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Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

We sought to assess the elasticity change of the paravertebral fascia and muscle in adolescent idiopathic scoliosis patients with Lenke Type 1, 2, or 3 curves after posterior selective fusion surgery.The shear wave elasticity imaging system was used to assess the elasticity of the thoracic paravertebral muscles and fascia both on the concave and convex sides. Three regions of interest, including the apex, upper end, and lower end of the main curve, were tested.Ten female patients, with an average age of 16.6 ± 2.7 years old, were included. The average post-operation follow-up period was 9.0 ± 2.4 months. The Cobb angle was significantly corrected from 63.6 ± 12.0° to 10.7 ± 5.4° (p 0.05). The length of the trunk increased from 40.4 ± 2.5 cm to 46.0 ± 2.8 cm (p 0.05). The elasticity of deep fascia didn't show a significant change post-operation (p 0.05). The elasticity of the paravertebral muscle on the concave side had a significant increase at the final follow-up (p 0.05). The elasticity of the paravertebral muscle on the convex side also increased at the upper end (p 0.05). The elasticity asymmetry of the deep fascia decreased, but the elasticity asymmetry of the paravertebral muscle increased at the upper end of the curve (p 0.05).The paravertebral muscle on the concave side is stiffer after surgery. Elastic asymmetry of paravertebral muscle increased and elastic asymmetry of the deep fascia decreased at the upper end of the curvature. Further study is needed to elucidate the mechanism by which the paravertebral soft tissue responds after surgery.

Additional file 1: Figure S1. Morphological changes of four other plants seed from dry seed to seedling. Figure S2. Correlation between different samples. Figure S3. Pathways shared among the four modules. Figure S4. Heat map of genes expression related to brassinosteroid biosynthesis.

Background Seed germination is the most important stage for the formation of a new plant. This process starts when the dry seed begins to absorb water and ends when the radicle protrudes. The germination rate of seed from different species varies. The rapid germination of seed from species that grow on marginal land allows seedlings to compete with surrounding species, which is also the guarantee of normal plant development and high yield. Pearl millet is an important cereal crop that is used worldwide, and it can also be used to extract bioethanol. Previous germination experiments have shown that pearl millet has a fast seed germination rate, but the molecular mechanisms behind pearl millet are unclear. Therefore, this study explored the expression patterns of genes involved in pearl millet growth from the germination of dry seed to the early growth stages. Results Through the germination test and the measurement of the seedling radicle length, we found that pearl millet seed germinated after 24 h of swelling of the dry seed. Using transcriptome sequencing, we characterized the gene expression patterns of dry seed, water imbibed seed, germ and radicle, and found more differentially expressed genes (DEGs) in radicle than germ. Further analysis showed that different genome clusters function specifically at different tissues and time periods. Weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that many genes that positively regulate plant growth and development are highly enriched and expressed, especially the gibberellin signaling pathway, which can promote seed germination. We speculated that the activation of these key genes promotes the germination of pearl millet seed and the growth of seedlings. To verify this, we measured the content of gibberellin and found that the gibberellin content after seed imbibition rose sharply and remained at a high level. Conclusions In this study, we identified the key genes that participated in the regulation of seed germination and seedling growth. The activation of key genes in these pathways may contribute to the rapid germination and growth of seed and seedlings in pearl millet. These results provided new insight into accelerating the germination rate and seedling growth of species with slow germination.

