Soybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq). SLAF-seq was performed to screen SLAF markers with 149 F_8:11 individuals from a cross between a semi wild soybean, ‘Huapidou’, and a cultivated soybean, ‘Qihuang26’, which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F_8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively. With SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.

Introduction: Sweet potato is an important food, feed and industrial raw material, and its tubers are rich in starch, carotenoids and anthocyanins.Methods: To elucidate the gene expression regulation and metabolic characteristics during the development of sweet potato tubers, transcriptomic and metabolomic analyses were performed on the tubers of three different sweet potato varieties at three developmental stages (70, 100, and 130 days (d)).Results: RNA-seq analysis revealed that 16,303 differentially expressed genes (DEGs) were divided into 12 clusters according to their expression patterns, and the pathways of each cluster were annotated. A total of 9118 DEGs were divided into three categories during the same developmental period. A total of 1566 metabolites were detected, which were mainly divided into 12 categories. DEGs and differentially regulated metabolites (DRMs) were significantly enriched in the starch and sucrose metabolism and flavonoid biosynthesis pathways. The DEGs associated with the flavonoid pathway showed greater expression with the development of tubers, with the highest expression occurring at 130 d; chalcone isomerase (CHI) was a key gene associated with 11 flavonoid compounds. The DEGs associated with the starch pathway presented relatively low expression during the development of tubers, with the highest expression occurring at 70 d; UDP-glucose pyrophosphorylase 2 (UPG2) and glycogen synthase (glgA) were able to regulate the key genes of 8 metabolites related to the starch biosynthesis pathway. The anthocyanin content is directly related to changes in the content of peonidin-3-O-(6”-O-feruloyl)sophoroside-5-O-glucoside, which is regulated by the IbCHI gene. The abundance of this starch is directly related to changes in the content of D-glucose 6-phosphate and is regulated by the IbUGP2 and IbglgA genes. A total of 14 candidate genes related to starch, carotenoids and anthocyanins in sweet potato tubers, including the IbCHI, IbUGP2 and IbglgA genes, were identified via weighted correlation network analysis (WGCNA).Conclusion: This research provides fresh insights into the levels of anthocyanins, starch, and carotenoids throughout the growth of sweet potato tubers and sheds light on the potential regulatory pathways and candidate genes involved in this developmental progression.

Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.

(1) The development of sweet potato storage roots is impacted by nitrogen (N) levels, with excessive nitrogen often impeding development. Starch synthesis enzymes such as sucrose synthase (SUS) and ADP-glucose pyrophosphorylase (AGPase) are pivotal in this context. Although the effects of excessive nitrogen on the formation of sweet potato storage roots are well documented, the specific responses of IbSUSs and IbAGPases have not been extensively reported on. (2) Pot experiments were conducted using the sweet potato cultivar “Pushu 32” at moderate (MN, 120 kg N ha⁻¹) and excessive nitrogen levels (EN, 240 kg N ha⁻¹). (3) Nine IbSUS and nine IbAGPase genes were categorized into three and two distinct subgroups based on phylogenetic analysis. Excessive nitrogen significantly (p < 0.05) suppressed the expression of IbAGPL1, IbAGPL2, IbAGPL4, IbAGPL5, IbAGPL6, IbAGPS1, and IbAGPS2 in fibrous roots and IbSUS2, IbSUS6, IbSUS7, IbSUS8, IbSUS9, IbAGPL2, and IbAGPL4 in storage roots, and then significantly (p < 0.05) decreased the SUS and AGPase activities and starch content of fibrous root and storage root, ultimately reducing the storage root formation of sweet potato. Excessive nitrogen extremely significantly (p < 0.01) enhanced the expression of IbAGPL3, which was strongly negatively correlated with the number and weight of storage roots per plant. (4) IbAGPL3 may be a key gene in the response to excessive nitrogen stress and modifying starch synthesis in sweet potato.

Background Although the role of the basic leucine zipper (bZIP) family of transcription factors in response to various abiotic stresses has been investigated, few studies have been conducted on their function in submergence stress. Results In this study, we localized a bZIP gene GmbZIP71-4 in the nucleus of soybean and constructed a GmbZIP71-4overexpressing tabocco line, which showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway enrichment analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the most significant differences were the expression levels of the factors in plant hormone signal transduction, especially those in response to ABA. Electrophoretic Mobility Shift Assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2, which is consistent with the ChIP-qPCR result. Conclusions Our study showed that GmbZIP71-4 was a negative regulator of submergence stress tolerance. The findings in this work will set a solid foundation for the understanding of submergence resistance in plants.

Rice is a short-day thermophilic crop that originated from the low latitudes of the tropics and subtropics; it requires high temperatures for growth but is sensitive to low temperatures. Therefore, it is highly important to explore and analyze the molecular mechanism of cold tolerance in rice to expand rice planting areas. Here, we report a phenotypic evaluation based on low-temperature stress in indica rice (R998) and wild rice (GZW) and a comparative transcriptomic study conducted at six time points. After 7 days of low-temperature treatment at 10 °C, R998 exhibited obvious yellowing and greening of the leaves, while GZW exhibited high low-temperature resistance, and the leaves maintained their normal morphology and exhibited no yellowing; GZW has a higher survival rate. Principal component analysis (PCA) and cluster analysis of the RNA-seq data revealed that the difference in low-temperature resistance between the two cultivars was caused mainly by the difference in low-temperature treatment after 6 h. Differential expression analysis revealed 2615 unique differentially expressed genes (DEGs) in the R998 material, 1578 unique DEGs in the GZW material, 1874 unique DEGs between R998 and GZW, and 2699 DEGs that were differentially expressed not only between cultivars but also at different time points in the same material under low-temperature treatment. A total of 15,712 DEGs were detected and were significantly enriched in the phenylalanine metabolism, photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. These 15,712 DEGs included 1937 genes encoding transcription factors (TFs), of which 10 have been identified with functional validation in previous studies. In addition, a gene regulatory network was constructed via weighted gene correlation network analysis (WGCNA), and 12 key genes related to low-temperature tolerance in rice were identified, including five genes encoding TFs, one of which was identified and verified in previous studies. These results provide a theoretical basis for an in-depth understanding of the molecular mechanism of low-temperature tolerance in rice and provide new genetic resources for the study of low-temperature tolerance in rice.