Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds

Genome-Wide Identification of GAST Family Members and Their Potential Roles in Epicotyl Dormancy in Chinese Cork Oak (Quercus variabilis)

Chinese cork oak (Quercus variabilis Blume) is a widespread tree species with high economic and ecological values. Chinese cork oak exhibits epicotyl dormancy, causing emergence heterogeneity and affecting the quality of seedling cultivation. Gibberellic acid-stimulated transcript (GAST) is a plant-specific protein family that plays a crucial regulatory role in plant growth, development, and seed germination. However, their evolution in Chinese cork oak and roles in epicotyl dormancy are still unclear. Here, a genome-wide identification of the GAST gene family was conducted in Chinese cork oak. Ten QvGAST genes were identified, and nine of them were expressed in seed. The physicochemical properties and promoter cis-acting elements of the selected Chinese cork oak GAST family genes indicated that the cis-acting elements in the GAST promoter are involved in plant development, hormone response, and stress response. Germinated seeds were subjected to gibberellins (GAs), abscisic acid (ABA), and fluridone treatments to show their response during epicotyl dormancy release. Significant changes in the expression of certain QvGAST genes were observed under different hormone treatments. QvGAST1, QvGAST2, QvGAST3, and QvGAST6 exhibited upregulation in response to gibberellin. QvGAST2 was markedly upregulated during the release of epicotyl dormancy in response to GA. These findings suggested that QvGAST2 might play an important role in epicotyl dormancy release. This study provides a basis for further analysis of the mechanisms underlying the alleviation of epicotyl dormancy in Chinese cork oak by QvGASTs genes.

Analysis and Identification of Genes Associated with the Desiccation Sensitivity of Panax notoginseng Seeds

Panax notoginseng (Burk.) F. H. Chen, a species of the genus Panax, radix has been traditionally used to deal with various hematological diseases and cardiovascular diseases since ancient times in East Asia. P. notoginseng produces recalcitrant seeds which are sensitive to desiccation and difficult to store for a long time. However, few data are available on the mechanism of the desiccation sensitivity of P. notoginseng seeds. To gain a comprehensive perspective of the genes associated with desiccation sensitivity, cDNA libraries from seeds under control and desiccation processes were prepared independently for Illumina sequencing. The data generated a total of 70,189,896 reads that were integrated and assembled into 55,097 unigenes with a mean length of 783 bp. In total, 12,025 differentially expressed genes (DEGs) were identified during the desiccation process. Among these DEGs, a number of central metabolism, hormonal network-, fatty acid-, and ascorbate-glutathione-related genes were included. Our data provide a comprehensive resource for identifying the genes associated with the desiccation sensitivity of P. notoginseng seeds.

Transcriptomic Analysis of the Dehydration Rate of Mature Rice (Oryza sativa) Seeds

In this study, a transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. We selected two rice cultivars for testing (Baghlani Nangarhar, an extremely rapid dehydration genotype, and Saturn, a slow dehydration genotype) based on the results determined by previous studies conducted on the screening of 165 germplasm materials for dehydration rate phenotypes. A rapid dehydration experiment performed on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified via transcriptome sequencing and real-time quantitative PCR (RT-qPCR). GO (Gene ontology) and KEGG(Kyoto Encyclopedia of Genes and Genomes) analyses were also conducted. In Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. In Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 were down-regulated. The results of the GO analysis show that the sites of action of the differentially expressed genes enriched in the rapid dehydration modes are concentrated in the cytoplasm, internal components of the membrane, and nucleosomes. They play regulatory roles in the processes of catalysis, binding, translocation, transcription, protein folding, degradation, and replication. They are also involved in adaptive responses to adverse external environments, such as reactive oxygen species and high temperature. The KEGG analysis showed that protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation were the main metabolic pathways that were enriched. The key differentially expressed genes and the most important metabolic pathways identified in the rapidly and slowly dehydrated genotypes were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism. They were presumed to have important regulatory roles in the mechanisms of stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during the dehydration and drying of mature seeds. The results of this study can potentially provide valuable information for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds, and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.

Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil

Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

Beta-Amylase and Phosphatidic Acid Involved in Recalcitrant Seed Germination of Chinese Chestnut

Chinese chestnut (Castanea mollissima), a species with recalcitrant seeds, is an important source of nuts and forest ecosystem services. The germination rate of recalcitrant seeds is low in natural habitats and decreases under conditions of desiccation and low temperature. The germination rate of cultivated Chinese chestnut seeds is significantly higher than that of wild seeds. To explore the reasons for the higher germination rate of cultivated seeds in Chinese chestnut, 113,524 structural variants (SVs) between the wild and cultivated Chinese chestnut genomes were detected through genome comparison. Genotyping these SVs in 60 Chinese chestnut accessions identified allele frequency changes during Chinese chestnut domestication, and some SVs are overlapping genes for controlling seed germination. Transcriptome analysis revealed downregulation of the abscisic acid synthesis genes and upregulation of the beta-amylase synthesis genes in strongly selected genes of cultivated seeds. On the other hand, hormone and enzyme activity assays indicated a decrease in endogenous ABA level and an increase in beta-amylase activity in cultivated seeds. These results shed light on the higher germination rate of cultivated seeds. Moreover, phosphatidic acid synthesis genes are highly expressed in seed germination stages of wild Chinese chestnut and may play a role in recalcitrant seed germination. These findings provide new insight into the regulation of wild seed germination and promote natural regeneration and succession in forest ecosystems.

Variations in Acorn Traits in Two Oak Species: Quercus mongolica Fisch. ex Ledeb. and Quercus variabilis Blume

Quercus mongolica Fisch. ex Ledeb. and Q. variabilis Blume are two main oak species in China, producing large amounts of acorns every year. However, the trait variations in acorns, as a promising energy crop material, are not fully understood, hence we compared the traits of acorns from the different populations with the altered geographic distribution in this study. Thirteen acorn traits, including phenotype, proximate compositions and functional compounds, were analyzed in both Quercus L. species collected from 44 populations across China. The results showed that, except large differences found among accessions in acorn sizes, the starch varied from 140.96–297.09 mg/g in Q. mongolica and 130.99–306.28 mg/g in Q. variabilis, indicating its substantial differences among populations. The total polyphenols, total flavonoids and soluble tannins varied from 41.76–158.92, 23.43–91.94, and 15.11–17.81 mg/g, respectively, in Q. mongolica, 89.36–188.37, 50.59–116.07, 15.24–17.33 mg/g, respectively, in Q. variabilis, demonstrating their large variations in the levels of polyphenols among populations. Moreover, the acorns of Q. mongolica in North China and Q. variabilis in Southwest China had higher levels of starch and polyphenols. As the geographical location approached in the distribution of two Quercus species, the difference in acorn sizes gradually increased, while that in polyphenols were opposite. Principal component analysis and cluster analysis further revealed that the acorn sizes became larger and polyphenols became less with the increasing latitudes in both species. In North China, the acorns of Q. mongolica had small sizes and high polyphenols, which was contrary to those in Q. variabilis. These findings indicated that acorn traits were closely associated with the geographical distribution. Thus, our results will provide references for the selection breeding of acorn with the high starch, high or low polyphenols in the different regions.