Soybean (Glycine max (L.) Merr.) was originally domesticated in China and is a significant leguminous crop, which can fix atmospheric nitrogen to bioavailable nitrogen. Ceramides, intermediates of sphingolipids, are crucial structural components in membrane formation and also function as signaling molecules, which play crucial roles in plant development and defense. Although Arabidopsis ceramide synthase genes AtLOH1 and AtLOH3 overexpression plants increased biomass compared to wild-type, its potential mechanism in plant growth was still unclear. A soybean ceramide synthase gene (GmCS1) has high expression level in the stem, and the protein is localized in the endoplasmic reticulum. Overexpression of GmCS1 promotes soybeans lateral branch development for effective branch formation, so as significantly increasing the number of lateral branches and pods. Using transcriptomic profiles, we found GmCS1 overexpression lines displayed the upregulation of plant hormone signal transduction pathway gene expression in developmental branches. Actually, Indole-3-acetic acid (IAA) induces bud outgrowth rather than initiation according to the determination of endogenous IAA andcytokinin (CKs) in soybean lateral branches. Collectively, these results suggest that GmCS1 may be a functional ceramide synthase gene in soybean, with the GmCS1-mediated regulatory network playing a crucial role in controlling branch development by IAA and CKs homeostasis. Understanding the ceramides regulation mechanisms by GmCS1 overexpression lines is essential for Ideal Soybean Architecture (ISA) innovation.

Soybean is a critical oil and protein crop for both food and forage production; however, its growth and development are severely impacted by drought stress. Nevertheless, the molecular regulatory mechanisms underlying drought tolerance in soybean remain poorly understood. In this study, two soybean varieties, Jindou 21 (JD21, drought-tolerant) and Suinong 26 (SN26, drought-sensitive), were used as experimental materials and subjected to 15% PEG6000 to simulate drought stress. Roots and leaves were sampled at 0 h, 6 h, and 12 h after treatment to determine physiological indicators and conduct RNA-seq analysis. The results showed that JD21 exhibited a lower malondialdehyde (MDA) content but higher soluble sugar and proline contents than SN26. A total of 2603 and 3128 osmotic-stress-responsive genes were identified in the roots and leaves of SN26 and JD21, respectively. Additionally, 256 genes in the roots and 215 genes in the leaves showed consistent differential expression between the two varieties across the three treatment time points. KEGG enrichment analysis revealed that the differentially expressed genes were significantly enriched in pathways related to glutathione metabolism, arginine and proline metabolism, glycolysis/gluconeogenesis, and starch and sucrose metabolism. Within these pathways, the functions of GmGST, GmAMD1, GmADH1, GmENO, GmsacA, and GmSUS3 were validated through transgenic hairy root assays, demonstrating that these genes play positive regulatory roles in osmotic stress response. This study provides valuable data for elucidating plant PEG-induced osmotic-stress-response mechanisms and offers theoretical support for drought-resistant soybean breeding.

Sphingolipids are essential regulators of plant growth and development, yet their functional specificity in soybean remains poorly understood. In this study, we focus on glucosylceramide (GluCer), a major sphingolipid end product, and identify GluCer d18:1/h16:0 as one of the most abundant sphingolipid molecular species in soybean roots. We identified and overexpressed the glucosylceramide synthase gene GmGCS1, one of four GmGCS genes in the soybean genome. GmGCS1 exhibited the highest expression level in roots. Functional assays demonstrated that overexpression promoted root development, increased seed size and yield, and enhanced phosphorus uptake and translocation. Conversely, suppression of GmGCS1 impaired root development and phosphorus uptake. Further mechanistic investigation revealed that the transcription factor GmPHR1 (PHOSPHATE STARVATION RESPONSE1) directly binds to the GmGCS1 promoter and activates its expression. Overexpression of GmPHR1 elevated GmGCS1 expression, enhanced root growth, increased root phosphorus content, and improved tolerance to phosphorus deficiency. Collectively, these results demonstrated that GmGCS1, regulated by GmPHR1, plays a role in soybean root and seed development through modulating phosphorus signaling. This study provides new insights into the interplay between sphingolipid metabolism and phosphorus regulation in soybean, offering a theoretical foundation and genetic target for improving soybean yield in phosphorus-limiting environments.

