Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

PE (Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant

Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line 'PI 381159' abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a cleaved amplified polymorphic sequences (CAPS) marker from a distinct SNP located at -735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.

Characterization and expression analysis of GLABRA3 (GL3) genes in cotton: insights into trichome development and hormonal regulation

BACKGROUND

GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) genes encode a typical helix-loop-helix (bHLH) transcription factors that primarily regulate trichome branching and root hair development, DNA endoreduplication, trichoblast size, and stomatal formation. The functions of GL3 genes in cotton crop have been poorly characterized. In this study, we performed comprehensive genome-wide scans for GL3 and EGL3 homologs to enhance our comprehension of their potential roles in trichome and fiber development in cotton crop.

METHODS AND RESULTS

Our findings paraded that Gossypium hirsutum and G. barbadense have 6 GL3s each, unevenly distributed on 4 chromosomes whereas, G. arboreum, and G. raimondii have 3 GL3s each, unevenly distributed on 2 chromosomes. Gh_A08G2088 and Gb_A09G2187, despite having the same bHLH domain as the other GL3 genes, were excluded due to remarkable short sequences and limited number of motifs, indicating a lack of potential functional activity. The phylogenetic analysis categorized remaining 16 GL3s into three subfamilies (Group I-III) closely related to A. thaliana. The 16 GL3s have complete bHLH domain, encompassing 590-631 amino acids, with molecular weights (MWs) ranging from 65.92 to 71.36 kDa. Within each subfamily GL3s depicted shared similar gene structures and motifs, indicating conserved characteristics within respective groups. Promoter region analysis revealed 27 cis-acting elements, these elements were responsive to salicylic acid, abscisic acid (ABA), methyl jasmonate (MeJA), and gibberellin. The expression of GL3 genes was analyzed across 12 tissues in both G. barbadense and G. hirsutum using the publicly available RNA-seq data. Among GL3s, Gb_D11G0219, Gb_D11G0214, and Gb_D08G2182, were identified as relatively highly expressed across different tissues, consequently selected for hormone treatment and expression validation in G. barbadense. RT-qPCR results demonstrated significant alterations in the expression levels of Gb_D11G0219 and Gb_D11G0214 following MeJA, GA, and ABA treatment. Subcellular localization prediction revealed that most GL3 proteins were predominantly expressed in the nucleus, while a few were localized in the cytoplasm and chloroplasts.

CONCLUSIONS

In summary, this study lays the foundation for subsequent functional validation of GL3 genes by identifying hormonal regulation patterns and probable sites of action in cotton trichome formation and fiber development. The results stipulate a rationale to elucidate the roles and regulatory mechanisms of GL3 genes in the intricate process of cotton fibre and trichome development.

A review of the types, functions and regulatory mechanisms of plant spines

Over a long period of evolution, plants have developed self-protection mechanisms, such as leaving seeds, dropping leaves, growing thorns, producing specific substances or emitting special odors to repel insects. Although studies on the taxonomic characteristics, functions and application of spines in spiny plants have been reported in China and abroad, a systematic overview of plant spines is currently lacking. This study therefore identifies the characteristics and types of plant spines based on domestic and international research on plant spines to provide clear criteria or bases for determining the types of plant spines. In addition, the functions, regulatory mechanisms, and factors influencing the formation of spines and the prospects for their development and application are described and summarized. This study will help to improve the understanding of the types, functions and regulatory mechanisms of plant spines and provide new ideas for the genetic improvement of plants from spiny to nonspiny varieties.

Transcriptome analysis reveals key genes and pathways for prickle development in Zanthoxylumarmatum

Zanthoxylum armatum is an economically important tree species. However, well-developed prickles on its stems and leaves pose serious challenges in terms of management and harvesting. To investigate the molecular mechanism underlying prickle development, we sequenced different stages of prickle morphological development and transcriptomes of different tissues in the root tips (Gen), leaf buds (Ya), and fruits of Z. armatum. The results revealed that proteins related to cell division and genes related to the growth hormone signaling pathway were highly expressed in the prickle just protrusion (PC1). In addition, a high expression of lignin biosynthesis genes was observed during the developmental onset of lignification (PC2) and prickle lignification (PC3). These findings indicate that phenylpropanoid biosynthesis and plant hormone signal transduction are key pathways for the completion of lignification development in the prickle. During prickle development, ZaMYB2 and ZaWRKY3 were significantly upregulated in PC2 and PC3, suggesting their possible involvement in prickle development. Transcriptome and qRT-PCR analyses revealed differential gene expression of zaPAL3, za4CLL1, zaCOMT1, ZaWRKY3, and ZaCCD31 in the Gen, Ya, newly formed fruit (ZaF1), newly oil-spotted fruits (ZaF2), PC1, PC2, and PC3 of Zarmatum. zaCCD31 was highly expressed in leaf buds, whereas Za4CLL1 was highly expressed in root tips. During the lignification of prickles, the relative expression of genes including zaMYB2 increased gradually; however, the relative expression of zaCCD31 decreased during this process. Therefore, we inferred that these genes might be closely related to prickle development. Notably, zaMYB2 was expressed at higher levels in PC2 and PC3 than in PC1 and was not expressed in Gen, Ya, ZaF1, and ZaF2. Therefore, zaMYB2 is a key gene involved in prickle development of Z. armatum that exhibited tissue-specific expression. This study establishes a foundation for future analyses of the molecular mechanism underlying prickle development in Z. armatum.

