Glucosinolates (GSLs) are unique sulfur-containing secondary metabolites in Brassica crops that critically influence stress resistance, nutritional quality, and economic value. This review systematically summarizes the chemical classification, tissue-specific distribution, and conserved three-phase biosynthetic pathway of GSLs in Brassica species. We dissect the core MYB-MYC-WRKY transcriptional regulatory network, elucidate how whole-genome duplication-driven gene functional diversification shapes species-specific GSL accumulation patterns, and outline the multi-layered regulatory system integrating endogenous and exogenous signals. Furthermore, we consolidate recent advances in the genetic dissection of GSL traits and molecular breeding strategies for targeted trait improvement. Finally, we propose a three-tiered regulatory cascade model for GSL metabolism and highlight future research priorities to address current breeding bottlenecks. This work provides a systematic theoretical framework for functional research and precision breeding of GSL metabolism in Brassica crops.

Cis-regulatory elements (CREs) orchestrate the spatiotemporal precision of gene expression that underlies plant development, adaptation, and domestication. Decoding the cis-regulatory grammar of plant genomes remains a central challenge in modern biology, with profound implications for programmable crop engineering. Here, recent conceptual and technological advances are synthesized to reshape our understanding of plant CREs. This review first argues that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three-dimensional genome topology, and cell type-specific regulatory landscapes. Furthermore, the convergence of single-cell epigenomics, high-throughput functional assays, and CRISPR-based dissection has begun to unravel this contextual grammar, revealing the computational principles governing transcriptional regulation. Critically, we propose that artificial intelligence (AI) platforms are catalyzing an ongoing transition from descriptive discovery to predictive engineering, wherein these platforms outperform natural evolution in designing synthetic CREs. Finally, a roadmap is outlined toward a plant regulatory grammar foundation model, which will enable truly predictive engineering of gene expression when fine-tuned for specific tasks. Collectively, the integration of single-cell resolution maps, precise genome editing, AI-driven design, and regulatory-compliant delivery systems promises to transform our ability to reprogram plant gene regulation for next-generation agriculture, bridging the gap between foundational regulatory biology and tangible crop improvement.

Long noncoding RNAs (lncRNAs) have been shown to play important roles in plant abiotic stress response and adaptation. However, the identification and characterization of genome-wide drought-responsive lncRNAs in rapeseed (Brassica napus L.) have been limited. Therefore, this study was the first to identify the expression profile of lncRNAs in rapeseed seeds responding to prolonged drought stress and subsequent short-term rewatering. A total of 6 000 lncRNAs were identified, among which 181 were classified as differentially expressed lncRNAs (DELs) in response to either drought stress or subsequent rewatering. Comparative analysis revealed that only 14 DELs were shared between the 159 DELs identified during drought stress and the 27 DELs detected upon rewatering. GO enrichment analysis showed that the co-expressed DEGs, primarily involved in photosynthesis, central carbon metabolism, stomatal movement, and strigolactone metabolism, were significantly down-regulated under drought stress but markedly up-regulated in subsequent rewatering. Furthermore, drought‑responsive competing endogenous RNA (ceRNA) networks were constructed based on the identified DETs and DEGs. Two ceRNA modules, MSTRG.57345.1-bna-miR164a/b/c/d-HSP2 and MSTRG.57345.1-bna-miR395d/e/f-HSFA7a, which are based on the newly identified lncRNA MSTRG.57345.1, were detected for the first time in rapeseed under drought stress and subsequent rewatering. The present study advances our understanding of the expression patterns and functional role of rapeseed lncRNAs in the response to drought stress and the subsequent rewatering. It provides novel insights into lncRNA-mRNA networks and lncRNA-miRNA-mRNA networks in the seeds of B. napus. These findings offer a valuable reference for further genetic research and molecular breeding programs aimed at rapeseed improvement.

