Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

SFMBT2 regulates plumage color via serum metabolites in Chinese Anyi tile-like gray chickens

Plumage color is an important characteristic of chicken breeds, and molecular genetic research is significant for resource conservation and product quality control. Anyi tile-like gray chicken is a high-quality local chicken breed resource generated through long-term natural selection and artificial breeding in China. However, the molecular mechanisms underlying plumage color formation in Anyi tile-like gray chickens remain unclear. In this study, nontargeted liquid chromatography and tandem mass spectrometry (LC-MS/MS) was performed to identify serum metabolites associated with plumage color in 93 Anyi tile-like gray chickens, including 60 tile-like gray and 33 black chickens. Notably, 12 serum metabolites were significantly enriched in Anyi tile-like gray chickens, including deoxyuridine and inosine, which were the key biomarkers distinguishing tile-like gray chickens from black chickens. Additionally, nine serum metabolites were significantly enriched in black chickens. Moreover, we identified 225 significant SNPs (P < 9.71 × 10-8) on chromosomes 1, 2, 3, 4, 11, 15, and 21 that were associated with deoxyuridine, inosine, 3-hydroxybenzoic acid, and L-methionine S-oxide through metabolome genome-wide association studies (mGWAS). Importantly, chromosome 1 harbored a region, 172.79-kb, which was the most likely quantitative trait locus (QTL) interval. RNA sequencing (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that SFMBT2 was the only differentially expressed gene in the QTL interval, and its expression was correlated with the abundance of specific serum metabolites. Conclusively, SFMBT2-mediated changes in serum metabolites contribute to plumage color development in Anyi tile-like gray chicken. This study provides important insights into the interaction between serum metabolites and host genes, and offers a theoretical basis for the breeding of Anyi tile-like gray chickens.

Flower morphology, flower color, flowering and floral fragrance in Paeonia L

Paeonia have diverse flower colors, rich flower types, varying bloom periods, and delightful fragrances, rendering them highly valuable for both ornamental and economic purposes in horticulture. Investigating the developmental mechanisms of morphology, flower color, flowering and floral fragrance in Paeonia holds significant value for enhancing their ornamental traits and conducting germplasm improvement. This review provides an overview of research progress on Paeonia flower morphology (including flower bud differentiation, classification, omics applications in shape studies, and functional genes regulating flower morphology), flower colors (omics applications in color research and functional genes regulating flower colors), bloom periods (flower bud dormancy, flowering time), and fragrances (preparation, analysis, components, and molecular biology research of flower fragrances) within the Paeonia. Additionally, it offers a comprehensive analysis of current research challenges and future directions.

Genome-wide analysis of two different regions of brain reveals the molecular changes of fertility related genes in rln3a-/- mutants in male Nile tilapia (Oreochromis niloticus)

Relaxin3 (rln3) has been associated with various emotional and cognitive processes, including stress, anxiety, learning, memory, motivational behavior, and circadian rhythm. Notably, previous report revealed that Rln3a played an indispensable role in testicular development and male fertility in Nile tilapia (Oreochromis niloticus). However, the underlying molecular mechanisms remain largely unknown. We found that Rln3a is expressed exclusively in the diencephalon* (Di*) of the brain. Deficiency of Rln3a resulted in a significant increase in serum dopamine level and an upregulation of gene expression of gnrh1 and kisspeptin2. To further elucidate the role of Rln3a in fish fertility, we collected two different regions of Di* and hypothalamus (Hyp) tissues for subsequent RNA-seq analysis of both wild-type (rln3a+/+) and rln3a-/- male tilapia. Upon the transcriptomic data, 1136 and 755 differentially expressed genes (DEGs) were identified in the Di* and Hyp tissues, respectively. In Di*, the up-regulated genes were enriched in circadian rhythm, chemical carcinogenesis, while the down-regulated genes were enriched in type II diabetes mellitus, dopaminergic synapse, and other pathways. In Hyp, the up-regulated genes were enriched in circadian rhythm, pyrimidine metabolism, while the down-regulated genes were enriched in type I diabetes mellitus, autoimmune thyroid disease, and other pathways. Subsequently, the results of both qRT-PCR and FISH assays highlighted a pronounced up-regulation of core circadian rhythm genes, cry1b and per3, whereas genes such as clocka, clockb, and arntl exhibited down-regulation. Furthermore, the genes associated with dopamine biosynthesis were significantly increased in the Hyp. In summary, the mutation of rln3a in male tilapia resulted in notable changes in circadian rhythm and disease-linked signaling pathways in the Di* and Hyp. These changes might account for the fertility defects observed in rln3a-/- male mutants in tilapia.