A NAC transcription factor ZaNAC93 confers floral initiation, fruit development, and prickle formation in Zanthoxylum armatum

Zanthoxylum armatum is a dioecious prickly plant which developed apomictic reproduction. The increases in male flowers and prickle density in female plants lead to low yield and picking efficiency. However, little is known concerning the mechanisms of floral development and prickle formation. NAC is a well-known transcription factor that participates in multiple aspects of plant growth and development. Herein, we characterize the functions and regulatory mechanisms of candidate NACs controlling both traits in Z. armatum. A total of 159 ZaNACs were identified, and 16 of these were male-biased, represented by the NAP subfamily members ZaNAC93 and ZaNAC34, orthologs of AtNAC025 and AtNARS1/NAC2 respectively. Overexpression of ZaNAC93 in tomato led to modifications in flower and fruit development, including earlier flowering, increased numbers of lateral shoots and flowers, accelerated plant senescence, and reduced size and weight of fruits and seeds. In addition, the trichome density in leaves and inflorescences was dramatically reduced in ZaNAC93-OX lines. Overexpression of ZaNAC93 resulted in the up-/downregulation of genes associated with GA, ABA and JA signaling pathways, such as GAI, PYL and JAZ, as well as several TFs, including bZIP2, AGL11, FBP24 and MYB52. Yeast two-hybrid analysis revealed that ZaNAC93 protein could interact with AP1, GAI, bZIP2 and AGL11 in Z. armatum, which might contribute to floral induction, fruit growth, and trichome initiation. This work provides new insights into the molecular mechanisms of ZaNAC93 in reproductive development and prickle formation in Z. armatum.

Comparative transcriptome analysis reveals hormone, transcriptional and epigenetic regulation involved in prickle formation in Zanthoxylum armatum

Zanthoxylum armatum is an evergreen plant with high economical and medicinal values. The presence of prickles on stems and leaves is undesirable for them make picking difficult. To date, little is known of prickle formation in Z. armatum. Herein, the morphological and molecular features of prickle initiation in prickless (WC) and three types of prickly Z. armatum were characterized. Compared to WC, the levels of cytokinin and auxin were increased, while GA and JA declined in prickly Z. armatum. Transcriptome analysis identified 6258 differentially expressed genes (DEGs)between prickless and prickly Z. armatum. Among them, several DEGs related to hormone metabolism and signaling, including LOG7, CKX3, AHK1, three DELLAs, six JAZs and TIR1, were candidate genes involved in prickle formation. Transcription factors associated with prickle formation was screened, including MYB6-1/MYB6-2, WER, GL3-2, SPL4/5, SOC1, and SCL32. Of them, MYB6-1 and WER might negatively regulate prickles initiation via interacting with GL3-2. Additionally, the histone acetylation and DNA methylation levels, the transcripts of histone acetyltransferase/deacetylase and DNA methyltransferases showed significant differences between prickless and prickly plants, indicating their involvements in prickle initiation. These findings illustrate the regulation of prickle formation might be mediated by phytohormones (especially cytokinin), transcription factors and epigenetic modifications in Z. armatum.

Comparative Transcriptome Analysis of Gleditsia sinensis Thorns at Different Stages of Development

G. sinensis thorn (called "zào jiǎo cì", ZJC) has important medicinal and economic value, however, little is known about the molecular mechanisms behind the development of ZJC. In this study, we measured the content of soluble sugar and starch during the growth and development of the thorn, and performed transcriptome sequencing of the thorn segment, non-thorn segment, apex, and root tip at five distinct stages of thorn formation. The results showed that, with the growth of ZJC, the soluble sugar content of the roots, hypocotyls, thorn stems, thornless stems, leaves, and the starch content of the roots and leaves all firstly increased and then decreased after the basic structure of thorns was formed; the soluble sugar content and starch content of ZJC showed an overall downward trend (decreased by 59.26% and 84.56%, respectively). Myb-like, YABBY2, Growth-regulating factor 3, TCP2, Zinc transporter 8, and another 25 genes may be related to the maintenance and growth of thorns. Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) between stems with thorn and thorn-free stems found that a significant number of DEGs were annotated with terms related to the positive regulation of development, heterochronic (GO:0045962), the positive regulation of photomorphogenesis (GO:2000306), and other biological process (BP) terms. The developmental initiation regulation of ZJC may be regulated by TCP transcription factors (TFs). Eight genes were selected randomly to validate the RNA-seq results using real-time quantitative PCR (RT-qPCR) and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the thorn development of G. sinensis.

