Root lodging is a physical stress that changes gene expression from sucrose accumulation to degradation in sorghum

Abstract

Background: Sorghum (Sorghum bicolor L.) is used as a raw material for biofuels because it accumulates sugars at high levels in the stem. Lodging of sorghum occurs when the soil is wet and very high winds blow across the field. In root lodging, the roots are pulled loose from the soil, causing the plant to fall over. Lodging reduces the yield of nonstructural carbohydrates. It is not yet clear which genes show changes in expression when sorghum falls over. We compared whole-gene expression in the mature stems of intact and lodged sorghum plants, with a focus on comparisons from the perspective of differences in sugar accumulation or degradation.

Results: Lodging decreased sucrose content, starch content, and ratio of sucrose to total sugars in the stems of the sorghum cultivar SIL-05. Particular paralogs of SWEET and TMT family genes, which encode sucrose or hexose transporters, or both, were significantly highly expressed in intact or lodged sorghum stems. In intact stems, genes encoding the glucose-6-phosphate translocator, aquaporins, and enzymes involved in photosynthesis and starch synthesis were highly expressed. In lodged sorghum stems, expression of genes associated with sucrose or starch degradation or energy production was increased. Notably, expression of genes encoding enzymes catalyzing irreversible reactions and associated with the first steps of these metabolic pathways (e.g. INV, SUS, and hexokinase- and fructokinase-encoding genes) was significantly increased by lodging. Expression of SUT, SPS, and SPP was almost the same in intact and lodged sorghum.

Conclusions: Specific paralogs of sucrose-associated genes involved in metabolic pathways and in membrane transport were expressed in the stems of sorghum SIL-05 at the full-ripe stage. Root lodging drastically changed the expression of these genes from sucrose accumulation to degradation. The changes in gene expression resulted in decreases in sugar content and in the proportion of sucrose to hexoses in the stems of lodged plants.

Keywords: Biofuel; RNA-seq; Stem; Sugar content; Sugar metabolism; Sugar transporter.

Fig. 1

Differences in sugar content, sugar composition, and starch content of stem between lodged and intact plants. a Brix and sucrose percentage. Horizontal axis represents Brix and vertical axis represents sucrose weight as a percentage of the total weights of sucrose, glucose, and fructose combined. Data on 36 intact plants (black) and 12 lodged plants (gray) are plotted. b Sugar composition. The contents (weight/volume) of sucrose, glucose, and fructose of three individual plants of intact (# 13, # 15, # 16) and lodged (# 33, # 37, # 48) sorghum are shown. c Starch content. The mean and standard deviation of the values of the starch content (dried starch weight (mg)/stem fresh weight (g)) for three individual intact (# 13, # 15, # 16) and lodged (# 33, # 37, # 48) plants are shown

Fig. 2

Changes in gene expression level with lodging. Fragments per kilobase of exon per million mapped sequence reads (FPKM) of 27,608 genes were plotted for lodged plants (vertical axis) and intact plants (horizontal axis). Values are log₁₀ of average FPKM calculated from three individual plants: intact (# 13, # 15, # 16) or lodged (# 33, # 37, # 48)

Fig. 3

Relative expression levels of metabolism-associated genes in lodged and intact plants. Each box represents 2778 predicted genes involved in metabolic pathways; these genes were annotated with MapMan software. Colors represent relative expression levels: significantly higher in intact plants (red); significantly higher in lodged plants (blue); no significant difference (white). Green numbers represent metabolic pathways discussed in the main text. 1: sucrose synthesis; 2: starch synthesis; 3: Calvin cycle; 4: pentose phosphate pathway; 5: TCA cycle; 6: fermentation; 7: trehalose synthesis; 8: sucrose degradation; 9: starch degradation

Fig. 4

Expression levels of genes involved in sucrose metabolism. a Sucrose synthesis. b Sucrose degradation. One arrowhead indicates an irreversible reaction, and double arrowheads indicate a reversible reaction. Colors of arrows and of gene names represent relative gene expression levels: significantly higher in intact plants (red); significantly higher in lodged plants (blue); no significant difference (black). Graphs indicate average numbers of FPKM (fragments per kilobase of exon per million mapped sequence reads) of intact (black) or lodged (gray) plants and standard errors from three individual plants. Green arrow represents the link from other metabolic pathways

Fig. 5

Expression levels of genes involved in starch metabolism. a Starch synthesis. b Starch degradation. Designations are as in Fig. 4

Fig. 6

Expression of putative transporter genes involved in sugar accumulation or release: 23 SWEET, six SUT, 19 TMT, 30 GPT, and 42 aquaporin genes. Constitutively expressed control genes, actin (Sb08g003970), elongation factor 1-alpha (EF1alpha; Sb10g023330), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH; Sb10g029870), are also shown. Designations are as in Fig. 4

Fig. 7

Representative genes involved in sugar accumulation or release. a Model of intact sorghum. Sucrose (Suc) is accumulated in the vacuoles or is degraded to glucose (Glc) and fructose (Frc) in the cytosol. These hexoses are stored or used for starch synthesis. Genes for sucrose accumulation were highly expressed in intact stems. b Model of lodged sorghum. Sucrose stored in vacuoles is translocated to other tissues. Sucrose is synthesized from stored starch or hexoses. Genes for release of stored sucrose to other tissues were expressed in the lodged stem. Illustrations on the left show schematically the enzymatic reactions or transport steps involved in sugar accumulation or release. Yellow numbers correspond to the numbers in the tables at right. In these tables, genes within each family with expression levels that changed with lodging (red: significantly higher in intact plants; blue: significantly higher in lodged plants) and genes that were expressed at high levels but not differentially between intact and lodged plants (black) are listed