OVATE family proteins (OFPs) are key regulators involved in plant development and stress responses. However, their biological roles in soybean remain largely unclear. In this study, we identified GmOFP8, a member of OVATE family in soybean, which exhibits root-specific expression and is transcriptionally responsive to both brassinolide and drought stress. Overexpression of GmOFP8 increased drought tolerance and nodule numbers, whereas knockout of GmOFP8 resulted in reduced drought resistance and fewer nodules, indicating its positive role in regulating drought stress responses and nodulation. Protein-protein interaction analyses demonstrated that GmOFP8 physically interacted with the glycogen synthase kinase 3-like kinase, GmSK2, and this interaction promotes the nucleocytoplasmic shuttling of GmOFP8. Furthermore, overexpression of GmSK2 in soybean hairy roots suppressed both drought tolerance and nodulation. Based on these findings, we propose that GmSK2 plays a conserved role in mediating the phosphorylation status of GmOFP8, as observed in rice, thereby contributing to the regulation of drought tolerance and nodulation in soybean. These results provide valuable genetic resources for molecular breeding strategies aimed at improving stress resilience and nitrogen fixation capacity in soybean.

Buckwheat is a fast-growing crop valued for its gluten-free grain, high rutin content, adaptability to suboptimal conditions, and minimal nutrient requirements, making it an ideal candidate for sustainable crop rotation systems. Crop rotations are known to profoundly shape the diversity, composition, and complexity of soil microbial communities, ultimately impacting the functioning and productivity of agroecosystems. While soil abundant and rare microbial communities serve distinct ecological roles, the specific effect of different rotation patterns and buckwheat species on these communities within the rhizosphere and their subsequent roles in agriculture functioning remain largely unknown. To address this gap, we conducted a three-year field trial to assess the relationships among soil properties, rhizosphere bacterial communities, and buckwheat yields under three rotation systems: wheat-buckwheat rotation (R1), continuous mono-buckwheat cropping (R2), and soybean-buckwheat rotation (R3), using both common and tartary buckwheat species. Compared to differences between buckwheat species, rotation systems more significantly influenced the attributes of both abundant and rare communities, soil chemical properties, and soil enzyme activities. Notably, R3 had a higher diversity of abundant taxa, enhanced complexity, cohesion, and robustness of abundant bacterial interactions, and a greater number of abundant biomarkers, relative to the monoculture practice in R2. This likely increased the resilience of abundant taxa in the diversified rotation system to stresses and facilitated belowground ecosystem functions, significantly contributing to higher buckwheat yield. In contrast, while R3 also increased diversity of rare taxa and altered their communities, these changes primarily affected soil chemical properties through modulating soil enzyme activities. These findings suggest that the attributes of abundant and rare taxa in the buckwheat rhizosphere, when intensified by the diversified rotation system, played distinct roles in different facets of agroecosystem functioning. Overall, our study highlights the importance of diversifying rotational diversity to bolster agricultural sustainability.

Background: Global food security faces mounting pressure from population growth, climate change, and overreliance on nutritionally inadequate staple cereals. Integrating climate-resilient orphan crops-with their multifunctionality and low-input requirements-enhances nutritional security and advances multiple Sustainable Development Goals (SDGs) through sustainable land use. Scope and approach: This review systematically examines buckwheat (Fagopyrum spp.), an orphan crop with persistent global cultivation despite limited research focus. Moving beyond existing literature on nutritional attributes, we analyze the relationships of its historical dissemination, evolutionary trajectory, and multifunctional roles, which bridges traditional and modern applications in food systems, pharmacology, and agriculture-while outlining future research perspectives. Key findings: By analyzing its historical dissemination from mountainous marginal lands to worldwide cultivation, highlighting socioeconomic variations in production, yield, and dietary roles. We argue that buckwheat's resilience to extreme environments and adaptability to diverse agricultural practices originate in its Himalayan evolutionary origins. This heritage, coupled with multifaceted societal benefits, bridges traditional uses and contemporary applications. Cutting-edge genomic research further substantiates buckwheat's enduring significance from past to future. Finally, we elucidate how the "Buckwheat Model"-defined by genetic plasticity, environmental buffering capacity, and multiple-utilization potential-provides a framework for climate-resilient agricultural systems. This model advances interconnected sustainability goals and offers actionable strategies for leveraging orphan crops to achieve SDGs.