A Compendium for Novel Marker-Based Breeding Strategies in Eggplant

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.

RrTTG1 promotes fruit prickle development through an MBW complex in Rosa roxburghii

Fruit prickles are widely distributed on the pericarp and exhibit polymorphic traits at different developmental stages. Although they are multicellular appendages that are well-known for helping plants defend against biotic and abiotic stresses, their origination and molecular mechanism are still less known. Here, we studied the origination and molecular mechanism of fruit prickles in Rosa roxburghii. Using morphological and histological observations, we found that the fruit prickle primordium of R. roxburghii originated from the ground meristem that underwent cell division to form flagelliform prickles, continued to enlarge, and finally lignified to form mature fruit prickles. We amplified a homolog of candidate gene TRANSPARENT TESTA GLABRA1 (TTG1) from R. roxburghii, named RrTTG1. RrTTG1 harbored four conserved WD-repeat domains and was exclusively nuclear-localized. Using qRT-PCR and in situ hybridization, we found that RrTTG1 was constitutively expressed and highly expressed during the initiation and cell expansion phases of fruit prickles. Ectopic expression analysis in Arabidopsis proved that RrTTG1 substantially enhanced the number of trichome and pigmentation production and inhibited root hair formation. Besides, RrTTG1 complemented the phenotypes of the ttg1 mutant in Arabidopsis, thus indicating that RrTTG1 played pleiotropic roles akin to AtTTG1. We demonstrated that the RrTTG1 only interacted with RrEGL3, a homolog of ENHANCER OF GLABRA3 (EGL3), via yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Briefly, RrTTG1 might positively regulate the initiation of fruit prickle primordium and cell enlargement by forming the RrTTG1-RrEGL3-RrGL1 complex in R. roxburghii. Therefore, our results help characterize the RrTTG1 in R. roxburghii and also elucidate the establishment of the prickles regulatory system in the Rosaceae plants.

Nonglandular prickle formation is associated with development and secondary metabolism-related genes in Rosa multiflora

Roses are among the most economically important ornamental plants worldwide. But prickles on the stem and leaves cause difficulties for cultivation or inconveniences during harvest and transportation, thus are an undesirable horticultural character. However, little is known about the molecular mechanisms of prickle development. In this study, we sought to develop Rosa multiflora (in the family Rosaceae) as a model plant to study prickle formation. The morphology, structure, and ontogeny of prickles were characterized, and transcriptome analysis of prickly and prickleless R. multiflora genotypes was performed. Morphological observation and microscopic analyses revealed that prickles of R. multiflora were non-glandular prickles (NGPs) and their maturation went through five developmental stages, which was accompanied by the accumulation of secondary metabolites such as lignin and anthocyanins. Comparative transcriptome analysis identified key pathways and hub genes potentially involved in prickle formation. Interestingly, among the differentially expressed genes (DEGs), several notable development and secondary metabolism-related transcription factors (TFs) including NAC, TCP, MYB, homeobox, and WRKY were up-regulated in prickly internodes. KEGG enrichment analysis indicated that DEGs were enriched in the pathways related to biosynthesis of secondary metabolites, flavonoids, and phenylpropanoids in the prickly R. multiflora. Our study provides novel insights into the molecular network underlying the regulation of prickle morphogenesis in R. multiflora, and the identified candidates might be applied to the genetic improvement of roses.

Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.

Identification of Quantitative Trait Loci Controlling the Development of Prickles in Eggplant by Genome Re-sequencing Analysis

Eggplant (Solanum melongena L.) is the third most important crop in the family of Solanaceae. Prickles are considered as the undesirable traits during the plantation of eggplant and the transportation of fruits. In this study, we constructed a high-quality genetic linkage Bin map derived from the re-sequencing analysis on a cross of a prickly wild landrace, 17C01, and a cultivated variety, 17C02. The major quantitative trait locus (QTL) controlling the development of prickles on the calyx (explained 30.42% of the phenotypic variation), named as qPC.12, was identified on a ~7 kb region on chromosome 12. A gene within qPC.12, which encodes a WUSCHEL-related homeobox-like protein, with higher expression levels in 17C01 calyx and 22-bp deletion in 17C02 was probably the functional gene for prickle formation. Results from this study would ultimately facilitate uncovering the molecular regulatory mechanisms underlying the development of a prickle in eggplant.