Plant height is a crucial agronomic trait that significantly influences plant architecture and yield in soybean (Glycine max (L.) Merr.). Identifying major genes regulating plant height and developing closely linked molecular markers are crucial for breeding soybean cultivars with ideal architecture. In this study, a recombinant inbred line (RIL) population (F2:7-8) developed from a cross between two soybean cultivars with contrasting plant heights was used to conduct quantitative trait loci (QTL) mapping for plant height across five environments based on a high-density genetic linkage map. As a result, 13 QTL associated with plant height were identified on seven chromosomes. Among these, four QTL (qPH-5, qPH6-1, qPH18, and qPH19-2) were consistently detected across multiple environments. Candidate genes for three stable QTL (qPH6-1, qPH18, and qPH19-2) with major effects on plant height were identified by annotating single-nucleotide polymorphisms within the parental haplotypes, combined with analyses of gene expression patterns and biological functions. Consequently, TCP13, Dt2, and Dt1 were predicted as strong candidate genes influencing plant height within these loci, respectively. Haplotype analyses within RIL population and across diverse soybean germplasm revealed that allelic variation in each of these genes significantly affected plant height. Moreover, different haplotype combinations of the three genes exhibited distinct phenotypic effects, indicating a pyramiding effect of these three genes on plant height. These findings will facilitate molecular breeding of soybean cultivars with ideal plant architecture.

Soybeans have garnered significant attention as a vital source of nutrients due to the growing demand for functional foods and the persistent issue of hidden hunger. Herein, we employed multiple cultivars and processing, including soy beverage, fermented soy beverage, natto, and soy sprouts, to systematically evaluate the effects of cultivar and processing technologies on key bioactive components. Results demonstrated that the genetic background was the primary determinant of product nutritional quality. Consequently, high-folate/ isoflavone cultivars retained significantly greater levels across all products. Processing exerted complementary effects: natto fermentation markedly increased tetrahydrofolate (up to 419%) and glycitein while degrading sucrose and forming melibiose. Liquid-based processing elevated beta-glucoside isoflavones (e.g., daidzin +6.18fold) but reduced malonylated forms (61.5-97.3%). Liquid-based processing and natto fermentation increased total folate content by 54.3% to 108% compared to raw soybean seeds. This study provides a scientific rationale for producing nutritionally enhanced soy foods through targeted cultivar selection and optimized processing.

Soybean seeds are rich in saponins, yet their variation across germplasm and environments is poorly explored. We developed an HPLC-MS/MS method to extract and quantify Group A and B saponins and profiled 711 soybean accessions across four environments. Genotype, accession type, ecoregion, seed coat colour, and seed tissue all significantly affected saponin content, with five-fold variation (1376.19-6764.67 μg/g). Group A saponins were dominant (77.5%), led by Ab (46.0%) and Aa (23.0%). Black-seeded accessions showed the highest total saponin content. Moreover, the hypocotyl exhibited high total saponin content (45,230.40 μg/g; 93.5% Group A). Total saponins positively correlated with all constituents (except Af) and with oil, but negatively with protein. Geographical distribution revealed that Northern and Huang Huai-Hai Region accessions had high levels of Group A and total saponins. This study provides comprehensive and novel insights into seed saponin profiles and identifies elite accessions to support breeding and industrial applications.

IntroductionMungbean [Vigna radiata (L.) R. Wilczek] has emerged as a highly valued crop owing to its unique functional properties. Improving seed quality represents a major goal in mungbean breeding; however, the systematic identification of quantitative trait loci (QTLs) governing key seed quality traits remains limited.MethodsIn this study, a recombinant inbred line (RIL) population derived from a cross between Zhonglv1 and HB211 was developed, and phenotypic data were collected across three distinct environments. Three complementary QTL mapping methods—composite interval mapping (CIM), inclusive composite interval mapping (ICIM), and multiple QTL mapping (MQM)—were utilized to detect genomic regions associated with protein, starch, oil, and moisture content.Results and discussionIn total, 162 QTLs were identified, including 44, 30, 43, and 45 QTLs were identified for protein, starch, oil, and moisture content, respectively. Among these, stable QTLs were consistently detected across multiple environments and methods, highlighting their potential utility in breeding applications. The putative candidate genes underlying these robust QTLs were further annotated, providing preliminary insights into the genetic control of seed quality traits. This study establishes a comprehensive genetic framework for future functional studies and the development of improved mungbean varieties with enhanced seed quality.