Soybean (Glycine max) constitutes one of the paramount oil and forage crops globally. High and uniform seed germination is essential for optimizing soybean yield. Sphingolipids are major constituents of membrane lipid rafts and exert pivotal roles in plant growth and stress responses. Nevertheless, comprehension regarding the functionalities of sphingolipids in seed germination remains elusive. Using chemicobiological approaches, we discovered that exogenous application of C24 phytoceramide t18:0/24:0 could facilitate seed germination in soybean. To elucidate the role of sphingolipids in soybean seed germination, we conducted an integrated time-course transcriptome and sphingolipidomic analysis on germinated soybean seeds. Through time-course transcriptome analysis, we identified two gene modules positively or negatively correlated with seed germination; the expression levels of these genes were successively up-or down-regulated during seed germination, respectively. Notably, numerous genes involved in sphingolipid biosynthesis exhibited down-regulation during seed germination, particularly LCB Delta 8 desaturases, which attracted our attention. Furthermore, our time-course sphingolipidomics outcomes indicated that the concentrations of ceramide d18:0/16:0, ceramide d18:0/22:0, and phytoceramide t18:0/24:0 increased during seed germination, suggesting a positive association between saturated ceramides and seed germination in soybean. Additionally, overexpression of GmSLD1 (encodes LCB Delta 8 desaturase) gave rise to strong seed dormancy in soybean by reducing the GA/ABA ratio within soybean seeds. In conclusion, through comprehensive time-course transcriptome profiling combined with sphingolipidomics and genetic evidence, we identified two sets of genes related to soybean seed germination and demonstrated that saturated simple ceramides play crucial roles therein.

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Seed yield and quality are quantitative traits that are controlled by multiple genes. Although several genes associated with hundred-seed weight have been reported, the underlying molecular mechanisms remain poorly understood. In this study, quantitative trait locus (QTL) mapping was employed using six generations derived from a cross between Changjiang Chun 2 (high hundred-seed weight) and Jiyu166 (low hundred-seed weight). A total of 64 QTLs, including 24 QTLs for hundred-seed weight (HSW), 17 QTLs for seed length (SL), and 23 QTLs for seed width (SW), were identified. Among these, six QTLs shared common intervals in both linkage mapping and bulked segregant analysis (BSA)-seq. Ninety genes contained variations in the region of the coding sequence within these genomic regions. Furthermore, transcriptome analysis revealed 24 differentially expressed genes (DEGs) within the QTL regions. In conjunction with QTL mapping, BSA-seq, and RNA-seq, a total of 6 genes were identified as candidate genes controlling hundred-seed weight- in soybean. These results provide valuable genetic resources for both candidate gene exploration and marker-assisted breeding aimed at enhancing the soybean yield potential.

Tartary Buckwheat [Fagopyrum tartaricum (L.) Garten, TB] is an annual herb, which has high nutritional value. Amino acid permease (AAP) can extensively absorb and transport various amino acids and participate in a series of physiological processes in plant growth. However, research on AAP genes in Tartary buckwheat remains limited. In this study, a total of 18 FtAAP proteins were identified and categorized into 3 phylogenetic subgroups. There was a similarity in gene structure and motif composition among proteins within the same subset. In addition, a variety of hormone responsive elements and abiotic stress response elements were detected in the promoter region of the FtAAP genes. An analysis of synteny showed that Tartary buckwheat was related to dicotyledons more than monocotyledons. Expression pattern analysis indicated that most FtAAP genes exhibited tissue-specific expression patterns. The expression of FtAAP genes exhibited significant responsiveness to diverse phytohormone treatments, including ABA, IAA, GA, SA, and MeJA by RT-qPCR analysis. This study integrated phylogenetic analysis with genome-wide expression profiling to provide valuable information for understanding the functional characteristics of AAP genes in Tartary buckwheat.

