaLTPs. They were predicted to be small unstable proteins with "Glycolipid transfer protein" and "Alpha-Amylase Inhibitors, Lipid Transfer and Seed Storage" domains, that are translocated to the extracellular region. CaLTPs were predicted to possess 3-4 introns and were located on all the eight chromosomes of chickpea with half of the CaLTPs being localized on chromosomes 4, 5, and 6, and found to be closely related to LTPs of Arabidopsis thaliana and Medicago trancatula. Gene duplication and synteny analysis revealed that most of the CaLTPs have evolved due to tandem or segmental gene duplication and were subjected to purifying selection during evolution. The promoters of CaLTPs had development-related, phytohormone-responsive, and abiotic and biotic stress-related cis-acting elements. A few CaLTP transcripts exhibited differential expression in diverse tissue types, while others showed no/very low expression. Out of 20 jasmonate-regulated CaLTPs, 14 exhibited differential expression patterns during Helicoverpa armigera-infestation, indicating their role in plant defense response. This study identified and characterized CaLTPs from an important legume, C. arietinum, and indicated their involvement in plant defense against H. armigera-infestation, which can be further utilized to explore lipid signaling during plant-pest interaction and pest management.

Mendelian randomization and clinical trial evidence supports TYK2 inhibition as a therapeutic target for autoimmune diseases.

To explore the associations of genetically proxied TYK2 inhibition with a wide range of disease outcomes and biomarkers to identify therapeutic repurposing opportunities, adverse effects, and biomarkers of efficacy. The loss-of-function missense variant rs34536443 in TYK2 gene was used as a genetic instrument to proxy the effect of TYK2 inhibition. A phenome-wide Mendelian randomization (MR) study was conducted to explore the associations of genetically-proxied TYK2 inhibition with 1473 disease outcomes in UK Biobank (N=339,197). Identified associations were examined for replication in FinnGen (N=260,405). We further performed tissue-specific gene expression MR, colocalization analyses, and MR with 247 blood biomarkers. A systematic review of randomized controlled trials (RCTs) on TYK2 inhibitor was performed to complement the genetic evidence. PheWAS-MR found that genetically-proxied TYK2 inhibition was associated with lower risk of a wide range of autoimmune diseases. The associations with hypothyroidism and psoriasis were confirmed in MR analysis of tissue-specific TYK2 gene expression and the associations with systemic lupus erythematosus, psoriasis, and rheumatoid arthritis were observed in colocalization analysis. There were nominal associations of genetically-proxied TYK2 inhibition with increased risk of prostate and breast cancer but not in tissue-specific expression MR or colocalization analyses. Thirty-seven blood biomarkers were associated with the TYK2 loss-of-function mutation. Evidence from RCTs confirmed the effectiveness of TYK2 inhibitors on plaque psoriasis and reported several adverse effects. This study supports TYK2 inhibitor as a potential treatment for psoriasis and several other autoimmune diseases. Increased pharmacovigilance is warranted in relation to the potential adverse effects. None.

Transcriptome annotation of 17 porcine tissues using nanopore sequencing technology.

The annotation of animal genomes plays an important role in elucidating molecular mechanisms behind the genetic control of economically important traits. Here, we employed long-read sequencing technology, Oxford Nanopore Technology, to annotate the pig transcriptome across 17 tissues from two Yorkshire littermate pigs. More than 9.8million reads were obtained from a single flow cell, and 69 781 unique transcripts at 50 108 loci were identified. Of these transcripts, 16 255 were found to be novel isoforms, and 22 344 were found at loci that were novel and unannotated in the Ensembl (release 102) and NCBI (release 106) annotations. Novel transcripts were mostly expressed in cerebellum, followed by lung, liver, spleen, and hypothalamus. By comparing the unannotated transcripts to existing databases, there were 21 285 (95.3%) transcripts matched to the NT database (v5) and 13 676 (61.2%) matched to the NR database (v5). Moreover, there were 4324 (19.4%) transcripts matched to the SwissProt database (v5), corresponding to 11 356 proteins. Tissue-specific gene expression analyses showed that 9749 transcripts were highly tissue-specific, and cerebellum contained the most tissue-specific transcripts. As the same samples were used for the annotation of cis-regulatory elements in the pig genome, the transcriptome annotation generated by this study provides an additional and complementary annotation resource for the Functional Annotation of Animal Genomes effort to comprehensively annotate the pig genome.

Identification of KFB Family in Moso Bamboo Reveals the Potential Function of PeKFB9 Involved in Stress Response and Lignin Polymerization.