Mungbean [Vigna radiata (L.) R. Wilczek] has gained increasing popularity in the food industry owing to its unique functional properties and high nutritional value. Improving the protein, starch, and water content of mungbean seeds is a fundamental breeding objective, as these traits are critical determinants of seed quality. However, there have been no systematic reports of identified quantitative trait loci (QTLs) associated with these traits in mungbean. In this study, we generated a recombinant inbred line (RIL) population from a cross between B031 and B2939 and conducted phenotypic evaluation across three distinct environments. Using three QTL mapping methods, we identified 19 QTLs associated with protein content, 16 QTLs for starch content, and 12 QTLs for water content. Among these, qPRO10-1, qSTA8-1, and qWAT7-2 were consistently detected across different environments and mapping methods. Our further investigation identified two candidate genes potentially regulating protein content, one for starch content, and one for water content. These findings provide a solid theoretical foundation for future functional studies on the genetic regulators of these key traits and support the breeding of high-quality mungbean germplasm.

Understanding the relationship between genomic variation and phenotype is fundamental to deciphering the genetic architecture underlying complex traits. Yet, existing statistical models struggle to balance massive genomic datasets with biological interpretability. Here, we introduce GP-WAITER, a deep learning framework integrating GWAS-derived SNP weights into a hybrid convolutional neural network and Transformer architecture. By utilizing a weighted embedding mechanism and multi-head self-attention, GP-WAITER effectively captures long-range dependencies across ultra-long genomic sequences. The model consistently outperforms seven state-of-the-art genomic prediction models across six datasets, achieving up to a 77.5% improvement in prediction accuracy, a 78% reduction in mean squared error, and a 1.8-2.4fold increase in computational efficiency. Furthermore, GP-WAITER offers biological transparency by pinpointing key genetic variants driving specific traits. This scalable, interpretable framework provides a powerful tool for precision breeding and the functional interpretation of trait-associated variants.

Vitamin B2, comprising riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) are essential micronutrient and plays a vital role in human health. Despite the nutritional value of soybean, its vitamin B2 profile remains beyond the realm of research lens. However, this study was designed to bridge this gap by optimizing a rapid, cost-effective UPLC-FLD method for simultaneous extraction and quantification of these compounds. The vitamin B2 compositions were assessed in 1186 soybean accessions, comprising landraces and cultivars obtained from different ecoregions of China across two years. The total vitamin B2 content varied 2.2-fold, ranging from 158.46 to 357.58 mu g/100 g FW, with the highest mean from the southern region. FAD was the dominant derivative, contributing over 42 % to total vitamin B2. Correlation analysis depicted a strong positive association between individual vitamin B2 and nutritional traits like isoflavone and polyunsaturated fatty acid. These findings provide foundational insights for soybean biofortification strategies to combat global vitamin B2 deficiency dilemma.

Soybean oil plays crucial roles in both food and biodiesel industries. Increasing oil content and improving the fatty acid composition are critical objectives in soybean breeding programs. In this study, we performed high-resolution QTL mapping for oil content and fatty acid composition using 192 F2:7-8 recombinant inbred lines (RILs) based on a high-density genetic map. We detected a total of 66 QTL, including 14 for oil content and 52 for individual fatty acids. Among these, seven QTL were stable across multiple environments, with qPA-05 and qLA-06 being novel loci for palmitic and linoleic acids, respectively. A total of 34 QTL were grouped into seven clusters. Through candidate gene mining for Cluster05-2 and qLNA-14 using single-locus ANOVA in 1025 soybean accessions, combined with gene expression profiling and annotation, we identified the MOTHER OF FT AND TFL1 (MFT) gene (Glyma.05G244100), the 2-acylglycerol O-acyltransferase (MGAT) gene (Glyma.05G248100), and three ubiquitination-related genes (Glyma.05g237500, Glyma.05G238500, and Glyma.05G238900) in Cluster05-2 as strong candidate genes for oil content, and the ω-3 fatty acid desaturase (FAD3A) gene (Glyma.14G194300) in qLNA-14 as strong candidate gene for linolenic acid. Haplotype analyses of these candidate genes revealed significant influence of specific haplotypes on oil and linolenic acid content, respectively. Notably, for MGAT, the frequency of the high-oil haplotype (Hap1-TA) exhibited a clear decreasing trend from north to south in China among the soybean accessions, which is consistent with the distribution trend of soybean oil content across China. The discovery of stable QTL and candidate genes associated with oil and fatty acid contents will enhance the efficiency of molecular breeding programs aimed at improving soybean quality.