Orchardgrass (Dactylis glomerata L.) is drought resistant and tolerant to barren landscapes, making it one of the most important forages for animal husbandry, as well as ecological restoration of rocky landscapes that are undergoing desertification. However, orchardgrass is susceptible to rust, which can significantly reduce its yield and quality. Therefore, understanding the genes that underlie resistance against rust in orchardgrass is critical. The evolution, cloning of plant disease resistance genes, and the analysis of pathogenic bacteria induced expression patterns are important contents in the study of interaction between microorganisms and plants. Genes with nucleotide binding site (NBS) structure are disease-resistant genes ubiquitous in plants and play an important role in plant attacks against various pathogens. Using sequence analysis and re-annotation, we identified 413 NBS resistance genes in orchardgrass. Similar to previous studies, NBS resistance genes containing TIR (toll/interleukin-1 receptor) domain were not found in orchardgrass. The NBS resistance genes can be divided into four types: NBS (up to 264 homologous genes, accounting for 64% of the total number of NBS genes in orchardgrass), NBS-LRR, CC-NBS, and CC-NBS-LRR (minimum of 26 homologous genes, only 6% of the total number of NBS genes in orchardgrass). These 413 NBS resistance genes were unevenly distributed across seven chromosomes where chromosome 5 had up to 99 NBS resistance genes. There were 224 (54%) NBS resistance genes expressed in different tissues (roots, stems, leaves, flowers, and spikes), and we did not detect expression for 45 genes (11%). The remaining 145 (35%) were expressed in some tissues. And we found that 11 NBS resistance genes were differentially expressed under waterlogging stress, 5 NBS resistance genes were differentially expressed under waterlogging and drought stress, and 1 NBS resistance was is differentially expressed under waterlogging and heat stress. Most importantly, we found that 65 NBS resistance genes were significantly expressed in different control groups. On the 7th day of inoculation, 23 NBS resistance genes were differentially expressed in high resistance materials alone, of which 7 NBS resistance genes regulate the "plant-pathogen interaction" pathway by encoding RPM1. At the same time, 2 NBS resistance genes that were differentially expressed in the high resistance material after inoculation were also differentially expressed in abiotic stress. In summary, the NBS resistance gene plays a crucial role in the resistance of orchardgrass to rust.

Additional file 7: Figure S3. WGD-related miRNAs’ targets expression.

Additional file 4: Figure S2. Top 20 enriched GO terms of ploidy- and drought-related DETs in 4X Alamo and 8X Alamo.

Additional file 8. Protocols of the physiological measurement.

Additional file 5: Table S3. Summary of samples miRNA sequencing results.

Additional file 1: Table S1. Summary of samples transcriptome sequencing results.

Additional file 2: Table S2. Summary of differently expressed transcripts among seven comparisons.

Background Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear. Result We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes. Conclusions This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding.

Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.

Using the material of Hemarthria compressa (L.F.) R.Br. cv. YA’AN, we carried out this research to study the influence of radiation on the genetic variation of plants. Genetic difference was analyzed with expressed sequence tag-simple sequence repeat (EST-SSR) molecular marker through the comparison of 60Co-γ radiation on H. compressa seed stems and original variety. By using 20 primer pairs, 176 polymerase chain reaction (PCR)-amplifications with clear and consistent bands were obtained. The results showed that 155 of 176 bands were polymorphic, which indicating an 88.07% polymorphism rate, and each pair of primers had 8.8 amplified bands on average; the amplitude of polymorphism information content was 0.4709–0.6952 with an average value 0.6081. The genetic similarity coefficient of H. compressa and its mutants ranged from 0.4318 to 0.8239 with an average of 0.6671. As a consequence, existence of genetic differences between the mutants and the basic material was proved., We gratefully acknowledge financial support from the Modern Agro-industry Technology Research System (CARS-34) and the Sichuan Province Breeding Research grant (2016NZ0098-11).

Genes or metabolites involved in the same biological process will have same or similar change rules, so association analysis of transcriptome and metabolome is an effective way to find key metabolic pathways, key genes and explain the molecular mechanisms. Anthocyanin-rich forage is rare but a powerful antioxidant, which is good for both humans and animals. Pennisetum purpureum cv. Purple is abundant in anthocyanins and has higher biomass than most forage grasses. To study the mechanisms underlying the purple color of P. purpureum, transcriptomic and metabolomics analyses were performed with the purple-leaved cultivar ‘Purple’ and the green-leaved cultivar ‘Mott’. Metabolites, including luteolin, kaempferol, quercetin, malvidin, apigenin, pelargonidin and cyanidin were present at different levels between the cultivars. High levels of malvidin correlated with purple color, suggesting that this compound probably plays a dominant role in making the purple leaves in P. purpureum considering its high content and strong correlation with the color expression. A total of 16 differentially expressed genes (DEGs) in the flavonoid biosynthesis pathway were discovered between the purple and green varieties, and these were selected as candidate genes possibly involved in purple color formation and accumulation. Moreover, 47 differentially expressed transcription factors (TFs) were identified, including 15 up-regulated and 12 down-regulated TFs between ‘Purple’ and ‘Mott’. Furthermore, 55 SNPs in 11 DEGs and 231 SNPs in 41 differentially expressed TFs were found between ‘Purple’ and ‘Mott’, suggesting that SNPs may play an important role in regulating gene expression. This study provides crucial information on leaf color development and anthocyanins production of P. purpureum, and will facilitate the development of breeding forage varieties with high-anthocyanins contents.