The Kelch repeat F-box (KFB) protein is an important E3 ubiquitin ligase that has been demonstrated to perform an important post-translational regulatory role in plants by mediating multiple biological processes. Despite their importance, KFBs have not yet been identified and characterized in bamboo. In this study, 19 PeKFBs were identified with F-box and Kelch domains; genes encoding these PeKFBs were unevenly distributed across 12 chromosomes of moso bamboo. Phylogenetic analysis indicated that the PeKFBs were divided into eight subclades based on similar gene structures and highly conserved motifs. A tissue-specific gene expression analysis showed that the PeKFBs were differentially expressed in various tissues of moso bamboo. All the promoters of the PeKFBs contained stress-related cis-elements, which was supported by the differentially expression of PeKFBs of moso bamboo under drought and cold stresses. Sixteen proteins were screened from the moso bamboo shoots’ cDNA library using PeKFB9 as a bait through a yeast two-hybrid (Y2H) assay. Moreover, PeKFB9 physically interacted with PeSKP1-like-1 and PePRX72-1, which mediated the activity of peroxidase in proteolytic turnover. Taken together, these findings improved our understanding of PeKFBs, especially in response to stresses, and laid a foundation for revealing the molecular mechanism of PeKFB9 in regulating lignin polymerization by degrading peroxidase.

Genome-Wide Identification of GASA Gene Family in Ten Cucurbitaceae Species and Expression Analysis in Cucumber

Gibberellic acid-stimulated in Arabidopsis (GASA), a unique small molecular protein of plants, plays an essential role in plant growth and development. The GASA family genes have been identified and studied in many plants. However, the identification of GASA gene family in Cucurbitaceae species has not been reported yet. Therefore, in this study, based on the available genome information on the Cucurbitaceae species, the GASA family genes in 10 Cucurbitaceae species including cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), pumpkin (Cucurbita moschata), wax gourd (Benincasa hispida), sponge gourd (Luffa cylindrica), bottle gourd (Lagenaria siceraria), bitter gourd (Momordica charantia), chayote (Sechium edule), and snake gourd (Trichosanthes anguina) were identified with bioinformatics methods. To understand the molecular functions of GASA genes, the expression pattern analysis of cucumber GASA family genes in different tissues and stress responses were also analyzed. The results showed that a total of 114 GASA genes were identified in the 10 Cucurbitaceae species, which were divided into three subfamilies. Synteny analysis of GASA genes among cucumber, Arabidopsis and rice showed that nine cucumber GASA genes were colinear with 12 Arabidopsis GASA genes, and six cucumber GASA genes were colinear with six rice GASA genes. The cis-acting elements analysis implied that the cucumber GASA genes contained many cis-elements associated with stress and hormone response. Tissue-specific expression analysis of cucumber GASA family genes revealed that only the CsaV3_2G029490 gene was lowly or not expressed in all tissues, the CsaV3_3G041480 gene was highly expressed in all tissues, and the other seven GASA genes showed tissue-specific expression patterns. Furthermore, nine cucumber GASA family genes exhibited different degrees of regulatory response under GA, abiotic and biotic stresses. Two cucumber GASA genes, CsaV3_3G042060 and CsaV3_3G041480, were differentially expressed under multiple biotic and abiotic stresses, which indicated that these two GASA genes play important roles in the growth and development of cucumber.

Integrated Analysis of Tissue-Specific Gene Expression in Diabetes by Tensor Decomposition Can Identify Possible Associated Diseases.

In the field of gene expression analysis, methods of integrating multiple gene expression profiles are still being developed and the existing methods have scope for improvement. The previously proposed tensor decomposition-based unsupervised feature extraction method was improved by introducing standard deviation optimization. The improved method was applied to perform an integrated analysis of three tissue-specific gene expression profiles (namely, adipose, muscle, and liver) for diabetes mellitus, and the results showed that it can detect diseases that are associated with diabetes (e.g., neurodegenerative diseases) but that cannot be predicted by individual tissue expression analyses using state-of-the-art methods. Although the selected genes differed from those identified by the individual tissue analyses, the selected genes are known to be expressed in all three tissues. Thus, compared with individual tissue analyses, an integrated analysis can provide more in-depth data and identify additional factors, namely, the association with other diseases.

Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.)

Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures persuaded threat to its wild habitat. Plant tissue culture and RNA-Seq-based molecular bioprospection of key regulatory genes aid the understanding of molecular dynamics involved in specialized metabolites (phenylethanoids and phenylpropanoids) biosynthesis and its sustainable production. Hence, comparative transcriptomic analysis was performed using leaf and root tissues from the wild and tissue-cultured plants, revealing tissue-specific production of salidroside and rosavin. The transcriptome profiling resulted in 345 million high-quality reads yielding 92,380 unique transcripts with an N50 of 1260 bp. Tissue-specific gene expression analysis revealed that both phenylethanoids and phenylpropanoids biosynthesis are predominantly associated with the shikimate pathway. In addition to RNA-Seq data, the downstream biosynthesis pathways genes viz., phospho-2-dehydro-3-deoxyheptonate aldolase (DAHPS), 3-dehydroquinate synthase (DHQS), shikimate kinase (SK), chorismate mutase (CM), arogenate dehydrogenase (TYRAAT), aromatic-L-amino-acid decarboxylase (TDC), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4-CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) showed higher expression pattern in wild plant tissues compared to tissue-cultured plants. The transcript fold expression determined by RT-qPCR results followed similar patterns as those observed in RNA-seq and targeted metabolite profiling data. Salidroside and rosavin content in wild plants exhibited 2.40 fold and 1.77 fold increase accumulation compared to the tissue-cultured plant. The present investigation explained the tissue and condition-specific significant differences between the expression of proposed biosynthetic pathway genes and salidroside and rosavin content. Additionally, NAC, bHLH, and ARF were the most abundant transcription factor families found in the transcriptomic analysis of R. imbricata. The generated transcriptome dataset provides a valuable gene(s)/transcription factors hub that can be used for the sustainable production of salidroside and rosavin in R. imbricata under tissue culture conditions.

Identification and Validation of Autophagy-Related Genes in Diabetic Retinopathy.

BackgroundDiabetic retinopathy (DR) is one of the most common microvascular complications of diabetes, which is associated with damage of blood-retinal barrier and ischemia of retinal vasculature. It devastates visual acuity due to leakage of retinal vessels and aberrant pathological angiogenesis in diabetic patients. The etiology of DR is complex, accumulated studies have shown that autophagy plays an important role in the pathogenesis of DR, but its specific mechanism needs to be further studied.MethodsThis study chose the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE146615 to carry on the research. Autophagy-related genes that were potentially differentially expressed in DR were screened by R software. Then, the differentially expressed autophagy-related genes were analyzed by correlation analysis, tissue-specific gene expression, gene-ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and protein-protein interaction (PPI) network analysis. Finally, retinal pigment epithelial cell line (ARPE-19) incubated with high glucose (HG) was used to mimic the DR model, and the mRNA level of key genes was verified by quantitative real-time polymerase chain reaction (qRT-PCR) in vitro.ResultsA total of 23 differentially expressed autophagy-related genes (9 up-regulated genes and 14 down-regulated genes) were identified by differential expression analysis. The analysis of tissue-specific gene expression showed that these differentially expressed autophagy-related genes were enriched in the retina. GO and KEGG enrichment analysis showed that differentially expressed autophagy-related genes were significantly enriched in autophagy-related pathways such as regulation of autophagy and macroautophagy. Then 10 hub genes were identified by PPI network analysis and construction of key modules. Finally, qRT-PCR confirmed that the expression of MAPK3 in the DR model was consistent with the results of bioinformatics analysis of mRNA chip.ConclusionThrough bioinformatics analysis, we identified 23 potential DR autophagy-related genes, among which the down-regulated expression of MAPK3 may affect the occurrence and development of DR by regulating autophagy. It provides a novel insight into the pathogenesis of DR.

Identification and Tissue-Specific Expression Analysis of CYP720B Subfamily Genes in Slash Pine and Loblolly Pine

Diterpene resin acids (DRAs) are major components of pine oleoresin that can effectively resist the invasion of insects and pathogenic microorganisms. The subfamily of cytochrome P450s, CYP720B, catalyzes diterpene products into DRAs. Identifying CYP720B subfamily members and revealing the characteristics of tissue-specific expression would help understand diterpene-rich structures and diverse types. Slash pine and loblolly pine are important pines that provide oleoresin products. In this study, we identified CYP720B candidate genes based on the Pinus taeda V2.0 genome and full-length transcriptome of slash pine by PacBio. A total of 17 genes in slash pine and 19 in loblolly pine were identified and classified into four main clades by phylogenetic analysis. An analysis of cis-acting elements showed that CYP720B genes were closely related to adversity resistance. The gene expression of these candidates in different tissues was quantified by real-time quantitative PCR (RT–qPCR) analysis. Most of the genes showed relatively higher expression levels in roots and stems than in the other tissues, corresponding with the results of DRA component detection by gas chromatography–mass spectrometry (GC–MS), which indicated that stems and roots might be important tissues in oleoresin biosynthesis. These results provide a valuable resource for a better understanding of the biological role of individual CYP720Bs in slash pine and loblolly pine.