Flavonoids are key secondary metabolites in soybean, contributing to the plant defense mechanism and human health. The isoflavones in soybean have been well studied, and non-isoflavone flavonoids remain unexplored. This study optimized and validated a highly sensitive high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS) method to quantify 13 flavonoids from five subclasses (chalcone, flavanols, flavanones, flavones, and flavonols), representing 82 % of total flavonoid content (TFC) in soybean seeds. Profiling 711 diverse soybean accessions from China's three main ecoregions revealed significant variation, with TFC ranging from 667 to 24503 mu g/100g, representing a 36-fold difference; four accessions exceeding 20000 mu g/ 100g. The Huang Huai Hai Valley Region (HR) had the highest mean TFC (3341 mu g/100g). Black seed coat accessions exhibited the highest flavonoid concentrations. The cumulative share of four major flavonoids, epicatechin, quercetin 3-galactoside, prunin, and apigenin, accounted for 77-81 % of TFC, particularly the darkpigmented seedcoat enriched with epicatechin and quercetin derivatives. TFC correlated positively with most flavonoids, isoflavones, and protein, but negatively with oil content. Major flavonoid components were negatively associated with longitude, suggesting that geographical origin affects flavonoid accumulation. The findings provide actionable insights for breeding nutritionally enriched soybean varieties, with implications for functional food development.

As the second important staple crop next to rice in China, common wheat (Triticum aestivum) plays a decisive role in national food security. Wild and semi-wild relatives of wheat provide abundant genetic resources for wheat genetic improvement. In China, wheat wide hybridization and chromosome engineering breeding initiated in the 1950s and developed into a well-defined theoretical and technical system over the next three decades through learning, exploration and practice. Subsequently, the technological innovation in alien chromatin identification and the isolation and analysis of alien resistance genes sponsored by continuous national projects have significantly enhanced China's impact on the world in this field. Eminent scientists such as Professor Li Zhensheng, who was awarded the Medal of the Republic before the National Day in 2024, have made outstanding contributions to the establishment and development of the research in this area in China. This article reviews the history of wheat wide hybridization and chromosome engineering breeding in China, aiming to honor the senior scientists and inspire future researchers to work hard in germplasm innovation and alien gene transfer, cloning and utilization in breeding.

Understanding the genetic architecture of soybean seed fatty acid (FA) compositions to enhance oil quality is crucial for nutritional value and industrial applications. This study elucidates the genomic determinants of seed FA composition in soybean (Glycine max [L.] Merr.) through comprehensive genome-wide association study (GWAS) analysis utilizing 1,550 diverse soybean accessions evaluated across five distinct environmental conditions. The phenotypic evaluation revealed significant genetic variability and environmental influences on the biosynthetic process of five essential FAs: palmitic (PA), stearic (SA), oleic (OA), linoleic (LA), and linolenic acid (LNA). High-throughput genomic association mapping identified 110,964 significant SNP-trait associations encompassing 18,841 putative genes. Notable genetic loci included chromosome 5 and 17 harboring GmFATB1A and GmFATB1B for PA biosynthesis; chromosome 2 and 8 containing Glyma.02G161200 and Glyma.08G279700 associated with SA regulation; chromosomes 10, 13, and 20 with GmKCS21, GmKAS2, and GmFAD2 affecting OA concentration; chromosomes 10 and 13 with GmKCS21 and GmKAS2 influencing LA content; and chromosome 14 containing GmFAD3 controlling LNA biosynthesis. Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed significant overrepresentation of lipid metabolic processes, particularly glycerolipid metabolic pathways. The haplotype characterization of three key regulatory genes GmKCS21, GmFAD2, and GmFAD3 revealed distinct geographic distribution patterns across the northern region, Huang-Huai-Hai region, and southern ecoregions of China, with varying allelic frequencies between improved cultivars and landraces, reflecting adaptive evolution and selection pressure during domestication and enhancement. This study provides a comprehensive genetic resource of 110,964 SNP-trait associations and functionally characterized haplotypes of key regulatory genes (GmKCS21, GmFAD2, and GmFAD3) that demonstrate ecoregion-specific allele frequency patterns, enabling marker-assisted selection strategies tailored to those soybean production ecoregions.