The Change in Whole-Genome Methylation and Transcriptome Profile under Autophagy Defect and Nitrogen Starvation

Through whole-genome bisulfite sequencing and RNA-seq, we determined the potential impact of autophagy in regulating DNA methylation in Arabidopsis, providing a solid foundation for further understanding the molecular mechanism of autophagy and how plants cope with nitrogen deficiency. A total of 335 notable differentially expressed genes (DEGs) were discovered in wild-type Arabidopsis (Col-0-N) and an autophagic mutant cultivated under nitrogen starvation (atg5-1-N). Among these, 142 DEGs were associated with hypomethylated regions (hypo-DMRs) and were upregulated. This suggests a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Examination of the hypo-DMR-linked upregulated DEGs indicated that the expression of MYB101, an ABA pathway regulator, may be regulated by DNA demethylation and the recruitment of transcription factors (TFs; ERF57, ERF105, ERF48, and ERF111), which may contribute to the growth arrest induced by abscisic acid (ABA). Additionally, we found that DNA methylation might impact the biosynthesis of salicylic acid (SA). The promoter region of ATGH3.12 (PBS3), a key enzyme in SA synthesis, was hypomethylated, combined with overexpression of PBS3 and its potential TF AT3G46070, suggesting that autophagy defects may lead to SA-activated senescence, depending on DNA demethylation. These findings suggest that DNA hypomethylation may impact the mechanism by which Arabidopsis autophagy mutants (atg5-1) respond to nitrogen deficiency, specifically in relation to ABA and SA regulation. Our evaluation of hormone levels verified that these two hormones are significantly enriched under nitrogen deficiency in atg5-1-N compared to Col-0-N.

Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

Great progress has been made in our understanding of floral organ identity determination and its regulatory network in many species; however, the quantitative genetic basis of floral organ number variation is far less well understood for species-specific traits from the perspective of population variation. Here, using a tree peony (Paeonia suffruticosa Andrews, Paeoniaceae) cultivar population as a model, the phenotypic polymorphism and genetic variation based on genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) analysis were analyzed. Based on 24 phenotypic traits of 271 representative cultivars, the transcript profiles of 119 cultivars were obtained, which indicated abundant genetic variation in tree peony. In total, 86 GWAS-related cis-eQTLs and 3188 trans-eQTL gene pairs were found to be associated with the numbers of petals, stamens, and carpels. In addition, 19 floral organ number-related hub genes with 121 cis-eQTLs were obtained by weighted gene co-expression network analysis, among which five hub genes belonging to the ABCE genes of the MADS-box family and their spatial-temporal co-expression and regulatory network were constructed. These results not only help our understanding of the genetic basis of floral organ number variation during domestication, but also pave the way to studying the quantitative genetics and evolution of flower organ number and their regulatory network within populations.

Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom

In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.

SlJAZ10 and SlJAZ11 mediate dark-induced leaf senescence and regeneration

During evolutionary adaptation, the mechanisms for self-regulation are established between the normal growth and development of plants and environmental stress. The phytohormone jasmonate (JA) is a key tie of plant defence and development, and JASMONATE-ZIM DOMAIN (JAZ) repressor proteins are key components in JA signalling pathways. Here, we show that JAZ expression was affected by leaf senescence from the transcriptomic data. Further investigation revealed that SlJAZ10 and SlJAZ11 positively regulate leaf senescence and that SlJAZ11 can also promote plant regeneration. Moreover, we reveal that the SlJAV1-SlWRKY51 (JW) complex could suppress JA biosynthesis under normal growth conditions. Immediately after injury, SlJAZ10 and SlJAZ11 can regulate the activity of the JW complex through the effects of electrical signals and Ca²⁺ waves, which in turn affect JA biosynthesis, causing a difference in the regeneration phenotype between SlJAZ10-OE and SlJAZ11-OE transgenic plants. In addition, SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. Together, SlJAZ10 and SlJAZ11 not only act as repressors of JA signalling to leaf senescence, but also regulate plant regeneration through coordinated electrical signals, Ca²⁺ waves, hormones and transcriptional regulation. Our study provides critical insights into the mechanisms by which SlJAZ11 can induce regeneration.