Ectopic expression ofGmRNF1aencoding a soybean E3 ubiquitin ligase affects Arabidopsis silique development and dehiscence.

A soybean E3 ubiquitin ligase, GmRNF1a, may affect pod dehiscence and seed development through MADS family genes. These results would be useful for the study of soybean pod and seed development. Pod dehiscence is one of the critical causes of yield loss in cultivated soybeans, and it is of great significance to understand the molecular mechanisms underlying pod dehiscence in soybeans. In this study, we identified a new RING family member of the E3 ubiquitin ligase, GmRNF1a, which was observed to interact with the MADS-box protein GmAGL1 to regulate siliques dehiscence. Tissue-specific gene expression analysis revealed that GmRNF1a was mainly expressed in flowers and pods in soybean. The subcellular localization assay showed the nuclear and cytoplasmic localization of GmRNF1a. In addition, it was found that GmRNF1a exhibits higher promoter activity in soybean hairy roots as well as in Arabidopsis leaves, flowers, and siliques. Heterologous expression of GmRNF1a in Arabidopsis showed that the transgenic Arabidopsis siliques had a faster maturation rate and cracked earlier than the wild-type plants. The functional and nucleotide diversity analysis suggests that GmRNF1a might play an important role in pod maturation and dehiscence and has been strongly selected for during soybean domestication.

Cyclic fertilin-derived peptide stimulates in vitro human embryo development

To study the cyclic fertilin peptide effects on preimplantation human embryogenesis. Cyclic fertilin peptide reproduces the structure of the binding site of the sperm Fertilin β (also named A Disintegrin and Metalloprotease 2: ADAM2) disintegrin domain. It binds to the oocyte membrane and increases sperm-oocyte fusion index in human and fertilization rate in mouse, providing healthy pups. It also improves human oocyte maturation and chromosome segregation in meiosis I and binds to human embryo blastomeres, suggesting that it has a membrane receptor. Thawed human embryos at the 3 to 4 cells stage were randomly included in a dose-response study with cyclic fertilin peptide. Inner cell mass (ICM), trophectoderm (TE), and total cell numbers were evaluated in top- and good-quality blastocysts. The study was performed in an academic hospital and research laboratory. Human embryos donated for research. This project was approved by the French "Agence de la Biomédecine." Immunofluorescence and tissue-specific gene expression analysis, using Clariom D microarrays, were performed to study its mechanism of action. Cyclic fertilin peptide improves blastocyst formation by almost 20%, the concentration of 1 μM being the lowest most efficient concentration. It significantly increases twice the TE cell number, without modifying the ICM. It increases the invitro hatching rate from 14% to 45%. Cyclic fertilin peptide stimulates TE growth. In the ICM, it induces transcriptional activation of intracellular protein and vesicle-mediated transport. Cyclic fertilin peptide dramatically improves human embryo development potential. It could be used to supplement culture medium and improve the invitro human embryo development. Starting supplementation immediately after fertilization, instead of day 2, could significantly upgrade assisted reproductive technology outcome.

Abstract 10863: Genome-Wide Assessments of 138 Inflammatory Markers Identified Inflammatory Pathways Confer Cardiovascular Disease Risk