QTL mapping, BSA-seq, and RNA-seq revealed key QTL/genes of protein and oil, some of which were aligned with previous QTLs. EMS-mutations and SoyGVD were applied to validate function of candidate genes. Protein and oil are the two principal economic components of soybean seed. Although several related genes regulating soybean protein and oil accumulation have been reported, the regulatory mechanisms remain largely unknown. In this study, quantitative trait loci (QTL) mapping was employed using four generations derived from a cross between Changjiangchun 2 (high protein and oil content) and Yushuxian 2 (low protein and oil content), resulting in the detection of 37 QTLs, including 16 QTLs for protein content and 21 QTLs for oil content. BSA-seq was performed on two parents and two offspring extreme pools from F2 population individuals. Two QTLs, qOIL1.2 and qPRO14.1, were found to overlap with the BSA-seq mapping interval, in which eight genes exhibited single nucleotide polymorphisms (SNPs) or insertion/deletion (InDel) variations within their coding sequences (CDS). RNA-seq was performed on seeds collected at 20, 30, and 40 days after-pollination (DAP) from two extreme pools of F2:3 population individuals. A total of 199 deferentially expressed genes (DEGs) were obtained within the QTLs regions. In conjunction with previous research, 10 protein and four oil QTLs intervals were aligned with previously identified QTLs. Notably, based on EMS-induced mutation lines and SoyGVD database, 12 potential candidate genes were screened out and preliminary validated the function for oil and protein in soybeans. These findings lay the groundwork for further research into candidate genes and marker-assisted selection (MAS) in soybean breeding to enhance seed protein and oil content.

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map. A genetic map containing 445 SSR markers with an average distance of 5.3 cM and a total length of 2375.6 cM was obtained. Based on constructed genetic map, 11 traits including hundred-seed weight (HSW), seed length (SL), seed width (SW), seed length-to-width ratio (SLW), oil content (OIL), protein content (PRO), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), palmitic acid (PA), stearic acid (SA) of yield and quality were detected by the multiple- d size traits and 113 QTLs related to quality were detected by the multiple QTL model (MQM) mapping method across generations F2, F2:3, F2:4, and F2:5. A total of 71 QTLs related to seed size traits and 113 QTLs related to quality traits were obtained in four generations. With those QTLs, 19 clusters for seed size traits and 20 QTL clusters for quality traits were summarized. Two promising clusters, one related to seed size traits and the other to quality traits, have been identified. The cluster associated with seed size traits spans from position 27876712 to 29009783 on Chromosome 16, while the cluster linked to quality traits spans from position 12575403 to 13875138 on Chromosome 6. Within these intervals, a reference genome of William82 was used for gene searching. A total of 36 candidate genes that may be involved in the regulation of soybean seed size and quality were screened by gene functional annotation and GO enrichment analysis. The results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean.

Soybean, a primary vegetable protein source, boasts favorable amino acid profiles; however, its composition still falls short of meeting human nutritional demands. The soybean amino acid content is a quantitative trait controlled by multiple genes. In this study, an F2 population of 186 individual plants derived from the cross between ChangJiangChun2 and JiYu166 served as the mapping population. Based on the previously published genetic map of our lab, we increased the density of the genetic map and constructed a new genetic map containing 518 SSR (simple sequence repeats) markers and 64 InDel (insertion-deletion) markers, with an average distance of 5.27 cm and a total length of 2881.2 cm. The content of eight essential amino acids was evaluated in the F2:5, F2:6, and BLUP (best linear unbiased prediction). A total of 52 QTLs (quantitative trait loci) were identified, and 13 QTL clusters were identified, among which loci02.1 and loci11.1 emerged as stable QTL clusters, exploring candidate genes within these regions. Through GO enrichment and gene annotation, 16 candidate genes associated with soybean essential amino acid content were predicted. This study would lay the foundation for elucidating the regulatory mechanisms of essential amino acid content and contribute to germplasm innovation in soybeans.