Plant tissue culture is a crucial part of biotechnology that supports crop improvement, plant conservation, and other related fields. Although tissue culture has been successfully used in many plants, low regeneration and transformation rates still exist in some species. Agrobacterium-mediated transformation is commonly used in genetic engineering, but its effectiveness depends heavily on establishing a reliable in vitro regeneration system through organogenesis or somatic embryogenesis. Over the past decade, substantial progress has been made in understanding the molecular basis of regeneration; however, most reviews have focused on individual aspects such as hormone regulation or transcription factor networks in isolation. In contrast, this review provides a comprehensive and integrated framework that systematically links four critical layers-wound signaling, hormonal regulation, developmental regulators, and epigenetic modifications-into a unified regulatory network governing plant regeneration. Furthermore, we highlight recent cutting-edge advances, including artificial intelligence-assisted prediction, single-cell and spatial transcriptomics, epigenome editing, and CRISPR-based activation systems, and we discuss their transformative potential in overcoming genotype-dependent recalcitrance. By synthesizing classical regulatory mechanisms with emerging technologies, this review offers a forward-looking perspective that distinguishes it from earlier publications and provides both theoretical foundations and practical strategies for improving plant regeneration and genetic transformation.

Abstract Lodging remains a significant agronomic challenge that limiting the yield potential of Brassica napus globally, making the elucidation of its molecular basis critical for breeding new germplasm. Lignocellulose components (including lignin, cellulose, and hemicellulose) play an essential role in the mechanical strength of the stem, and they are regarded as the key determinants of lodging. In a doubled haploid (DH) population, 61 consensus quantitative trait loci (QTLs) associated with the lignocellulose content in the stem were identified through QTL analysis. Integrating QTL mapping with transcriptomic data revealed 1035 candidate genes potentially involved in stem lignocellulose biosynthesis, of which 52 high-confidence candidates were selected. Among them, BnaC01.MYB85, BnaA04.WRKY12, and BnaC03.ASMT exhibited stem-specific expression. A stem-specific lignocellulose biosynthetic pathway characterized by the coordinated expression of these high-confidence genes was delineated. Haplotype analysis in a natural population showed that BnaC03.ASMT segregated into two major haplotypes, with hap01 exhibiting a significantly higher hemicellulose content (HC) than hap02. These findings provide novel insights into the genetic regulation of lodging resistance and offer a valuable foundation for breeding B. napus cultivars with higher stem strength and lodging tolerance.

Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. In our previous work, we generated a high-throughput CRISPR library whereby a knockout collection was established for rapeseed breeding and functional genomics. However, the collection remains small and several promising candidate genes still await functional validation. Here, we report an update of this collection by constructing a small-scale CRISPR mutant library based on the elite commercial cultivar Zhongshuang 11 (ZS11). We first generated 326 independent T0 lines using an optimized protocol for ZS11 transformation and regeneration with a high positive rate of 94.2%. Analysis of the editing outcomes revealed a mutagenesis frequency of 68.4%. We then phenotyped this new collection and unraveled possible key genes underlying the variations in seed oil content (SOC) and plant height. Finally, we functionally validated BnFAB1B and BnEDA32, two candidate genes identified from our knockout collection. The results confirmed that loss of function of BnFAB1B significantly increases SOC, indicating its great agronomic potential, whereas knockout of the nuclear-localized BnEDA32 severely disrupts seed oil accumulation. This study provides a valuable knockout collection of the elite cultivar ZS11 and new genes for creating superior rapeseed germplasm.

Brassica napus is a member of the cruciferous family with rich glucosinolate (GSL) content, particularly glucobrassicin (3-indolylmethyl glucosinolate, I3M), that can be metabolized into indole-3-carbinol (I3C), a compound with promising anticancer properties. To unravel the genetic mechanism influencing I3C content in rapeseed seedlings, a comprehensive study was undertaken with a doubled haploid (DH) population. By quantitative trait loci (QTL) mapping, seven QTL that were located on A01, A07, and C04 were identified, with the most significant contribution to phenotypic variation observed on chromosome A07 (11.78%). The genes within the QTL confidence intervals (CIs) include transcription factors (TFs) and glycosyltransferases. After co-expression analysis, GSL-related regulatory network of TFs-targets was constructed and two TFs, BnaA07.ERF019 and BnaA07.NAC92, were identified as possible regulators in GSL biosynthesis. Three IGMT (glucosinolate methyltransferases) genes were found within the CIs that expressed higher in seedlings with more I3C, indicating their roles in I3C synthesis regulation. Molecular docking studies validated the binding capability of I3M to IGMTs, and those within the I3C QTL CIs have the strongest binding energy. These new discoveries offer critical insights into the genetic regulation of I3C content in rapeseed seedlings and establish a foundation for breeding high-I3C rapeseed varieties with potential health-promoting properties.

