- To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition.. - We found evidence that differences in transposition and defense related genes may arise due to the complex nature of the polyploid Saccharum genomes. - However, most genes coding for photosystem components or those coding for phosphoenolpyruvate carboxylases (PEPCs) were upregulated in the high biomass group. - Sucrose synthase (SuSy) coding genes were upregulated in the low biomass group, showing that this enzyme class can be involved with sucrose synthesis in leaves, similarly to sucrose. - Genes in pathways related to biosynthesis of cell wall components and expansins coding genes showed low average expression levels and were mostly upregulated in the high biomass group.. - Full list of author information is available at the end of the article. - As a result, sugarcane leaves form part of the straw remaining in the field after harvesting. - Sugarcane species are members of the genus Sac- charum, of the Poaceae family. - The former was the ancestor of the cultivated S. - Polyploidy is an inherent char- acteristic of the Saccharum genomes, with S. - More than 80% of the chromosomes of modern hy- brids come from S. - There is also aneuploidy in the homeologous groups [12]. - Genes coding for enzymes of the lignin pathway were stimulated in a high-biomass genotype [18], and their expression levels were higher in bottom rather than top internodes [17]. - Singh and colleagues [19] found that high-biomass genotypes of an F2 population were more photosynthetically active, as a result of the upregulation of genes coding for photorespiration, Calvin cycle and light reaction proteins.. - In addition to their direct use as a biomass source, leaves are the source tissue with which plants produce photoassimilates used to maintain leaf activities and for cell wall synthesis or sucrose accumula- tion in vacuoles of the stalks and sink organs [21]. - 1 in Additional file 1), the first dimension basically separated the high and low biomass groups, and genotypes of the former were farther from each other, revealing higher gene expression variability within the high biomass group. - Investigation of the low biomass group (Fig. - 1 Dendrogram of the twelve sugarcane genotypes based on phenotypic traits. - We performed a hierarchical clustering of the genotypes based on Euclidean distances calculated for all evaluated traits. - Points at the bottom represent the gradient of the scaled phenotypic measures of each accession, where larger green points represent higher phenotypic values. - polarization or sucrose percentage in the juice (POL % Juice). - percentage of sucrose in the total solids of the juice (Purity). - percentage of fiber in the bagasse (Fiber). - ii) Krakatau, IN84–88 and US85–1008 in the middle. - Curiously, in the latter group, an ac- cession classified as S. - This resulted in 10,903 down- regulated and 10,171 upregulated genes in the low biomass group. - Also, the high biomass genotypes showed significant differences in the expression level of genes related to cell division, replication and post- replication repair terms. - 3 Bar chart of the number of DEGs in each enriched functional class for the differences within the high biomass group. - We also found changes in genes coding for proteins in- volved in the response to salicylic acid in both tests.. - 4 Bar chart of the number of DEGs in each enriched functional class for the differences within the low biomass group. - Cellular components of chloroplasts were found in five modules of the network: three, seven, eight, eleven and sixteen (Table 3 in Additional file 3). - This is explained by the expression profile of the genes present in this module, for which the expression level in the low biomass group was higher and similar among the samples (Figure 10 in Additional file 3).. - The results of the comparison between the main groups identified up and downregulated DEGs in all metabolic processes provided by the M AP M AN 4 func- tional BINs (Figure 11 in Additional file 3). - Many genes involved in photophosphorylation were downregulated in the low biomass group, annotated as components of the photosystem II (Psb) proteins, photosystem I (Psa) and cytochrome (Pet) subunits and photosystem I assem- bly (YCF3 and YCF4) (Figure 12 in Additional file 3).. - Other genes of the photosynthesis light reactions were differentially expressed within the two groups, in both cases consistently upregulated in the genotypes with the lowest fiber content (Figure 13 and Figure 14 in Add- itional file 3). - spontaneum genotypes were similar in the expression of genes coding for enzymes of the lignin metabolism, with significant differences for five genes - a 4CL, a β-glucosidase, a Caffeoyl-CoA O-methyltransferase and two cinnamoyl-Coa reductases (CCR) (Figure 18 in Additional file 3).. - We observed that many genes coding for enzymes act- ing on xylan were upregulated in high biomass geno- types, even in the within-group comparisons (Fig. - Regarding cell modifica- tion and degradation, a 1,6-alpha-xylosidase was highly expressed in the low biomass group (Figure 19-B in Additional file 3). - This is expected given that the Golgi apparatus synthesizes most polysaccharides of the cell wall, where transferases catalyze the synthesis of the xyloglucan backbone and side branches [25]. - We also found significant differences in the expression levels of genes associated with cell wall flexibility. - In particular, DEGs coding for expansins of the β subfamily were more highly expressed in S. - an enzyme family mainly in- volved with sucrose degradation - were upregulated in the low biomass group and in US85–1008 (Fig. - Although SUT4 was strongly upregulated in the low bio- mass group (Figure 22 in Additional file 3), SUT1 was highly expressed in the high biomass genotypes (Fig. - We found different expression profiles of genes coding for sugar transporters of the same family. - Gene expression in each biomass group was calculated using the mean of the normalized counts per million. - acting on geranylgeranyl diphosphate in the carotenoid synthesis pathway. - As an ex- ample, we considered the annotated genes of