In plants, senescence is the final stage of development, but regeneration can help them beyond the stage. Plants regeneration is essential for propagation, and in cultivated crops to maintain excellent traits as close as possible. JA signaling can sense environmental signals and integrate various regulatory mechanisms to ensure plants regeneration occurs under optimal conditions. In this work, the JAZ-JAV1-WRKY51 complexes with reported was further optimized, the function of SlJAZ10 and SlJAZ11 was identified to promote inhibitory activity of SlJAV1-SlWRKY51 complex which negatively regulated JA biosynthesis by direct binding of the W-box of the SlAOC promoter. The results of further investigation suggest that the differences in regulation of electrical signals, Ca²⁺ waves, hormones and transcriptional regulation are responsible for the regeneration between SlJAZ10 and SlJAZ11. In addition, we have found that SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. In summary, despite both SlJAZ10 and SlJAZ11 can function as senescence, only SlJAZ11 has an important promoting function for regeneration.

Bacillus thuringiensis and Chlorantraniliprole Trigger the Expression of Detoxification-Related Genes in the Larval Midgut of Plutella xylostella

Background: Diamondback moth (DBM), Plutella xylostella (L.), has developed resistance to many insecticides. The molecular mechanism of DBM resistance to Bt-G033A combined with chlorantraniliprole (CL) remains undefined. Methods: In this study, field-resistant strains of Plutella xylostella to three pesticides, namely, Bacillus thuringiensis (Bt) toxin (Bt-G033A), CL, and a mixture of Bt + CL, were selected to evaluate the resistance level. Additionally, transcriptomic profiles of a susceptible (SS-DBM), field-resistant (FOH-DBM), Bt-resistant (Bt-DBM), CL-resistant (CL-DBM), and Bt + CL-resistant (BtC-DBM) strains were performed by comparative analysis to identify genes responsible for detoxification. Results: The Bt-G033A was the most toxic chemical to all the DBM strains among the three insecticides. The comparative analysis identified 25,518 differentially expressed genes (DEGs) between pairs/combinations of strains. DEGs were enriched in pathways related to metabolic and catalytic activity and ABC transporter in resistant strains. In total, 17 metabolic resistance-related candidate genes were identified in resistance to Bt-G033A, CL, and Bt + CL by co-expression network analysis. Within candidate genes, the majority was upregulated in key genes including cytochrome P450, glutathione S-transferase (GST), carboxylesterase, and acetylcholinesterase in CL- and BtC-resistant strains. Furthermore, aminopeptidase N (APN), alkaline phosphatase (ALP), cadherin, trypsin, and ABC transporter genes were eminent as Bt-resistance-related genes. Expression patterns of key genes by the quantitative real-time PCR (qRT-PCR) proved the credibility of transcriptome data and suggest their association in the detoxification process. Conclusion: To date, this study is the most comprehensive research presenting functional transcriptome analysis of DBM using Bt-G033A and CL combined insecticidal activity.

Characterization of the DNA molecular sequence of complete plastid genome of Paeonia rockii subsp. taibaishanica, an endemic species in China

Paeonia rockii subsp. taibaishanica (Paeoniaceae), one of the tree peony species, is endemic to the Qinling Mountains in central China. In this study, we characterized its whole plastid genome sequence using the Illumina sequencing platform. The complete plastid genome size of P. rockii subsp. taibaishanica is 153,368 bp in length, including a large single copy (LSC) region of 85,030 bp, a small single copy (SSC) region of 17,042 bp, and a pair of inverted repeats (IRs) of 25,648 bp. The genome contains 131 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC contents in chloroplast genome, LSC region, SSC region, and IR region were 38.3%, 36.6%, 32.6%, and 43.1%, respectively. A total of 16 species are used to construct the phylogenetic tree of Paeoniaceae, the results showed that P. rockii subsp. taibaishanica is more closely related with congeneric Paeonia suffruticosa and Paeonia ostii, these species were clustered into a clade with high bootstrap support.

Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.)

BACKGROUND

Signal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues. The working system of CLE genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis of CLE genes in such plants.