The improvement of soybean seed carotenoid contents is indispensably important owing to its beneficial role to human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed the next generation sequencing-based bulked-segregant analysis for identifying new genomic regions governing seed carotenoids in 1551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotype were pooled to form two bulks with high (50 accessions) and low (50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gbp of clean bases and 89.82% of Q30 were obtained and the average alignment efficiency was 99.45% with average coverage depth of 62.20× and 99.75% genome coverage. Based on the G’ method analysis, a total of 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant region displaying the highest elevated G’-value was found in chromosome 06 at a position of 18.53-22.67 Mb, and chromosome 19 at a genomic region intervals of 8.36-10.94, 12.06-13.79 and 18.45-20.26 Mbs, and were preferably taken to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to get 90 significantly enriched (P<0.05) gene ontology (GO)-terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of which, following their gene annotation function and high significant haplotype variation in various environments, five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and suggested for further functional validation studies. Collectively, understanding the genetic bases of carotenoid pigments and identifying genes underpinning carotenoid accumulation via bulked-segregant analysis sequencing (BSA-seq) approach provide new insight for exploring future molecular breeding of high carotenoid content in soybean cultivars.

Mungbean [Vigna radiata (L.) R. Wilczek] has gained significant popularity in the food industry, due to its distinctive functional properties and exceptional nutritional value. Increasing yield is a central objective in mungbean breeding programs; however, systematic studies identifying quantitative trait loci (QTLs) associated with key yield-related traits remain limited. In this study, the recombinant inbred line (RIL) population (AH20 × SX36) was generated, and phenotypic assessments were conducted in three distinct environments. Three methods genome-wide composite interval mapping (GCIM), multiple QTL mapping (MQM) and inclusive composite interval mapping (ICIM) were employed to detect QTLs linked to HSW (hundred-seed weight), SPP (number of seeds per pod), PL (pod length), PW (pod width), and YP (yield per plant). Consequently, 33, 19, 26, 22, and 20 QTLs were identified for HSW, SPP, PL, PW, and YP, respectively. Notably, 10 QTLs were consistently detected across all environments and by all three mapping methods, indicating their robustness and potential for breeding applications. Candidate genes associated with these stable QTLs were also predicted, offering insights into the genetic regulation of yield traits. These findings provide a valuable genetic framework for functional validation and the cultivation of high-yielding mungbean germplasm.

Soybean seed physical characteristics are crucial for quality assessment, but the link between these characteristics and biochemical composition across different maturity groups (MGs) remains unclear. This study examined the relationships between seed physical characteristics (color and weight) and biochemical constituents, including oil content (OC), protein content (PC), and fatty acid (FA) composition in 191 diverse soybean accessions across eight MGs (0-VII) at three locations over two years. The results indicated that black-seeded accessions demonstrated a notably higher average of PC (47.33

The intricate relationships between plants and insects are essential for understanding ecological dynamics. Among these interactions, HIPVs serve as a pivotal defense mechanism. Our findings reveal the highly conserved nature of the GOX gene within the Lepidoptera order, highly expressed in the salivary glands of S. frugiperda, and its role in mediating maize’s defense responses. Notably, salivary GOX activity expression significantly decreases subsequent gene knockout. The presence of GOX in the saliva of S. frugiperda significantly modulates the emission of HIPVs during maize consumption. This research delineates that GOX selectively inhibits the emission of certain green leaf volatiles (GLVs) while concurrently enhancing the release of terpene volatiles. This study unveils a novel mechanism whereby S. frugiperda utilizes GOX proteins in OS to modulate volatile emissions from maize, offering fresh perspectives on the adaptive evolution of phytophagous insects and their interactions with their preferred host plants.

