Identification of miRNA–mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree (Camellia oleifera)

Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal value that is widely planted in southern China. However, there is no report on the identification of the miRNAs involved in lipid metabolism and seed development in the high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the key periods of oil formation and accumulation in the seeds of tea oil camellia and identified miRNA–mRNA regulatory modules involved in lipid metabolism and seed development. Sixteen small RNA libraries for four development stages of seed oil biosynthesis in high- and low-oil cultivars were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families, and 40 novel miRNAs were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 upregulated miRNAs, and 21 downregulated miRNAs. An integrated analysis of the miRNA and mRNA transcriptome sequence data revealed that 10 miRNA–mRNA regulatory modules were related to lipid metabolism; for example, the regulatory modules of ath-miR858b–MYB82/MYB3/MYB44 repressed seed oil biosynthesis, and a regulation module of csi-miR166e-5p–S-ACP-DES6 was involved in the formation and accumulation of oleic acid. A total of 23 miRNA–mRNA regulatory modules were involved in the regulation of the seed size, such as the regulatory module of hpe-miR162a_L-2–ARF19, involved in early seed development. A total of 12 miRNA–mRNA regulatory modules regulating growth and development were identified, such as the regulatory modules of han-miR156a_L+1–SPL4/SBP2, promoting early seed development. The expression changes of six miRNAs and their target genes were validated using quantitative real-time PCR, and the targeting relationship of the cpa-miR393_R-1–AFB2 regulatory module was verified by luciferase assays. These data provide important theoretical values and a scientific basis for the genetic improvement of new cultivars of tea oil camellia in the future.

Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development

Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.

Identification of miRNA-mRNA regulatory modules involved in lipid metabolism and seed development in a woody-oil tree (Camellia oleifera)

BackgroundTea oil camellia ( Camellia oleifera ), an important woody oil tree, is a source of seed oil of high nutritional and medicinal values and has been being widely planted in southern China. However, there is no report on the identification of miRNAs involved in lipid metabolism and seed development in high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the critical period of oil formation and accumulation in tea oil camellia, and identified miRNA-mRNA regulatory modules involved in lipid metabolism and seed development. ResultsSixteen small RNA libraries for high- and low-oil cultivars of the critical period of oil biosynthesis were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families and 40 novel miRNAs, were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 up-regulated miRNAs and 21 down-regulated miRNAs. An integrated analysis of miRNA and mRNA transcriptome sequence data and qRT-PCR-based information was performed and revealed that nine miRNA-mRNA regulatory modules were related to lipid metabolism, such as the negative regulatory modules of ath-miR858b- MYB82 / MYB3 / MYB44 represses seed oil biosynthesis and a positive regulation module of csi-miR166e-5p- S-ACP - DES6 for formation and accumulation of oleic acid. Twenty-tree miRNA-mRNA regulatory modules were involved in the regulation of seed size, such as a negative regulatory module of hpe-miR162a_L-2- ARF19 involved in early seed development. Twelve miRNA-mRNA regulatory modules regulating growth and development were identified, such as the negative regulatory modules of han-miR156a_L+1- SPL4 / SBP2 promoting early seed development. The targeting relationship of the cpa-miR393_R-1-AFB2 regulatory module were verified by luciferase activity assays. ConclusionMultiple microRNAs (miRNAs) were identified to involve in developing seeds of tea oil camellia, especially discovering several miRNA-mRNA regulatory modules involving in seed development and lipid metabolism. These data provide important theoretical value and a scientific basis for the genetic improvement of new varieties of tea oil camellia in the future.

Effect of Drought Stress during Soybean R2–R6 Growth Stages on Sucrose Metabolism in Leaf and Seed

Sucrose is the main photosynthesis product of plants and the fundamental carbon skeleton monomer and energy supply for seed formation and development. Drought stress induces decreased photosynthetic carbon assimilation capacity, and seriously affects seed weight in soybean. However, little is known about the relationship between decreases in soybean seed yield and disruption of sucrose metabolism and transport balance in leaves and seeds during the reproductive stages of crop growth. Three soybean cultivars with similar growth periods, “Shennong17”, “Shennong8”, and “Shennong12”, were subjected to drought stress during reproductive growth for 45 days. Drought stress significantly reduced leaf photosynthetic rate, shoot biomass, and seed weight by 63.93, 33.53, and 41.65%, respectively. Drought stress increased soluble sugar contents, the activities of sucrose phosphate synthase, sucrose synthase, and acid invertase enzymes, and up-regulated the expression levels of GmSPS1, GmSuSy2, and GmA-INV, but decreased starch content by 15.13% in leaves. Drought stress decreased the contents of starch, fructose, and glucose in seeds during the late seed filling stages, while it induced sucrose accumulation, which resulted in a decreased hexose-to-sucrose ratio. In developing seeds, the activities of sucrose synthesis and degradation enzymes, the expression levels of genes related to metabolism, and the expression levels of sucrose transporter genes were enhanced during early seed development under drought stress; however, under prolonged drought stress, all of them decreased. These results demonstrated that drought stress enhances the capacity for unloading sucrose into seeds and activated sucrose metabolism during early seed development. At the middle and late seed filling stages, sucrose flow from leaves to seeds was diminished, and the balance of sucrose metabolism was impaired in seeds, resulting in seed mass reduction. The different regulation strategies in sucrose allocation, metabolism, and transport during different seed development stages may be one of the physiological mechanisms for soybean plants to resist drought stress.

