Model of the photoperiod flowering time pathway in sorghum.

<p>Phytochrome B (PhyB) is mediates light signaling that modulates flowering time in response to photoperiod in sorghum. In LD, PhyB up-regulates the expression of <i>PRR37</i> and <i>GHD7</i>, two central floral repressors, during the evening phase of LD but with minimal influence in SD. Induction at this time of day is also dependent on output from the circadian clock. PhyB may stabilize and interact with PhyC, a candidate gene for <i>Ma5</i> a locus that also contributes to photoperiod regulation of flowering time. SbPRR37 activates <i>SbCO</i> expression peaking at dawn. SbPRR37 and SbGhd7 repress expression of the floral inductors <i>SbEHD1, SbCN8, SbCN12</i> and <i>SbCN15</i>, leading to delayed flowering in long days. In SD or 58 M (<i>phyB-1</i>), expression of the floral repressors Sb<i>PRR37</i> and Sb<i>GHD7</i> is reduced which results in floral initiation once plants have satisfied other requirements for flowering. PhyB was found to mediate repression of <i>SbCN15</i> regardless of day length.</p

Genome-Wide Association Study of Grain Polyphenol Concentrations in Global Sorghum [<i>Sorghum bicolor</i> (L.) Moench] Germplasm

Identifying natural variation of health-promoting compounds in staple crops and characterizing its genetic basis can help improve human nutrition through crop biofortification. Some varieties of sorghum, a staple cereal crop grown worldwide, have high concentrations of proanthocyanidins and 3-deoxyanthocyanidins, polyphenols with antioxidant and anti-inflammatory properties. We quantified total phenols, proanthocyanidins, and 3-deoxyanthocyanidins in a global sorghum diversity panel (<i>n</i> = 381) using near-infrared spectroscopy (NIRS), and characterized the patterns of variation with respect to geographic origin and botanical race. A genome-wide association study (GWAS) with 404,628 SNP markers identified novel quantitative trait loci for sorghum polyphenols, some of which colocalized with homologues of flavonoid pathway genes from other plants, including an orthologue of maize (<i>Zea mays</i>) <i>Pr1</i> and a homologue of <i>Arabidopsis</i> (<i>Arabidopsis thaliana</i>) <i>TT16</i>. This survey of grain polyphenol variation in sorghum germplasm and catalog of flavonoid pathway loci may be useful to guide future enhancement of cereal polyphenols

Expression of <i>SbCO</i>, <i>SbEhd1</i>, <i>SbCN8/12/15</i> in 100 M (<i>Ma3/PHYB</i>) and 58 M (<i>ma3^R/phyB-1</i>) in LD and SD.

<p>Relative RNA levels in leaves of 100 M (solid black lines) and 58 M (dashed red lines) entrained and sampled in LD (14 h light/10 h dark) or SD (10 h light/14 h dark) for 24 h followed by 24 h in LL (continuous light and temperature). Relative expression levels were determined every 3 hours by qRT-PCR analysis. The gray shaded areas represent the dark periods. (A) <i>SbCO</i>, (B) <i>SbEHD1</i>, (C) <i>SbCN8</i>, (D) <i>SbCN12</i>, (E) <i>SbCN15</i>. Each data point of relative expression is based on three technical replicates and three biological replicates. Error bars indicate SEM.</p

Sequence analysis of <i>PHYB</i> coding alleles in different sorghum lines.

<p>Sequence analysis of <i>PHYB</i> coding alleles in different sorghum lines.</p

Relative expression of <i>SbPRR37</i> and <i>SbGHD7</i> in 100 M (<i>Ma3/PHYB</i>) and 58 M (<i>ma3^R/phyB-1</i>) in LD and SD.

<p>100 M (solid black line) and 58 M (dashed red line) plants were entrained LD (14 h light/10 h dark) or SD (10 h light/14 h dark) and sampled for one 24 h cycle, followed by 48 h in LL (continuous light and temperature). The grey background corresponds to time when plants are in darkness. Relative gene expression was determined every 3 hours by qRT-PCR. Arrows represent morning peaks of expression and arrowheads represent evening peaks of expression. (A) In LD, the second peak (arrowhead) of <i>SbPRR37</i> expression in the evening (∼15 h) is missing in the <i>phyB</i> deficient line, 58 M. (B) In SD, the second peak (arrowhead) of <i>SbPRR37</i> is absent in both 100 M and 58 M. (C) In LD, the second peak (arrowhead) of <i>SbGHD7</i> expression in the evening (∼15 h) is attenuated in 58 M. (D) In SD, the second peak of <i>SbGHD7</i> is attenuated in both 100 M and 58 M. Each data point of relative expression was based on data from three technical replicates and three biological replicates. Error bars indicate SEM.</p

Flowering time QTL and analysis of epistasis in populations derived from 58MxR.07007.