Soybean is a major source of protein and edible oil worldwide. Originating from the Huang-Huai-Hai region, which has a temperate climate, soybean has adapted to a wide latitudinal gradient across China. However, the genetic mechanisms responsible for the widespread latitudinal adaptation in soybean, as well as the genetic basis, adaptive differentiation, and evolutionary implications of theses natural alleles, are currently lacking in comprehensive understanding. In this study, we examined the genetic variations of fourteen major gene loci controlling flowering and maturity in 103 wild species, 1048 landraces, and 1747 cultivated species. We found that E1, E3, FT2a, J, Tof11, Tof16, and Tof18 were favoured during soybean improvement and selection, which explained 75.5% of the flowering time phenotypic variation. These genetic variation was significantly associated with differences in latitude via the LFMM algorithm. Haplotype network and geographic distribution analysis suggested that gene combinations were associated with flowering time diversity contributed to the expansion of soybean, with more HapA clustering together when soybean moved to latitudes beyond 35°N. The geographical evolution model was developed to accurately predict the suitable planting zone for soybean varieties. Collectively, by integrating knowledge from genomics and haplotype classification, it was revealed that distinct gene combinations improve the adaptation of cultivated soybeans to different latitudes. This study provides insight into the genetic basis underlying the environmental adaptation of soybean accessions, which could contribute to a better understanding of the domestication history of soybean and facilitate soybean climate-smart molecular breeding for various environments.

Soybeans are grown worldwide owing to their protein, oil, and beneficial bioactive compounds. Genetic and environmental factors influence soybean seed isoflavones. In the present study, we profiled the seed isoflavones in world diverse soybean germplasm grown in two locations over two years in China. Significant differences (p < 0.001) were observed between the accessions, accession origins, seed coat colors, and maturity groups for individual and total isoflavone (TIF) content. TIF content of the soybean accessions ranged from 677.25 μg g−1 to 5823.29 μg g−1, representing an 8-fold difference. USA soybean accessions showed the highest mean TIF content (3263.07 μg g−1), followed by Japan (2521.26 μg g−1). Soybean with black seed coat showed the highest (3236.08 μg g−1) TIF concentration. Furthermore, isoflavone levels were significantly higher in late-maturity groups. Correlation analysis revealed significant positive associations between individual and TIF content. Malonyldaidzin and malonylgenistin showed higher correlations with TIF content (r = 0.92 and r = 0.94, respectively). The soybean accessions identified as having high and stable TIF content can be utilized in the food and pharmaceutical industries and breeding programs to develop soybean varieties with enhanced isoflavone content.

The oral secretions of insect herbivores are complex mixtures of organic and inorganic solutes and enzymes that are deposited onto plant tissues during the feeding process. Some specific components of insect oral secretions have been shown to confer important functions in mediating plant-insect interactions at the molecular level. In this review, we examined the biochemical studies of insect oral secretions to summarize the current knowledge of their compositions. We then moved beyond the functional studies of components of oral secretions, and focused on the literature that pinpointed specific molecular targets of these compounds. Finally, we highlighted the investigations of oral secretion components in the context of insect physiology, which shed light on the potential evolutionary trajectory of these multi-functional molecules.

Thiacloprid, a neonicotinoid pesticide, is known to affect the gut microbiome of honeybees, yet studies often focus on immediate alternations during exposure, overlooking long-term microbiological impacts post-exposure. This study investigates the influences of sublethal thiacloprid administered during the larval developmental stage of honeybees on physiological changes and gut microbiota of adult honeybees. We found that thiacloprid exposure increased mortality and sugar intake in emerged honeybees. Using 16S rDNA sequencing, we analyzed intestinal microbial diversity of honeybees at one and six days post-emergence. Our findings reveal a significant but transient disruption in gut microbiota on day 1, with recovery from dysbiosis by day 6. This study emphasizes the importance of evaluating chronic sublethal exposure risks of thiacloprid to protect honeybee health.

Watermelon seed kernels (WSK) are prone to oxidative rancidity, while their evaluation biomarkers and changes in volatile flavor are still unknown. The research tracked the changes in volatile compounds and lipid components before and after rancidity using HS-SPME-GC-O-MS and lipidomic techniques. The results showed the flavor of watermelon seed kernels changed significantly before and after rancidity, from mild aroma to rancidity. A total of 42 volatile compounds were detected via GC-O-MS, and a total of 220 lipid molecules were detected via lipidomic technology. 55 lipids with significant differences were screened via multivariate statistical analysis. Combining the above analysis, it found that glycerol phospholipid and glyceride pathways were the most important metabolic pathways and 1-Pentanol and styrene could be used as potential biomarkers to judge the rancidity process of watermelon seed kernels. The research could provide powerful technical support for the storage, transportation and freshness preservation of watermelon seed kernels.