the photo- synthesis biological process. - Lowly expressed isoforms did show significant differential ex- pression when the fold changes were very high, i.e., when expression occurred almost entirely in one of the biomass groups (Fig. - A higher BCV when contrasting groups was expected because we used different genotypes as replicates of the same group (Fig. - Previously, using SSR genotyping of a subset of the Brazilian Panel of Sugar- cane Genotypes, TUC71–7 and SP80–3280 were assigned to the same subpopulation, RB72454 and RB855156 to another and, separately, White Transparent and IN84–58 to the two remaining subpopulations [26].. - Indeed, the third dimension of the multidimensional scaling based on gene expression showed that SP80–. - We hypothesize that the lower number of DEGs in the low biomass group reflects sugarcane breeding, because the hybrids in this group have a higher genomic contribution from S. - Samples of the S. - The wild sugarcane genotypes of the high biomass group showed substantial differences in their expression profiles and we did not find any evi- dence of kinship among them in the scientific literature.. - This may partly be explained by the higher contribution of the S.. - officinarum genome in hybrids and by large differences between the genomes of the wild canes. - Clearly, sucrose storage is higher in the hybrids and S. - In leaves, higher expression of SPS and SPP coding genes in the low biomass group may indicate that the stalk of these genotypes requires more sucrose. - Color intensity represents the logarithm of the counts per million (cpm) of the corresponding transcript. - For each gene identifier we also show the log2 of the average counts per million. - How- ever, the SUT1 coding gene was downregulated in the low biomass group but had a higher overall expression level that SUT4 (Fig. - sponta- neum [27], but we found a SWEET14 gene repressed in the low biomass group, with no evidence of differential expression within this group. - Carbohydrate metabolism in culms also includes gene products from members of the SuSy family. - One DEG was also de- tected in the two other contrasts. - Although SuSy is possibly syn- thesizing sucrose, we also stress the importance of SPS for sucrose synthesis in the low biomass group (Figure 21-A in Additional file 3).. - Genes coding for proteins of the lignocellulose pathways were upregulated in high biomass genotypes.. - Expansins are a class of enzymes that can modify the structure of the cell wall, promoting its expansion [45]. - In our study, the high biomass group showed higher expression of expansin genes, possibly promot- ing the development of the leaf. - Because structures of the sugarcane top are relevant as biomass sources for energy cane, leaf growth is a desirable trait. - More directly related to the cell wall, many genes coding enzymes that assemble polysaccharides were upregulated in the high biomass genotypes. - This distinct variability within each of the two groups reflects the genomic differences of the ac- cessions (Figure 1 in Additional file 3). - This work presented a broad view of the expression of many coding genes in sugarcane leaves of different geno- types. - With regard to cell wall, most genes were upregu- lated in the high biomass group, but in general with low average expression levels. - Expression profiles in other plant parts of wild and cultivated acces- sions are needed to provide knowledge about the action of the genes involved in carbohydrate metabolism and biomass production. - This panel is managed by the sugarcane breeding program of the Inter-University Network for the Development of the Sugarcane Sector (RIDESA), at the Federal University of São Carlos (Araras, Brazil). - Genotypes of the high bio- mass group were IN84–58, IN84–88, Krakatau, SES205A, IJ76–318 and US85–1008. - In the high biomass group, there were four S. - Samples of the low biomass group include four hybrid cultivars - TUC71–7, RB72454, SP80–3280 and RB855156 - and two S. - Portions of the first visible dewlap leaves. - RNA extraction, sequencing and quality of the libraries We used the RNeasy Plant Mini Kit (Qiagen, cat. - The background set was composed of the expressed genes passing the cpm filter. - Co-expression network and gene set enrichment analysis A co-expression network was built with WGCNA [61], using as input the logarithm of the normalized cpm matrix of the expressed genes. - Our choice was to build an adjacency matrix preserving the sign of the connection. - Next, we checked the enrichment of the gene set formed by each co-expression module by ranking genes based on their absolute LFC for each contrast. - Because the expression quantification was done at the gene level, the transcript identifiers of the M ERCATOR 4 mapping file were changed to gene identifiers. - Supporting information of the genotypes. - Additional tables and figures showing a phenotypic characterization of the genotypes.. - Additional information about the methods used in the manuscript: basic statistics and comparison of the de novo assemblies. - Annotation of the de novo assembly used as reference.. - The first draft of the manuscript was written by FHC and GRAM, and all authors commented on previous versions of the manuscript. - Worldwide Genetic Diversity of the Wild Species and Level of Diversity Captured within Sugarcane Breeding Programs. - Genomic resources for energy cane breeding in the post genomics era. - Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane. - Golgi-Mediated Synthesis and Secretion of Matrix Polysaccharides of the Primary Cell Wall of Higher Plants. - Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. - Genome-wide analyses of miniature inverted-repeat transposable elements reveals new insights into the evolution of the triticum-Aegilops group. - The significance of responses of the genome to challenge.. - Association of variation in the sugarcane transcriptome with sugar content.. - High- throughput profiling of the Fiber and sugar composition of sugarcane biomass. - An assessment of the genetic diversity within a collection of Saccharum spontaneum L
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