Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG (W = A or T) methylation in the whole genome of these hybrids and their parents at the middle development period of contemporary seed. We were able to prove that changes in DNA methylation patterns occurred in immature hybrid seeds and the parental variation was to some degree responsible for differential expression between the reciprocal hybrids. Non-additive differential methylation sites (DMSs) were also identified in large numbers in hybrids. Interestingly, most of these DMSs were hyper-methylated and were more concentrated in gene regions than the natural distribution of the methylated sites. Further analysis of the non-additive DMSs located in gene regions exhibited their participation in various biological processes, especially those related to transcriptional regulation and hormonal function. These results revealed DNA methylation reprogramming pattern in the hybrid soybean, which is associated with phenotypic variation and heterosis initiation.

The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies have mapped SPB-resistant quantitative trait loci (QTLs) and deciphered the response mechanism in soybean. Here, we selected two soybean varieties, JY93 (SPB-resistant) and K6 (SPB-sensitive), to construct F₂ and F_2:3 populations for QTL mapping and collected pod shells before and after SPB larvae chewed on the two parents to perform RNA-Seq, which can identify stable QTLs and explore the response mechanism of soybean to the SPB. The results show that four QTLs underlying SPB damage to seeds were detected on chromosomes 4, 9, 13, and 15. Among them, qESP-9-1 was scanned in all environments, hence it can be considered a stable QTL. All QTLs explained 0.79 to 6.09% of the phenotypic variation. Meanwhile, 2298 and 3509 DEGs were identified for JY93 and K6, respectively, after the SPB attack, and most of these genes were upregulated. Gene Ontology enrichment results indicated that the SPB-induced and differently expressed genes in both parents are involved in biological processes such as wound response, signal transduction, immune response, and phytohormone pathways. Interestingly, secondary metabolic processes such as flavonoid synthesis were only significantly enriched in the upregulated genes of JY93 after SPB chewing compared with K6. Finally, we identified 18 candidate genes related to soybean pod borer resistance through the integration of QTL mapping and RNA-Seq analysis. Seven of these genes had similar expression patterns to the mapping parents in four additional soybean germplasm after feeding by the SPB. These results provide additional knowledge of the early response and induced defense mechanisms against the SPB in soybean, which could help in breeding SPB-resistant soybean accessions.

The high isoflavones content of soybeans is an important breeding goal due to the demonstrated benefits of isoflavones to human health and their association with plant resistance. In this study, quantitative trait loci (QTL) mapping for soybean isoflavone aglycones, including daidzin, glycerin, and genistin, and total isoflavones content was performed in a population of 178 F_2:6 recombinant inbred lines (RILs) which was generated from a cross between varieties Jinong 17 and Jinong 18. A genetic linkage map covering 1248 cM was constructed using the simple sequence repeat (SSR) molecular markers. The results revealed 22 isoflavone-related QTLs, 5 for daidzin, 7 for genistin, 6 for glycerin, and 4 for total isoflavone content. Seven of these represented new QTLs. All QTL regions contained 6462 genes, of which 58 have been annotated for flavonoid synthesis. Using public databases, three candidate genes, namely Glyma.11G164400, Glyma.16G158400, and Glyma.19G217700, were subsequently identified. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) demonstrated that the three genes exhibited specific, high expression in soybean seeds and a positive correlation with flavonoid content. These findings might be helpful in the efforts to breed new soybean varieties with improved isoflavone composition and content.

Tiger nut (Cyperus esculentus L.) is recognized for its high oil and oleic acid content in underground tubers. However, the molecular mechanisms governing growth, development, and fatty acid accumulation in these tubers are not well understood. This study employed gas chromatography–mass spectrometry (GC–MS) and small RNA sequencing on tiger nut tubers across five developmental stages. The findings indicate that the critical period for accumulating dry matter and oils, particularly oleic acid, occurs between 35 and 75 days after tuber formation. A total of 183 microRNAs (miRNAs) were identified, comprising 31 known and 152 novel miRNAs. Approximately half of these miRNAs (such as ces-miR156b-3p and ces-miR166a-3p) exhibited differential expression during and around the key periods of metabolite synthesis. The predicted target genes of these miRNAs were significantly enriched in glycerate 3-phosphate metabolism and cell growth processes. Furthermore, 13 miRNA–mRNA interaction modules related to oil accumulation and tuber growth were identified, and these target genes’ expression levels showed significant differences during the tuber developmental stages. These findings advance the understanding of the molecular mechanisms underlying tuber development and oil accumulation in tiger nut.

Castor bean (Ricinus communis L.) is an important industrial oil crop worldwide. In China, western Jilin Province represents a major production region for this species, where spring drought severely constrains its yield and quality.This study aimed to comprehensively evaluate drought resistance in castor bean and explore its underlying mechanisms. A total of 40 common castor bean germplasms in Jilin Province were used as materials. Seedling drought resistance was evaluated using 25% polyethylene glycol (PEG) simulated drought stress, and agronomic traits were assessed under natural drought field conditions. Based on these evaluations, eight drought-tolerant and eight drought-sensitive germplasms were selected. Physiological indices and transcriptome sequencing (RNA-seq) were performed on the drought-tolerant genotype Baibi 22 and the drought-sensitive genotype Nongxuan 1. The 40 germplasms were classified into three drought resistance categories: drought-tolerant (8), moderately drought-tolerant (24), and drought-sensitive (8). Under 25% PEG stress, chlorophyll content decreased continuously, while peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activities were higher than in the control, and malondialdehyde (MDA) content showed a unimodal increase. RNA-seq was used to identify 94 consistently differentially expressed genes (uDEGs) between the two germplasms at 3 and 7 days after stress, which were enriched in calcium signaling, redox balance, antioxidant stress, and the proteolytic ubiquitination pathway. Quantitative real-time PCR (qRT-PCR) verification confirmed the reliability of the RNA-seq results. This study screened elite drought-tolerant castor bean germplasms and identified 17 key genes related to abiotic stress regulation, providing germplasm resources and a molecular basis for improving abiotic stress resistance in castor bean through gene editing or molecular breeding.