Introduction: Atherosclerosis, the main underlying causes of coronary heart disease (CHD) and ischemic stroke, is an inflammatory condition. However, therapeutics targeting inflammation for CHD and stroke are limited, partially due to insufficient evidence for causal inflammatory pathways and druggable targets. Objectives: We aimed to identify causal inflammatory markers for CHD and ischemic stroke, and to characterize the genetic architecture shared between such an inflammatory profile and CHD/stroke. Methods: Pooling multiple databases, we curated the largest genome-wide association summary statistics for 138 markers including 126 inflammatory proteins (C-reactive protein [CRP], N>450k; others such as cytokines, N~3.6k-45k) and 12 blood immune cell types (N>450k) and subsets (N~2.5k); as well as for CHD (N~547k) and stroke (N~521k). We conducted Mendelian randomization (MR) analysis using Causal Analysis Using Summary Effect Estimates and Mode-Based Estimate; and the genome-wide cross-trait meta-analysis using Association analysis based on SubSETs. Results: Of the 138 inflammatory markers, MR analyses identified 3 cellular and 4 protein markers showing significant causal effects for CHD (including white blood cell count, CD8+ T count, interleukin 6, and interleukin 22 receptor subunit alpha 1; FDR <0.05); and 4 protein markers showing significant causal effects for ischemic stroke (including interleukin 6 and macrophage migration inhibitory factor; FDR <0.05). Genome-wide cross-trait analysis identified 456 independent genetic loci that significantly co-regulated cardiovascular disease (CHD or stroke) and at least one of its causal inflammatory markers (e.g., APOC1-4 coregulated CHD and 5 causal markers for CHD; lead SNPs showing P <5e-8 in each pair of marker-disease meta-analysis and FDR <0.01 with each trait). In tissue-specific gene expression analysis, the expressions of genes harboring these loci showed a significant enrichment in blood, blood vessels, and adipose tissue ( FDR <0.05), and a marginal enrichment in the liver and lung ( P <0.05). Conclusions: We identified cellular and protein inflammatory markers that potentially have a causal role in the development of CHD and ischemic stroke, based on genetic evidence.

SlCCD1A Enhances the Aroma Quality of Tomato Fruits by Promoting the Synthesis of Carotenoid-Derived Volatiles.

The loss of volatiles results in the deterioration of flavor in tomatoes. Volatiles are mainly derived from fatty acid, carotenoid, phenylpropane, and branched chain amino acids. In this study, the tomato accession CI1005 with a strong odor and accession TI4001 with a weak odor were analyzed. The volatile contents were measured in tomato fruits using gas chromatography-mass spectrometry. The scores of tomato taste and odor characteristics were evaluated according to hedonistic taste and olfaction. It was found that the content of fatty acid-derived volatiles accounted for more than half of the total volatiles that had grassy and fatty aromas. Phenylpropane-derived volatiles had irritation and floral aromas. Branched-chain amino acid-derived volatiles had a caramel aroma. Carotenoid-derived volatiles had floral, fruity, fatty, and sweet-like aromas, preferred by consumers. A lack of carotenoid-derived volatiles affected the flavor quality of tomato fruits. The accumulation of carotenoid-derived volatiles is regulated by carotenoid cleavage oxygenases (CCDs). A tissue-specific expression analysis of the SlCCD genes revealed that the expression levels of SlCCD1A and SlCCD1B were higher in tomato fruits than in other tissues. The expression levels of SlCCD1A and SlCCD1B were consistent with the trend of the carotenoid-derived volatile contents. The expression of SlCCD1A was higher than that for SlCCD1B. A bioinformatics analysis revealed that SlCCD1A was more closely linked to carotenoid metabolism than SlCCD1B. The overexpression of SlCCD1A indicated that it could cleave lycopene, α-carotene, and β-carotene to produce 6-methyl-5-hepten-2-one, geranylacetone, α-ionone, and β-ionone, increasing the floral, fruity, fatty, and sweet-like aromas of tomato fruits. The flavor quality of tomato fruits could be improved by overexpressing SlCCD1A.

Anthocyanin Accumulation and Related Gene Expression Profile in ‘Red Zaosu’ Pear and Its Green Mutant

Red-skinned pear is a promising commercial fruit due to its attractive appearance and nutritious value. Anthocyanin is the determinant of the red coloration of the pear peel. However, differences in anthocyanin accumulation exist among red pear cultivars with different genetic backgrounds. In this study, we analyzed the anthocyanin content and gene expression patterns in the fruits and different tissues of the red pear ‘Red Zaosu’ at different developmental stages and found a difference in anthocyanin accumulation between ‘Red Zaosu’ pear and its green mutant. The data showed that the expression profiles of transcripts that encoded critical anthocyanin biosynthetic genes were basically consistent with a tendency to a decreased anthocyanin content during fruit development, indicating that a synergistic effect of these genes was responsible for anthocyanin biosynthesis and regulation. Tissue-specific expression analysis of anthocyanin biosynthetic genes showed that they could be expressed in all tissues but at different levels. PbF3H, PbDFR, and PbANS were mainly expressed during the early flowering period, which explained the reduced levels of anthocyanin content in petals. Additionally, the content of anthocyanins and the expression levels of PbDFR, PbANS, and PbMYB10 significantly decreased in the green mutant of ‘Red Zaosu’, suggesting that PbDFR, PbANS, and PbMYB10 probably play a decisive role in determining the skin coloration of ‘Red Zaosu’ and its green mutant.