A core interaction network associated with cluster buds trait was discovered in Brassica napus, and indoleacetic acid-induced protein 8 (IAA8) might affect the shoot apical meristem (SAM) development through IAA8-ARF5 complex → DRN → CLV3 pathway. B. napus is one of the important oilseed crops in China. However, the low level of mechanized production restricts the industry due to the infinite inflorescence characteristics of B. napus. Therefore, the cultivation of new varieties suitable for mechanized harvesting is one of the main objectives of rapeseed breeding. In this study, a screened natural mutant of B. napus with no branching or short branches in the bolting stage and a relatively shorter flowering period showed distinct traits of cluster buds and uniform maturity, which made it suitable for high-density cultivation and mechanized harvesting. Microscopic examination between the wild-type (WT) and the cluster buds mutant (cbm) lines was performed across developmental stages. The results showed that the SAM regions of the mutants were widened and exhibited multiple growth points due to the loss of apical dominance. Transcriptome sequencing of SAM regions in the WT and cbm lines identified 2497 differentially expressed genes (DEGs). Bulk segregant analysis (BSA) pinpointed five significant genomic regions associated with the cluster buds trait and identified 799 candidate genes. Finally, an interaction network associated with the cluster buds trait was constructed, within which IAA8 was revealed as a candidate gene to regulate the SAM development in B. napus. Taken together, the present study elucidates the potential molecular regulation mechanism of cluster buds trait and laid a solid theoretical foundation for the cultivation of new varieties suitable for close planting and mechanized harvesting in B. napus.

Yellow seed coat color (SCC) is a valuable trait in Brassica napus , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus . In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 ( dominant gene of yellow seed coat color and improved seed oil content 1 ) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus , which has excellent potential for yellow SCC and high SOC rapeseed breeding.

Leaf senescence in rapeseed (Brassica napus), a globally important oilseed crop, is essential for yield optimization through nutrient remobilization. This study investigates the role of lipid signaling in rapeseed leaf senescence, focusing on the acyl-CoA-binding protein BnACBP1-like. Upregulation of BnACBP1-like induced premature leaf senescence, as evidenced by chlorophyll degradation, increased ion leakage, and jasmonic acid (JA) accumulation (other phytohormones showed no significant differences). Genetic analyses confirmed that this phenotype was dependent on the JA pathway. In contrast, CRISPR/Cas9 knockout lines resembled wild-type plants. Integrated multi-omics analysis revealed that BnACBP1-like overexpression triggered extensive lipid remodeling, characterized by decreased glycerophospholipid levels -including phosphatidic acid, phosphatidylcholine and phosphatidylethanolamine, and increased lysophospholipid levels, such as lysophosphatidylcholine, lysophosphatidylethanolamine, and free fatty acids (FFAs). Transcriptome profiling showed upregulation of lipoxygenases (LOX3, LOX3-like, LOX4 and LOX5) and phospholipase A2β (PLA2β), contributing to JA biosynthesis. Protein interaction assays confirmed direct binding between BnACBP1-like and PLA2β, while pharmacological inhibition of PLA2β activity suppressed senescence. These results suggest that their interactions may promote phospholipid hydrolysis and the release of FFA substrates for JA synthesis. Thus, the study reveals a critical role for lipid signaling in leaf senescence and elucidates the molecular mechanism by which BnACBP1-like regulates lipid metabolism, offering potential strategies to enhance photosynthetic product reutilization by controlling leaf senescence.