>Crop domestication has long been regarded as an evolutionary process because the development of new and improved cultivars is based on selection. Many domesticated crops possess a suite of selected characteristics such as plant architecture, seed shattering, and inflorescence-related traits (Shi and Lai, 2015). Alteration of secondary metabolites has also become a common domestication trait. However,it seems to be somewhat overlooked (Alseekh et al., 2021).

Potato–legume intercropping has been confirmed to increase productivity in modern agricultural systems. However, the physiological and ecological mechanisms of potato–soybean intercropping for promoting tuber yield formation in potato remain unclear. Field experiments were conducted in 2022 and 2023 to explore the responses of tuber yield formation, rhizosphere soil quality, root growth, and plant physiology of potato in potato–soybean intercropping. The soil at the experimental site is Cambisols. The treatments included sole cropping potato, sole cropping soybean, and potato–soybean intercropping. Our results indicated that potato –soybean intercropping decreased the water content, increased the total K content and activities of urease and catalase in rhizosphere soil, and enhanced the root mean diameter, root projected area, and root length density in the 0–5 cm and 15–20 cm soil layers of potato. Moreover, potato–soybean intercropping improved the plant photosynthetically active radiation and light transmittance rate of the middle and lower layers as well as the leaf area index, enhanced the leaf chlorophyll b content and ribulose-1,5-diphosphate carboxylase/oxygenase activity, and increased the leaf net photosynthetic rate and organ dry matter accumulation amounts of potato. The changes in the above parameters resulted in an increased tuber weight per plant (19.4%) and commercial tuber number (42.5%) and then enhanced the equivalent tuber yield of potato (38.2%) and land equivalent ratio (1.31 in 2022 and 1.33 in 2023). Overall, potato–soybean intercropping greatly increased the equivalent tuber yield by improving the rhizosphere soil quality, root growth, and plant physiology of potato and then achieved a higher land equivalent ratio.

Background Soybean (Glycine max) is one of the most important oil and fodder crop worldwide. High and uniform seed germination is crucial for soybean yield. Sphingolipid is one of the major components of membrane lipid raft, which has crucial roles in plant growth and stress responses. However, Knowledge regarding the functions of sphingolipid in seed germination is elusive. Results Through chemicobiological methods, we found that exogenous application of C24 phytoceramide t18:0/24:0 could accelerate seed germination in soybean. In order to explore the functions of sphingolipid in soybean seed germination, we performed integrated time-course transcriptome and sphingolipidomics with germinated soybean seeds. We identified two modules of gene set that were positively or negatively associated with seed germination by time-course transcriptome analysis, and the expression of these genes were gradually up- or down- regulated during seed germination, respectively. Among which, many genes involved in sphingolipid biosynthesis were down-regulated during seed germination, especially, the LCB Δ8 desaturases attracted our attentions. Moreover, our time-course sphingolipidomics results indicated that the amounts of ceramide d18:0/16:0, ceramide d18:0/22:0, and phytoceramide t18:0/24:0 were elevated during seed germination, suggesting that saturated ceramides is positive related to seed germination in soybean. Conclusion Through time-course transcriptome analysis, we identified two set genes that related to soybean seed germination. Moreover, consider with time-course sphingolipidomics and chemicobiological assays, we demonstrated that saturated simple ceramides have positive roles in soybean seed germination.

Soybean (Glycine max) is an important crop, rich in proteins, vegetable oils and several other phytochemicals, which is often affected by light during growth. However, the specific regulatory mechanisms of leaf development under shade conditions have yet to be understood. In this study, the transcriptome and metabolome sequencing of leaves from the shade-tolerant soybean 'Nanxiadou 25' under natural light (ND1) and 50% shade rate (SHND1) were carried out, respectively. A total of 265 differentially expressed genes (DEGs) were identified, including 144 down-regulated and 121 up-regulated genes. Meanwhile, KEGG enrichment analysis of DEGs was performed and 22 DEGs were significantly enriched in the top five pathways, including histidine metabolism, riboflavin metabolism, vitamin B6 metabolism, glycerolipid metabolism and cutin, suberine and wax biosynthesis. Among all the enrichment pathways, the most DEGs were enriched in plant hormone signaling pathways with 19 DEGs being enriched. Transcription factors were screened out and 34 differentially expressed TFs (DETFs) were identified. Weighted gene co-expression network analysis (WGCNA) was performed and identified 10 core hub genes. Combined analysis of transcriptome and metabolome screened out 36 DEGs, and 12 potential candidate genes were screened out and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assay, which may be related to the mechanism of shade tolerance in soybean, such as ATP phosphoribosyl transferase (ATP-PRT2), phosphocholine phosphatase (PEPC), AUXIN-RESPONSIVE PROTEIN (IAA17), PURPLE ACID PHOSPHATASE (PAP), etc. Our results provide new knowledge for the identification and function of candidate genes regulating soybean shade tolerance and provide valuable resources for the genetic dissection of soybean shade tolerance molecular breeding.