Genome-wide identification and expression analysis of SWEET gene family in Litchi chinensis reveal the involvement of LcSWEET2a/3b in early seed development

Background SWEETs (Sugar Will Eventually be Exported transporters) function as sugar efflux transporters that perform diverse physiological functions, including phloem loading, nectar secretion, seed filling, and pathogen nutrition. The SWEET gene family has been identified and characterized in a number of plant species, but little is known about in Litchi chinensis, which is an important evergreen fruit crop. Results In this study, 16 LcSWEET genes were identified and nominated according to its homologous genes in Arabidopsis and grapevine. Multiple sequence alignment showed that the 7 alpha-helical transmembrane domains (7-TMs) were basically conserved in LcSWEETs. The LcSWEETs were divided into four clades (Clade I to Clade IV) by phylogenetic tree analysis. A total of 8 predicted motifs were detected in the litchi LcSWEET genes. The 16 LcSWEET genes were unevenly distributed in 9 chromosomes and there was one pairs of segmental duplicated events by synteny analysis. The expression patterns of the 16 LcSWEET genes showed higher expression levels in reproductive organs. The temporal and spatial expression patterns of LcSWEET2a and LcSWEET3b indicated they play central roles during early seed development. Conclusions The litchi genome contained 16 SWEET genes, and most of the genes were expressed in different tissues. Gene expression suggested that LcSWEETs played important roles in the growth and development of litchi fruits. Genes that regulate early seed development were preliminarily identified. This work provides a comprehensive understanding of the SWEET gene family in litchi, laying a strong foundation for further functional studies of LcSWEET genes and improvement of litchi fruits.

Effect of drought stress during soybean R2-R6 growth stages on sucrose metabolism and its transport from leaf to seed

Background Sucrose is the main photosynthesis product of plants and the fundamental carbon skeleton monomer and energy supply for seed formation and development. Drought stress induces decreased photosynthetic carbon assimilation capacity and seriously affects seed weight in soybean. However, little is known about the relationship between decreases in soybean seed yield and disruption of sucrose metabolism and transport balance in leaves and seeds during the reproductive stages of crop growth.Results Three soybean cultivars with similar growth periods, ‘Shennong17’, ‘Shennong8’, and ‘Shennong12’ were subjected to drought stress during reproductive growth for 45 days. Drought stress significantly reduced leaf photosynthetic rate, shoot biomass, and seed weight. Drought stress changed the distribution of carbon assimilation products in leaves, thus decreasing starch content and increasing soluble sugar content. Drought stress increased the activities of sucrose phosphate synthase, sucrose synthase, and acid invertase enzymes, and up-regulated the expression levels of GmSPS1 , GmSuSy2 , and GmA-INV in leaves. Drought stress decreased the contents of starch, fructose, and glucose in seeds during the late seed filling stages, while it induced sucrose accumulated, which resulted in a decreased hexose-to-sucrose ratio. In developing seeds, the activities of sucrose synthesis and decomposition enzymes and the expression levels of genes related to metabolism were enhanced during early seed development under drought stress; however, under prolonged drought stress, all of them decreased. The expression levels of sucrose transporter genes in seeds were up-regulated under drought stress during early seed development, but down-regulated in leaves and seeds during the middle and late seed filling stages.Conclusion These results demonstrated that drought stress enhances the capacity for unloading sucrose into seeds and activated sucrose metabolism in seeds during early seed development. At the middle and late seed filling stages, sucrose flow from leaves to seeds was diminished, and the balance of sucrose metabolism was impaired in seeds, resulting in seed mass reduction. The different regulation strategies in sucrose allocation, metabolism, and transport during different seed development stages may be one of the physiological mechanisms for soybean plants to resist drought stress.