<p>(A) Flowering time QTL labeled <i>Ma3, Ma5</i> and <i>Ma6</i>, were identified through analysis of flowering time variation in LD in the F2 population derived from 58MxR.07007. LOD values are shown on the Y-axis and sorghum chromosome numbers on the X-axis. The percent of the variance explained by each QTL is noted. The additive plot is shown in the lower portion of 2A where a positive value corresponds to alleles from R.07007 that delay flowering time. (B) Boxplot of flowering time distribution in the subset of the population with <i>Ma1Ma5-</i> genotypes but varying for alleles of <i>Ma3/ma3^R</i> and <i>Ma6/ma6</i>. (C) Boxplot of flowering time distribution in the subset of the population having <i>Ma1Ma3</i>- genotypes but varying for <i>Ma5/ma5</i> and <i>Ma6/ma6.</i> Median values for flowering time are represented by horizontal lines within boxes.</p

Flowering time of F2/F3 progeny from 58MxR.07007 in LD.

<p>Flowering time of F2/F3 progeny from 58MxR.07007 in LD.</p

Case_Study_1_plant_height_Sorghum

Raw individual images with gps log and ground truth data for the sorghum plant height estimate in case study 1

Image_2_Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation.tiff

Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development. Genes involved in RFO biosynthesis (SbMIPS1, SbInsPase, SbGolS1, SbRS) were more highly expressed in leaves compared to stems and roots, with peak expression early in the morning in leaves. SbGolS, SbRS, SbAGA1 and SbAGA2 were also expressed at high levels in the leaf collar and leaf sheath. In leaf blades, genes involved in myo-inositol biosynthesis (SbMIPS1, SbInsPase) were expressed in bundle sheath cells, whereas genes involved in galactinol and raffinose synthesis (SbGolS1, SbRS) were expressed in mesophyll cells. Furthermore, SbAGA1 and SbAGA2, genes that encode neutral-alkaline alpha-galactosidases that hydrolyze raffinose, were differentially expressed in minor vein bundle sheath cells and major vein and mid-rib vascular and xylem parenchyma. This suggests that raffinose synthesized from sucrose and galactinol in mesophyll cells diffuses into vascular bundles where hydrolysis releases sucrose for long distance phloem transport. Increased expression (>20-fold) of SbAGA1 and SbAGA2 in stem storage pith parenchyma of sweet sorghum between floral initiation and grain maturity, and higher expression in sweet sorghum compared to grain sorghum, indicates these genes may play a key role in non-structural carbohydrate accumulation in stems.</p

Image_1_Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation.tiff

Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development. Genes involved in RFO biosynthesis (SbMIPS1, SbInsPase, SbGolS1, SbRS) were more highly expressed in leaves compared to stems and roots, with peak expression early in the morning in leaves. SbGolS, SbRS, SbAGA1 and SbAGA2 were also expressed at high levels in the leaf collar and leaf sheath. In leaf blades, genes involved in myo-inositol biosynthesis (SbMIPS1, SbInsPase) were expressed in bundle sheath cells, whereas genes involved in galactinol and raffinose synthesis (SbGolS1, SbRS) were expressed in mesophyll cells. Furthermore, SbAGA1 and SbAGA2, genes that encode neutral-alkaline alpha-galactosidases that hydrolyze raffinose, were differentially expressed in minor vein bundle sheath cells and major vein and mid-rib vascular and xylem parenchyma. This suggests that raffinose synthesized from sucrose and galactinol in mesophyll cells diffuses into vascular bundles where hydrolysis releases sucrose for long distance phloem transport. Increased expression (>20-fold) of SbAGA1 and SbAGA2 in stem storage pith parenchyma of sweet sorghum between floral initiation and grain maturity, and higher expression in sweet sorghum compared to grain sorghum, indicates these genes may play a key role in non-structural carbohydrate accumulation in stems.</p