Leaf senescence in rapeseed (Brassica napus), a globally important oilseed crop, is essential for yield optimization through nutrient remobilization. This study investigates the role of lipid signaling in rapeseed leaf senescence, focusing on the acyl-CoA-binding protein BnACBP1-like. Upregulation of BnACBP1-like induced premature leaf senescence, as evidenced by chlorophyll degradation, increased ion leakage, and jasmonic acid (JA) accumulation (other phytohormones showed no significant differences). Genetic analyses confirmed that this phenotype was dependent on the JA pathway. In contrast, CRISPR/Cas9 knockout lines resembled wild-type plants. Integrated multi-omics analysis revealed that BnACBP1-like overexpression triggered extensive lipid remodeling, characterized by decreased glycerophospholipid levels -including phosphatidic acid, phosphatidylcholine and phosphatidylethanolamine, and increased lysophospholipid levels, such as lysophosphatidylcholine, lysophosphatidylethanolamine, and free fatty acids (FFAs). Transcriptome profiling showed upregulation of lipoxygenases (LOX3, LOX3-like, LOX4 and LOX5) and phospholipase A2(3 (PLA2 beta), contributing to JA biosynthesis. Protein interaction assays confirmed direct binding between BnACBP1-like and PLA2(3, while pharmacological inhibition of PLA2(3 activity suppressed senescence. These results suggest that their interactions may promote phospholipid hydrolysis and the release of FFA substrates for JA synthesis. Thus, the study reveals a critical role for lipid signaling in leaf senescence and elucidates the molecular mechanism by which BnACBP1-like regulates lipid metabolism, offering potential strategies to enhance photosynthetic product reutilization by controlling leaf senescence.

Plant oil production is crucial for meeting the global demand for vegetable oils providing essential fatty acids and energy and for various industry uses. Plant oil biosynthesis is a complex biological process. Understanding the process is essential for improving oil crop productivity and nutritional quality. To target genetic improvement strategies of oil content, this review attempts to provide a broad view of oil biosynthesis in terms of the oil biosynthesis chain and was thus arranged into four sections: the code/control center of oil production-genetic and genomic insight into seed oil content control; the manufacturing center of oil production-oil biosynthesis and its regulation; the upstream raw material supply chains of oil production-carbon source, energy, and reductants; and the progresses, challenges, and strategies-oil content improvement by conventional and biotechnological breeding in the past and future. Within these sections, we highlight major-effect quantitative trait loci of oil content and the WRINKLED1- and SEEDSTICK-centered regulatory networks of oil biosynthesis and then revisit/update the significance of both photosynthetic and maternal effect on oil content and the central metabolic pathways and related bypasses in oil accumulation. Strategies for further improvement of oil content are discussed toward constructing integrated frameworks for increasing oil productivity. Overall, with this review we aim to consolidate the recent progress regarding oil biosynthesis in crops and provide insights into future research and practical applications to crop oil production.

Crocus sativus is an autotriploid hybrid with many medicinal benefits from its stigmas. The crocin level, along with the number and weight of flowers, greatly affects the quality and yield of the stigmas. However, limited resources are available for studying the key genes responsible for these important agronomic traits. This study presents the first complete assembly of the C. sativus genome. It uncovers genomic rearrangements among the three chromosome sets and the loss of two large syntenic regions, which may influence the rates of genome divergence. By combining this new genome assembly with time-course mRNA transcriptome analyses across multiple developmental stages of stigma and flower bud tissues, we identified key candidate genes involved in carotenoid biosynthesis and flowering. We then experimentally verified the specific role of one gene, CsFT3-like, discovering that it acts as a positive regulator of flowering and pistil weight. Lastly, the putative flowering regulatory network in C. sativus was examined and compared with that of Arabidopsis, revealing many additional potential flowering-related genes that may function at distinct stages of development. The present study provides a valuable resource for understanding the genomic evolution of C. sativus and offers insights for enhancing its stigma quality and yield.

Brassica carinata has gained traction as an alternative biofuel feedstock in many countries, and serves as a well-known dual-purpose crop for both oilseed and leafy vegetable production. The purple varieties, which are rich in anthocyanins, are usually more eye-catching and beneficial to health. In this study, eleven cyanidin 3-glycoside-5-glucoside derivatives with different acyl modifications were characterized in two purple varieties of B. carinata (ZJC, which has an obvious purple stem, and ZJ, which has both purple stems and leaves) using an ultra-high performance liquid chromatography (UHPLC) system coupled with a high-resolution mass spectrometer (HRMS). In ZJ, the main anthocyanins are modified with a malonyl group at the C5 position, whereas such modifications are not found in ZJC. A total of 141 anthocyanin biosynthetic genes (ABGs) were identified in the B. carinata genome, and these genes were combined with the comparative transcriptome analysis based on RNA-Seq of leaves and stem peel from two purple varieties and one green variety to investigate the mechanisms underlying anthocyanin accumulation. A comprehensive synthetic and regulatory pathway for anthocyanin biosynthesis was proposed for B. carinata, and the ABGs in the pathway, particularly the late biosynthetic and transport genes, were predominantly regulated at the transcriptional level in pigmented tissues. Furthermore, the R2R3 MYB transcription factor BcaB05. MYB114 was verified as a crucial and conserved regulator of anthocyanin biosynthesis through its interactions with TT8 and TTG1 in Brassica species. This study opens new avenues for engineering anthocyanin-enriched B. carinata with improved horticultural quality.

Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78

For the past decade, research on constructing large-scale plant protein–protein interaction (PPI) networks has mainly focused on model plants, and the capability of experimental-based large-scale PPI networks in these plants was thought to be significantly inferior to the actual number of protein interactions in plants (Altmann et al., 2020; Jones et al., 2014; Smakowska-Luzan et al., 2018; Wang et al., 2023). Currently, there is still a lack of experimentally-derived, large-scale PPI data in plants, especially with respect to protein interaction networks specific to seed organs (Rhee and Mutwil, 2014). In this study, we selected Brassica napus, one of the most important oil crops extensively cultivated worldwide, to construct BnSTINet: an experimental-based seed transcription factor (TF) interaction network. CrY2H-seq is a method that utilizes high-throughput screening of PPIs and relies on precise protein expression libraries (Trigg et al., 2017). Nonetheless, the relatively high cost of this method restricts its extensive application (Pruneda-Paz et al., 2014). We have innovated a method for constructing precise yeast expression vectors, referred to as In-Gate, resulting in a remarkable cost reduction of 93% and a nearly 50% reduction in experimental time compared to the conventional CrY2H-seq method (Figure S1). To screen the candidate TFs for constructing the interaction networks, the developing seeds at the linear embryo, early curved embryo, mid- curved embryo, late curved embryo and green embryo stages were collected for RNA-seq (Figure 1a). The expression patterns of TFs were evaluated, and 10 gene clusters potentially related to seed development and organic accumulation were identified (Figures S2 and S3). Totally, a data set consisting of 932 non-redundant TFs (NRTFs) was proposed to construct the TFs interaction network (Table S1). Almost all NRTFs with FPKMs value greater than 5 were included in the data set (99.1%) (Figure 1b). Those TFs were involved in seed development, such as hormone response, embryo development, seed coat development, lipid metabolism and light response, etc. (Table S2). In total, a precise protein expression library consisting of 1886 Y2H strains expressing TFs was constructed one by one. Identification of self-activating TFs and utilization of nanopore sequencing for detection of interacting recombinant sequences in TF interaction screening enhances the efficiency of detecting protein–protein interactions compared to the original CrY2H-seq (Figure 1c,d). Based on the above optimization and modification of CrY2H-seq technology, we term it mCrY2H-seq which lowers the application threshold for the construction of experimental-based large-scale PPI networks (Figure 1e,f). We loaded a set of 1886 TFs into the mCrY2H-seq pipeline. Self-activating pre-screen showed that 96 TFs were with self-activating characteristics in the bait library (Figure S4; Table S3). Nanopore sequencing generated a total of 64 113 valid reads, while 62 747 of these reads were concurrently mapped to two different TFs, accounting for 97.9% of the entire set of valid reads. Totally, 805 pairs of PPIs were obtained and the unannotated TFs occupied 25.9% of total TFs in the network (Figure 1g; Table S4). The reliability of the interacting pairs within the TF interaction network was confirmed through one-to-one verification using the array yeast two-hybrid method (Figures S5–S11). In the interaction network, multiple interaction subnetworks conserved in model plants were found, such as the Bzip family homodimers, nuclear factor complex, auxin and brassinosteroid (BR) signalling pathway TF interaction network (Figure S12). Some unreported interactions, such as the interaction between indole-3-acetic acid inducible protein 2 (BnaIAA2)/BnaIAA9, auxin response factor 6 (BnaARF6)/BnaIAA18 and BnaARF8/BnaIAA10 (Figure 1h). A total of 24 pairs of direct interactions and 54 pairs of indirect crosstalk were found between IAA, jasmonic acid (JA), abscisic acid (ABA), gibberellic acid (GA), BR and ethylene (ET) hormone signal pathways, which involved direct hormone crosstalk (Figure S13). The BnSTINet can be readily accessed and made available through a publicly accessible website with a simple three-step process (https://yanglab.hzau.edu.cn/BnIR/TF_regulation_network) (Figures 1i and S14). A candidate G-box regulating factor 6 (BnaGRF6) that interacts with WRINKLED1 (BnaWRI1, a star molecule known to control fatty acid synthesis) was selected for the function investigation. The interaction between BnaGRF6 and BnaWRI1 was confirmed by Y2H, bimolecular fluorescence complementation (Figure S15a,b). Overexpression of BnaGRF6 significantly increased seed oil content by 0.9%–4.38% compared with the control (Figure S15c,d). Overexpression of the BnaGRF6 gene in seeds facilitated the elevation of transcriptional levels of downstream regulatory target genes of BnaWRI1 (Figure S15e). In 2274 B. napus germplasm in BnIR, a frameshift mutation from A to ACT in the reading frame of BnaGRF6 homologous gene BnaA03G0592400ZS was found (Figure S 16 a, b and c) (Yang et al., 2023). The frameshift mutation variant mainly appears in semi-winter and spring rapeseed and is distributed in Asia, followed by Europe and North America (Figures 1j and S16d). Among 258 germplasm resources growing in the same environment, the average seed oil content of B. napus germplasm of the mutant variant was 41.74%, which was significantly lower than that of the reference type (43.42%) (Figure 1k). Here, we present a comprehensive research strategy for exploring the functions of polyploid crop genes and achieving molecular breeding advancements. This work was funded by the National Key Research and Development Program of China (2022YFD1200400) and the National Natural Science Foundation of China (32172087, 32072098). The authors declare no conflict of interest. ML and YY designed the research. YY wrote the article. YY, ZG, JJ, HH, WC, NR, JL, YL, HZ and ZL optimized the CrY2H-seq method, the expression vector construction, yeast mating and the recombinant plasmid information sequencing. YY, KC, HL, JH, WZ and YD collected and screened the transcript factors. ML, LZ, CF and YL revised the manuscript. Figure S1 Workflow of the In-Gate method. Figure S2 and S3 NRTF clusters in B. napus seed. Figure S4 Reads number of self-activating TFs in the mCrY2H-seq screen by nanopore sequencing. Figures S5–S11 Point-to-point validation of interactions by array yeast two-hybrid method. Figure S12 Conserved subnetwork within BnSTINet. Figure S13 The hormone crosstalk in BnSTINet. Figure S14 A simplified tutorial on retrieving TF interactions in BnSTINet database. Figure S15 Functional verification of BnaGRF6 affecting seed oil accumulation. Figure S16 Variation and phenotypic distribution of BnaGRF6. Table S1 Comprehensive TF list and expression data used for the BnSTINet construction. Table S2 Enriched metabolic pathways list of the candidate NRTFs for mCrY2H-seq interaction network construction. Table S3 List of self-activated transcription factors detected in the TF interaction network of seeds. Table S4 List of all interaction pairs in the transcription factor interaction network of seeds. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Yellow Camellia is an endangered and protected wild plant with unique medicinal value. Among the Camellia Sect. Chrysantha Chang, certain species (e.g. Camellia limonia) can grow in karst regions. The karst region is a highly sensitive ecosystem with low environmental capacity. However, the molecular mechanisms underlying the adaptation of yellow camellia to karst regions remain unclear. Here, we present a high-quality genome with 15 chromosome groups with an N50 of 198.92 Mb. The divergence between C. limonia and Camellia sinensis occurred approximately 6 million years ago, indicating that the Himalayan uplift event may led to species differentiation. This enables C. limonia to thrive in a unique ecological environment like the karst region. Flavonoid compounds play a significant role in the interaction between plants and their environment. In comparison to Theaceae family genomes, C. limonia exhibits an increased number of gene family members involved in the flavonoid biosynthesis pathway, including UDP-glycosyltransferases and chalcone reductase. Additionally, two gene clusters associated with flavonoid biosynthesis were identified in the genome of C. limonia. Furthermore, comparative genomics analysis revealed the expansion of genes associated with karst environment adaptation in the genome of C. limonia, such as calmodulin genes and genes related to Calcium ion transmembrane transport. Additionally, at the gene expression level, it was observed that the secondary metabolism-related genes may be involved in the calcium tolerance of C. limonia. These findings provide important insights into the evolution of C. limonia, offering references for the study of plants in karst areas.

BACKGROUND:Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. RESULTS:In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. CONCLUSIONS:The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.