RESULTS

A total of 26 individual CLE genes were identified in Chinese long '9930' cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes among Arabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of all CsCLEs genes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumber CLE genes indicates a possible relationship between CsCLE genes and certain functions of hormone response elements. Cucumber resulted closely related to Arabidopsis and melon, having seven and 15 orthologous CLE genes in Arabidopsis and melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process, CLE genes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber gene CLV3 was overexpressed in Arabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type.

CONCLUSIONS

In this study, 26 CLE genes were identified in Chinese long '9930' cucumber genome. The CLE genes were mainly composed of alkaline hydrophilic unstable proteins. The genes of the CLE family were divided into seven classes, and shared close relationships with their homologs in Arabidopsis and melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, and CLV3, which the representative gene of the family, was overexpressed in Arabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.

Genetic Diversity of Paeonia rockii (Flare Tree Peony) Germplasm Accessions Revealed by Phenotypic Traits, EST-SSR Markers and Chloroplast DNA Sequences

Research Highlights: This study, based on the first collection of cultivated Paeonia rockii (flare tree peony, FTP) germplasm across the main distribution area by our breeding desires, comprehensively evaluates these accessions by using phenotypic traits, expressed sequence tag (EST)-simple sequence repeat (SSR) markers and chloroplast DNA sequences (cpDNA). The results show that these accessions collected selectively by us can represent the genetic background information of FTP as a germplasm of tree crops. Background and Objectives: FTP has high cultural, ornamental and medicinal value traditionally, as well as recently presenting a significance as an emerging edible oil with high α-linolenic acid contents in the seeds. The objectives of this study are to reveal the characteristics of the genetic diversity of FTP, as well as to provide scientific suggestions for the utilization of tree peony breeding and the conservation of germplasm resource. Materials and Methods: Based on the phenotypic traits, EST-SSR markers and chloroplast DNA sequence variation, we studied the diversity of a newly established population of 282 FTP accessions that were collected and propagated by ourselves in our breeding project in recent years. Results: (1) There was an abundant variation in phenotype of the accessions, and the phenotypic variation was evenly distributed within the population, without significant hierarchical structure, (2) the EST-SSR data showed that these 282 accessions had relatively high genetic diversity, in which a total of 185 alleles were detected in 34 pairs of primers. The 282 accessions were divided into three distinct groups, and (3) the chloroplast DNA sequences (cpDNA) data indicated that these accessions had a higher genetic diversity than the population level and a lower genetic diversity than the species level of wild P. rockii, and the existing spatial genetic structure of these accessions can be divided into two branches. Conclusions: From the results of the three analyses, we found that these accessions can fully reflect the genetic background information of FTP germplasm resources, so their protection and utilization will be of great significance for genetic improvement of woody peonies.

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

BACKGROUND

Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS).

RESULTS

The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%).

CONCLUSIONS

Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.

Tree peony variegated flowers show a small insertion in the F3'H gene of the acyanic flower parts

BACKGROUND

The tree peony (Paeonia suffruticosa Andr.) cultivar 'Er Qiao' is appreciated for its unstable variegated flower coloration, with cyanic and acyanic flowers appearing on different branches of the same plant and occasionally in a single flower or petal. However, the variegation mechanism is still unclear.

RESULTS

In this study, we found significantly higher contents and more diverse sets of anthocyanins in the cyanic petals than in the acyanic petals. Comparative transcriptome analysis between the two flower types revealed 477 differentially expressed genes (DEGs). Quantitative real-time PCR results verified that the transcript levels of the flavonol synthase (FLS) gene were significantly increased in the acyanic petals. Furthermore, we found that a GCGGCG insertion at 246 bp in the flavonoid 3'-hydroxylase (F3'H) gene-coding region constitutes a duplication of the 241-245 bp section and was consistently found only in acyanic flowers. Sequence alignment of the F3'H gene from different plant species indicated that only the acyanic petals of 'Er Qiao' contained the GCGGCG insertion. The transformation of Arabidopsis tt7-1 lines demonstrated that the ectopic expression of F3'H-cyanic, but not F3'H-acyanic, could complement the colors in the hypocotyl and seed coat.

CONCLUSION

In summary, we found that an indel in F3'H and the upregulation of FLS drastically reduced the anthocyanin content in acyanic petals. Our results provide molecular candidates for a better understanding of the variegation mechanisms in tree peony.

Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies

Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.