硅为地壳中含量第二丰富的元素,其作为肥料施用,对农作物增产具有十分显著的效果.选取苦荞品种酉荞一号作为试验材料,于 2019 年与 2020 年进行重复试验,采用随机区组试验设计,设置 4 个硅肥水平,0(A1)、30 kg/hm2(A2)、60 kg/hm2(A3)和 90 kg/hm2(A4)以及 3 个纳米土墒材料水平,0(B1)、75 kg/hm2(B2)和 150 kg/hm2(B3).通过配施不同水平的硅肥和纳米土墒材料,研究其对苦荞倒伏表现、产量及茎秆生理特性的影响,结果表明:① 合理配施硅肥和纳米土墒材料可以延后倒伏时期,明显降低苦荞倒伏率和倒伏级别;② 施用硅肥和纳米土墒材料可以显著提高苦荞的产量,并且配施硅肥与纳米土墒材料的处理产量提升更为显著,与对照 A1 B1 相比,A3 B2 处理产量提高了 109.82%;③ 施用硅肥和纳米土墒材料可以提高苦荞茎秆抗折力,显著降低倒伏指数,提高茎秆强度,并且配施硅肥与纳米土墒材料的效果更为显著且稳定;④ 施用硅肥和纳米土墒材料一定程度上可以降低苦荞重心高、第二节间长度、株高和增加第二节间直径、茎壁厚度、节间充实度,且配施硅肥与纳米土墒材料效果更优;⑤ 硅肥和纳米土墒材料适当单施或者两者配施有利于苦荞茎秆中硅、木质素、纤维素、半纤维素的积累,从而增强茎秆韧性,降低倒伏的发生,且配施硅肥与纳米土墒材料提升效果优于单施.本试验条件下,配施 60 kg/hm2 硅肥与 75 kg/hm2 纳米土墒材料效果最佳,能够有效优化苦荞的茎秆结构,降低倒伏的发生,提高苦荞产量.

芦丁是一种黄酮类化合物,具有强化血管、抗氧化等生物活性.苦荞籽粒富含芦丁,是重要的药食兼用作物.了解和研究苦荞芦丁含量的遗传规律,开发与苦荞籽粒芦丁含量相关的分子标记对选育高芦丁苦荞种质具有重要意义.本研究以 263 个苦荞种质资源为材料,检测并统计分析芦丁含量,263 个种质籽粒芦丁含量的变幅为0.46%～1.43%,变异系数为 21.64%,利用实验室已有的 77 对 SSR标记检测结果,聚类分析将 263 份苦荞资源分为 3 个类群,群体结构分析将 263 份种质划分为 3 个亚群.亲缘关系分析结果说明材料间亲缘关系较远,对关联分析影响较小.GLM和 MLM模型的p 值 QQ plot图显示两个模型都适用于 263 份苦荞资源的芦丁关联分析,结果表明:TatG0085,TatG0131,TatG0155,TatG0156,TatG0164,TatG0187,TatG0188,S6763,SWU_Ft029,SWU_Ft177,SWU_Ft394,SWU_Ft420 这 12 对 SSR标记与苦荞芦丁含量显著关联,其中 TatG0164 和 SWU_Ft394 在两个模型中均与芦丁含量呈显著性关联,与前人研究相比,8 个标记可能存在一因多效的功能.该研究结果可以为分子标记辅助选择高芦丁苦荞种质资源及苦荞芦丁含量重要功能基因挖掘提供重要科学依据.

Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F2 population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding.